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What type of RNA is the most common and what is its function?

rRNA and it makes up ribosomes


Explain the metaphor to software and hardware used to describe mRNA, rRNA and tRNA.

mRNA is like a software which tells the machinery what it should produce
RRNA and tRNA are like hardware which allow ribosomes to fulfill the “commands” given by mRNA


What is the purpose of microRNA’s?

They regulate the amount of protein that is produced by interfering with mRNA preventing them from being translated


What type of bonds unite nucleotides in both DNA and RNA?

Phosphodiester bonds


Outline major differences between DNA and RNA. (6)

1 Ribose vs deoxyribose (2’OH in ribose)
2 Uracil vs Thiamine
3 Single Stranded vs double stranded
4 RNA is less stable due to 2’ OH
5 RNA can have secondary and tertiary structure
6 RNA has a higher amount of non-Watson Crick base pairing


Draw a diagram explaining the important function of palindromic sequences in RNA molecules.

They create hairpin structures:
X. X


What is the open reading frame ORF?

The area between the start and stop codons which will actually be translated


Describe the modifications that take place to pre-mRNA before it becomes mature mRNA when possible give reasoning behind these modifications.(3)

1 Splicing- introns are removed leaving only exons
2 5’ cap is added consisting of 7 methyl guanosine linked by a triphosphate linkage- This prevents degradation of mRNA by phosphatases and nucleares and allows the ribosome to recognize it
3 3’ Poly A tail is added which protects the mRNA from degradation


Describe some of the main features of tRNA.(3)

1 CCA at 3’ end- amino acids are bound to the 2’ or 3’ OH of the A at the carboxyl group
2 Have a high number of unusually modified bases
3 Exhibit clover leaf secondary and L-shaped tertiary structure


What is non Watson-Crick base pairing and when can it occur?

Any base pairing between bases other than those which normally pair (AT and GC). It can occur between any two bases as long as they each have a hydrogen bond donor and a hydrogen bond acceptor and they come in close proximity of each other.


Why is the difference in stability between DNA and RNA important?

DNA is more stable which avoids the loss of genetic material over the life course of an organism
RNA is much less stable which makes it easier to regulate the amount of protein being produced at different times


Compare and contrast promoters and enhancers.

Promoters bind RNA polymerase so that it can begin transcription. Enhancers bind other protein factors which interact with RNA polymerase to increase the rate of transcription.
Promoters are like putting a car into drive- they allow transcription to begin at a regular slow speed and enhancers are like pushing the gas pedal, they cannot start transcription by themselves but they can increase the speed if transcription has been initiated.
Another major difference is location. Promoters are always located directly upstream from the start sequence while enhancers may be located anywhere including thousands of base pairs away from the start site and the DNA bends to bring them close to the transcription site.


Compare and contrast enhancers and silencers.

Enhancers upregulate transcription and silencers downregulate transcription.
They may both be located very far away from the start site


Define cis-acting elements and trans-acting elements and explain how they relate to enhancers, promoters, etc.

Cis-acting elements are short DNA sequences which attract certain proteins. These proteins which bind to cis-acting elements are trans-acting elements and they affect the rate of transcription by interacting with RNA polymerase.
Enhancers, promoters and silencers are made up of many cis-acting elements near each other.


Differentiate between general and sequence specific transcription factors.

General transcription factors are required for transcription to occur. These factors must be present at a location for RNA polymerase to bind and for transcription to occur so all promoters have these near the start site
Sequence-specific transcription factors up/down regulate RNA polymerase and may or may not be present in DNA elements


What are some of the major differences between transcription and replication besides the end product (3).

1 Transcription is de novo synthesis- meaning that it does not require a primer, instead a triphosphate A or G begins at the 5’ end
2 Transcription has a lower fidelity because errors are less costly
3 Only one strand is created in transcription in the 5’-3’ direction so only one strand of DNA is used as a template in the 3’-5’ direction


Explain the importance of the concept of a combinatorial mechanism in promotion of replication.

Cis acting elements are not unique to individual promoters, enhancers etc. Instead what is unique is the combination and arrangements of elements
In addition, all of the transcription factors relating to the specific cis-acting elements must be present for a promoter to function. This explains tissue specific gene expression because different factors are present in different cell types leading to only the expression of those genes whose factors are present.


Make up an example to illustrate the principle of modularity in transcription.

Transcription factors are made up of multiple domains such as a DNA binding domain and a regulatory domain. These domains if switched to another protein would still function.
For example, assume you had a transcription factor with a DNA binding domain that binds to an element that regulates expression of TNF alpha and that same transcription factor has a regulatory domain that enhances transcription. Then say you transfer the regulatory domain to a factor with a different DNA binding domain. NOw, the new transcription factor would cause the upregulation of transcription of whatever gene the binding domain binds to.


On what characteristics are transcription factors separated into families?

The sequences to which they bind


Explain what signal sequences are and their function in protein localization.

THey are a part of the amino acid sequence of a protein either at the N or C terminus that targets that protein for its destination and will often be removed after reaching the destination.


Diagram a nuclear pore.

Should show 2 membranes of nuclear envelope
Projections toward the outside of the nucleus that look like tentacles
Projections toward the inside from a "basket"


What is the purpose of nuclear pores?

They allow small hydrophilic molecules and ions to travel freely between the cytosol and the nucleus while allowing those larger molecules with the correct signals to travel as well.


Explain and diagram the process by which a protein destined for the nucleus arrives there

Proteins destined for the nucleus will contain a nuclear localization signal which is a short sequence of positively charged amino acids. This signal binds to nuclear import receptors in the cytosol. These receptors then bind to cytosolic fibriles of nuclear pores which transport protein through pores into nucleus
nuclear localization signal --> nuclear import receptors--> cytosolic fibriles--> pass through nuclear pore


Explain and diagram the process by which a protein gains entry into the mitochondria.

Proteins have an N-terminus signal sequence which binds to import receptors on the cytosolic side of the outer mitochondrial membrane. import receptors are bound to translocators which feed the protein through the outer membrane toward translocators on the inner membrane which will feed them through to the matrix
N-terminus signal sequence --> import receptors on membrane --> outer translocator --> inner translocator --> mitochondrial matrix


What differentiates free ribosomes from ER bound ribosomes?

They are structurally identical and it only depends on which protein they are currently translating. If it is bound for the ER the ribosome will move to the ER and if not the ribosome will remain free.


The ER acts as a distribution center for proteins going to what destinations? (5)

ER, golgi, lysosomes, endosomes and cell surface


How do proteins bound for the ER get there?

When the protein begins to be translated, the beginning N terminus will contain a signal sequence for the ER. The signal sequence is recognized by signal recognition particle (SRP) which binds to an SRP receptor on the ER membrane which allows the growing protein to pass through a translocator as it is translated.
signal sequence --> signal recognition particle (SRP) --> SRP receptor --> translocator--> ER


Compare and contrast soluble and embedded ER proteins.

Soluble proteins pass completely through the membrane as they are translated and end up free floating within the ER. These proteins are ultimately bound for the lumen of an organelle or else to be secreted outside of the cell completely.
Embedded proteins are held in the ER membrane after translation based on transmembrane portions. These proteins will be membrane bound in their destination and are transferred to their final location by vessicular transport.


Outline the process by which a protein becomes embedded in the ER membrane.

As it is being translated, a hydrophobic stop sequence occurs causing the translocator to "spit" the protein out into the surrounding membrane. This hydrophobic portion remains embedded into the membrane while the protein continues to be translated anchoring the protein there. A single protein may have several stop hydrophobic stop and start sequences causing it to make multiple passes through the membrane.


What protein removes the signal sequence from ER proteins?

Signal peptidase


Describe the symptoms and causes of Swyer syndrome or XY gonadal dysgenesis and how it relates to protein localization.

Symptoms: XY individuals form female external genitalia but no ovaries
Cause: non-functional SRY gene
Connection: May result from lack of nuclear localization signal on SRY gene causing the gene to not perform its function in the nucleus as a transcription factor


Describe the process of adding polyadenylation.

An endonuclease recognizes the sequence AAUAAA and cleaves at this site allowing polyadenylate polymerase to add a poly A tail.


What does codon degeneracy mean?

More than 1 codon code for the same amino acid


Contrast insertion and deletion mutations at the protein level to frameshift mutations

Insertion and deletion mutations at the protein level refer to addition or deletion of 1 or more amino acids without causing a frameshift whereas frameshift mutations occur when a number of nucleotides not divisible by 3 was added or deleted from the reading frame which shifts the reading frame causing major changes to the product.


What is a poly some?

A group of ribosomes that are working independently of each other to translate the same piece of mRNA.


Draw how you would represent monozygotic and dizogotic twins on a pedigree

One vertical line coming from the sibling line with two diagonal lines to individuals represents twins. Monozygotic twins will have a horizontal line between them while dizogotic twins will not


What is consanguinity and how would it be represented on a pedigree chart?

It represents that a mating couple are related by blood. It is represented by a double mating line instead of the normal single line


What does a diagonal line through a person on a pedigree chart mean?

That person is deceased


Draw your own pedigree chart.

Make sure it follows all of the normal rules (squares = male circle female, mating lines etc.)


Name the major components of chromatin (3)

Non-histone proteins


What is meant by saying that DNA-histone interactions are “fluid”?

They are not always exactly the same but are constantly changing leading to changes in gene expression patterns


What is a nucleosome?

A “bead” made up of 8 histones with DNA wrapped around it


What is cohesion and what proteins make it happen?

The binding of sister chromatids together. Cohesin protein complex accomplishes this by acting like a napkin ring around sister chromatids


Describe the changes that occur to the cohesin complex over the course of the mitosis and meiosis

-Cohesion loads onto sister chromatids at replication
- majority dissociates at prophase but some remains at the centromere until anaphase

- Loads along homologous pairs in meiosis 1
- Exists only between centromeres of sister chromatids in meiosis 2 similar to mitosis


Describe the role of condensin proteins

They cause the chromatin to condense at the beginning of mitosis

CDK protein triggers M phase and causes condensin to accumulate


Describe the major differences between euchromatin and heterochromatin

Euchromatin is less densely packed, more transcriptionally active and appears lighter than heterochromatin in G-banding


What is G-banding?

It is a way to visualize chromosomes. Trypsin partially digests histones and allows dye to bind to DNA so that they can be visualized. Each chromosome has a fairly standardized pattern of bands that allow geneticists to identify them. Each band is made up of 50-100 genes.


When in the cell cycle is best for G-banding and why?

During prometaphase. The chromosomes can be visualized then or during metaphase but the bands are clearer during prometaphase than metaphase


What is the centromere?

A repetitive sequence of DNA on each chromosome that allows the proteins of the mitotic spindle to bind during mitosis.


Describe the three subtypes of chromosomes based on centromere positioning

1 meta centric: centromere basically in the center
2 Submetacentric: centromere halfway between the center and one end
3 Afrocentric: centromere is near the end


Differentiate between the p and q arms of chromosomes.

The centromere divides the chromosome into 2 arms. The smaller arm is the p arm (petite) and the q arm is the larger arm


Explain the purpose of telomeres and the normal function of telomerase

Telomeres are repeats of a 6 base pair sequence (TTAGGG) that occur over and over near the end of the chromosome. They protect the coding regions of the chromosome from degradation since some DNA is lost in each cell cycle. Short telomeres trigger apoptosis. Telomerase is a protein that replaces telomeres and is active in germ cells but normally becomes inactive afterwards. Active telomerase is a trait of neoplastic (cancer) cells


What are the three types of chromosomal abnormalities?

Numerical: wrong number of chromosomes
Structural: changes to the structure of a given chromosome
Mosaicism: 2 or more genetically distinct cell lines within the same individual


Give the karyotype nomenclature for a normal female and a male with Down syndrome.



Compare and contrast polyploidy and aneuploidy

Polyploidy involves the wrong number of copies of all chromosomes ie triploidy or 69 (n =3) while aneuploidy refers to an incorrect number of only some of the chromosomes but not all of them (most often just one) polyploidy occurs in 1% of all conceptions accounting for 10-20% of chromosomally abnormal miscarriages but is basically always lethal. Aneuploidy usually results in spontaneous abortion but in some cases can result in a live birth usually with serious defects


What is the most commonly occurring aneuploidy? Which ones can result in live births?

16 is the most common but basically always lethal
Trisomies 21, 18, and 13 can all result in live births as well as monosomy X or XXY


What are the most common causes of structural abnormalities of chromosomes?

1 Non homologous recombination
2 double strand breaks of sister chromatids
3 telomere instability


What is a translocation? Compare and contrast reciprocal translocations and Robertsonian translocations.

An exchange of info between non homologous chromosomes
A reciprocal translocation occurs when 2 non-homologous chromosomes essentially undergo crossing over
A Robertsonian translocation occurs when 2 Acrocentric chromosomes join at the centromere resulting in one large chromosome that is a combination of the other two and the loss of the small p arms of both chromosomes


What are the main clinical features of trisomy 21?

Down Syndrome
Mild to moderate intellectual disability
Characteristic facial appearance
hypotonia (weak muscle tone) at birth
Higher risk of:
Gastroesophageal reflux
Celiac disease
Hearing/vision problems


What are the common clinical features of Trisomy 18?

Edward Syndrome
Slow intrauterine growth/low birth weight
Heart defects
Small abnormally shaped head
Small jaw and mouth
Clenched fist with overlapping fingers
Most die within a month and those that don’t usually have severe intellectual disabilities


What are the common clinical features of Trisomy 13?

Patau Syndrome
Severe intellectual disabilities
Many physical abnormalities especially along the midline: cleft lip/palate, micropthalmia (small underdeveloped eyes), extra fingers, toes
Heart and spinal chord defects


What is Turner Syndrome? What are the common clinical features?

Monosomy X
Results in female sex characteristics
Short stature
Early loss of ovarian function and infertility
Most do not undergo puberty without hormone treatment
30% have extra skin folds on the back of the neck
1/3 coarctation (unusually narrow) of the aorta


What is Klinefelter’s syndrome and what are the common clinical features?

XXY karyotype
Male sex characteristics
Taller than average
small testes —> low testosterone —> delayed puberty
Can develop some feminine feature such as breasts, feminine belly fat placement patterns, hip structure, etc.


What is the cause of most aneuploidies?

Nondisjunction during Meiosis 1 of oogenesis


What are two main exceptions to the central dogma?

1 Reverse transcriptase - goes backward from RNA to protein
2 RNA as the final product- tRNA, miRNA, snRNA, rRNA are not meant to be translated into protein


What are the 3 ways that gene expression can be controlled by physical modifications to DNA?

1 DNA/gene loss
2 DNA/Gene amplification
3 DNA rearragement- Ex: immunoglobulin subunits can be rearranged to create many unique proteins


What are 3 real world examples of DNA methylation in gene expression?

1 Globin gene is methylated in all cells besides red blood cells
2 X-inactivation
3 Imprinting


What DNA sequence is usually methylated and why is that?

CpG islands or regions with a high number of C’s followed by G’s. The reason is because C’s are generally methylated and this sequence is a palindrome that allows both strands to be methylated


Draw and explain how imprinted DNA stays methylated across cell divisions.

Each division there one strand comes from the parent cell and one new strand. The parent strand if it was methylated will remain methylated and the new strand is not methylated. This is referred to as hemimethylated. All hemimethylated cells are recognized and methylated.


Summarize the different ways that red blood cell expression is controlled through various mechanisms. (4)

1 All DNA is deleted from mature RBC’s stopping expression entirely
2 Globin gene is methylated in all cells except red blood cells to keep it from being expressed
3 As RBC’s mature, the chromatin becomes more condensed limiting expression
4 When iron is not present, Globin mRNA’s are prevented from being translated since they will not be able to form hemoglobin


Label all of the following inhibitors of translations as affecting eukaryotes, prokaryotes or both:
Diphtheria toxin
Alpha amantin
Actinomycin D

Ricin: E
Kanamycin P
Tetracycline P
Puromycin B
Cycloheximide E
Streptomycin P
Gentamicin P
Neomycin P
Diphtheria toxin E
Erythromycin P
Chloramphenicol P
Rifamycin P
Alpha amantin E
Actinomycin D B


Compare and contrast Loss of function and gain of function mutations and the diseases they cause.

Loss of function refers to a mutation which reduces or eliminates the function of a protein. These disorders are generally recessive since one functional copy is often enough to prevent a disorder. An example of this is Duchenne muscular dystrophy. However in the case of proteins that are required in high quantities, loss of function disorders may be dominant as is the case for osteogenesis imperfecta
Gain of function mutations are when the mutation causes the protein to have a function that the normal protein did not have either within the same pathway as is the case in achondroplasia or in an unrelated pathway as is the case in Huntington’s disease. These disorders are generally dominant with the main exception being sickle cell anemia.


Describe the clinical presentations of osteogenesis imperfecta

Group of disorders characterized by brittle bones
Type 1 = milder leads to frequent fractures of long bones with any exertion which heal normally
Type 2 = more severe, many fractures present at birth and patients normally die within a few weeks of birth


Describe the mutations that cause osteogenesis imperfecta type 1 and 2.

This is caused by a reduction in the amount of collagen which is important in bone formation
Collagen is made up of 2 Alpha 1 chains and 1 Alpha 2 chain
Type 1 - mutation results in no production of alpha 1 —> heterozygotes produce 1/2 normal alpha 1 and therefore 1/2 normal collagen
Type 2 - point mutation to alpha 1 chain that makes any collagen chain with defective alpha 1 chain non-functional. This leads to 3/4 of collagen becoming non-functional and only 1/4 of the normal amount of collagen


In what ways are serious genetic disorders perpetuated even though affected members may be unable to reproduce?

1 Novel mutations and mosaicism/chimerism, a novel mutation could occur which is only present in some fo the cells which could make it so that the phenotype is not present but if the mutation is present in any germline cells, it could be passed on.
2 For recessive disorders, carriers could be at an advantage in some ways such as sickle cell


Compare and contrast mosaicism and chimerism

Both result in different genetic cell lines within the same organism but the mechanism is different.
Mosaicism: Mutation occurs early in cell divisions of the embryo. The earlier the mutation occurs, the more cells will be affected
Chimerism: two genetically distinct zygotes fuse to form one organism early in cell division. Often as a result of one zygote holding a fatal abnormality that would otherwise cause spontaneous abortion


Describe the clinical presentations of achondroplasia.

Autosomal dominant Gain of function mutation to the fibroblast growth factor receptor (FGFR3) gene. Mutation leads to ligand independent stabilization of dimers activating downstream signaling. Results in lack of normal growth in long bones but otherwise healthy individuals.
80-90% are de novo mutations


What is anticipation in genetics and what explains it?

A genetic disease that occurs earlier and more severely in each successive generation. This is explained by triplet repeat expansion where a disease is caused by an abnormally high number of repeats of a 3 nucleotide sequence. The number of repeats generally increases each generation and the higher number of repeats the more sever the disorder.


Describe the clinical manifestations of Huntington’s disease

Autosomally dominant gain of function disease caused by expansion of the number of CAG repeats in a specific gene.
Normal is 10-30 repeats
Affected is 36+
Average onset is 37 years with 100% penetrance by age 80
Begins with mild motor function deficiencies memory loss and progresses to uncontrollable movements, extreme personality changes, severe memory loss and severe psychiatric conditions until the patient is immobilized and cognitively non functional. Death 10-20 years after onset.


Describe the clinical manifestations of Spinal Muscular atrophy (SMA).

Autosomal recessive loss of function mutation to Survival motor neuron 1 (SMN).
Leads to motor neuron degeneration the severity of which is dependent on the number of copies of SMN2 that an individual has.
Type 1: born with little muscle tone - death within 2 years
Type 2: sits but never stands childhood lethal
Type 3 and 4: most mild with some adult survival but generally loss significant mobility

Recent gene therapy has been successful to date in treating SMA


Describe the clinical manifestations of Duchenne muscular dystrophy (DMD)

X-linked recessive disorder
Delayed motor development, proximal muscle weakness, classic microscopic myopathy can changes, muscle fiber breakdown results in high serum levels of muscle enzymes such as creatine kinase, dilated cardiomyopathy, wheelchair bound by 12, typically die by late 20’s


Define allelic heterogeneity, locus heterogeneity, and clinicalheterogeneity.

Allelic: same phenotype caused by different mutations to the same gene
Locus: Same phenotype caused by mutations to different genes often within the same pathway
Clinical: Very different phenotypes resulting from mutations in the same gene


What patterns does mitochondrial inheritance follow?

Similar to X-linked dominant transmission, variability in symptoms based on mixed population of normal and affected mitochondria
Mostly affect aerobic tissues (nervous system, eyes, cardiac and skeletal muscle)


Describe how chromosome analysis or karyotype works, what it can be used to detect and what it cannot be used to detect.

A chemical is added to cells to arrest them in metaphase and cells are dyed and dropped onto a microscope slide so that chromosomes and banding patterns can be analyzed.
Used for- detection large chromosomal abnormalities such as aneuploidy, translocations, deletions, duplications etc.
Can’t be used for Uniparental disomy, methylation changes or abnormalities smaller than 5Mbps


How does Fluorescent in situ hybridization (FISH) work? What can it and can’t it be used for?

Fluorescent probes are created to be complimentary to certain DNA regions. They are then hybridized to the cellular DNA and visualized.
Can tell: Deletions, duplications, translocations and mosaicism (limited by size of probes and knowledge of the target)
Can’t tell: Uniparental disomy or methylation changes


How does Array CGH work? What can it and can’t it be used for?

Oligonucleotide probes are placed on a glass slide. Patient and control DNA are labeled with different colors and then allowed to hybridized with probes. The fluorescent patterns are then compared.
Can tell: deletions and duplications
Can’t tell: Balanced rearrangements, UDP, Anything smaller than 10-30Kbps, changes in methylation


What can PCR and microsatellite PCR be used for?

Microsatellite PCR targets short repeats that occur a different number of times for different people.
Can be used for: Crime scene identification, paternity testing, changes in methylation and UDP


How does Sanger sequencing work? What can it be used for and what can’t it be used for?

It is like PCR but it also includes labeled dideoxyribonucleotides which terminate the chain and be used to tell which base is present at each location.
Can tell: Small alterations in targeted regions
Can’t tell: UDP or methylation (clinically )


How does multiple probe ligations MLPA work and what can it and can’t it be used for?

Nucleotide probes are fused to universal PCR primers and hybridized with DNA. Then PCR is performed which amplifies only those probes that hybridized.
Can tell: Small deletions and duplications no larger than one gene
Can’t tell: Single base mutations, UDP, methylation, translocations and inversions


Describe how massively parallel sequencing works and what its potential uses are.

The genome is fragmented and bound to adapters then ligated to a flow cell. Bridge amplification is used to create clusters of identical DNA strands. Fluorescently tagged reversibly terminating nucleotides are added and lasers are used to tell what base was added at each location. They are then removed and cycled through for each location until a sequence is created.
This can sequence much more information including a whole exime at a much lower cost than Sanger sequencing but is more error prone.
Can be used to find small abnormalities and could eventually be used to look for larger ones.


What are the major differences between hemoglobin and myoglobin?

Hemoglobin is a tetramer and myoglobin is a tetramer this causes hemoglobin to exhibit cooperativity and have a lower oxygen affinity in the tissues than myoglobin. Because of this difference, hemoglobin is used to transport oxygen throughout the body and myoglobin is used to store oxygen to be used during exercise in skeletal muscles


What structural changes occur to hemoglobin as a result of O2 binding?

In the deoxygenated state, the iron atom of hemoglobin is pulled out of the plane of the heme ring and when oxygen binds it pulls the whole helix to which iron is bound so that the iron is back in the plane. This difference is characterized as the T-state (deoxygenated) and the R-state (oxygenated).


What interactions are destabilized in the R state vs the T state of hemoglobin?

Several ionic interactions between amino acids that stabilize alpha-alpha and alpha1-beta2 and alpha2-beta1 subunit interactions in the T-state are no longer possible in the R state due to the conformational changes that take place


How does CO binding affect hemoglobin?

CO binds at the oxygen binding site with 300 times more affinity than oxygen blocking O2 from binding. CO is constantly present in small amounts in the body but Hb bound CO is removed in a matter of hours


Describe the cooperativity of hemoglobin.

The T-state of hemoglobin has a lower affinity for oxygen than the R-state. When 2 oxygen molecules are bound to a Hb the two states are in equilibrium. However when 1 O2 is bound the T-state becomes favored and when 3 are bound the R state is favored. This increases the affinity for oxygen in high concentrations of O2 and decreases affinity for O2 at low concentrations


What are the 3 allosteric inhibitors of hemoglobin and how does each affect it?

All three lower the affinity for oxygen by favoring the T-state
1pH- low pH causes H+ ions to bind to hemoglobin favoring the T-state. Low pH results from exercise
2 2,3BPG- occurs as a short term result of high altitude
3 CO2 - also occurs as a result of exercise


Describe the natural Hemoglobin variants.

Hemoglobin A is the major type present in adults consisting of two alpha and two beta subunits
Hemoglobin A2 is present in smaller concentrations in adults and is made up of 2 alpha and 2 delta subunits
Hemoglobin F is found in fetuses and consists of 2 alpha and 2 gamma subunits
Embryonic hemoglobin consists of 2 alpha and 2 epsilon subunits
Pre-embryonic hemoglobin consists of 2 zeta and two epsilon subunits
Fetal and embryonic hemoglobin variants have higher O2 affinity than adult hemoglobin


Describe alpha thalassemia.

Any mutation to the alpha subunit of hemoglobin which causes insufficient production of hemoglobin
Most are deletions
1 deletion = silent carrier w/o symptoms
2 deletions = alpha thalassemia trait and mild anemia
3 deletions = hemoglobin H disease- moderate to marked anemia but not lethal
4 deletions = hemoglobin Bart’s no O2 carrying capacity, neonatal death


Describe beta thalassemia.

Any of over 100 mutations to the beta subunit of hemoglobin which causes insufficient hemoglobin production
Clinically heterogenous
From mild to major (Cooley’s)
Cooley’s = transfusion dependent, infants are listless and pale, grow slowly and may be jaundiced, internal organs can be enlarged


Describe Heinz body hemolytic anemias

Results from point mutations in the hydrophobic center of the hemoglobin usually in the beta subunit
Results in desaturation of the molecule and coagulation within the erythrocytes (Heinz bodies)


Describe Sickle cell anemia.

Results from a single point mutation causing an amino acid change from glutamate to valine in beta subunit of hemoglobin that causes them to become “sticky” in T state resulting in sickle shaped RBC’s


What is the average lifespan of a normal RBC?

120 days


What is a reticulocyte?

The step before a mature RBC in Erythropoiesis. You can often see them on blood smears they will appear larger than erythrocytes and purple with a mesh-like network of rRNA. They normally make up about 1% of RBC’s


Why could a count of reticulocytes be important? And what is the best way to measure them?

They can be measured in a complete blood count. They are useful to understand the rate of Erythropoiesis


If a patient has a higher or lower than normal amount of reticulocytes what could that indicate?

Higher: blood loss or hemolytic anemias
Lower: vitamin deficiency or Myelodysplastic syndromes


Outline the important components of the RBC cellular structure.

Biconcave discs with central pallor 1/3 of diameter- this increases the surface area for gas exchange
Unique membrane and cytoskeleton allow for flexibility and deform ability which is important for fitting through blood vessels
No nucleus


What is a schistocyte?

Fragmented RBC’s that look like triangles or helmets. Are caused by shearing or mechanical force
Only present under severe pathological conditions such as artificial heart valves or microangiopathic hemolytic anemia, malignant hypertension


Describe the shape and lifespan of sickle cell RBC’s.

They are crescent shaped with pointed ends. Typical lifespan is 10-20 days


What are spherocytes? What causes them?

RBC’s shaped like spheres with no central pallor due to loss of membrane. This causes decreased surface area to volume ratio. Can result from pathology such as burns and autoimmune hemolytic anemia or it can be hereditary


What causes hereditary Spherocytosis?

An autosomal dominant gene usually affecting the cytoskeleton protein ANK1 (ankyrin)


What are target cells and when are you likely to see them?

Abnormal RBC’s with too much membrane increasing the surface area to volume ratio to higher than normal. THey are seen in liver disease and after removal of the spleen and sometimes in thalassemia


What are ovalocytes? When are you likely to see them?

They are elongated oval shaped RBC’s. They look kind of like sickle cells but with rounded edges. They are most commonly seen in iron and vitamin B12 deficiencies as well as hereditary ovalocytosis


What causes hereditary elliptocytosis/ovalocytosis?

Autosomal dominant gene in the cytoskeleton protein spectrum


What is basophilic stippling and when does it usually present?

RBC’s with small blue dots dispersed throughout which are caused by clusters of rRNA
OFten seen in lead and arsenic poisoning, alcoholism and thalassemia


What conclusions did Anfinsen make about protein folding?

All of the information necessary for proper folding is inherent in the primary structure and there is no energy necessary for them to properly fold


What is Levinthal’s paradox and what realization did it lead to?

There is not enough time for proteins to try every conformation and choose the best one. This leads to the idea that there is a predetermined pathway


Why is crowding in cells a challenge for proper protein folding?

Interactions of amino acids with other proteins toward aggregation competes with proper folding. When folding takes place in a crowded environment there are many other proteins around with which the protein may aggregate


Explain the excluded volume effect and how it makes it so that the effective concentration inside cells is smaller than the actual volume.

In a crowded cell, a small molecule could fit into essentially any part of the open space. However larger molecules require a larger space which excludes much of the open space because. This makes the protein act as though the concentration was higher than it actually is (effective concentration vs actual concentration).


What proteins are at an elevated risk for aggregation?

New, unfolded proteins
Mutated proteins
Nuclear proteins
Proteins that become unfolded as a result of stress conditions


What mechanism do cells use to overcome the challenge to proper protein folding that crowding presents?

Helper proteins such as chaperones which protect the unfolded protein from unwanted interactions and allow it to fold properly


What is the function of peptidyl-prolyl cis trans isomerase (PPI)

It catalyze the inter conversion of cis and trans isomers of proline peptide bonds allowing for better protein folding


What is the role of protein disulfide isomerase (PDI) in protein folding?

IT catalyze disulfide bond formation


What are the three broad classes of chaperone proteins briefly describe each.

Small heat shock proteins- very small, ATP independent aid in the formation of oligomeric complexes
Low MW - relatively small, ATP dependent, bind to hydrophobic regions until they can properly fold
High MW- large proteins, ATP dependent, form a cage-like structure around the protein preventing it from interacting with anything else and allowing it to fold


What are the two main classes of protein folding diseases? Give an example of each.

Loss of function and gain of function
Cystic fibrosis is an example of loss of function because the disease is caused by misfolded and ineffective CFTR protein
Systemic amyloidosis is an example of gain of function because proteins that wouldn’t normally aggregate do forming plaques that damage tissues


Explain how alpha-1 antitrypsin deficiency is both a loss of function and gain of function disease.

Normally, alpha-1 antitrypsin coats and protects the lungs from damage. However the misfolded protein does not fulfill this role and leaves the lungs to be damaged (loss of function) in addition, misfolded protein accumulates in the liver causing liver damage (gain of function)


What is congo red?

It is a dye that is used to diagnose systemic amyloidosis. It turns fluorescent green when positive for amyloidosis


What protein structure often defines systemic amyloidosis aggregates?

Cross Beta sheets


Briefly differentiate between the three main types of systemic amyloidosis.

Primary- the most common, caused by overexpression of light chain immunoglobulin which aggregates
Secondary occurs as a result of chronic inflammation
Familial is hereditary based on a mutation to the TTR protein


What are prions?

Misfolded proteins which when in contact with properly folded versions of that protein act as a template for the properly folded protein to take on the misfolded form. Thus they are like protein infections


Compare and contrast foldases and chaperone proteins.

Both are used by cells to promote proper folding of proteins under crowded conditions. Foldases actively catalyze reactions related to folding while chaperones similar protect the protein from interacting with other proteins to allow it to fold by itself


How much DNA is found within the nuclear genome?

About 6000 Mbps


Where does most of the variability between the DNA of individuals occur?

In repeated DNA elements


Describe the structure of mitochondrial DNA

Circular similar to bacteria, contains about 37 genes 5-10 copies of genome per mitochondrion


How much of the variation in gene expression between individuals is explained by SNP’s?



What differentiates between a SNP and a mutation?

A SNP is relatively common, occurring in at least 1% of the population while mutations are more rare


How much of the variation in gene expression between individuals is explained by copy number variants?



What are copy number variations? What roles do we know that they play?

Deletions or duplications of sections of DNA of 1kb to 1Mb in size. They are important in the normal function of special senses and play a role in diseases such as cancer, autism, schizophrenia


What is a tandem repeat? What are the 3 types?

A specific pattern of nucleotides repeated over and over right next to each other. They occur mostly in non-coding regions
1 satellite DNA
2 mini satellite DNA
3 microsatellite DNA


Describe the two main types of satellite DNA.

Alpha-satellites = centromeres
Beta satellites - variable regions on acrocentric chromosomes. They occur near the centromeres


Differentiate between Satellite DNA, Microsatellite DNA and Minisatellite DNA.

All are tandem repeats and they are different classifications based on size
Satellites are larger than 100bp
Mini satellites are 10-100 bp
Microsatellite are 2-4 bp


What type of tandem repeat are telomeres?

Minisatellites because they are. 6 bp repeats


Why are mini satellites extremely variable?

They are hotspots for recombination and replication errors because of their similarity


What is a splice site mutation?

A mutation that occurs in the 2bp before or after an exon that determines splicing. These are almost always harmful


Give an example of the nomenclature of all of the following:
A nonsense mutation
A frameshift mutation resulting in a premature stop codon
A point mutation in cDNA
A point mutation in genomic DNA
A single amino acid change
A mutation to the splice site before an exon
A mutation to the splice site after an exon

C.397delAG (p.Gly47Ilefs*80)


Compare and contrast exogenous and endogenous DNA damage.

Exogenous occurs when the damaging factors comes from without the cell while endogenous is when the damaging factor comes from within the cell


What are the 2 main types of exogenous DNA damage and what kind of damage does each one cause?

1 UV- irradiation- tends to cause thymine dimers which are repaired by nucleotide excision repair
2 Alkylating agents- tend to affect guanine residues and may add small or large chains that can distort the helix and cross link strands. Alkylating agents tend to cause cancer


Describe depurination.

Adeline’s and guanine are often spontaneously lost during replication. This is one major cause of mosaicism


Describe deamination of cytosine.

An amine group is lost from cytosine turning it into uracil. Because uracil bonds with adenine, the base is changed in the next replication. This is a common cause of endogenous DNA mutations


How can reactive oxygen species cause DNA damage?

They add carbonyls onto guanine which makes it as likely to pair with adenine as with cytosine which then results in DNA mutations during replication

8 oxo guanine


What common mistakes occur during replication that can lead to mutations?

1 Slippages occur during microsatellites leading to deletions or duplications of genes
2 Tandem repeats can lead to unequal crossing over in meiosis leading to deletions and duplications of major portions of DNA


What is haploinsufficiency?

When 50% of a protein is not enough to be functional. This causes heterozygous individuals with a null mutation to have a disease phenotype


What is a dominant negative?

A mutant protein that loses its normal function and also interferes with the normal protein product such as through competitive inhibition in transcription factors and multimeric proteins


What types of errors will base excision repair fix?

Purine loss and 8-oxo-guanine


What is the function of MUTYH protein and what happens when it is mutated?

It is involved in 8-oxo-guanine DNA repair mutations cause a recessive phenotype leading to many colon polyps and increased risk for colorectal cancer called MUTYH associated polyposis


What types of errors can nucleotide excision repair fix? What kind of phenotypes result from mutations to this machinery?

Repairs bulky DNA lesions such as thymine dimers. Mutations to machinery lead to recessive phenotypes increasing sensitivity to the sun and risk of skin cancer


What 4 genes are responsible for mismatch repair? Which of them dimerize?

MLH1, MSH2, MSH6, and PMS2
MLH1 and PMS2 dimerize as do MSH6 and MSH2


Outline the steps of the double stranded DNA damage signal and repair system including what protein (s) are involved and what results from mutation to that protein.

1 Maintenance of structure and integrity of DNA - BLM (helicase) - Bloom Syndrome (recessive)
2 Signal the repair process - ATM - ataxia telangiectasia
3 Locate damage and trigger repair- FANC genes - Fanconi anemia
4 Repair of DNA - BRCA1 and BRCA2- Hereditary breast and ovarian cancer (dominant)
5 End joining of dsDNA - NBN, Rad50 and MRE11A - Nijmegen breakage syndrome


What protein is involved in single stranded DNA repair?



Why could PARP1 potentially be used as a therapeutic agent for cancers related to a mutated BRCA1 or BRCA2?

PARP 1 is involved in single stranded DNA repair and BRCA1 and 2 are related to double stranded repair. These processes have some overlap and if both are compromised, cell death is triggered. Cancers where BRCA1 or 2 is mutated would then trigger cell death if PARP1 is compromised


What is the difference between a nucleotide and a nucleoside?

Nucleosides do not contain phosphate groups


How many rings do purines have? How about Pyrimidines?

Purines: 2
Pyrimidines: 1


What is the major source of nucleotides in humans?

De novo synthesis of nucleotides


Outline the Pentose Phosphate pathway and explain its importance. Include the rate limiting enzyme

Glucose 6 phosphate from glycolysis is converted to Ribose 5 phosphate by the reduction of 2 NADP to NADPH. Then Ribose 5-phosphate is converted to 5 Phosphoribosyl-1-pyrophosphate PRPP which is important in nucleotide synthesis. NADPH is also an important antioxidant.
The rate limiting enzyme is glucose 6 phosphate dehydrogenase


What occurs as a result of glucose 6 phosphate dehydrogenase deficiency and why? What is the inheritance pattern?

Results in hemolytic anemia in response to infection, certain drugs and fava beans which all increase levels of reactive oxygen species. this occurs because glucose 6 phosphate dehydrogenase catalyzes the rate limiting step of the pentose phosphate pathway which produces NADPH an important antioxidant

X-linked recessive


Outline the major steps of purine biosynthesis from Ribose 5-phosphate. Include the key enzyme and major substrates.

Ribose 5P—> PRPP—> 10 steps —> IMP—> 2 steps—> AMP or GMP
Key enzyme: glutamine PRPP aminotransferase
Important substrates: Amino acids (glutamine x2, glycine, aspartate), Carbon sources (HCO3- and THF)


Outline the pathway of adenosine catabolism. Include 2 key enzymes

AMP-> Adenosine->Inosine->Hypoxanthine->Xanthine->Uriel acid
Key enzymes: Adenosine deaminase - catalyzes adenosine to inosine
Xanthine oxidase- catalyzes hypoxanthine to Xanthine and Xanthine to Uric acid


OUtline the pathway for catabolism of Guanine.
Include 1 key enzyme

GMP->Guanosine->Guanine->Xanthine->Uric acid
Key enzyme Xanthine oxidase- catalyzes Xanthine to Uric acid


What symptoms would occur as a result of a deficiency of adenosine deaminase and why?

Severe combined immunodeficiency called (scid) occurs because ADA leads to the buildup of ATP which inhibits RNR which catalyzes dNTPS. Without dNTP’s cells can’t divide and this kills T lymphocytes and B lymphocytes which constantly divide


Describe how gout and its treatment relates to purine metabolism.

Gout occurs when Uric acid builds up and forms crystals leading to chronic inflammatory arthritis. This occurs as a result overactivity of purine catabolism. It can be treated with allopurinol which resembles hypoxanthine and inhibits Xanthine oxidase lowering the production of Uric acid


Describe the major and minor pathways of purine salvaging and the enzymes for each.

Adenine + PRPP-> AMP + ppi
Enzyme: Adenine phosphoribosyltransferase APRT
Hypoxanthine + PRPP->IMP +PPI->AMP or GMP
Enzyme: Hypoxanthine-guanine phosphoribosyltransferase HPRT


What disorder results from HPRT deficiency and why?

Lesch Nyhan syndrome- severe hyperuricemia and compulsive self-mutilation.
This occurs because HPRT salvages purines and if they are not salvaged they will produce Uric acid in over abundance and create hyperuricemia


What is the committed step of purine biosynthesis?

Conversion of PRPP to 5-phosphoribosyl amine (2nd step)


List the substrates and key enzyme of Pyrimidines biosynthesis

Substrates: amino acids (glutamine and aspartate) and Carbon sources: CO2 and THF
Key enzyme: carbamoyl phosphate syntheses II


What is the committed step of pyrimidine biosynthesis?

Production of carbamoyl phosphate by carbamoyl phosphate synthetase II (CPSII)


Outline the major steps in synthesis of Cytosine.

CO2+Glutamine + ATP->4 Steps-> +PRPP-> 2 steps-> UMP->UDP->UTP->CTP->dCTP


Outline the major steps in Thymine biosynthesis

CO2 + Glutamine +ATP->4 Steps->+PRPP-> 2 Steps-> UMP-> dUMP-> dTMP

methylene tetrahydrofolate (THF) is required for final step


How are Pyrimidines salvaged?

Cytidine + ATP -> CMP +ADP


What are the end products of catabolism of Pyrimidines? HOw are they different from the end product of purine catabolism?

Cytidine and uridine -> alanine
Thymidine-> amino butyrate

Their rings are no longer intact making them water soluble so they don’t cause disorders unlike uric acid the product of purine biosynthesis.


What causes orotic aciduria and what are its symptoms?

Symptoms: megaloblastic anemia, crystalline sediment of orotic acid in urine, slow growth
Caused by a deficiency in UMP synthetase which prevents biosynthesis of Pyrimidines. Lack of Pyrimidines leads to the above symptoms


What is a major difference between the biosynthesis of purines and that of Pyrimidines.

In pyrimidine biosynthesis, heterocyclic rings are synthesized first and then bound to ribose phosphate. The opposite is true in purine biosynthesis.


How is the production of deoxyribose thymine different from that of other Pyrimidines?

All other Pyrimidines are converted to deoxyribonucleotides from their corresponding ribonucleotide. However, thymine is converted from deoxyribouracil.


What enzyme catalyzes the conversion of ribonucleotide of cytosine to deoxyribonucleotide?

Ribonucleotide reductase


Describe how ribonucleotide reductase is allosterically regulated. What disorder does this relate to?

ATP activates it and dATP inhibits it. This relates to SCID in which adenosine deaminase is deficient leading to accumulation of dATP’s which inhibit ribonucleotide reductase preventing the production of dNTPs


What is folate? How is it converted to its active form?

Folate is a B-vitamin that plays an important role in nucleotide synthesis by being a carbon source. It’s active form is tetrahydrofolate (THF) it is converted from folate by successive reductions with NADPH by the enzyme dihydrofolate reductase


Describe how each of the following function as chemotherapeutic agents:
5 fluorouracil

All function in some way by inhibitting pyrimidine biosynthesis preventing the production of nucleotides needed for replication
5-fluorouracil is a structural analog of thymine and blocks the conversion of dUMP to dTMP
Methotrexate is a structural analog of folate and competitively inhibits dihydrofolate reductase preventing the formation of THF which is necessary for nucleotide synthesis including conversion of dUMP to dTMP
Hydroxyurea inhibits ribonucleotide reductase preventing the formation of deoxyribonucleotides from their corresponding ribonucleotides


Briefly describe the structure of the ER import sequence.

It is found near the N-terminus and is made up of hydrophobic amino acids


Briefly describe the mitochondria import sequence.

It is found near the N-terminus and contains regularly distributed basic (Positively charged) amino acids


Briefly describe the structure of the nuclear import and nuclear export signal sequences.

Import: Short and made up of positively charged amino acids
Export: short and made up of hydrophobic amino acids


What is the ER retention signal? What is it like?

It signals that a protein is to be maintained within the lumen of the ER rather than to be transported to another organelle. It is 4 amino acids at the C terminus with varying characteristics


Define paternal and maternal imprinting.

In paternal imprinting, the father’s copy of a gene is methylated and turned off. IN maternal imprinting it is the mother’s copy that it methylated and turned off


Explain how the transferrin receptor is an example of RNA stability used to control gene expression

Transferrin gene is constantly transcribed but its mRNA is degraded and not translated unless iron is low in which case it is immediately translated. Allows the body to react immediately to low iron


What is the function of snRNA?

They regulate splicing


What is aplastic anemia?

A rare form of anemia caused by failure of the bone marrow to produce all blood cell types


Where do most achondroplasia mutations come from?

80 to 90% are de novo mutations and all de novo mutations come from the father


Explain the function of the two gene therapies to treat SMA.

Spinrata-causes inclusión of exon 7 to be more likely in smn2.
Zolgensma delivers the smn1 gene in adeno associated virus


What is the haldane hypothesis?

It states that a genetically inherited disease causing death before eproduction should decrease by 1/3 each generation. This shows us that 1/3 of Duchenne muscular dystrophy cases are de novo mutations because the frequency is remaining constant


What is heteroplasmy?

A specific form of mosaicism that results from differences in the number of normal and abnormal mitochondria within each cell


What is the natural, resting state of DNA?

30nm fiber


What are the possible causes of polyploidy?

1 Fertilization of ovum by 2 sperm
2 an error in meiosis 2 of oogenesis


Is the father or mother more likely to contribute a structurally abnormal chromosome?

The father


What is the likely phenotype for an individual with a chromosome translocation?

They may be phenotypically normal if they have a full compliment of genetic material but have problems with reproduction because of difficulties of lining up chromosomes in meiosis


What other sex chromosome abnormalities exist in addition to turner’s Syndrome and klinefelter’s syndrome. What are the symptoms?

47,XXX and 47,XXY- these usually show no significant physical phenotype and only a mild learning disability


What is the usual cause of Turner’s syndrome?

Lack of a paternally inherited X chromosome


What is a cystic hydroma? What condition is it associated with?

A sac of fluid that forms during development near the back of the neck associated with Turner’s syndrome


Give the cause and major symptoms of Williams disease.

Caused by a deletion on chromosome 7
Symptoms: delayed speech and development, unique face, mild to moderate mental retardation, feeding issues, and cocktail personality


For which if the genetic testing methods can SNPs be a problem?

Any of them that use probes or primers such as PCR, Sanger sequencing and multiple probe ligations MLPA


Where does erythrophoiesis occur?

In the bone marrow, specifically the medullary space of long bones and especially in the hip


What is erythropoietin?

A hormone that is released in response to low levels of oxygen and causes increased erythropoiesis


What is extramedullary erythropoiesis? What is it an indication of?

Production of red blood cells occurring outside of the bone marrow. Most often in the liver, spleen and lymph nodes. Occurs normally in embryos but in adults it is a sign of RBC turnover or bone marrow failure. It is also associated with hereditary spherocytosis


What structural changes occur to forming red blood cells across each stage of erythropoiesis (generally)?

They get smaller, more hemoglobin and more chromatin condensation with each step


What is a holoprotein? Describe how both hemoglobin and myoglobin can be classified as holoproteins?

A holoprotein is a protein that contains at least one non-protein prosthetic group. The heme group is a non-protein prosthetic group


Describe the structure of the heme group.

It is a porphyrin ring with 4 nitrogen containing rings each of with interacts with Fe which is at the center


What protein structures are most prevalent in myoglobin and the hemoglobin subunits?

Alpha hélices


What is the Bohr effect?

The effect of low pH on hemoglobin binding curve. Namely, at low pH protons bind to hemoglobin stabilizing the T state and dramatically lowering the affinity for oxygen


How are all of the different hemoglobin genes arranged in the genome?

The various hemoglobin genes are arranged so that the genes for like subunits are grouped together.
Chromosome 16 contains 1 zeta gene and 2 alpha genes close to each other
Chromosome 11 contains 1 delta, 1 epsilon, 2 gamma and 1 beta gene all close together


Suppose 1 mutant hemoglobin variant lowers the affinity for oxygen and another raises the affinity for oxygen. Which will likely be more damaging to the individual?

The one that raises affinity


Describe hemoglobin C gene.

Caused by a mutation at the exact same locus as sickle cell disease that changes to a positively charged amino acid instead of a hydrophobic amino acid (like in sickle cell). It is homozygous recessive and causes a milder anemia than sickle cell. Individuals who are heterozygous for the hemoglobin C allele and sickle cell allele have sickle cell anemia but it is usually milder than those who have homozygous for sickle cell trait


What other factors besides a mutation could lead to a gain of function disease of protein folding?

Abnormal protein concentration and protein infections


What acronyms correspond with each type of systemic amyloidosis?

Primary = AL
Secondary = A
Familial = ATTR


What is the difference between synonymous and non-synonymous SNPs?

Synonymous do not cause amino acid changes while non-synonymous do


What is another name for a minisatellite? What is another name for a microsatellite?

Minisatellite = variable number tandem repeat
Microsatellite = short tandem repeat


Explain the term compound heterozygote.

An individual who has inherited two partially functional genes. Phenotype depends on the severity of the reduced function of each gene. An example would be someone who inherited one sickle cell allele and one hemoglobin C allele. In this case they would display a phenotype more severe than homozygous for hemoglobin C but less severe than homozygous for sickle cell


What is the role of mismatch repair in DNA repair?

It fixes replication errors, mismatched nucleotides, and problems with microsatellites


Where does metabolism of purines take place?



What enzyme catalyzes the formation of deoxyribonucleotide thymine?

Thymidine synthetase


What are the 3 main functions of the plasma membrane?

1 Receiving information
2 Import and export
3 Movement and change of shape


What is meant by the fluid mosaic model of the plasma membrane?

Describes the way the membrane acts which is like a fluid in 2 dimensions


Describe the general components that make up the plasma membrane and how they are arranged.

The major component is phospholipids which contain a hydrophilic head and 2 hydrophobic tails. These form a lipid bilayer with hydrophilic heads on the outside and hydrophobic tails in the center. Another major part of membranes are proteins. Cholesterol is present inside of the membrane and fills in the gaps between hydrophobic tails as well as making the membrane less permeable. Finally sugars are found on the outside of the membrane covalently attached to either proteins or lipids.


Diagram the structure of a general phospholipid in the plasma membrane.

A hydrophilic head attached to phosphate which is attached to a glycerol molecule with 2 hydrophobic tails coming off of it. On one of the fatty acid tails, a cis double bond causes a kink


What is meant by the term amphipathic and how does it relate to molecules in the plasma membrane?

Amphipathic means having both a hydrophobic and hydrophillic region in the same molecule. Proteins and lipids in the membrane are amphipathic allowing them to form a bilayer


What are the four major types of phospholipids? Briefly describe how they differ. What is the minor 5th? And what is its importance?

1 Phosphatidyl ethanolimine
2 Phosphatidylserine
3 Phosphatidylcholine
4 Sphingomyelin

1-3 are exactly the same other than the hydrophilic head group which is reflected in their name.
Phosphatidyl serine is - charged while the rest are neutral

4 has a choline head group but is attached to the hydrophobic portion by a different molecule other than glycerol

5 (minor) Phosphatidyl inositol- important for recruiting signaling molecules


Describe the ways that lipids move within the plasma membrane.

They move freely in: lateral diffusion (side to side), flexión (movement of tails), and rotation (spinning in place)

Flip flop or changing from one side of the bilayer to the other is rare and requires flipase or flopase enzymes. This type of movement is important in membrane synthesis


Describe the asymmetry of the lipid bilayer.

There are differences between the outer and inner layers of the bilayer. Mainly glycolipids and proteins are found only on the outer layer and the inner layer is more negatively charged due to the presence of Phosphatidyl serine and Phosphatidyl inositol


What types of things will and won’t pass freely through the plasma membrane.

Will: hydrophobic molecules small or large such as O2 or steroids

Rarely will: Very small hydrophilic molecules

Won’t: large hydrophilic molecules or charged molecules of any size


What are lipid rafts?

Regions of the membrane with distinctive structure and function. They contain a lot of cholesterol and glycosphingolipids which makes them thicker and less fluid and this determines what proteins will be present here. They are often involved in cell signaling


What are the 2 major categories of membrane proteins and the subgroups within each category.

1 Integral- directly attached to the membrane and require detergents to be separated
A Transmembrane- passes through the entire membrane
B Membrane associated
C lipid linked - B and C are covalently bound to membrane components

2 Peripheral- interact non-covalently with membrane proteins and can be separated without detergent
A Protein attached


What are the 4 main functions of membrane proteins?

1 Transporters
2 Anchors
3 Receptors
4 Enzymes


Describe the primary structure of transmembrane proteins.

They are amphipathic with regions of hydrophobicity which pass through the center of membranes and hydrophilic regions that remain on the outside of the bilayer


Describe the common secondary structures of transmembrane proteins.

They often form alpha helices in their hydrophobic regions which allow them to show hydrophobic amino acids on the outside of the helix. Sometimes multiple amphipathic alpha helices will combine together to form a hydrophilic pore where hydrophilic molecules can pass through the membrane

Less often, beta sheets can be found which can form beta barrels which appear barrel like and function similarly to hydrophilic pores formed by alpha helices


In what ways can the lateral diffusion of membrane proteins be restricted? (4)

1 They can be bound to cytosolic proteins
2 they can be bound to extracellular proteins
3 they can be bound to proteins on other cells
4 The cell can form barriers to diffusion


What is the cell cortex?

A framework of fibrous proteins that links proteins in the membrane together to strengthen the otherwise weak membrane


What are glycoproteins and proteoglycans?

Glycoproteins are proteins linked to sugars that are common in the outer side of the plasma membrane. Proteoglycans are a specific kind of glycoprotein that is heavily glycosylated with long, repeating, unbranched amino containing sugars unlike the shorter non-repeating and branched sugars on most glycoproteins. Proteoglycans are especially important in forming the extracellular matrix and connective tissues


Describe the glycocalyx. What are its functions? (3)

The layer of sugars on the outside of the plasma membrane made up of glycolipids and glycoproteins. It functions to protect the membrane from mechanical damage, cell-cell signaling and lubrication of extracellular space in vascular system


Describe radiography in terms of energy , how it shows tissue differenc, benefits and limitations.

Energy: X-rays
How it shows differences: different electron densities
Benefits: Fast, great resolution
Limitations: Poor tissue contrast, uses radiation


Describe Computed tomography (CT) in terms of energy , how it shows tissue differenc, benefits and limitations.

Energy: X-rays
HOw it shows differences: Different attenuation of x-rays relative to water
Benefits: Very good contrast at all tissue densities
Limitations: TOns of radiation


Describe magnetic resonance imaging (MRI) in terms of energy , how it shows tissue differenc, benefits and limitations.

Energy: Radio waves
How it shows differences: different rates of nuclear relaxation
Benefits: Best tissue contrast, no radiation
Limitations: Slow and expensive, magnet dangers


Describe Ultrasound in terms of energy , how it shows tissue differenc, benefits and limitations.

Energy: Sound waves
How it shows difference: Different acoustic impedance
Benefits: Real time imaging, no radiation
Limitations: User dependent, many artifacts


Describe nuclear medicine in terms of energy , how it shows tissue differenc, benefits and limitations.

Energy: Gamma rays
How it shows difference: different levels of radioactivity
Benefits: See physiology and pathophysiology in action
Limitations: Worst resolution, Radiation


Compare and contrast simple diffusion and protein-assisted diffusion.

Diffusion always refers to passive movement of molecules down their concentration gradient. In simple diffusion they cross the membrane directly- this is only possible for small, hydrophobic molecules. In protein assisted diffusion, proteins embedded in the membrane allow movement of larger or hydrogphilic compounds


What is flux? What is net flux?

Flux is the amount of molecules crossing a membrane at any given time. Molecules are always crossing in both directions so net flux is the difference between the two one-way fluxes


What is Fick’s law?

It explains how much of a given molecule will diffuse across a membrane.
Diffusion is directly proportional to:
K- permeability of solute
A- Surface area of membrane
C = solute concentration gradient
Diffusion is inversely proportional to :
delta x - distance the solute must travel


What factors influence permeability constant (K)?

Lipid solubility- directly proportional
Solute size- indirectly proportional


What are the two main types of protein-assisted diffusion?

Ion channels
Facilitated diffusion


Compare and contrast ion channels and facilitated diffusion in terms of how they work, how quickly they work, what they can transport and how they select for solutes.

They both function on passive diffusion that is they do not require energy and transport only in the direction of the concentration gradient. Ion channels simply work by creating a very small pore in the membrane that will allow ions through, they work very quickly, can only transport ions and use size and charge of amino acids within the pore to select solutes.

Facilitated diffusion works by binding the solute at a specific site causing a conformational change which allows the solute to be released within the cell, they work much slower, they can transport ions or larger molecules, and they select based on the specific molecule’s ability to bind at the active site.


In what 3 ways can ion channels be gated?

1 Ligand gated - activated by binding of a signaling agent
2 Voltage gated- activated by changes in membrane potential
3 Mechanically gated- activated by physical deformation of the surrounding membrane


What is an electrochemical gradient?

Diffusion of ions depends not only on the concentrations of that specific ion but also concentrations of charge on either side of the membrane


What is membrane potential? What is the resting potential of cells like?

Membrane potential is the difference in charge on either side of the membrane. Generally, cells have more negative charge inside than out (-70mv)


What are the 2 types of active transport how are they different?

Primary- uses ATP for energy
Secondary uses ion gradient for energy


Diagram how primary active transport works.

Solute binds to pump protein-> ATP is hydrolyzed -> Pi binds to pump-> conformational change of pump allows solute to enter/exit the cell


Describe how the sodium potassium pump works. What type of transport is it and why?

It transports 3 sodium out of the cell and 2 potassium into the cell against their gradients with the use of 1 ATP.

This makes them primary active transport


What are the two types of secondary active transport? What is the usual energy source in the body?

The usual energy source is the sodium gradient.
1 Co-transport = solute moves in the same direction as sodium
2 Counter-transport/antiport = solute moves in the opposite direction of sodium


Why can water move across the membrane even though it is polar?

It can’t unless there are channels called aquaporins which are present in different concentrations in most cells. Amount of aquaporins determines speed of osmosis.


What is the typical osmolarity of body fluids?

300 mOsm


What is the difference between osmolarity and tonicity?

Osmolarity is the concentration of all solutes
Tonicity is the concentration of only non-permeable solutes

Most solutes in the body function as if they were non-permeable so the two are usually very similar


How does the cell respond to a hypertonic, isotonic and hypotonic solution?

Hypertonic- water leaves, cell shrinks
Isotonic- no net movement of water, no change in cell size
Hypotonic- Water enters cell, cell swells


Why do sodium and potassium behave as non-penetrating solutes even though they can pass through channels in the membrane?

Because they are quickly pumped by the sodium potassium pump to maintain their gradients.


What is the role of the Smooth endoplasmic reticulum? What is its structure?

It is made up of roles rolls of membrane which may be contiguous with the rough ER but does not contain ribosomes.
It’s function is to synthesize fatty acids and phospholipids


What types of cells would you expect to have abundant smooth endoplasmic reticulum?

Cells which produce a large quantity of lipids such as steroid producing cells for example the adrenal cortex or the leydig cells in the testes


What is smooth endoplasmic reticulum called in skeletal cells? What is its specialized function?

Sarcoplasmic reticulum, it sequesters calcium ions which play an important role in the contractile impulse


Describe the specialized role of the smooth endoplasmic reticulum in liver cells.

It helps to detoxify some hydrophobic compounds turning them into water soluble compounds which can be excreted in the urine. These include toxins such as carcinogens and pesticides and drugs like ethanol and the barbiturates thiopentanal and phenobarbital


What are the 3 main functions of vesicular transport?

1 Deliver newly made molecules to destinations
2 Communicate with extracellular environment
3 Ingest extracellular particles and solutes


Distinguish between the 2 major pathways of vesicular transport

Secretory pathway- in to outmoves from the ER to the golgi and from there it can move to the plasma membrane or lysosomes

Endocytic pathway - out to in
Moves from outside of the cell to components within the cell


What is budding? What is fusion?

Budding is when the vehicle breaks off from the membrane at its origin

Fusion is when the vesicle joins the membrane at its target


What is vesicle coating? What are its 2 functions?

Proteins that cover the outside of vesicles during budding and will be removed prior to fusion
They function to help vesicle bud off and to aid in sorting of proteins


Describe the structure of clathrin. What is its function?

It is the most important vesicle coating protein
It has 3 light and 3 heavy chains that form a 3 armed spiral structure called a triskelion. When coating vesicles it creates a honeycomb like lattice structure around the outside of the forming vesicle forcing the membrane into a circular shape


Diagram and describe how clathrin and other proteins are involved in protein sorting.

Clathrin binds to adaptin which binds to a receptor that is specific for a type of cargo. Different forms of adaptin exist in different areas which allow different receptor/cargo pairs to enter vesicles. After budding, clathrin and adaptin are released from the vesicle but the receptor and cargo remain


What protein pinches budding vesicles off from the membrane?



Describe the process and proteins involved in docking and fusion of vesicles.

First, Rab protein on the vesicle binds to a tethering protein on the target which pulls the vesicle closer to the membrane. Here v-Snare on the vesicle binds to T-snare on the target and the two pull each other so close together that fusion occurs


What are the 3 most common post-transcriptional modifications that take place in the ER?

1 Disulfide bonds- both intrachain and interchain
2 Lipid membrane anchors are added covalently
3 Glycosylation- usually to the N-terminus of asparagine residues but occasionally also to serine or threonine


Detail the process of glycosylation in the ER?

Dolichol protein embedded in the ER membrane holds the oligosaccharide until it will be added to the asparagine residue by the enzyme oligosaccharyl transferase


Describe the protein quality control that occurs in the ER.

ER does not allow proteins that either misfolded or did not join with the proper subunits to leave the ER. This is accomplished by chaperone proteins which bind to the unfolded protein and prevent other interactions until it is properly folded. If the protein never folds properly it is held by chaperones until it is eventually exported to the cytosol for degradation


Explain the connection between cystic fibrosis and ER quality control of proteins.

The mutated protein in the cystic fibrosis gene could be at least partially functional if it reached the plasma membrane but instead it is prevented by the quality control mechanisms of the ER leading to its degradation and a severe phenotype


Describe the structure of the golgi.

The golgi is made up of several long, flattened membranes piled on top of each other kind of like a stack of pancakes. One end is called the cis face which is where vesicles enter and the other is the trans face where vesicles exit. Cargo moves by vesicles from one membrane bound layer to another throughout the golgi until reaching the trans face


What actions occur to proteins as they move through the golgi?

They are sorted and oligosaccharides are added or removed


Differentiate between the two types of exocytosis.

Constitutive secretion- occurs at all times unregulated in all cells. It carries new proteins and lipids to the plasma membrane and transports other cargo outside of the cell

Regulated secretion occurs only in specialized secretory cells such as those that release hormones. In this case vesicles storing tightly packed cargo are produced and wait near the membrane until a signal is received that causes them to fuse to the membrane releasing their contents.


What are acid hydrolases?

The proteins in the lysosome that degrade different types of molecules and function under the lower pH of the lysosome relative to the rest of the cell. They are highly glycosylated to allow them to withstand the low pH.


Describe how lysosomal enzymes are targeted to the lysosome from the ER.

These proteins contain a short amino acid sequence that targets them to lysosomes. Once in the golgi, a mannose-6 phosphate is added to these proteins. In the trans face of the golgi, the mannose-6phosphate binds to mannose-6phosphate receptors in clathrin coated pits with then form vesicles bound for early or late endosomes which will mature into lysosomes


Describe the causes and symptoms of lysosomal storage diseases. Give a few of the most common and the most severe.

Diseases caused by a defected hydrolase or cofactor that functions in the lysosome to degrade a specific molecule. This causes that molecule to build up and become toxic. Babies with these diseases appear normal at birth but show symptoms very early. Life expectancy is 15 years. Most common are : Gaucher disease, Hurler syndrome and Hunter syndrome.
The most severe is I-cell disease which causes is a defect in the enzyme that adds mannose-6-phosphate to hydrolases so none of them reach the lysosome.


What are the 3 types of endocytosis?

1 Phagocytosis- injestion of large particles only in specialized immune cells
2 Pinocytosis- non-specific constitutive injestion of fluid and solutes that occurs in all cells
3 Receptor mediated endocytosis- very specific uptake of molecules which bind to receptors in the membrane


How are constitutive exocytosis and pinocytosis related to each other?

Both are occurring constantly and non-specifically and they compliment each other so that one process doesn’t significantly change the amount of membrane in a cell


Briefly describe how phagocytosis works.

Membrane extends projections called pseudopods out to engulf whatever large particle it is trying to injest until it covers the entire particle and brings it in


What is the fate of endocytosed molecules?

They first go to early endosomes near the plasma membrane. This causes most receptors to release their substrate because of the slightly acidic environment. Endosomes sort cargo and most of the cargo released from receptors ends up in the lysosomes for degradation


Explain how LDL cholesterol gets into cells.

LDL cholesterol is a complex containing cholesterol surrounded in a lipid monolayer which is surrounded by an organizing protein. This allows transport of cholesterol in blood although it is hydrophobic. This entire complex binds to receptors and is endocytosed. In the early endosomes, the cargo is released from the receptor and in the lysosome, it is degraded, releasing cholesterol which diffuses out through the membrane and into the cytosol of the cell


Describe the cause and symptoms of familial hypercholesterolemia.

Caused by a mutation in the LDL receptor that would normally allow for receptor-mediated endocytosis that causes it to be either missing or non-functional. Thus LDL doesn’t enter cells and accumulates in the blood stream which can lead to atherosclerosis and early cardiovascular disease. Patients are treated by controlling their diets and using cholesterol lowering drugs such as statins


Why does signal transduction usual occur over many steps instead of a few?

This allows:
1 Signals to be regulated at each step
2 Signals to be amplified
3 Signals to be distributed to several processes at the same time


What 3 actions/molecules often form part of a signal cascade?

1 Enzyme activity- ex kinases
2 Protein-protein interactions
3 Second messenger molecules


How can different cells respond differently to the same signal?

Different receptors could be present on each cell that start differing cascades or the signaling pathways could be different downstream


Why is withdrawal of a signal important? What actions can be taken to withdraw the signal?

Proper withdrawal is as important as signaling itself because it if is withdrawn too quickly it can’t have a large enough effect and if it is withdrawn too slowly it could have too dramatic of effects or the receptor could be downregulated as a result. Withdrawal can occur by removing the signal molecule via diffusion, degradation or endocytosis by neighboring cells or it could occur by downregulation of the receptors either by reduced synthesis or internalization


Describe the cause, symptoms and treatment for myasthenia gravis

Myasthenia Gravis is an autoimmune disease in which antibodies are formed against acetylcholine receptors in skeletal muscle preventing reactivity to acetylcholine. Symptoms include severe fatigue, a droopy eyelid, unsteady walking and difficulty swallowing. It can be treated by acetylcholinesterase inhibitors which prevent degradation of acetylcholine and increase its concentration


What type of signals might cause immediate modifications? What signals might cause slower, long-term changes?

Immediate changes could be caused by changes in protein activity for example in changing the shape of the cell.

Slower long-term results take place from signals which affect gene expression because time is needed to transcribe, translate, modify and transport protein that is expressed


Compare and contrast the structure of G-protein coupled receptors and Receptor tyrosine kinases.

Both contain an extracellular domain which binds to the signal molecule and both contain intracellular domains which bind to proteins. The main difference is that GPCR’s pass through the membrane 7 times while RTK’s pass through only once.


Describe the general process of activation of a G-protein coupled receptor.

The GPCR is bound to a trimer of G-proteins alpha, beta and gamma. The alpha is bound to a GDP but once the signal molecule is bound to the receptor, it causes the GDP to be replaced with GTP. This change causes the alpha and beta/gamma subunits to dissociate from the receptor and become active. These subunits bind to their targets to affect some change which they causes phosphorylation of the GTP back to GDP and the trimer reforms and binds to the GPCR once again.


What are some of the classes of GPCR functions?

They can regulate ion channel activity or regulate membrane bound enzymes such as adenylyl ciclases


What are the functions of Gi Gs and Gq GPCR’s?

Gi- inhibits adenylyl cyclase
Gs activates adenylyl cyclase
Gq activates phospholipase C


What pathways are enzyme linked receptors generally involved in?

Pathways related to growth, proliferation, differentiation and survival. Their substrates are often growth factors. For this reason dysregulation of these pathways often results in cancers


What is the most common type of enzyme linked receptor?

Receptor tyrosine kinases


Generally describe how receptor tyrosine kinases are activated.

When the signal molecule binds to the receptor, it causes them to dimerize. Each receptor cross phosphorylates the other. The negative charge from phosphorylation attracts new proteins and a large protein complex forms around the receptor which can begin signal transduction pathways


What are ion channel linked receptors? Where are they commonly found?

Receptors that when bound to signal molecule open or close ion channels changing the electrical charge across the membrane. These are common in neural signals.


What type of molecule might bind to an intracellular receptor? What will its function be?

A small hydrophobic molecule so that it can pass through the membrane
These are basically always involved in changing gene expression


Explain how the gas nitrous oxide functions as a signal molecule.

The enzyme NO synthase converts arginine to NO which diffuses across membranes into other cells. NO binds to gauntly cyclase which produces cyclic GMP a second messenger. The result of increased cGMP is relaxation of smooth muscles which causes dilation of blood vessels.


How far reaching are the effects of NO synthesis and why?

They are very localized due to the instability of NO.


Explain why nitroglycerin is an effective treatment for patients with angina. Why would it be problematic to take nitroglycerin with other drugs such as ED medications?

Angina is caused by inadequate blood flow to the heart. Nitroglycerin is converted to NO which causes dilation of blood vessels by creating cGMP. This lowers the blood pressure so if taken with other drugs that work in the same pathway, blood pressure could be lowered to dangerous or even fatal levels.


What is cAMP? How is it produced and degraded?

Cyclic AMP is a second messenger molecule common to signal transduction pathways. It is produced by adenylyl cyclase from ATP and degraded by phosphodiesterase to AMP.


What does cAMP do once created?

It activates protein kinase A which phosphorylates enzymes in the cytosol or can travel into the nucleus and activate other proteins which regulate gene expression


Explain how cholera affects the body at the cellular level.

Creates a toxin which irreversibly modifies the alpha subunit of Gs proteins by adding ADP-ribose. This prevents hydrolysis of GTP to GDP so the pathway is always active. This results in high cAMP levels causing a massive flow of water into the intestine and severe, life threatening diarrhea.


How is cGMP created and degraded?

It is synthesized by guanylyl cyclase and degraded by cGMP phosphodiesterase


What is PIP2? Describe how it is produced and what its effects are.

Phosphotidyl inositol in the plasma membrane can be phosphorylated in a variety of ways by PI kinases. One of these forms is PIP2. It can be broken down by phospholipase C to produce DAG and IP3. DAG remains in the membrane and binds to protein kinase C. IP3 triggers the opening of calcium ion channels in the ER causing the cytosol to be flooded with calcium. Calcium also binds to Protein kinase C and along with DAG activates it so that it will go on to phosphorylation other proteins


What is Ras? How is it activated and what does it do?

It is a monomeric G-protein that is activated downstream of almost all RTK’s. It activates the Map-kinase cascade which results in protein activity and gene expression related to survival. For this reason it is often mutated in cancers and is an important oncogene.


Outline the PI-3 kinase pathway including how it is stimulated what it does etc.

It is stimulated by Ras and other G-proteins. As a result of stimulation, Phosphatidyl inositol is phosphorylated at the 3 position hence PI3. This stays in the membrane but becomes active and activates other membrane proteins mostly related to growth and survival


Describe the JAK STAT pathway.

It is a short pathway involved in inflammation and immunity


Describe the TGF beta-SMAD pathway.

A short pathway involved in development. It uses serine/threonine kinases
THF beta binds to its receptor which dimerizes and cross phosphorylates. Then it activates SMADs which travel to the nucleus to affect gene expression


What are 3 methods by which membrane receptors become desensitized? When might this occur?

1 Downregulation: Decrease in receptor synthesis or increase in degradation (occurs slowly)
2 sequestration: receptors internalized by endocytosis (occurs rapidly)
3 Inactivation of GPCR’s: GPCR’s are phosphorylated preventing interaction with G-proteins (occurs rapidly)

This would occur in response to constant activation because of prolonged high concentration of substrate


How do GPCR’s become inactivated by phosphorylation?

G-protein-coupled receptor kinases (GRK’s) phosphorylated them and once phosphorylated they bind to arrestin molecule rather than G-protein


How are Beta adrenergic receptors in the heart activated? What pathway do they follow after activation and what is the end result?

They are activated in response to epinephrine and norepinephrine. They are GPCR’s that activate a Gs protein which activates adenylyl cyclase pathway and protein kinase A. The end result is increasing contractility and heart rate.


Describe the relationship between heart failure and Beta adrenergic receptor signaling. How can it be treated?

Damage to the heart -> sympathetic response-> prolonged response -> desensitization of beta-adrenergic receptors-> decreased contractility and heart rate -> further weakens the heart

Beta blockers can be used to treat heart failure because paradoxically they actually correct the beta adrenergic receptor number and GRK activity


Draw the structure of the insulin receptor.

2 transmembrane tyrosine kinase domains bound to two completely extracellular domains by disulfide bonds. The extracellular domains are bound together by disulfide bonds as well and together they form an active site for insulin binding


What pathways are activated by the insulin receptor?

MAPK and PI3K-AKT pathways to induce glucose uptake, cell survival and proliferation
Major effects on glucose regulation come through the PI3K-AKT pathway


Explain the role of calcium ions in signaling generally.

Calcium ions are at a lower concentration in the cytoplasm than in the extracellular environment and in the ER because of ion pumps. Calcium ion channels can be opened in either location as a result of signaling which floods the cytoplasm with ions and can activate or deactivate other proteins


What gene is responsible for cystic fibrosis? Where is the gene located? What is its basic function?

CFTR cystic fibrosis transmembrane conductance receptor

It is located on exon 7

Functions as a Cl- ion channel in the ABC transporter family


What are some of the symptoms of cystic fibrosis?

Salty sweat
Severe cough with thick mucus
Digestive problems including leading to malnutrition
Obstruction and infection of airways
Damage to respiratory system and pulmonary disease (90% of mortality)


Describe and/or diagram the general structure of the CFTR gene.

It has two membrane spanning domains with 6 transmembrane domains each. Each also bound to a nucleotide binding domain and one is attached to the cytoskeleton. The two subunits are attached by the R (regulatory) domain in between them. The R domain is unique and not similar to other ABC transporters.


Describe how the CFTR gene is gated?

Gating refers to the regulation that takes place to determine when it is open or closed.
1 cAMP activates PKA
2 PKA phosphorylates R domain
3 ATP is hydrolyzed in NBD1 to open channel
4 PKA phosphorylates more sites on R domain
5 NBD2 binds ATP which further opens channel
6 ATP hydrolysis at NBD2 results in release of ADP and channel closing
7 R domain dephosphorylation closes channel


What are the 6 classifications of CFTR mutations? Which is the most common? Which are the most severe? Relate them to some of the pancreatic symptoms.

I lack of CFTR
II defective, misfolded CFTR (does not reach membrane)
III defective gating
IV Restricted Cl- movement thru channel
V reduced protein (alternative splicing)
VI accelerated turnover
>85% are type II
I-III are the most severe leading to pancreas insufficient phenotype
V-VI are the most mild and lead to pancreas sufficient phenotype


Diagram/Explain on a molecular level how CFTR mutation leads to salty sweat.

Sweat ducts are divided into secretory coil and reabsorptive duct. Secretory coil does not contain CFTR and simply passes isotonic solution into the duct. This solution then passes through the reabsorptive duct where CFTR is found which normally causes uptake of chlorine leading to uptake of sodium but not water (because there are no aquaporins) this results in a hypotonic sweat solution. However, defected CFTR in CF patients limits reabsorption of salts leading to salty sweat


Describe/diagram on a molecular level how cystic fibrosis affects the lungs and how those affects lead to symptoms.

CFTR is located in bronchial ciliated cells. Goblet cells throughout the lungs secrete mucus into this area. Normally CFTR transports chlorine out of cell into the mucus where sodium remains and water is pulled out by osmosis to thin out the mucus. In CF patients, chlorine is not transported out and as a result sodium is reabsorbed into cells. These combine to cause water to move out of mucus into cells instead of the reverse and the resulting mucus is very thick. This thick mucus builds up obstructing airways and leading to inflammation and infection and ultimately scarring and lung disease.


Describe/diagram how cystic fibrosis affects the pancreatic duct on the molecular level and how those affects lead to symptoms.

Similar to the lungs, CF patients do not secrete chlorine leading to absorption of sodium and retention of water leading to viscous pancreatic juice. In addition, chlorine gradients created in part by CFTR are used for counter transport of bicarbonate out of the cells. In CF patients the chlorine gradient is not created and bicarbonate cannot be secreted. This leads to thick mucus blocking the release of enzymes into digestive tract and much of the food is not digested or absorbed which can lead to malnutrition. In addition, pancreatic beta cells can be damaged by mucus limiting insulin production and resulting in diabetes.


What percentage of CFTR function is required to show no symptoms of CF?

>10% function


What is the most common mutation leading to cystic fibrosis.

Deletion of phenylalanine at position 508 of the gene. In the NBD1. Causes misfolding of protein which prevents it from reaching the plasma membrane


What are some potential future treatments for Cystic Fibrosis?

1 Gene therapy attempting to deliver functioning CFTR gene
2 Pharmacotherapy focused on trafficking protein with F508del mutation to the membrane that will be at least partially functional and may reduce or eliminate symptoms


Why has Cystic fibrosis gene become and remained so prevalent in European populations even though it is so harmful?

It is possible that it confers a heterozygous advantage against cholera. Heterozygotes don’t show symptoms of CF but show less fluid loss and dehydration than the homozygous dominant phenotype. Cholera toxin enters intestinal cells and perpetually activates cAMP which activates CFTR in addition to other ion channels causing massive secretions of ions and water into the lumen leading to severe often fatal diarrhea. CF heterozygotes potentially are less harmed by cholera.


What are the two main pathways of degradation of intracellular proteins? Explain how they differ in terms of what they degrade and when?

1 Ubiquitin proteasome- degrades short lived and damaged or misfolded proteins, it is selective

2 Lysosomal pathways- degrade long lived proteins and organelles, can be selective or random and is unregulated in response to cellular stresses.


How does a protein get tagged with ubiquitin for degradation?

Ubiquitin ligases E1 E2 and E3

With the use of ATP, ubiquitin is added to E1, it is then transferred to E2 and finally to the target protein with the help of the E3 enzyme.


How are specific proteins targeted for Ubiquitination?

There are hundreds of different E3 Ubiquitin ligase which each only add ubiquitin to a specific target protein


Describe the structure of proteasomes and their function.

They are large protein structures made up of a central core which contains protease and ends which bind to target proteins and feed them thru the core where they are degraded by proteases and Ubiquitin is removed by ubiquitinases to be recycled in the cytoplasm.


What is autophagy?

It is the pathway by which cellular proteins and organelles reach the lysosome for degradation.


What are the 3 types of autophagy?

1 Macroautophagy- selective or random, large particles are engulfed in a double membrane which fuses with the lysosome
2 Microautophagy- selective or random- small particles and organelles invaginate directly into the lysosome to form a vesicle which is degraded along with its contents
3 Chaperone mediated autophagy- highly selective, Proteins with a specific amino acid motif are shuttled to the lysosome and transported through the membrane for degradation


Describe/diagram the process of macroautophagy.

Bits of membrane called isolation membrane or phagophore that are believed to be from the golgi or SER begin surrounding the target until they completely engulf it enclosing it within a double membrane. This is called an autophagosome. The outer membrane then fuses with the lysosome and the inner membrane is degraded along with the target.


What diseases can be caused by non-functioning ubiquitin related proteins?

Cancer, neurodegenerative diseases and many others


Describe/diagram the process of microautophagy.

The lysosome begins to invaginate to engulf a target creating an autophagic tube which is more narrow especially at the ends. Eventually this buds off inside the lysosome to create a vesicle which is degraded along with its contents


Describe/diagram the process of chaperone mediated autophagy.

Proteins with KFERQ motif bind to chaperone called hsc70 or hsc73 and are targeted to the lysosome. At the lysosome membrane they bind to LAMP2 which changes shape to become a transporter and allow them through to the inside of the lysosome where they are degraded.


What types of cellular stress could upregulate autophagy? (5) What are genes responsible for this upregulation called?

1 Nutrient deficiency
2 Growth factor withdrawal
3 Infection
4 Hypoxia
5 DNA damage

Genes responsible are called autophagy related genes or ATGs


What is mTOR and what is its importance in relation to protein degradation? What conditions can result from its disregulation?

It is a master regulator
It activates genes related to growth/proliferation and inhibits autophagy related genes ATG limiting autophagy. Under cell stress, mTOR is inhibited allowing expression of ATGs and ultimately increased autophagy.

Disregulation of mTOR can lead to obesity diabetes and cancer


What is pharmacodynamics? What is pharmacokinetics?

Pharmacodynamics: What a drug does to the body
Pharmacokinetics: What the body does to a drug


What are the 4 main drug targets?

1 Receptors
2 Enzymes
3 Structural proteins
4 Transport proteins


Compare and contrast agonists and antagonists

Both bind with high affinity to the target. However agonists cause an effect upon binding and antagonists don't cause an effect. Usually this results in agonists activating a process and antagonists inhibiting a process


Differentiate between orthosteric and allosteric binding.

Orthosteric binding occurs at the active site and allosteric binding occurs away from the active site


Draw the chart to illustrate the ways that antagonists can function. Which one is competetive

Receptor vs non receptor
(W/in non receptor) Chemical vs physiological
(W/in Receptor) Orthosteric vs allosteric
Both orthosteric and allosteric branch to be either reversible or non reversible.
Orthosteric reversible is competetive


Compare and contrast competitive and non competitive antagonists

Competitive antagonists bind reversibly to the active site of the receptor while non-competitive bind away from the active site. Competitive antagonists reduce potency and can be overcome by increasing agonist concentration. non-competitive antagonists decrease efficacy and cannot be overcome by increasing concentration of agonist.


What do physiological antagonists and chemical antagonists do?

Physiological antagonists activate an opposite pathway
Chemical antagonists use some chemical interaction without the involvement of a receptor


Define efficacy and potency and use a Dose-response curve and the concepts of Emax and ED50 to illustrate

Efficacy = how effective a drug is at a certain concentration. An effective drug has a high Emax or a high maximum effectiveness at high concentration
Potency = at what concentration a drug becomes effective a potent drug has a low ED50 meaning it reaches half of its maximum effectiveness at a very low concentration. A dose-response curve is a graph of effictiveness vs concentration of a drug


What is a quantal dose curve? Use it to define ED50 TD50 and LD50

A graph of % of people exhibiting an effect (therapeutic, toxic or lethal) vs concentration of drug. ED50 is the concentration at which 50% of people saw therapeutic effects. TD50 and LD50 are the same but for toxic and lethal effects respectively


Define therapeutic index and therapeutic window

TI = TD50/ED50. Therapeutic window is the dosage at which a drug will be effective for most people without being toxic to anybody. A narrow window is illustrated by a low TI and a wide window is illustrated by a high TI.


What is the margin of safety?

MS= LD1/ED99


What is selectivity of a drug? Selective drug action? What are the relationships between selectivity and side effects? Selectivity and safety?

Selectivity refers to whether the drug binds only to one receptor and not to any others. Selective drug action includes binding to only 1 receptor but also includes that receptor controlling only one process. High selectivity produces fewer side effects and highly selective drugs are usually safer although selectivity does not guarantee safety


What are the 4 main factors affecting pharmacokinetics?

1 Absorption- how much of it actually makes it to the blood stream
2 Distribution- Where in the body does it go
3 Metabolism - Breakdown of drug
4 Excretion- removal of drug in urine


What are the 4 ways a drug could be absorbed? Which one is by far the most common?

1 Passive diffusion- most common
2 Facilitated diffusion
3 Active transport
4 Endocytosis


Describe how pH could affect drug absorption.

Different pH's could cause drugs that are weak acids or bases to change between protonated and non protonated states which results in differences in net charge between states. The uncharged state will always be absorbed better than the charged state. So weak bases should be in weak basic drugs to promote deprotonation and weak acids should be in weak acidic drugs to encourage protonation


What is bioavailability and what factors affect it?

What portion of the drug actually reaches systemic circulation. This is affected by absorption and metabolism in the liver


What is the volume of distribution?

Amount of drug/concentration in the plasma This gives you the apparent volume in which the drug is distributed


Describe the two compartment model of drug distribution for an iv administered drug.

Alpha- initial rapid decrease in plasma concentration due to distribution into the tissues and away from the central compartment
Beta- gradual decrease in plasma concentration due to metabolism and excretion


Differentiate between phase I and phase II drug metabolism.

Phase I = oxidation, hydrolysis, hydroxylation, deamination, and dealkylation
Phase II = addition of large substituent groups to increase hydrophilicity


What are cytochrome P450's (CYP)?

A class of enzyme that participates in phase I of drug metabolism under the following reaction
NADPH + D + O2 + H+ -> NADP+ + H2O + DO
Where d is the drug


What equations explain the metabolism of first order and zero order drugs respectively? What major takeaways can we get from these?

First order: V = Vmax [C]/KM
V is proportional to drug concentration
Zero order: V = Vmax
Velocity is constant at the maximum because of saturation


What determines whether a drug will act as a first order or zero order in regards to metabolism?

If the concentration is much higher than Km it will act as zero order
If it is much lower than Km it will act as first order.


What is the half life of a drug? How can you find it for a drug that is under first order and zero order metabolism?

The amount of time it takes to remove half of the concentration of a drug from the plasma.
First order: t1/2 = 0.693/k
It is inversely proportional to the rate constant
Zero order: there is no fixed half life because the rate of elimination is independent of concentration


Define clearance in pharmacokinetics. Use equations to relate it to rate of elimination and half life.

Clearance is the volume of plasma cleared of a drug per unit time.
Rate of elimination = CL * [drug]
Half life = 0.693Vd/CL


Explain the concept of drug accumulation and steady state.

When a drug is taken continuously or repeatedly before it is cleared from the system, it will build up. As the drug reaches higher concentrations, the rate of elimination increases until it equals the rate accumulation at the steady state. At this point, the concentration does not change as long as the drug is administered at the same rate. The steady state is reached after about 5 halflives. The time it takes to reach the steady state is the same no matter the rate of administration but that means that the concentration at the steady state is higher under more rapid administration


What factors could contribute to differing pharmacokinetics between people? (5)

1 Health
3 Weight
4 interference by other drugs
5 Genetic variations


What are the three ways that pharmacogenomics is relevant clinically and explain how for each way and give an example for the first 2.

1 Avoid adverse drug reactions- genetic testing before prescription of drugs for those that are known to have adverse effects in individuals with certain genotypes. Example warfarin can cause severe bleeding in patients with CYP2C9 mutations
2 Improve efficacy of treatments- testing can be done before to determine how effective a drug could be based on genotype.- Example Trastuzumab is much more effective in patients with HER2-positive breast cancer
3 Improve cost-effectiveness of treatments- the previous 2 will necesarily cause this


Diagram/describe the levels of CFTR function at which each the major symptoms of vas deferens, airway, sweat glands and pancreas are present.

Above 10% = no functions
4.5-10% = absence of vas deferens
1-4.5 = airway and sweat symptoms
<1% = pancreas


What is the best test to diagnose CF in a based on clinical suspicion?

The sweat chloride test


Describe the way newborn screening works in ohio to diagnose CF.

All babies receive an immunoreactive trypsinogen test (IRT) those with highest IRT receive a genetic panel including 23 of the most common mutations, if at least one mutation is present, a diagnostic sweat chloride test is undertaken


What are some clinical clues toward a diagnosis of CF.

Meconium ileus (neonate)
Failure to thrive (at any age)
Chronic respiratory or sinus disease especially with sinus polyps
Rectal prolapse


What two bacteria are most likely to affect CF patients?

P. Aeruginosa
S. Aureus


List some of the common treatments for symptoms of Cystic fibrosis.

Airway clearance
Hypertonic saline
Bacterial suppression
Inhaled antibiotics
Digestion aids
Pancreatic enzymes
Vitamin supplementation
Lung transplant
Ivacaftor- potentiator which increases the function of CFTR at the membrane (only treats 4% of mutations)
Combined therapies of potentiators and correctors


Define how correctors, potentiators and compounds allowing read-through of stop codons could be used to treat CF and why different types are recommended for different mutations

Compounds allowing read through of stop codons would prevent truncation and possibly produce an at least partially functional protein in mutations resulting in premature stop codons Class I
Correctors would allow proteins which do not reach the membrane because of misfolding to at least reach the membrane where they could show at least some function - class II
Potentiators- improve the function of proteins which are already at the membrane- classes iii-vi
All three combined could treat most mutations and could show greater improvements to class i and II mutations than any one alone


What is the poly T tract in the CFTR gene? Explain how it can cause it can combine with the TG tract.

The poly T tract is a string of repeated thymine in the intron between exons 8 and 9 in CFTR gene. Individuals have varying numbers of T’s. 9 and 7 T’s are normal while 5T’s cause exon 9 to not be included in the transcript many times resulting in fewer functional copies of CFTR protein. Individuals homozygous for 5T usually have about 10% CFTR function and therefore usually do not show symptoms. The TG tract is another locus adjacent to the poly T tract which also has a variable number of repeats. Normal is 9-11 TG’s. If an individual has 12 or 13 TG’s on the same gene where they are 5T, exon 9 is included less often leading to a more severe phenotype. It can be difficult to tell by genetic testing if these two traits are cis (on the same gene) or trans on opposite copies) so genetic testing of one parent of an individual may be necessary. Compound heterozygotes for 5T and other disease causing CFTR mutations could have varying disease symptoms
Of note is that combination of 5T allele with the Arg117His mutation can lead to disease phenotype although neither mutation alone does


What are the three main types of genetic testing for CF? Explain some pros and cons of each.

Targeted testing- only focuses on a few mutations so should only be used in those individuals whose families have a history of specific mutations
Panels- tests for 23 mutant alleles- cheapest and easiest option for most people but may not catch more rare mutations
Sequence analysis + duplication deletion testing- very expensive and slow, will catch almost everything but may catch unknown mutations or mutations with unknown phenotypic effects


What are the major products of glycolysis? How many ATP produced under anaerobic and aerobic conditions?

2 ATP (net) 2NADH pyruvate will be turned into acetyl coa and enter the TCA cycle.
Anaerobic: Only those 2 ATP per glucose
Aerobic 30-36


Draw out the steps of glycolysis (not on bus)
Include which steps form NADH and ATP
What are the two phases

glucose 1-> glucose 6P 2-> fructose 6P 3-> fructose 1,6BP 4-> GAP 5-> 1,3BPG 6-> GAP3P 7-> Gap2P 8-> PEP 9-> Pyruvate
ATP used: 1, 3
ATP produced: 6, 9
NADH produced: 5
Preparative phase 1-4
ATP generating phase: 5-9


What are the two major steps of amino acid catabolism?

1 Conversion of amine nitrogen to urea to be excreted
2 Conversion of carbon skeleton into one of 7 metabolites depending on whether amino acid is ketogenic glucogenic or both


Describe the process by which fatty acids are produced, transported through the blood, and to the mitochondrial matrix including the names of necessary proteins. What is the most common inherited disorder affecting this process?

In response to hormonal signals, lipases create fatty acids from triacyl glycerols in fat cells. These are transported through the blood attached to albumin until they reach the cell and transported across the membrane by fatty acid binding proteins. In the cytosol, fatty acyl coa synthetase attaches COA to the carboxylic acid portion. Carnitine palmitoyl transferase 1 CPT1 then replaces coa with carnitine and a translocase protein moves the carnitine fatty acid into the mitochondrial matrix where CPT 2 converts it back to a fatty acyl COA. Deficiency of CPT 2 is the most common disorder affecting this process


Draw out the steps of beta oxidation of a short chain saturated fatty acid. (not on the bus)

1 Creation of trans double bond between alpha and beta carbons with the reduction of FAD to FADH2
2 Addition of water at the beta carbon
3 Oxidation of the beta carbon to a ketone with the reduction of NAD+ to NADH
4 Attack by COASH to produce acetyl coa and a shorter fatty acyl coa


What is the most common deficiency affecting beta oxidation.

Different enzymes exist for beta oxidation of short, medium and long chain fatty acids. Medium chain acyl coa dehydrogenase MCAD deficiency is the most commonly deficient


Explain how beta oxidation is different in a fatty acid with an odd number of carbons and in an unsaturated fatty acid.

Odd number: it is the same until the last round where the products are 1 acetyl coa and 1 propionyl coa (3 carbons) propionyl coa is converted to succinyl coa which enters the TCA cycle
Unsaturated: Enoyl coa isomerase shifts double bond into correct position. If needed before enoyl coa isomerase functions, dienoyl coa reductase will remove a double bond by reducing it with FADH2


How does beta oxidation of very long chain fatty acids and branched fatty acids differ from simpler fatty acids?

Oxidation begins in the peroxisome instead of the mitochondrial matrix. For VLCFA's they are oxidized into smaller pieces which are sent to the mitochondria for further oxidation. Branched fatty acids can undergo alpha oxidation which removes one carbon as co2 to line up branches in the alpha position and then undergo beta oxidation where half of the products are propionyl coa.


Briefly describe omega oxidation.

A form of fatty acid metabolism that occurs in the ER of kidney and liver cells in which the omega end of the fatty acid is first oxidized three times to form a carboxyllic acid and then beta oxidation occurs until you are left with a small molecule with carboxylic acid groups on either end. This molecule can be succinate which enters TCA cycle or adipate which is excreted. This occurs primarily under conditions where beta oxidation is limited.


Describe 2 ways in which beta oxidation is regulated. At what times would you expect it to be turned on?

1 Hormonal stimulation leads to breakdown of triacylglycerols increasing beta oxidation
2 Malonyl coA, a substrate in fatty acid metabolism inhibits CPT1 which prevents fatty acids from entering the mitochondria and therefore inhibits beta oxidation
It is high under fasting, exercise conditions and after eating a meal high in fat


What is ketogenesis?

The production of ketone bodies from acetyl coA in the liver. 2 of the three ketone bodies travel elsewhere in the body where they are converted back to acetyl coA for TCA cycle. This process is overseen by HMG-coA synthase


What is the TCA cycle? What does it stand for? What are its inputs and outputs? What is its purpose?

TCA stands for Tricarboxylic acid cycle, it is the process that occurs with acetyl coa produced in metabolism of lipids carbohydrates and proteins and its purpose is to create NADH and FADH2 to power oxidative phosphorylation.
Inputs: Acetyl Coa, oxaloacetate
Outputs: 3NADH 1 FADH2 1 GTP 2CO2


Draw the steps of the TCA cycle including names of intermediates and all enzymes involved as well as where NADH GTP and FADH2 are produced (not on the bus)

1 Oxaloacetate + acetyl coa to citrate
Enzyme: citrate synthase
2 Citrate to isocitrate
Enzyme: Aconitase
3 Isocitrate to alpha ketoglutarate
Enzyme: isocitrate dehydrogenase
4 Alpha ketoglutarate to succinyl coA
Enzyme: alpha ketoglutarate dehydrogenase
5 Succinyl coA to Succinate
Enzyme: Succinate synthetase
6 Succinate to fumarate
Enzyme: Succinate dehydrogenase
7 Fumarate to malate
Enzyme: Fumarase
8 Malate to oxaloacetate
Enzyme: Malate dehydrogenase


What is oxidative phosphorylation?

The process by which oxidation of NADH and FADH2 with oxygen as the electron acceptor is paired to the phosphorylation of ADP. It is the major source of cellular ATP


What enzyme is needed to transfer the phosphate group from GTP to ADP to form ATP?

Nucleotide diphosphate kinase


In oxidative phosphorylation, how many ATP are produced per molecule of NADH and FADH2

FADH2: 2


Draw a representation of the electron transport chain and diagram the path electrons would take from NADH to O2. (Not on the bus)

NADH-> Complex I (transmembrane and pumps 4 H+)-> Coenzyme Q (lipid soluble within the membrane and moves to next complex) -> Complex III (transmembrane and pumps 4 H+ -> cytochrome C (water soluble on the outside of the membrane moves to next complex) -> Complex IV (transmembrane and pumps 2 H+) -> O2 (becomes H20)


What protein carries out phosphorylation of ADP in oxidative phosphorylation? How does it do this?

F0F1-ATP synthase
It uses the electrochemical gradient of protons formed by the electron transport chain for energy. As protons pass through the enzyme which is transmembrane, they cause the C subunit to rotate which results in structural changes to the alpha and beta subunits resulting in phosphorylation of ADP


Where does the extra energy produced by the electron transport chain but not used in oxidative phosphorylation go?

It is used for ion transport across the inner membrane and is released as heat


Use acetyl choline effects on the heart, salivary glands and skeletal muscle to illustrate the concept that one signal may have different effects in different places.

Heart cell: results in decreased rate and force of contraction
Salivary cell: secretion
Skeletal muscle: contraction


What cellular molecule is the building block for NO? What enzyme catalyzes this reaction?

Arginine, NO synthase (NOS)


What are cytokines? What receptors do they generally stimulate?

They are signaling proteins involved in the immune system and inflammation, they generally bind to JAK -STAT receptors


What type of receptor are beta adrenergic receptors, JAK-STAT receptors, insulin receptors, TGF beta receptors?

beta adrenergic: GPCR’s
JAK-STAT- enzyme associated ie they are not built in
Insulin- Receptor with a built in tyrosine kinase (RTK)
TGF beta - Receptor with a built in serine threonine kinase


Diagram the possible pathways that could be followed by GPCR activation (Not on the bus) (3 pathways)

Adenylyl cyclase-> cAMP -> PKA-> gene expression and protein changes in cytosol
guanylyl cyclase-> CGMP-> smooth muscle relaxation and vasodilation
PI kinases-> PIP-> DAG + IP3 -> PKC


Diagram the main pathways that could follow stimulation of an RTK. (Not on the bus) (2)

Ras-> Map kinase -> protein activity and gene expression -> cell survival

PI kinases -> PI3 -> protein activation -> cell survival and growth


What is transcytosis?

Transport from one side of the cell to another by vesicles. This is one of the possible fates of receptors taken up into the early endosome by receptor mediated endocytosis


What is the function of COP1 and 2 proteins?

They are vessicle coating proteins involved in transport from the ER to the golgi


Explain why CF causes fibrosis of the pancreas and pancreatitis?

Pancreatic acinar cells produce and excrete exocrine digestive enzymes. This thick juice and lack of bicarbonate blocks pancreatic ducts and prevents exocrine secretions. Eventually this causes the acinar cells to die leading to pancreatic fibrosis and pancreatitis


What is eNAc? Explain its relationship to cystic fibrosis.

It is a major sodium ion transporter Channel in cellular membranes. Normally, the CFTR protein inhibits eNAc reducing sodium reabsorption but in cystic fibrosis, it is active because CFTR cannot inhibit it so sodium flows into the cells making symptoms worse.


What was the first cystic fibrosis mutation that the drug ivacaftor was cleared to treat and what class does it belong to?

Class III - protein reaches plasma membrane but has gating issues


What complications arise from a failure to diagnose CF early in infancy (6)

1 Hypochloremia - (Alkalosis)
2 Hyponatremia - (dehydration, failure to thrive)
3 Hypoproteinemia
4 Vitamin E deficiency (Hemolytic anemia)
5 Vitamin K deficiency- (bleeding diathesis)
6 Zinc deficiency- (acrodermatitis)


What results from a sweat test indicate CF or the possibility of CF?

> 60 mmol/liter = diagnosis
30-59 = Grey zone possible CF
<30 = NOrmal


What gene is respobsible for metabolizing nearly half of the most commonly used drugs?



Which 4 phase 1 metabolism proteins show the most genetic variation and therefore are key targets for pharmacogenetic testing?

1 CYP2D6
2 CYP2C19
3 CYP2C9
4 CYP2A6


What categories can patients be separated into based on CYP2D6 genotype? What effect would this have on dosage of drugs and prodrugs metabolized by CYP2D6?

Poor intermediate efficient and ultra rapid metabolizers. This determines how much drug or prodrug they will need. For example a poor metabolized would need very low dose of drugs and very high dose of prodrug


What drugs are metabolized by CYP2D6? (4)

Anti psychotic drugs
Tricyclic antidepressants
Metoprolol (antihypertensive)
Tamoxifen (anti-estrogen)


What two genes are known to be involved in adverse drug reactions to warfarin?



What two shuttle systems can transport NADH produced in glycolysis into the mitochondria?

1 Glycerol 3-phosphate shuttle
2 Malate aspartate shuttle


What are the 4 major dietary fatty acids?

1 palmitate (c16)
2 stearate (C18)
3 oleate (C18:1)
4 inoleate (C18:2)


Compare and contrast the major fatty acid types found in animal fat, dairy fat and Vegetable oil.

Animal fat: saturated and monounsaturated long chain fatty acids
Dairy fat: medium chain fatty acids (C6-C12)
Vegetable oils: linoleate and other polyunsaturated fatty acids


Aside from producing NADH and FADH2 for oxidative phosphorylation, what is the other important function of the TCA cycle?

It produces precursors to important processes:
Heme synthesis
Amino acid synthesis


What is lactic acidosis? What causes it?What are some situations in which it might present?

Buildup of Lactic acid because it is the breakdown product of pyruvate when the citric acid cycle is being underutilized. This is a common symptom of metabolic disorders. It occurs under anaerobic conditions such as strenuous exercise, or under disease conditions preventing full functioning of TCA cycle and/or oxidative phosphorylation


What does pyruvate kinase do? What are some of the major symptoms and treatments for pyruvate kinase deficiency?

Pyruvate kinase catalyzes the final step of glycolysis from PEP to pyruvate (with the production of 1 ATP)
Chronic hemolytic anemia- reduction of ATP limits sodium-potassium pump in RBC’s leading to ion imbalance
Increased 2,3BPG levels- converted from 1,3BPG which builds up. Inhibits hexokinase resulting in further reductions in ATP productions. Also alters hemoglobin to allow more oxygen to be released in tissues which counteracts some of the symptoms
Blood transfusions, splenectomy, iron chelation, bone marrow transplant


What is the function of pyruvate dehydrogenase? Describe the inheritance pattern, symptoms (2 types) and treatments for pyruvate dehydrogenase deficiency.

Pyruvate dehydrogenase catalyzes the conversion of pyruvate to acetyl coA to enter the citric acid cycle and generates 1 NADH in the process.
X-linked recessive because most mutations affect E1alpha subunit
Metabolic form- severe presents with overwhelming lactic acidosis
Chronic neurological form- moderate lactic acidosis and severe brain dysfunction and abnormalities. (Most common in females)
Treatment: high fat/low carb diet, thiamine supplement, sodium bicarbonate and citrate for acidosis, dicholoroacetate (inhibits E1 regulatory kinase which lowers protein function)


What is the action of pyruvate carboxylase? What cofactor (s) involved?

Converts pyruvate to oxaloacetate for entrance into TCA cycle and other pathways
Cofactor = biotin


Describe the symptoms and treatments for pyruvate carboxylase deficiency.

Symptoms: Lactic acidosis, hypoglycemia (decreased gluconeogenesis), failure to thrive, decrease in myelin sheaths leading to developmental delay, recurrent seizures and neurological dysfunction
Can attempt: hydration, glucose, citrate, biotin, aspartate, avoidance of fasting, high carb/protein diet (to prevent gluconeogenesis which uses up oxaloacetate)


Describe the cellular cause and effects of cyanide poisoning? What treatment could be used?

Cyanide binds to Fe3+ in cytochrome oxidase in complex 1 of the electron transport chain. Prevents oxidative phosphorylation and causes switch to anaerobic metabolism leading to massive acidosis and hyperventilation and rapid death.
Treatment: Nitrite (oxidizes hemoglobin to Fe3+ state to bind cyanide and remove it from cytochrome oxidase)


How is naturally occurring cyanide from dietary sources metabolized?

Rhodanase in the liver converts it to thiocyanate which is harmless


What are some of the common characteristics of mitochondrial mutation disorders? (4)

1 Maternal inheritance
2 heteroplasmy (replicative segregation)
3 high mutation rate -> late onset
4 affects tissues with high energy demand- vision, hearing, smell and neurons generally affected


List 7 mitochondrial diseases.

3 Kearns-sayer syndrome
6 Pearson syndrome
7 Leigh disease


What are some symptoms of Kearns-sayre syndrome?

Late onset Ptosis (drooping of eyelids due to inability to open them)
Ophthalmoplegia paralysis of muscles in and around the eye


What is MERRF? Describe cause, symptoms and treatments.

Myoclonic epilepsy and ragged-Red Fiber disease
Late onset in late childhood or in adulthood. Caused by a mutation to the mitochondrial gene which codes for lysine tRNA.
Symptoms: myoclonic epilepsy (muscle twitching) short stature, poor night vision, hearing loss, lactic acidosis and exercise intolerance
Treatment: none effective but can try coenzyme q and L-carnitine


What is LHON? Describe its cause, symptoms and treatment.

Leber’s hereditary optic neuropathy
Caused by 1 of 3 mutations to mitochondrial gene for NADH dehydrogenase subunits (complex 1 of ETC)
Symptoms: acute, sudden onset of blindness in young adults caused by degeneration of retinal ganglion cells of optic nerve.
Treatment: Idebenone (experimental)- boosts electron transport chain and allows bypass of complex 1


What’s are the signs, symptoms and treatments for MCAD deficiency?

Inability to breakdown medium chain fatty acids (C6-C12) leads to acute energy deficiency, hypoketotic hypoglycemia and elevated levels of C8 acylcarnitine and DICARBOXYLIC ACIDS (results from omega oxidation)
Commonly presents in healthy children 3-24 months as sudden hypoketotic hypoglycemia triggered by illness or prolonged fasting. Symptoms also include: vomiting, lethargy, liver failure, seizure, coma and death. If caught early, prognosis is very good but can be fatal if undetected
Treatment: avoidance of fasting, glucose supplementation, low-fat diet, carnitine suplementation


Describe the three types of CPTII deficiency along with their symptoms. What are possible treatments?

1 Adult: mild myopathy form. Presents as rhabomyolysis (breakdown of muscle fibers leading to myoglobin the urine causing it to be rust colored) induced by exercising, fasting, high fat diet, cold temperature or infection
2 Infantile- severe hypoketotic hypoglycemia, liver failure, cardiomyopathy, and peripheral myopathy
3 Neonatal- lethal within 4 days. Respiratory failure, hypoglycemia, seizures, hepatomegaly, liver failure, cardiomegaly
Treatments: Avoidance of fasting, extreme exercise and lipid intake
High carb/low fat diet, high intake of medium chain fatty acid triheptanoin and others, carnitine supplement


What are the two common propionyl coA associated metabolic disorders? Where do they act in the conversion of propionyl coA to succinyl coA and what cofactor (s) are involved? What are symptoms and treatments?

Propionic academia- acts on first step from propionyl coA to D-methylmalonyl coA. Biotin is a cofactor
Methylmalonic acidura - acts on the third step from L-methylmalonyl coA to succinyl coA. B12 is a cofactor
Symptoms: poor feeding, lethargy, vomiting, acidosis, hypotonia, seizures, coma can be life threatening
Treatment: Low protein diet, specialized amino acids, antibiotic against gut bacteria which produce propionyl coA


Describe the cause, sign, symptoms and treatments for adult refuse disease.

Caused by defect in alpha oxidation in the peroxisome leading to a build up of phytanic acid (branched fatty acid) which becomes toxic at high levels
Clinical features: retinitis pigmentosa, anosmia, progresses to blindness, deafness, sensory neuropathy, cerebral ataxia, cardiomyopathy
Treatment: dietary restrictions to avoid phytanic acid


What are the three disorders within Zellweger spectrum disorder? Describe causes, signs/symptoms.

1 Zellweger syndrome (ZS): severe
2 Neonatal adrenoleukodystrophy (NALD): intermediate
3 Infantile refsum disease (IRD): least severe
Caused by a defect in peroxisome biogenesis leading to a build up of very long chain fatty acids and branched fatty acids (phytanic acid) and decreased levels of some lipids
ZS- present as newborns or early childhood with hypotonia (decreased muscle tone) and distinct facial dysmorphism, seizures and liver dysfunction. No sight, hearing or psychomotor development and death within 1 year
IRD- present with progressive loss of hearing, vision, smell and motor function


Describe the causes, signs/symptoms of the two distinct phenotypes of X-linked adrenoleukodystrophy (ALD).

Caused by a defect in ABCD 1 gene that encodes transport of VLCFA’s into peroxisome leading to accumulation in plasma and tissues and damage to the myelin sheath and adrenal cortex resulting in progressive motor dysfunction and adrenal insufficiency
heterozygous females show some symptoms later in life
1 Cerebral demyelination form: presents in childhood (4-10) as inflammatory demyelination with rapid progression to vegetative state
2 Adrenomyeloneuropathy (AMN): milder form. Presents in young adults as non-inflammatory distal axonopathy with gradual progression to a spastic paraplegia.
No treatment


What are the 5 units commonly used to measure the energy content of food? How do they compare to each other?

1 calorie
2 Kilocalorie
3 Calorie
4 Joule
5 Kilojoule
1000 calories = 1 Kilocalorie = 1 Calorie = 4180 Joules = 4.18 Kilojoules


Compare and contrast the 2 methods used to determine how much energy is in a given food.

1 Direct calorimetry - measures the amount of energy that is released when the food is combusted completely
2 Indirect calorimetry - estimates the amount of energy in food in the body by measuring oxygen consumed, CO2 produced and Nitrogen excreted while metabolizing that food
Indirect calorimetry is more commonly used and is usually slightly lower than direct calorimetry


How many calories are in a gram of each of the following nutrients: Carbohydrates, fats, protein, alcohol? What determines the amount of energy?

Carbohydrates: 4 Kcals per gram
Proteins: 4 Kcals per gram
Fat: 9 Kcal per gram
Alcohol 7 Kcal per gram
The energy is a function of how reduced the nutrient is


How do the common nutrients carbohydrates, fat and protein compare in calories per liter of oxygen used? How do they compare in calories per liter CO2 produced?

The nutrients are nearly the same in calories per oxygen but vary more in calories per CO2 with Protein being the highest then fat and finally carbohydrates


What is the respiratory quotient? Why is it used? What are the values for carbohydrates, fat and protein?

The ratio CO2 produced/O2 used during metobolism of a given substance. This is used to determine how much energy is contributed by different foods in a mixed diet
Carbohydrates = 1
Protein = 0.8
Fat = 0.7


Draw a chart showing the major contributors to fuel during various lengths of time exercising.

10 minutes : muscle glycogen
10-20 : muscle and liver glycogen
>20 minutes: muscle and liver glycogen and fatty acids
> 2 hours : fatty acid
At this point gluconeogenesis is used to maintain blood glucose levels but can only do so for a short period of time thus if exercise is continued longer, hypoglycemia may occur.


What is energy density?

The number of calories per gram of a food


What three processes account for the total energy expenditure (TEE) of the human body? What percentage does each represent?

1 Basal metabolism (energy required to run cellular functions to stay alive) 50-70%
2 Physical activity: 15-30%
3 Thermic effect of food (energy required to process certain foods) 10%


What is the largest factor accounting for differences in Basal metabolic rate of adults?

Lean body mass. Muscle takes more energy to maintain than adipose tissue so the more muscle you have as a percentage of body weight, the higher the BMR


What is the thermic effect of food? What is it for carbohydrates, protein and fat?

The amount of extra heat produced during ingestion of a food because of energy required to digest, absorb and distribute its nutrients (the energy lost from food)
Carbohydrates: 10%
Fat: 5%
Protein: 20-30%


Compare and contrast macronutrients and micronutrients.

Macronutrients are needed in large quantities: carbohydrates, proteins and fats
Micronutrients are needed in much smaller quantities: vitamins and minerals


What is the recommended daily amount of dietary protein?

0.8 g/kg body weight/day


Where and how are amino acids absorbed?

Small intestine, by active transporters. More than one amino acid uses the same transporter so there can be competition for absorption


Which amino acids are essential? (10)



What are conditional amino acids?

Amino acids that are not normally essential but become essential for an individual because of disorders that make them unable to produce that amino acid


What is protein quality? What makes a protein complete, partially complete and incomplete?

Protein quality refers to the mix of essential amino acids that a protein contains and the amounts of each compared to the ideal
Complete = Can maintain life and normal growth as the sole source of protein
Partially complete = can maintain life but not growth
Incomplete = cannot maintain life


Define each of the following metrics of protein quality and tell how it is determined: Biological value, Net protein utilization, Protein efficiency ratio, Chemical score and protein digestibility corrected amino acid scoring

Biological value- measures percentage of absorbed amino acids retained for protein synthesis
BV = Dietary N - (UrinaryN-UrinaryN0)-(FecalN-FecalN0)/DietaryN-(FecalN-FecalN0) *100
Net protein utilization- percent of nitrogen intake that is retained in the body
NPU = DietaryN-(UrinaryN-UrinaryN0)-(FecalN-FecalN0)/FoodN eaten *100
Protein efficiency ratio
PER = weight gain in an animal/weight of protein ingested during that period of time
Chemical score- compares amino acids of a protein to egg (a high quality protein) to determine limiting amino acid
CS = mg essential amino acid per gram of test protein/mg essential amino acid per gram of egg protein *100
Protein digestibility corrected amino acid scoring- compares amino acids in a protein to the human requirement pattern of a 2-5 year old to determine limiting amino acid
AAS = mg of EAA in 1g test protein/mg of EAA in 1g protein requirement pattern
PDCAAS = lowest AAS ratio *true protein digestibility


What is amino acid sparing effects?

Some amino acids can fulfill one of the demands of another amino acid reducing the amount of the second amino acid that is needed. For example, cysteine like methionine can provide sulfur so if there is a lot of cysteine present in a food, methionine is not needed in as high of quantities


What are complimentary proteins?

Two poor quality proteins which differ in the limiting essential amino acid will form a higher quality protein when mixed together or ingested within about 24 hours of each other


Name and compare the two types of protein malnutrition.

Kwashiorkor- severe protein deficiency leading to edema and extended abdomen, mental apathy, changes in skin and hair pigmentation, Retarded growth and muscle wasting, rapid progression and high mortality. Often occurs when a second baby is born and the first is abruptly weaned from the mother’s milk and fed a diet of inadequate protein
Marasmus- Protein calorie malnutrition. Condition develops gradually over several months or years and shows growth retardation and wasting away of fat and muscle tissues but with mental alertness and appetite present. Low mortality


What are the 3 recommendations made by nutritionists generally about carbohydrate intake?

1 >100 grams per day
2 50% of calorie intake
3 Rely mostly on complex carbohydrates


What adverse health outcomes can result from extremely low carbohydrate intake?

Ketosis, loss of cations, dehydration, excessive breakdown of body protein


What are available and unavailable carbohydrates? What are the 2 types of unavailable carbohydrates?

Available are those which can be digested by the body and used for energy
Unavailable cannot includes Insoluble and soluble


What are dietary fiber, crude fiber, and added fiber?

Dietary fiber is what remains after intestinal digestion- soluble, insoluble and non-carbohydrate
Crude fiber is what remains after acid and alkaline digestion in a lab- Insoluble and non-carbohydrate only
Added fiber is what is often isolated and added to foods for the benefits associated with fiber Soluble and insoluble


What are the benefits associated with fiber in the diet? (5)

1 Reduce incidence of diseases such as diverticulitis, hemorrhoids, cardiovascular disease and hyperlipidemia
2 Promote weight loss by creating a feeling of fullness
3 Stimulate peristalsis and prevent constipation
4 Facilitate removal of cholesterol and other sterols in the feces
5 In diabetes, promote glycemic control and reduction of hyperlipidemia


What are exchange groups and what is their purpose?

Lists a number of groups and foods within those groups along with serving levels which all have approximately the same composition as other members of the group. This is meant to allow for easy exchanges without extensive calculations


What is glycemic index? And Glycemic load?

A measure of how much a certain carbohydrate raises the blood glucose levels. High glycemic index foods are linked to diabetes and heart disease
Glycemic load is the glycemic index multiplied by the grams of carbohydrate and divided by 100


What are the 3 types of fats in our diets?

Glycerides, phospholipids and sterols


What are essential fatty acids?

Humans cannot produce omega 3 and omega6 double bonds so we require these in our diet (linoleum acid omega 6 and alpha linolenic acid omega 3) If not present in the diet the condition essential fatty acid deficiency occurs causing dermatitis, alopecia, thrombocytopenia, and growth retardation


What are trans fats? What are their 5 main characteristics?

Fats with a trans double bond. Naturally occurring fats are all cis double bonds but in some food processing trans bonds occur. They act more like saturated fatty acids and are known to elevate risk of cardiovascular disease
1 higher melting point
2 increasing LDL/HDL ratio
3 inhibit delta six desaturase: catalyzes production of arachidonic acid
4 Increases shelf life of foods
5 present in fried foods


Define malnutrition and the two different types.

A disorder that results from too little or too much of essential nutrients
Primary occurs as a result of imbalanced or insufficient diet
Secondary occurs from defective assimilation or utilization of nutrients
Primary can be fixed by dietary changes alone but secondary may require medication and/or surgery


What are recommended dietary allowances (RDA)?

Amounts of various nutrients that provide adequate nutrition for 97.5% of people within a group of the same sex and age
Note that it is meant mainly to avoid insufficient nutrition and is therefore set 2 standard deviations above what is necessary for the average person in that group


Define and describe the dietary reference intakes.

Newer guidelines than RDA which aim to avoid chronic diseases in addition to insufficient nutrition.
Estimated average requirement (EAR): like RDA but for the average person in the group instead of 2 standard deviations above
Adequate intake (AI)- amount that appears to sustain good health in a group of people. For foods with insufficient scientific evidence to be an RDA
Tolerable upper intake level (UL)- the highest level of a nutrient that will pose no risk of adverse effects for 98% of people


What is the most accurate method of classifying obesity and what are the cutoffs for obesity?

Body fat percentage.
Men: > 25% = obese
Women: > 32% = obese


How is BMI calculated? Outline the guidelines for underweight, healthy overweight and stages 1-3 obesity.

BMI = body weight (kg)/height in meters^2 or body weight (lbs) *703/height in inches^2
Underweight = <18
Healthy = 18-25
Overweight = 25-30
Stage 1 obesity = 30-35
Stage 2 = 35-40
Stage 3 = 40+


Describe the 2 categories of fat location and how they relate to health/disease.

Abdominal/visceral: located between organs and abdominal wall. More highly associated with increased risk of CVD, diabetes etc.
Subcutaneous (peripheral) : just below the skin especially in the hips, thighs and buttocks. Poses less of a health risk


Describe the obesity classification method of waist to hip ratio (WHR).

The waist is measured at the narrowest point and the hips measured at the widest point.
WHR = waist circumference/hip circumference
>1 means at higher risk for diseases
It shows much higher correlation than BMI with risk for diseases because it takes into account location of fat deposits however it is more difficult and awkward for the patient to be measured


What 3 factors contribute to the alarming upward trends in obesity since 1970?

1 Increased sedentary lifestyle
2 Availability and marketing of cheap processed energy dense foods
3 genetics does not fit our lifestyle


Which population groups worldwide and in the US are most at risk of being obese?

Worldwide: developed countries have a higher risk
US: poor and minorities at higher risk


Why is the age of onset of obesity an important factor?

During periods of weight gain adipocytes grow in size but also proliferate however during periods of weight gain, they only shrink but their numbers do not decrease. This can stifle weight loss because it is hard to reduce adipocytes size below a threshold. In juveniles weight gain contributes more to the number of adipocytes than in adults. Thus if a young person becomes obese they will have a larger number of adipocytes that will contribute to problems accumulating fat throughout their life


What percentage of obesity is heritable? Is it possible for single gene mutations to contribute to obesity?

40-70% heritable
Yes there are some monogenetic disorders leading to obesity but they are extremely rare and do not account for rising obesity


Give the example of the Pima native Americans to illustrate the principle of heritability of obesity/diabetes.

Many Pima Native Americans migrated from Mexico to Arizona after the Mexican American war leaving two distinct populations. In the early 1900’s American Pimas had similar incidence of diabetes as the US population however by 1950 prevalence was 10X higher than US population. When compared to Mexican Pimas, prevalence is much higher in the US population due to adoption of an American diet. This shows that this group is genetically predisposed to diabetes, so environmental factors such as poor diet have a huge effect on them


What is the set point theory and how does it relate to obesity?

The theory that certain processes in our body maintain equilibrium at a set point and will resist if we try to deviate too far in either direction from that set point.
This is applied to obesity to say that there is a certain set point weight for each person that their body gravitates towards and will resist changes from that weight. This is supported by evidence showing that people who lose weight often cannot keep it off and that after weight loss people report feeling more hungry in the time after the meal than they did before weight loss


List the 4 major hormones involved in regulation of body weight and appetite and explain where they are produced and what is their function.

1 Leptin- produced in adipocytes and acts to decrease food intake. Leptin secretion is lowered after weight loss and highered (to a lesser degree after weight gain) supporting the set point theory
2 Ghrelin - peptide released in the stomach and acts to stimulate the hypothalamus to release hormones and increase food intake. Fasting and hypoglycemia bring it on
3 PYY- polypeptide produced in the ileum and colon that suppresses appetite and food intake and slows the passage of nutrients through the gut
4 Orexin (a and B)- peptides made in the lateral hypothalamus which stimulate appetite and cause increased food intake- they also promote wakefulness in the day and sleep at night


How is sleep related to obesity?

People who are sleep deprived have less leptin and more ghrelin and are therefore more likely to intake more food and gain weight


Describe the 3 types of surgeries common to improve health and fight obesity? Who is indicated to receive them?

1 Adjustable gastric banding- a band is placed on the stomach to limit the amount of space available in the stomach
2 Gastric bypass- the opening of the stomach is attached to the small intestine so that food does not pass through the stomach or much of the small intestine leaving only a small pouch. This limits the amount of food that patients eat and also limits their ability to absorb nutrients
3 Sleeve gastrectomy- A portion of the stomach is removed so that the stomach pouch is much smaller.
These are recommended only for patients with stage 3 obesity


What are the 3 defining characteristics of a vitamin?

1 Organic compound
2 Cannot be synthesized in sufficient quantities and therefore some must come from the diet
3 Are not metabolized to directly provide energy


Which vitamins are fat soluble? Which are water soluble?

Fat soluble
D,E, A, K
Water Soluble
C, B complex


How are fat soluble vitamins taken up? What about water soluble vitamins? What conclusions can be drawn from this?

Fat soluble by passive diffusion
Water soluble by facilitated transport
Fat soluble vitamins unlike water soluble vitamins cannot become saturated and therefore it is more likely to have an over abundance of fat soluble vitamins than of water soluble vitamins


What is the active form of vitamin D called? What is the structure like generally? How can we get it? What is its function? What happens if it is deficient?

Active form = calcitriol
It is similar to cholesterol with 4 hydrophobic rings
We can obtain it in our diet from animals but not plants or we can make it from cholesterol but this requires UV light which can be problematic in some places
It functions to alter gene expression in order to increase intestinal absorption of calcium ions in response to parathyroid hormone
In a deficiency, parathyroid hormone relies instead on uptake of bone calcium to raise plasma concentration leading to defective mineralization of the bone called rickets in children presenting with bowed legs, retardation of growth and plump appearance or osteomalacia in adults


Can vitamin D be toxic? What are its effects?

Yes in very high doses it can become toxic. It is extremely rare and seen mostly in response to abuse of supplements. Causes anorexia, excessive thirst, vomiting, weight loss, hypercalcemia, calcium deposits in soft tissue and if chronic enough can lead to atherosclerosis and cardiac myopathy


Name the 3 active forms of vitamin A. What is the structure like? Where do we get it?

Retinal, retinol, and retinoic acid
It is a single 6 membered ring with a long branched unsaturated carbon containing one polar group
It is rich in both animal and plant foods


What are the two main biological functions of Vitamin A? How could a deficiency occur and what symptoms would present?

1 Retinal is important in vision. It is bound to opsin to create rhodopsin and the retinal portion undergoes a change from cis to trans double bond when hit with UV light which is important for vision
2 Modifies gene expression to enhance differentiation and proliferation especially in epithelial and immune cells and in development
A deficiency could occur as a result of malabsorption disorders or a diet that is too heavily based on one thing such as white rice with little vitamin A. It presents as night blindness, hyperkeratosis of epithelial cells where immature skins cells accumulate are dry with a high production of keratin, also xerothalmia or hyperkeratosis of the cornea can occur which ultimately can lead to infection and blindness


How does our body get vitamin K? What are its functions in the body and what results from a deficiency?

We get about half of our vitamin K from animal and plants in our diets and the other half from intestinal bacteria
It allows the post-translational modification of adding CO2 to glutamate which is important for several clotting factor proteins.
Deficiency leads to severe bleeding
Deficiencies are rare and occur in adults in response to malasorptive syndromes or prolonged use of certain antibiotics or warfarin. It is assumed in infants b/c they don’t have gut bacteria and vitamin K and limited amounts in placenta and breast milk so all infants are given supplements


What is the biological function of vitamin E? What happens if it is deficient?

Function is not well understood. It is thought to have non specific antioxidant effects
Deficiency can occur from a mutation called AVED which results in retinopathy and neuropathy related to oxidative damage of the photoreceptors and neurons respectively. Can also result from malabsorptive syndromes


Make a chart for fat soluble vitamins showing their sources deficiencies and toxicity. (Not on the bus)

Vit. Source. Deficiency. Toxicity
Endow Plant. Animal. Gut. Risk. Disorder
A. Y. Y. Diet Visión, hyperkeratosis Y
D. Y. Y. Sunlight, diet Rickets, osteomalecia. Y
E. Y. Y. Genetics. AVED
K. Y. Y. Y. Birth. Bleeding and bruising


What is the name of B1 and its active form? What biological processes is it involved in?

Thiamine Active form = TPP
Cofactor for decarboxylation reactions such as pyruvate dehydrogenase and alpha ketoglutarate and amino acids
Used in citric acid cycle, pyruvate dehydrogenase, amino acid catabolism and pentose phosphate pathwat


What could cause a deficiency in vitamin B1 and what are the signs and symptoms?

Limited commodities diet such as only eating white rice or alcoholism
Symptoms include Wernicke-Korsakoff syndrome of neurological impairments and the more severe beriberi leading to anorexia, muscle weakness, peripheral paralysis and edema


Give the name for vitamin B2 and its active form? What is its function within the body?

Riboflavin Active forms FMN and FAD
Cofactors which catabolize oxidation reduction reactions in metabolism. Involved in electron transport chain, TCA cycle, beta oxidation


Give the signs/symptoms of vitamin B2 deficiency.

Pathology of skin and mucous membranes
Glossitis- tongue, Cheilosis- lips, sebhorreic dermatitis-scalp face and torso


Give the name and function of vitamin B3 and its active form.

Niacin active form nicotinamide NAD and NADP
Cofactor for oxidation reduction reactions in many pathways of metabolism


What are the causes and signs/symptoms of vitamin B3 deficiency?

Diet consisting of a limited commodity: corn
Hartnup disease- mutation affecting absorption of niacin precursor
Isoniazid antibiotic over long times
Signs / symtoms: pellagra- dermatitis,diarrhea and dementia


Give the name for vitamin B5 and its active form along with its function.

Pantothenate active form coenzyme A
Cofactor and acyl group carrier for a variety of metabolic processes


Give the name and active form of B6 along with its function.

Pyridoxine active form = pyridoxal 5-phosphate
Coenzyme for transamination reactions in amino acid metabolism thus it is required for synthesis of all amino acids


What are the causes signs and symptoms of vitamin B6 deficiency?

Isoniazid antibiotic
Macricytic anemia (large immature RBC’s), pathology of skin and mucous membranes


Why can vitamin B6 be toxic even though it is water soluble? What are the symptoms of toxicity?

It can be de phosphorylated which makes it less hydrophilic and allows some passive diffusion uptake. Toxicity occurs as a result of abuse of supplements
Nerve damage to arms and legs and sensitivity to sun all are reversible if supplement is stopped


What is the name and active form of vitamin B7, what is its function?

Biotin active form: biotin
Cofactor for carboxylases in many processes of metabolism


How can a vitamin B7 deficiency occur and what would be the signs and symptoms?

Genetic, long term antibiotic use, over reliance on raw eggs in diet
Signs/symptoms: Neurologic and dermatitis


Give the name, active form and function for vitamin B9.

Folic acid Active form THF
Important in one carbon metabolism such as synthesis of amino acids, purines and thymidine
Necessary for any rapidly dividing tissues


What are risks and signs/symptoms of a Vitamin B9 deficiency?

Over reliance on goat’s milk
Macrocytic anemia
Tongue lesions
Birth defects including spinal bífida


Give the name and function of Vitamin B12.

Required to synthesize active folate


Describe how vitamin B12 is absorbed. Why the intricate process?

It is ingested bound to proteins -> haptocorrin in the stomach -> Intrinsic factor in the intestine-> translocator in intestine -> transcobalamin i, II or iii in blood
It is much larger than other water soluble vitamins


What are the risks and signs/symptoms of vitamin B12 deficiency?

Strict vegan diet
Loss of intrinsic factor
Megaloblastic macrocytic anemia
Pins and needles and numbness in hands and feet, psychiatric disorders


What is the name and function of vitamin C?

Ascorbic acid
It is an important water soluble antioxidant especially functioning in neutrophils against infection it is also an electron donor for hydroxylations such as the formation of collagen


what are risks and symptoms of a deficiency of vitamin C?

Scurvy - Rupture of small blood vessels, weakening of bones and swelling of joints


What disorder results from a deficiency of the mineral selenium?

Keshan disease- cardiomyopathy in selenium deficient children triggered by stress, viral infection or chemical exposure


Create a chart summarizing the sources, deficiencies and toxicities of Water soluble vitamins.

Vit. Source. Deficiency. Toxicity
Endo Plant Animal Gut. Risk. Disorder
B1 Y. Y. alcoholism Beriberi and Wernicke-Korsakoff
B2. Y. Y. Light
B3. Y. Y. Y. Hartnup, low B6. Pellagra. y
B5 Y. Y
B6 Y. Y. Isoniazid macrocytic anemia. Y-passive uptake
B7 Y. Y. Y. Antibiotics
B9. Y. Y. Pregnancy. Macrocytic anemia/birth defects
B12. Y. Diet, loss of IF macrocytic anemia, nerve damage
C. Y. Diet. Scurvy


Describe the signs and symptoms of anorexia nervosa.

Weight loss or improper growth
Extreme fear of weight gain
Weighs less than 85% of expected weight


Describe the signs and symptoms of bulimia nervosa.

Repeated binge consumption followed by compensating behaviors which include: vomiting, fasting, laxatives, and excessive exercising


Describe the signs and symptoms of muscle dysmorphia.

Repeated obsession with appearance of body parts often muscle size followed by inappropriate compensating behavior.


Describe the DASH diet.

Dietary approaches to stop hypertension
Shown to lower blood pressure in normotensive and hypertensive patients
Consists of eating foods high in potassium and low in sodium along with fruits vegetables whole grains and lean meats and dairy


What is the role of lipoprotein lipase (LPL)?

It hydrolyzes triglycerides in blood borne lipoproteins allowing adipose tissue to take up free fatty acids


What is the role of Hormone sensitive lipase?

Hydrolyzes stored triglycerides in adipose tissue to release free fatty acids to be used for energy


Describe the normal role of Adiponectin.

Think adiponectin is good for you!
It is produced by adipocytes and has anti-atherosclerotic effects and increases insulin sensitivity.
It is lower in obesity, insulin sensitivity, metabolic syndromes and type 2 diabetes


How does insulin interact with adipose tissue proteins and hormones?

Inhibits HSL and activates LPL -> results in more fat storage
Stimulates leptin


What are some physiological functions that make visceral fat worse than subcutaneous? (4)

1 Higher angiotensin expression -> increases blood pressure
2 Leptin is mainly produced in subcutaneous
3 Elaborates most of the IL-6 and TNF-alpha which result in inflammation
4 Believed to be responsible for lower adiponectin in obese and diabetic patients


Diagram the mechanisms behind adipose tissue dysfunction.

1 Adipocytes enlarge due to obesity and release more FFAs
2 FFAs lead macrophages to produce more TNF-alpha
3 TNF-alpha activates adipocytes
4 Activated adipocytes increase lipolysis releasing more FFAs, secreting more IL-6 and recruiting more macrophages
5 More macrophages and more FFAs further leads to higher TNF-alpha in a vicious cycle
The result is high amounts of inflammation and macrophages in adipose tissue of obese patients. This is adipose dysfunction


How is adipose dysfunction related to insulin?

High levels of FFAs and TNF-alpha along with low levels of adiponectin in adipose dysfunction lead to greater insulin insensitivity


How is obesity related to atherosclerosis?

High triglycerides and low HDL along with hypertension increase the risk of atherosclerosis and result from obesity related adipose dysfunction
In addition obese people have high levels of angiotensinogen, ACE and renin which are all parts of the renin-angiotensin aldosterone pathway leading to increased blood pressure
Dysfunctional adipocytes produce angiotensinogen and angiotensin 2


What is the best intervention for adipose tissue dysfunction?

Physical activity and calorie restriction
Not only does this decrease the amount of adipose tissue and lead to weight loss, this decreases TNF-alpha, IL-6 while increasing adiponectin. All of this works together to decrease inflammation and increase insulin sensitivity even before weight loss occurs


Use intervention to bedding to explain classical conditioning.

An alarm is placed in the child’s pants that goes off in response to the first drops of urine.
In this case the Neutral stimulus is the feeling of a full bladder, the unconditioned stimulus is the alarm noise and the unconditioned response is waking up. Eventually by pairing the alarm to a full bladder for several weeks, children learn to associate the two stimuli and eventually if the alarm is removed, they will wake up to a full bladder alone


Explain the idea of systematic desensitization to treat a fear or anxiety.

This is a form of classical conditioning and follows these steps
1 Learn incompatible response besides fear and anxiety such as deep relaxation (breathing exercise)
2 Create an anxiety hierarchy- rank situations from little fear to a lot of fear
3 Gradually expose the patient to more and more threatening stimuli and allow them to experience each situation long enough until the anxiety subsides
Eventually, the situation becomes less threatening


Describe aversive conditioning.

A way to use classical conditioning to create more fear toward a situation
For example, you could give an alcoholic something that makes them nauseated each time they drink and eventually the idea of drinking alone will cause them discomfort or fear


What are the 4 main challenges of using classical conditioning?

1 Controlling the exposure to feared object/situation- sometimes it can be hard to give a small exposure without giving anything bigger for example a phobia of flying
2 Identifying the focus of the fear- for example someone with panic attacks may not understand what sets them off
3 Timing the exposure to feared object- the exposure can’t be too short, it must be long enough for the anxiety to go away
4 Make the exposure challenging enough- for example someone with a social phobia must experience difficult social situations such as someone being rude in addition to positive ones or else they will struggle with those in the real world


What are some of the challenges inherent in using operant conditioning? (4)

1 Shape behavior little by little-instead of offering an award for the perfected final product, small rewards should be offered for smaller steps along the way
2 Frequency of consequences- continuous reinforcement is required in the beginning to acquire the behavior and after that intermittent reinforcement is enough to maintain
3 Timing of consequence- there must be a close temporal link between action and consequence
4 Clarity of consequence- must be clear and specific about the action being reinforced or punished


Describe how operant conditioning could be applied clinically to help a child with feeding disorder of infancy or early childhood.

These patients either do not eat enough or enough variety of foods by mouth to sustain proper growth and development
Positive reinforcements could be made for each bite of a non-preferred food such as a bite of a preferred food
Negative reinforcement could be used when a disliked food is place close to the child’s face so that they must see and smell it until it is removed when they eat it
Punishment could be used such as a firm tone of voice if the child is spitting or acting out in another way
Extinction could be used by withdrawing attention and eye contact until the child takes a bite


Give the definition of a developmental disability with the 5 criteria.

A severe, chronic condition that:
1 is attributable to mental or physical impairment or a combination
2 is manifested before the age of 22
3 Is likely to continue indefinitely
4 Results in limitations in 3 or more areas of major life activity
Self care, Language, learning, mobility, self-direction, economic self-sufficiency, and independent living
5 Reflects a need for support and services that are lifelong or extended duration


What are the criteria for an intellectual disability?

Diagnosed by age 18
IQ below 70 AND deficits in adaptive behaviors (ability to accomplish tasks of daily living)


What are the three categories of adaptive behaviors used to diagnose someone with an intellectual disability. Give some examples within each category.

1Conceptual - ability to understand time, do math, read, write and communicate
2 Social- avoid being tricked or manipulated and follow social rules and expectations
3 Practical- Hygiene, money, technology


Give the defining criteria of autism spectrum disorder (3) and explain how they might affect a clinical situation.

1 Persistent deficits in social communication and interaction across multiple contexts
2 Restricted, repetitive patterns of behavior, interests or activities
3 Symptoms present in early developmental period (even if not fully manifested until later)
IN the clinic
Patients could be sensitive to touch or certain sounds so be aware
May engage in self-stimulatory behaviors- don’t tell them to stop
May talk excessively about a topic of interest- don’t get frustrated just try to redirect them


Describe the cause and symptoms of cerebral palsy and how it might affect a clinical visit

Results from brain damage, before during or right after birth
Usually affects individuals ability to move, balance or speak
In the clinic
They may have difficulty with physical movements ie moving limbs or getting onto an exam table
They may have difficulty speaking- this doesn’t mean they have an ID
Ask if they need assistance before touching or repositioning them


What is spina bifida? What are the 3 types? How could this affect a clinical visit?

A birth defect in which the spinal column does not close completely
1 Spina bifida oculta- most common and mild form
2 Meningocele- the split creates a sac of nerve fluid on the back
3 Myelomeningocele- spinal cord and nerves enter the sac of fluid- most severe and disabling form
In the clinic
May have mobility issues
Likely to have allergies such as latex
May have bowel or bladder incontinence


What are the common symptoms of Down syndrome? How could it affect a clinical visit?

Most have ID
Low muscle tone is common and they often receive physical therapy to improve speech and articulation and other movements
In the clinic
Low muscle tone may affect their speech but it doesn’t mean they can’t speak or don’t understand so ask them to repeat themselves or say it another way if necessary to understand them
Weight is a common problem in Down syndrome so discuss exercise and diet


Describe fragile X and how it could affect a clinical visit.

Genetic condition causing ID, symptoms of autism spectrum disorder, ADHD and anxiety
In the clinic
Be attentive to anxiety levels and other mental health issues
Be aware of common ADHD


What things should be taken into consideration for someone with a developmental disability in infancy? (2)

1Caregivers are vulnerable and uncertain about future so be positive but don’t make promises about future ability, be aware of financial burdens, give basic information about getting ready for preschool
2 Make sure caregivers take care of their own health as well


What special considerations should be made for a patient in childhood with developmental disability? (3)

1 Need primary healthcare like all other children (well visits)
2 May be uncomfortable or afraid of doctor’s offices so do your best to engage with them and help them be comfortable
3 May need extra time for examinations and procedures


What special considerations need to be made for an adolescent patient with a developmental disability? (4)

1 They need the conversation about sexual health just like all other teens- may need additional education on this topic
2 May be more likely to engage in risky behaviors
3 Transitions and failure to achieve milestones can be especially difficult
4 Plan for transition to adult care provider


What things need to be taken into consideration during adulthood of a patient with a developmental disability?

1 Give them normal guidelines for preventive care
2 Be aware of disability-specific risks
3 May have lost access to many services offered through school systems-ask if their needs are being met


What special considerations need to be made for an aging patient with a developmental disability? (3)

1 Parents pass away and caregiver responsibilities may change
2 Especially vulnerable to elder abuse
3 May not fully understand aging and dying- have conversations about end of life decision making with them, family and caregivers being sure to respect their autonomy


What is the difference between screening and diagnostic tests?

Screening is less expensive and administered to healthy populations in order to identify those with a high probability of disease but not to diagnose
A diagnostic test is used for diagnosis and only given to those suspected to have the disease


What are the 3 requirements for successful screening? Describe each briefly.

1 Suitable disease- the disease should have serious consequences, be progressive with treatment most effective at earlier stages and it must have a detectable pre-clinical phase
2 Suitable test- must be inexpensive, quick, safe, easy and relatively painless to administer and should have high validity and reliability
3 Suitable screening program


What are the three types of disease prevention?

1 Primary- Prevent the disease before its onset
2 Secondary- delay the onset of symptom appearance
3 Tertiary- slow disease progression, alleviate symptoms and prolong life


What is the lead time in screening?

The time by which the diagnosis of a disease is advanced because of screening.
For example, if onset of symptoms would have been 60 but you detect the disease at 55 by screening, the lead time is 5 years


Describe the terms, sensitivity, specificity and criterion of positivity in terms of screening. Explain how they are related.

Sensitivity = how many of the people with the disease are characterized as positive. Sensitivity = True positives/True positives + false negatives
Specificity = how many people who don’t have the disease are characterized as negative. Specificity = true negatives/true negatives+ false positives
Criterion of positivity is the test value determined to represent a positive score
As you move the CP in one direction you will improve either sensitivity or specificity but make the other worse so researchers must choose a point that best accomplishes what they want


What is the overall accuracy of a test?

A measure of the proportion of true results among all results
Overall accuracy = True positives + true negatives/ All results


Describe positive and negative predictive value in screening.

Positive predictive value is a measure of how likely someone who tested positive is to actually have the disease
PPV = True positive/True positive + False positive
Negative predictive value is a measure of how likely someone who tested negative is to actually be disease free
NPV = True negative/True negative + false negative


Give an example of a situation where you would prioritize sensitivity over specificity and vice versa.

You prioritize sensitivity any time it is more important to identify all people with a disease than make sure you don’t have false positives. Thus whenever you would rather have a false positive than a false negative you optimize sensitivity.
This might occur with a disease that can be transmitted because you want to identify all cases to avoid further transmission
You prioritize specificity any time you would prefer to have false negatives over false positives
This could be the case with an untreatable, fatal disease because a false diagnosis would cause serious harm to a patient and there is little to gain from knowing that you have the disease since nothing can be done to improve the situation


How does prevalence of a disease influence interpretation of screening?

Low disease prevalence -> higher false positives
High disease prevalence -> higher false negatives


What are the 4 main types of measures of disease frequency? Briefly describe each.

1 Count - Simply the number of people
2 Ratio - Comparison between two groups
3 Proportion - Comparison between one part of a group and the total group to which that part belongs
4 Rates - ratios or proportions that include an element of time


Compare and contrast fixed and dynamic populations? Which is more common?

Fixed = permanent membership based on defined event or characteristic
Dynamic = transient membership based on being in or out of a state
Dynamic is more common and makes things more complicated


What is incidence of a disease and what are the two types?

Incidence = frequency of new cases within a population
I = new cases/population over specific Time period
1 Cumulative incidence = # of new cases/# at risk at beginning of follow up over a specific time period- this works better for a fixed population
2 Incidence rate = # new cases/Sum of disease free person-time over specific time period. Instead of assuming everyone remains part of the group for the entirety of the study, it attempts to account for a dynamic population by counting the amount of time a person was a part of the group during the period of time


What are the three ways to measure person-time for an incidence rate?

1 Add up all the risk periods for each individual in the study - hardest but most accurate method
2 Average number of people in study * duration of study
3 Number of people in the study * average duration per person


What is the prevalence of a disease? What are the two types?

A measure of the proportion of the population with the disease over at a time. Includes both new and existing cases]
1 Point prevalence = # of cases /total population at a specific point in time
2 Period prevalence = existing cases + new cases/population at midpoint over a period of time


What is the relationship between incidence and prevalence?

Prevalence is a function of incidence and duration of disease.


Name and describe 4 types of data.

1 Binary- two options
2 Categorical - more than two and fewer than infinity options
3 Continuous- infinite number of options- numerical data
4 Time to event data


What are the two types of categorical data?

1 nominal- no implied order
2 Ordinal- implied order


What are the ways that continuous data could be described?

Measures of central tendency- mean and median

Measures of variability - Range and standard deviation


Give the mean, median, and standard deviation of the following data set:
4, 5, 1, 8, 3, 9

Mean: 5
Median: 4.5
Standard deviation: Square root(7.67) = 2-3 around 2.8


What is normality and how would you measure it?

Normality describes how close the data resembles a normal bell shaped distribution where the mean, median and mode are equal and the curve is symmetrical
You could graph the data either in a histogram and see if it looks like a bell curve or in a quantile quantile plot and see if points fall on or near the line of best fit
The most accurate way is to do a Shapiro-Wilk test. Null hypothesis is normally distributed so p


Make a simple diagram to show all of the pathways involved in amino acid metabolism. (Not on the bus)

Should include the following groupings
Ingested proteins
Amino acid biosynthesis
Both of these feed into the amino acid pool Which feeds into
Protein (also feeds back to amino acid pool)
Deamination which produces NH4+ and Carbon Skeletons
NH4+ feeds into excreted nitrogen
Carbon skeletons produce either acetyl coA or TCA cycle intermediates/pyruvate depending on whether they are Ketogenic or glucogenic


What is another important function of amino acid catabolism besides producing energy?

It provides precursors to many important nitrogen-containing compounds such as nucleotide bases, heme and creative


Explain the concept of nitrogen balance as well as quantity and quality requirements of amino acids.

Nitrogen balance is the amount of ingested nitrogen - excreted nitrogen. Nitrogen equilibrium is when nitrogen balance = 0. Nitrogen balance can also be positive meaning more nitrogen is entering the body than is leaving or negative meaning more is leaving than is entering
In order to maintain adequate nitrogen balance, a person must meet quantity and quality requirements of amino acids meaning they are eating enough total and they are getting a complete complement of essential amino acids


What are some situations in which someone would need a positive nitrogen balance?

Attempting to gain lean body mass


What could cause a negative nitrogen balance?

A negative nitrogen balance occurs when proteins within the body are being catalyzed in high quantities to produce energy and their nitrogen is being excreted in higher levels than the nitrogen being ingested
This can result from a lack of protein in the diet or from catabolic diseases such as cachexia which causes a hypercatabolic state


How does the synthesis and catabolism of essential and nonessential amino acids differ?

In general nonessential amino acids are much simpler to synthesize and catabolize and require many fewer enzymes. They are also generally glucogenic this may be a reason why the body retains the ability to synthesize them
Essential amino acids on the whole are more complex to synthesize and catabolize requiring many enzymes


Describe the cause, symptoms and treatments of phenylketonuria (PKU).

Cause: genetic deficiency in phenylalanine hydroxylase enzyme which converts phenylalanine to tyrosine
Symptoms: Tyrosine becomes an essential amino acid
Phenylalanine builds up mostly as phenylpyruvate and phenylacetate these can be toxic to the brain leading to mental disabilities and seizures
Treatment: avoidance of phenylalanine (contained in aspartame)
Supplementation of tyrosine


Describe the pathway by which cysteine is produced along with the 2 disorders affecting that pathway.

Methionine is converted to homocysteine which provides the sulfur to convert serine to cystathionine by the enzyme cystathionine synthetase. Cystathionine is then converted to cysteine by cystathionase
1 Homocystinuria occurs by deficiency of cystathion synthetase and results in cysteine becoming conditionally essential as well as accumulation of homocysteine and methionine
2 Cystathioninuria occurs by deficiency of cystathionase resulting in cysteine being conditionally essential and buildup of cystathionine.This is more benign than homocystinuria


Describe how asparagine is synthesized. How does this pathway related to cancer and cancer treatment?

A transamination occurs in which the nitrogen from glutamine is transferred to aspartate to produce asparagine. The enzyme is asparagine synthetase
In acute lymphocytic leukemia, leukocytes are deficient in asparagine synthetase and must rely on the extracellular environment to take up asparagine. A common treatment is L-asparaginase which breaks down asparagine in the extracellular environment depriving cancer cells of their only access to asparagine and causing them to undergo cell death


Draw the reaction by which amino acid nitrogen is released as ammonia.

Amino acids undergo transamination where their nitrogens are transferred to alpha ketoglutarate to produce glutamate and alpha ketoacids. Glutamate can then undergo oxidative deamination producing ammonia and alpha ketoglutarate


What is the purpose of the urea cycle? Draw the cycle including names of intermediates and enzymes and where each reaction takes place. (Not on the bus)

The purpose is to convert ammonia into urea which is less toxic to be excreted. Ammonia easily crosses the blood-brain barrier and causes damage to neurons.
1 HCO3- + NH4+ -> carbamoyl phosphate
Enzyme: Carbamoyl phosphate synthetase
2 Carbamoyl phosphate + ornithine-> citrulline
Enzyme ornithine transcarbamoylase
3 Citrulline + aspartate -> argininosuccinate
Enzyme: argininosuccinate synthetase
4 Argininosuccinate -> fumarate + arginine
Enzyme: argininosuccinate lyase
5 Arginine -> Urea + ornithine
Enzyme: Arginase
Urea cycle occurs mainly in the liver
1-2 occur in the mitochondrial matrix
3-5 occur in the cytosol


Why is blood urea nitrogen (BUN) measured?

Sharp rises in BUN indicate renal failure since the kidneys are responsible for excreting the urea produced in the liver


What is hyperammonemia and how can it occur? How can it be treated?

Too much ammonia leading to neurological damage
Symptoms include: tremors, slurred speech, vomiting, cerebral edema, blurred vision, coma and death
Can occur:
1 Congenital- rare mutations to one of the 5 urea cycle enzymes. The earlier in the process the enzyme acts the more severe. Infants show no signs at birth but have symptoms within 24 hours
2 Acquired : can occur as a result of liver cirrhosis (hepatic encephalopathy) or bacterial infection - some bacteria can convert urea back to ammonia leading to both hyperammonemia and kidney stones
Can be treated by restricting protein in the diet and supplementing with essential amino acids or by using sodium benzoato or sodium phenylbutyrate which lead other pathways of nitrogen excretion besides urea


What do the ketogenic amino acids have in common? Which ones are they?

They are the most hydrophobic ones which resemble fatty acids


What is triheptanoin? What 2 conditions could it be used to treat?

A medium chain fatty acid with 7 carbons. It produces propionyl coA when oxidized and also can produce a 5 carbon ketone body. It can be used to treat pyruvate carboxylase deficiency and cptii deficiency


What is respiratory quotient? How does it differ between nutrients?

The ratio of CO2 exhaled / O2 inhaled during metabolism of a certain food
Carbs = 1
Protein = 0.8
Fat = 0.7


What are the major parts of the pancreas and the roles of each?

1 Acinar cells- exocrine secretions make up vast majority of mass of pancreas
2 Islets of langerhans- endocrine secretions (1-2% of pancreas mass)
Within islets,
Alpha cells- glucagon
Beta cells- insulin
Gamma cells- somatostatin


Compare and contrast insulin and glucagon in terms of what they do, what they respond to and where they are produced.

They are exact opposites
Insulin- activates uptake of glucose from blood at target cells in response to high blood glucose levels and is produced in beta cells
Glucagon- activates release of glucose in response to low blood glucose and is produced in alpha cells


What are the targets of insulin secretion? (3)

1 Skeletal muscle
2 Adipocytes
3 Liver


Describe the process by which insulin exhibits its effects at target cells.

1 Insulin binds to its receptor (a pre dimerized RTK)
2 Receptor activates IRS1 (insulin receptor substrate 1)
3 IRS1 activates the PI3 kinase pathway
4 Vesicles containing GLUT4 (glucose transporter) are send to the plasma membrane increasing glucose uptake


Describe the structure of insulin as well as how it is formed.

Insulin is a small peptide hormone made up of an A and a B chain which are bound together by disulfide linkages
1 Translated to preproinsulin containing A, B and C chains along with signal peptide into ER
2 Signal peptidase removes signal peptide to form proinsulin
3 In ER proinsulin folds and disulfide linkages form between A and B chains
4 In secretory vesicles, the protein is cleaved so that the C chain is removed producing mature insulin


What is the C chain of insulin and why is it important clinically?

Part of the pro hormone which is removed during the formation of mature insulin. It is secreted along with insulin and produced in amounts equal to insulin. It is also much more stable than insulin and so its concentrations give clinicians an idea of the amount of insulin that is being produced


Describe the way insulin is stored prior to secretion.

Insulin is stored in secretory vesicles or storage granules
In these vesicles, they form a quaternary structure consisting of 3 dimers around a Zn ion where His from B chain of insulin is interacting with Zn ion


Why are islets highly vascularized?

The increased blood flow allows both the ability to sense glucose levels in the blood and to quickly distribute insulin into circulation.


How does glucose sensing occur in beta cells in the pancreas?

GLUT2 transporters bring glucose into the cell-> high glucose means more glycolysis -> high glycolysis means more ATP -> ATP closes K+ channels leading to more + charge within the membrane -> voltage gated calcium channels open -> Ca2+ leads to secretion of insulin


What is meant by biphasic secretion of insulin? How does it occur?

Insulin secretion occurs in 2 phases
1- rapid, transient secretion
2 - slow, sustained secretion
This occurs because there are two pools of storage granules. Rapid phase occurs as a result of secretion from vesicles near the cell surface and slow, sustained secretion results from vesicles stored near the center of the cell


Compare and contrast GLUT2 and GLUT4 transporters.

Both transport glucose into cells
GLUT4 transports glucose into cells in response to insulin secretion
GLUT2 transports glucose into beta pancreatic cells as a part of glucose sensing prior to glucose release


Describe the structure and processing of glucagon.

Glucagon consists of a single short peptide chain that creates an alpha helix
It is synthesized as a preprohormone which contains insulin along with other chains which serve other functions. The preprohormone is cleaved differently in different tissues in the body but in the pancreas it is cleaved in a way that separates the glucagon hormone from the other chains. In other tissues, the glucagon hormone forms part of a larger protein


Describe the process that leads to secretion of glucagon.

Low glucose in the blood triggers voltage gated opening of calcium channels in alpha cells of the pancreas. The influx of calcium causes vesicles containing glucagon to fuse with the membrane allowing release of glucagon


Describe the methods and findings of the Carolina abecedarian study.

Randomized poor children into two groups, 1 receiving daily childcare for the first 5 years of life in addition to other services and the other receiving all other services but not childcare. They followed those children over more than 40 years and tracked the differences between the two groups. They found marked differences in social and health outcomes including lower blood pressure, cholesterol, metabolic syndromes and CV risk scores in the childcare group. The childcare group had better outcomes in all areas. This illustrates the importance of the environment especially during the early years of development


Describe the study carried out on children born during the Dutch winter famine of 1944-1945 and what its findings mean.

Compared children born during the famine when rations were limited to 400-1000 Calories per day (far less than a pregnant mother needs) to children born before and after that time. In addition to low birth weight, neurological and other health issues were more common in children born to malnourished mothers during the famine. These included CVD, glucose-insulin disorders, obesity, renal dysfunction, airway disease and breast cancer. This showed that the circumstances facing the pregnant mother affect the baby and can have long-lasting effects


What are the three main ways that gene expression can be altered in response to experiences?

1 Modifications of DNA activity
2 Histone modifications
Acetylation, methylation, phosphorylation, etc.
3 Modifications of micro-RNA
MiRNAs downregulate translation of specific mRNA transcripts


Describe the honeybee and killer bee experiment and what it teaches about epigenetics.

Honey bees are generally docile while killer bees are much more aggressive. Researchers placed honey bee larvae with killer bees and vice versa and then measured their behavior. Honeybees raised around killer bees acted just like killer bees and killer bees raised with honey bees acted just like honeybees. Further when DNA microarrays were used to measure expression, it was found that expression had been changed in both cases to match the expression of the bees with which they were raised. This shows how environmental factors or experiences can alter DNA expression leading to dramatic changes in behavior/life course


Explain how the timing of midbrain and frontal cortex of the brain affect behavior and how they are related to ability to cope with stress.

The midbrain which controls the emotions, fear and stress among other things develops first while the frontal cortex develops much more slowly and will not be completely developed until after adolescence. The frontal cortex includes areas involved in planning, calculating and importantly impulse control. Children often throw temper tantrums and have difficulty controlling emotions as a result of a developed midbrain but immature frontal cortex. In order to handle emotions and stress in a way that will be less damaging, a child must have a well developed frontal cortex


What is the difference between tolerable and toxic stress for children?

Though some limited stress can be positive, both of these refer to negative stress. The difference between the two is in how developed the frontal cortex of the brain is and how well the child can handle the stress. If a child is developed enough to handle the stress in a way that is minimally harmful than it is tolerable but if they cannot, then it is toxic


What are ACEs what effects do they have?

Adverse childhood experiences. These are specific events or experiences known to cause a lot of harmful stress on a child. People with a high number of ACEs in childhood often develop social, emotional and cognitive impairments, they often engage in health-risk behaviors, they are more susceptible to diseases and they often die early


Explain the results of the lickers and groomers experiment.

Baby Rats were removed from their parents and then returned after a short time. Some parents licked and groomed their rats while others did not. The lickers and groomers showed a rapid decrease in stress hormones after being returned while those that did not receive licking and grooming did not. Also over the course of their lives, rats receiving licking and grooming were healthier in a variety of ways. This was true of all rats receiving licking and grooming whether it was from their biological parent or not. This teaches us that certain behaviors on the part of parents or other caregivers are important for helping children respond to stress and these behaviors can have long-lasting and far-reaching affects on the child’s life


What are some important strategies parents or other caregivers can adopt to raise children with well-developed social and emotional skills? (7)

1 Breastfeeding
2Back and forth communication
3 Stimulating environment
4 Daily routine
5 Teaching through play
6 Disciple aimed at teaching
7 Practice social-emotional skills


compare and contrast focused and comprehensive ultrasound.

Focused (point of care) is done by a clinician at the bedside with the purpose of answering a specific question
Comprehensive is generally performed by a technologist and interpreted by an imaging specialist and seeks to get a more thorough view of an entire system


What are the three colors on ultrasound and what does each represent?

1 Black or anechoic
Fluid and artifacts such as posterior acoustic shadowing
2 Gray or hypoechoic
Medium to low density tissues and some artifacts
3 White or hyperechoic
High density tissues and air


What are the four sides of an ultrasound image. If possible draw a picture to illustrate.

1 Near field- the top-represents more superficial
2 Far field- the bottom usually more deep tissues
3 Leading edge- the side closest to the indicator (often the left)
4 Receding edge- the side farthest from the indicator (often the right)


What is the piezoelectric effect?

The conversion between electrical and mechanical energy. Ultrasound uses crystals that vibrate to produce sound waves (mechanical energy) from electrical energy. The waves that bounce back off body tissues to the ultrasound machine are then converted back into electrical energy so they can be understood


Briefly describe Doppler ultrasound.

Uses the Doppler effect to estimate movement of particles such as blood cells based on the change in frequency caused when they run into each other.


What are the five probe motions?

1 Fan- change the angle of the probe perpendicular to the indicator without moving the probe
2 Sweep- move the probe perpendicular to the indicator without changing the angle
3 Rotate
4 slide - move the probe parallel to the indicator without changing the angle
5 rock = Change the angle of the probe parallel to the indicator without moving it


What are the three types of cytoskeleton filaments? Briefly describe the structure and main function of each.

1 Intermediate filaments- strong, flexible rope like structure thicker middle thickness. Mainly protects cells from mechanical stresses
2 Microtubules- stiff hollow rod like structures important in transport of cargo, formation of cilia and flagella and cell division
3 Actin- thin fibers with a wide variety of structures and functions regulated by actin binding proteins


What is the nuclear lamina?

A mesh on the inside of the nuclear envelope made up of intermediate fibers


What are desmosomes?

Plaque like structures that anchor intermediate filaments to the plasma membrane


How are intermediate filaments arranged in the cytoplasm generally?

They form a network surrounding the nucleus which extends out to the periphery of the cell


How are intermediate filaments built up?

They are made up of alpha helical monomers with coil together to form dimers called coiled-coil dimers. 2 dimers come together in a staggered way to form a tetramer. 8 tetramers are arranged side by side to form a bundle and bundles arrange end to end to create filaments with no polarity.


What are the 4 classes of intermediate filaments? Where in the body is each found?

1 Keratin filaments- epithelial cells
2 Vimentin and vimentin related filaments- connective tissues, muscles, glial cells
3 Neurofilaments- neurons
4 Nuclear lamins - in the nucleus of all cells


Explain the cause and symptoms of epidermolysis bullosa simplex.

Caused by mutations to skin specific keratin genes causing the skin to be sensitive to minor mechanical stress such that even small amounts of mechanical pressure cause skin blisters


Explain the cause and symptoms of Progeria.

Caused by a rare mutation to the gene encoding nuclear lamin A. The nuclear lamin therefore doesn’t form correctly and the nucleus is irregularly shaped and chromatin, gene expression and division are affected. Symptoms are prematurely aging: limited growth, wrinkling of skin, loss of hair, CV and kidney problems, musculoskeletal degeneration. Symptoms appear in first few months of life and the lifespan is generally into the teens


Explain how microtubules are built.

Alpha and beta tubulin form a dimer. These timers stack end to end to form a protofilament. 13 protofilaments associate side by side to form a hollow tubed structure which is a microtubule. One end has an alpha tubulin while the other has beta tubulin. Beta tubulin end is the + end where tubulin are incorporated more rapidly and the alpha end is the - end where tubulin are incorporated more slowly


Describe how microtubules are generally arranged in the cytosol.

Microtubules extend from outward from an organizing center called a centrosome which is located near the nucleus. A centrosome is made up of two centrioles and a matrix made up of hundreds of gamma tubulin rings. The - ends of microtubules become embedded in the gamma tubulin rings and the + ends are left exposed to grow outward


What is the structure and what are the functions of centrioles?

Centrioles are made up of perpendicular arrays of short microtubules. They are contained within the centrosome but in most cells their function is unknown. In ciliated cells, centrioles called basal bodies act as organizing centers for cilia. In dividing cells, 2 centrioles act as organizing centers for the mitotic spindle


What is dynamic instability of microtubules?

Microtubules can rapidly polymerize or depolymerize at their + end and they undergo periods of each


What is the role of GTP binding in microtubule polymerization.

Tubulin dimers bind to GTP before incorporating into the microtubule. Eventually this GTP is hydrolyzed to GDP. While GTP bound, dimers bind tightly to neighboring dimers however, once GTP is hydrolyzed, they bind less tightly and if exposed can fall off the microtubule. As long as dimers are being added quickly, no GDP bound dimers are exposed and so polymerization continues however if dimers cease to be added, GDP bound dimers become exposed and depolymerization occurs


What 3 cancer drugs affect microtubules? How is this effective in fighting cancer?

1 Taxol- stabilizes microtubules
2 Colchicine- prevents polymerization
3 Vinblastine- prevents polymerization

Microtubules are required for dividing cells such as cancer cells so cancer cells will be destroyed by lack of microtubules


What 2 types of molecules move cargo along microtubules and how do they do it?

Kinesins- move toward the + end or the outside of the cell
Dyneins move toward the - end or inside of the cell

They both have 2 head groups which bind to microtubules and walk along them. Their tail groups differ and bind to cargo


Describe the structure of cilia and flagella and how they move.

Cilia and flagella are made up of microtubules arranged in a 9+2 array so that there are 9 microtubule doublets around the outside circled around 2 single microtubules in the center. The heads of dyneins bind to one doublet while their tails bind to an adjacent doublet. Thus walking of the dyneins leads to movement of the cilia or flagella


How is actin arranged structurally and how does it polymerize?

Actin monomers bind together to form a thin 2 stranded helix structure with a + end (rapid growth) and a - end (slower growth) Monomers are bound to ATP which causes them to bind tightly to other actin monomers but when they become part of the polymer ATP is hydrolyzed to ADP causing it to bind less tightly and allowing depolymerization.


What are 4 examples of the many shapes that actin can take up in cells? What determines the shape that actin will form?

1 Microvilli
2 Stress fibers- contractile fibers within non muscle cells
3 Transient cellular projections
4 Contractile ring- separates dividing cells

The presence of different binding proteins determines the shape that they will take


Compare and contrast microvilli and cilia.

Cilia- Long and wide, made up of microtubules, motile

Microvilli- Smaller, made of actin, do not move


What is treadmilling of actin fibers?

Because actin is not attached to an organizing center at either end, polymerization and depolymerization can occur at either end. Treadmilling occurs when depolymerization occurs at the - end while polymerization occurs at the + end such that monomers move through the filament but its size doesn’t change


Outline actin’s role in cell migration. What two types of projections can it form?

Actin can allow cell migration by creating projections when its + end is facing the plasma membrane. These projections adhere to surroundings and allow the cell to drag itself forward.

1 Lamellipodium- broad, thin sheets of membrane with a dense meshwork of actin within

2 Filipodium- long, stiff finger like projections with parallel actin filaments


What are the motor proteins for actin? Which one is involved in contraction?

Myosin- many different types, all have actin-binding head and different tail shapes and walk along actin with their heads.

Myosin II is involved in contraction. It can bind tail to tail and in muscle cells in forms thick filaments made up of myosin. Myosin II is arranged so that when each myosin moves toward the + end of the actin to which it is bound, it brings them together causing contraction


What are Rho family of GTPases?

They are important proteins regulating actin organization. They activate downstream actin binding proteins which determine the shape and function of actin within the cell


Describe the cause and symptoms of congenital myopathy.

A broad spectrum of disorders caused by mutations to muscle specific actin.
This can result in heterogenous symptoms of muscle weakness which can be severe enough to cause neonatal death or can be mild muscle weakness in adults


What is the incretin effect? How does it appear in diabetic patients. Draw a graph to illustrate.

Graph insulin secretion offer time after a meal vs after intravenous glucose infusion. The incretin effect is the difference in the amount of insulin secreted after a meal and the amount secreted after intravenous injection. After a meal insulin is higher. The incretin effect is decreased in diabetic patients.


Graph and describe the effect of type 2 diabetes ion glucose levels, insulin levels, and glucagon levels around a meal.

Glucose levels are increased much more than normal patients after a meal
Insulin levels rise much higher after a meal in normal patients than in diabetic patients
Glucagon levels fall after a meal in normal patients but do not fall nearly as much in diabetic patients


What are the 2 incretin? Where are they produced and what are their effects?

GLP-1 - L-cells of the ileum and colon- can be used therapeutically
GIP- Kcells of jejunum cannot be used therapeutically
Stimulate glucose dependent insulin secretion
Suppress glucagon secretion
Slows gastric emptying
Reduces food intake
Improves insulin sensitivity
Long term: may improve beta cell mass and function


What is DPP4?

Enzyme that cleaves GLP-1 to inactive form

DPP4 inhibitors are an option in treatment of type 2 diabetes since they increase levels of GLP-1


What are the two secretin based options for treating type 2 diabetes? How do they differ?

1 GLP-1 agonists
2 DPP4 inhibitors

GLP1 agonists must be administered intravenously while DPP4 inhibitors can be taken orally. In addition, GLP-1 agonists reduce gastric emptying and promote weight loss while DPP4 inhibitors do not. They also cause nausea which is not observed in DPP4 inhibitors


Compare and contrast the mechanisms against hypoglycemia in a normal and type 1 diabetic patient.

Normally, insulin is suppressed but in type 1 diabetes there is no insulin in the first place
Normally glucagon is released in response but not in type 1 diabetes
Epinephrine is normally released after glucagon but in type 1 diabetes it is the first defense and eventually may be lost (hypoglycemia-associated autonomic failure)
Cortisol and growth hormone are the last thing released to combat hypoglycemia in both cases


Describe the causes And pathology of diabetic ketoacidosis.

Occurs mainly in type 1 diabetes and only rarely in type 2.
Lack of insulin -> intracellular starvation -> release of Counter-regulatory hormones -> increase severe increase in blood glucose, ketones and prostaglandin I2 and E2

Body cannot use glucose for energy even though it is in the blood leading to the breakdown of fat for ketone bodies which can become toxic in high concentrations


What are the symptoms and physical findings of diabetic ketoacidosis?

Abdominal pain
Shortness of breath
Respiratory distress
Abdominal tenderness


What are the four main counter regulatory hormones to insulin?

1 Glucagon
2 Catecholamines
3 Glucocorticoids
4 Growth hormone


What are the two main GLP-1 agonists being considered for use in treatment of type 2 diabetes?

1 Liraglutide
2 Exenatide


Differentiate between type 1 and type 2 diabetes.

In type 1, an autoimmune disorder attacks pancreatic beta cells so that no insulin is produced. Type 1 diabetics therefore all need insulin and don’t respond to some of the other treatments used for type 2 diabetes. It is also generally diagnosed in childhood to early adulthood. Symptoms are often severe such as hypoglycemia and diabetic ketoacidosis
Type 2 diabetes begins with insulin resistance and usually progresses to a point where not enough insulin is being produced. It is often diagnosed later in life than type 1 diabetes and has a stronger connection to diet and lifestyle factors than type 1 symptoms are often too mild to be noticed until permanent damage is done


What are the general symptoms of diabetes? What are symptoms in an emergency?

Blurry vision
Weight loss
In an emergency:
Vomiting/abdominal pain


What are the 3 methods of diabetes screening? What scores indicate diabetes and prediabetes for each method?

Method. Healthy. Prediabetes. Diabetes
1 Fasting blood glucose <100. 100-125. 125+
2 2 hr oral glucose tolerance test <140. 140-199. 200+
3 HbA1c. <5.7. 5.7-6.5. 6.5+


When should you test an adult for diabetes?

Overweight (BMI 25+) and additional risk factors
Family history
High-risk race/ethnicity (black, latino, Asian, Native American, Pacific Islander)
Physical inactivity
Or Over the age of 45 every 3 years (more often depending on initial results)


List 6 common drugs besides insulin that could be used to treat type 2 diabetes along with how each works. Indicate which should be the first one attempted in each patient. Which ones can improve cardiac outcomes?

1 Metformin- gold standard first tried. Decreases gluconeogenesis in the liver
2 Sulfonurea- causes pancreas to produce more insulin
3 TzD - makes muscle and fat more sensitive to insulin
4 DPP4 inhibitors - increase the concentration of natural GLP-1
5 GLP-1 analogues- adds additional GLP-1 which stimulates insulin after meals, slows gastric emptying, reduces glucagon after meals, and makes you feel full
6 SGLT-2 inhibitors- decrease renal reabsorption glucose causing glucose to be lost in the urine
GLP-1 analogues, DPP4 inhibitors and SGLT-2 inhibitors have been shown to improve cardiac outcomes


When should insulin be used to treat diabetes patients?

1 Always in type 1 diabetes
2 Type two diabetes that is not well controlled by metformin and other drugs or where contraindications to those other drugs exist
3 Type 2 diabetes with severe symptoms


What are the 3 types of synthetic insulin used to treat diabetes? How are they different?

1 Basal insulin- slow and long acting
2 Bolus insulin- rapid and short acting (taken with meals)
3 Pre mixed insulin


What is the definition of hypoglycemia? What can lead to hypoglycemia in diabetic patients? What are some of the symptoms? How should it be treated?

Blood glucose <70
Missed meals/eating less
Over exercising
Too much medication: high insulin doses
Shaking, sweating, dizziness, hunger, tachycardia, impaired vision, fatigue, headache
Consume 15 grams of glucose or carbs
Check glucose again after 15 minutes
Repeat if necessary until resolved


What are the macrovascular complications of diabetes?

Macrovascular = injury to large blood vessels
Myocardial infarction
heart failure
Cognitive impairment


What are the microvascular complications of diabetes?

Microvascular = injury to small vessels
Kidney failure


Show how glucose 6-phosphate, pyruvate and acetyl coa are key junctions in metabolism.

Glucose 6 phosphate can be converted to fructose 6 phosphate to continue glycolysis or it can be converted to ribose 5 phosphate a precursor to nucleotide synthesis or it can be converted to glucose 1 phosphate a precursor to glycogen synthesis

Pyruvate can be converted to Acetyl coa for TCA cycle, lactate in anaerobic respiration, alanine or oxaloacetate for gluconeogenesis

Acetyl coa can enter the TCA cycle but it can also be converted to fatty acids, cholesterol or ketone bodies


What are the 5 common ways that metabolic pathways are regulated?

1 Allosteric interactions- binding away from the active site changes the activity of an enzyme
2 Covalent modification- phosphorylation etc.
3 Adjustment of enzyme levels
4 Compartmentation- enzymes present in only certain areas of a cell with specific conditions
5 Metabolic specialization of organs


What is the mechanism by which epinephrine leads to glycogenolysis.

1 Binding to the receptor activates adenylyl cyclase leading to cAMP formation
2 cAMP activates protein Kinase A
3 PKA activates phosphorylase kinase and inactivates glycogen synthase by phosphorylation
4 Phosphorylase kinase activates glycogen phosphorylase b turning it to glycogen phosphorylase a
5 Glycogen phosphorylase a breaks down glycogen


Describe the action of catecholamines in skeletal muscle, liver and adipose tissue.

Skeletal muscle:
Increased glycolysis
Increased glycogenolysis
Increased triglyceride utilization
Decreased glycogen synthesis
Increased glycogenolysis
Increased gluconeogenesis
Decreased glycolysis
Decreased glycogen synthesis
Decreased fatty acid synthesis
Increased lipolysis
Decreased triglyceride utilization


How is glycolysis allosterically regulated?

The rate limiting and committed step of glycolysis is conversion of fructose 6-p to fru 1,6 bisphosphate by phosphofructokinase
This step is activated by
Fru 2,6 bisphosphate (produced from 1,6 bisphosphate)
Inhibitted by


How does the same catecholamine hormone have different effects on metabolism in skeletal muscle, liver and heart?

Enzyme isoforms are different in each location and are regulated differently
Phosphofructokinase 1 is on the same protein as the phosphatase that drives the reverse reaction (fru-1,6Bisphosphatase)
F26Bphosphatase is activated by PKA in response to catecholamines
Skeletal muscle
PFK1 and F26Bphosphatase are activated by levels of substrate alone
PFK1 is activated by PKA in response to catecholamines


What is the affect on metabolism in skeletal muscle, liver and adipose tissue of glucocorticoids?

Skeletal muscle:
Increased protein degradation
Increased lipolysis/expression of lipases
Increased gluconeogenesis
Increased glycogen synthesis

Glucocorticoids respond to chronic stress by preparing the body to be able to respond rapidly to acute stress at a later time


Describe the 2 pathways by which alcohol can be metabolized.

1 Alcohol dehydrogenase converts ethanol to acetaldehyde which is then converted to acetate each step reduces 1 NAD+- this is the primary process
2 CytP450 converts ethanol to acetaldehyde by a more complex process requiring one NADPH. Acetaldehyde will ultimately be converted to acetate- this process generates ROS and is induced only by heavy drinking


How does alcohol metabolism throw off the rest of metabolism?

1 Increased NADH from alcohol metabolism leads to conversion of pyruvate to lactate this leads to lactic acidosis as well as the shutdown of gluconeogenesis which requires pyruvate as a substrate leading to hypoglycemia.
2 Increased NADH leads to higher levels of G3P which feeds into production of triacylglycerols. This combined with the effect of low NAD+ blocking fatty acid oxidation leads to hyperlipidemia
3 High NADH also drives the TCA cycle to run in reverse leading to high levels of Acetyl coa which is converted to ketone bodies producing ketoacidosis


What are some of the psychosocial factors affecting nutrition in adulthood (20-64)?

Often busy with little time for meal planning and preparation
Food as comfort, fuel, tradition, celebration, enjoyment, etc.
Increased eating out today
Exploration of fad diets
Growth is completed and goal is maintenance of lean mass and good health
Risk of chronic diseases such as obesity diabetes and hypertension are up from earlier in life


What are the macronutrient recommendations and key nutrients for adults (22-64)?

Women: 25-35 Kcals/kg
Men: 25-45 Kcals/kg
Fats = 30%
Carbohydrates = 50%
Proteins = 20%
Key nutrients
Fiber, folate, Calcium, Iron, Magnesium, vitamin D


What developmental and psychosocial circumstances influence the nutrition of a toddler (1-3)?

Rapid growth
Increasing in fine motor skills
Increases in independence over what they put in their mouth
Often show strong likes and dislikes
Development of healthy eating habits and food preferences during this time is essential for greater health later in life


What are the macronutrient guidelines and key nutrients for a toddler (1-3)?

70-90 Kcals/kg
Varies dependent on activity level and energy needs
Protein 5-20%
Fats 25-35%
Carbs 45-65%

Key nutrients
All of these needed for growth


What are the circumstances surrounding nutrition in childhood (4-12)?

More independence with food choices but for the most part parents still provide options
Constantly growing
Nutritional needs and growth rate vary from child to child
Overweight and obesity becomes more of a problem


What are the macronutrient guidelines and key nutrients in childhood (4-12)?

70-90 Kcals/kg
Must be enough to promote growth but not allow excess weight gain
Carbs: 45-65%
Fat 25-35%
Protein 10-30%

Key nutrients
Vitamin D


What are the circumstances surrounding nutrition in adolescents (12-20)?

Rapid growth and development
Psychologic and cognitive transformation
Lean mass deposition
Sexual maturity
erratic eating patterns
Some risks of eating disorder behavior and body image concerns
Overweight and obesity in adolescents is also on the rise


What are the macronutrient guidelines for adolescents (12-20)?

47-65 Kcals/kg depending on gender and other factors
Carbs: 45-65%
Fat: 25-35%
Protein: 10-30%

Key nutrients
Folic acid


What are the circumstances surrounding nutrition of senior adults (65+)?

Time of uncertainty- retirement, lack of respect/purpose, isolation, diseases etc
Body is in decline
Lower BMR
Loss of muscle mass


What are the macronutrient guidelines and key nutrients for senior adults (65+)?

20-35 Kcals/kg
Decreased from adulthood
Carbs: 45-65
Fats: 30%
Protein 10-20%

Key nutrients
Vitamins A, D
Saturated fat


What proportion of fertilizations result in spontaneous abortions? What is the major cause of these?

1/3 of pregnancies end in spontaneous abortion
40-50% of these are chromosomal abnormalities


Give an overview of the first week of embryonic development.

FERTILIZATION occurs usually in the uterine tube
After about 30 hours CLEAVAGE begins to producing early embryonic cells called BLASTOMERS while the zygote travels toward the uterus in the uterine tubes
After 3-4 days as the embryo is reaching the uterus it reaches the 12-32 cell stage and becomes a MORULA the morula is organized into inner cell mass which will become the embryo and the outer cell mass which will become the fetal component of the placenta
After 4 days the morula becomes a BLASTOCYST when it absorbs fluid creating a BLASTOCYST CAVITY
At this point the inner cell mass gathers on one end of the blastocyst and becomes the EMBRYOBLAST while the outer cell mass surrounds the embryoblast and the blastocyst cavity and is called the TROPHOBLAST
Soon after arriving at the uterus near the end of week 1, the embryo attaches to the posterior or anterior uterine wall


What are the 3 stages of fertilization?

1 Sperm penetrates corona radiata
2 Sperm penetrates zona pellucid a- at this point the zona pellucida changes to not allow any other sperm to penetrate
3 Fusion of cell membranes of sperm and oocyte and fusion of nuclei


What is compaction in embryonic development?

The early cell divisions create smaller and smaller cells that remain inside the zona pellucida


Draw a picture of a blastocyst prior to implantation in the uterine wall.

The following should be shown:
Trophoblast- cells surrounding the outside of the blastocyst
Embryoblast- clump of cells at one end of the blastocyst
Blastocyst cavity
Embryonic pole- side with the embryoblast
Abembryonic pole side without the embryo


Tell the story of week 2 of embryonic development.

Just after implantation into the uterine wall, the trophoblast differentiates into CYTOTROPHOBLAST outer layer of the blastocyst and the SYNCYTIOTROPHOBLAST the part directely embedded in the endometrium of the uterus
Around day 8, the embryoblast differentiates into the EPIBLAST columnar cells on the external side and HYPOBLAST cuboidal cells on the internal side facing the blastocyst cavity. at this point it becomes known as the BILAMINAR EMBRYONIC DISC.
Next, fluid fills in the space between the epiblast and the cytotrophoblast to form the AMNIOTIC CAVITY and epiblast cells migrate to surround this cavity.
New tissue forms within the trophoblast cavity called the EXTRAEMBRYONIC MESODERM which then separates into 2 layers with a space between called the CHORIONIC CAVITY which separates the embryo from the outer wall of the blastocyst which is now called the CHORION
Around day 8, Hypoblast cells proliferate and migrate once to form the PRIMARY YOLK SAC the membrane of which is known as HEUSER’S MEMBRANE. Later around days 12-13, the hypoblast cells migrate again to form the DEFINITIVE YOLK SAC which displaces the primary yolk sac which now becomes a collection of vesicles at the abembryonic end.
At this point, the embryonic disc is suspended in the middle of the chorionic cavity held only be a thin extension of extraembryonic mesoderm called the CONNECTING STALK


What is an ectopic pregnancy? What symptoms does it cause? How can it be treated?

An embryo that implants outside of the uterus most commonly in the uterine tubes but sometimes also in the abdomen or other areas. It can be life threatening for the mother because it could rupture important blood vessels as the embryo grows
Abdominal pain
Vaginal bleeding
Treatment: Medications or surgical intervention to interrupt the pregnancy


Draw a picture of an embryo at the end of week 2 of development.

Should include:
Connecting stalk
Amniotic cavity
Definitive yolk sac
Chorionic cavity
Remnants of primary yolk sac


Why is week 2 of embryonic development sometimes called the “week of twos”? (4)

1 Trophoblast differentiates into two layers (cytotrophoblast and syncytiotrophoblast)
2 Embryoblast differentiates into epiblast and hypoblast
3 Extraembryonic mesoderm divides into 2 layers
4 Two cavities form - amniotic cavity and chorionic cavity


What is gastrulation? In what week does it occur? Walk through the process.

Gastrulation is the process by which the 3 germ layers are formed from the epiblast in the 3rd week of embryonic development
First a part of the epiblast thickens to form the PRIMITIVE STREAK which eventually invaginates and epiblast cells migrate toward it, through it and away from it on the other side. Those cells which displace the hypoblast will form the ENDODERM those that form on top of that are the MESODERM and those that don’t migrate through the primitive streak and remain on top will become the ECTODERM


What tissues form from the ectoderm? (5)

1 Nervous system
2 Epidermis
3 glands within the hypodermis
4 Sensory epithelial or eyes ears nose and pituitary
5 mammary glands


What tissues form from the mesoderm? (9)

1 Connective tissue
2 Cartilage and bone
3 muscles
4 heart
5 vasculature
6 kidneys
7 gonads
8 spleen
9 Suprarenal cortex


What tissues form from the endoderm? (6)

1 Epithelial lining of digestive and respiratory tracts
2 thyroid and parathyroid
3 thymus
4 liver
5 pancreas
6 epithelial lining of urinary bladder


What are the 4 main events that occur during weeks 3-6 of embryonic development?

1 Notochord formation
2 Neurulation
3 Differentiation of mesoderm
4 Body folding


Describe and diagram the process of notochord formation. When does it occur

Days 17-18 Cells extend along the midline from the primitive node toward the cranial end of the embryo forming a hollow tube called the NOTOCHORDAL PROCESS
Around day 20, the notochordal process fuses with the endoderm to form the NOTOCHORDAL PLATE which is flattened and connected to the endoderm on both ends
The notochordal plate then pulls away from the endoderm folding in on itself until it detaches to from a solid cylinder called the NOTOCHORD


Describe and diagram the process of neurulation.

The NOTOCHORD induces cells above it in the ectoderm along the midline to thicken forming the NEURAL PLATE
The neural tube invaginates to create the NEURAL GROOVE which has NEURAL FOLDS on each side
The neural folds eventually come together starting at the midline and fuse forming a hollow tube of cells called the NEURAL TUBE closure of the neural tube begins at the midline and progresses in both directions until openings are left only at the ends, called the CRAINIAL NEUROPORE and the CAUDAL NEUROPORE respectively. These eventually close on day 25 and 27 respectively completing neurulation


Where do neural cells come from?

They originate at the lateral edges of the neural plate and separate during neurulation to migrate and form a variety of cells


Describe the differentiation that occurs in the mesoderm during weeks 3-6 of embryonic development.

The mesoderm differentiates into 3 types
1 Paraxial mesoderm- thickened plate nearest to the midline which will eventually form somites which are balls of mesoderm cells along the midline that eventually form major mesoderm structures
2 Lateral plate mesoderm- thin layer of mesoderm farthest laterally which will eventually split into 2 layers (visceral and somatic) and surround organs of the body cavity
3 Intermediate mesoderm- Between lateral plate and paraxial mesoderm and will eventually form much of urogenital system


Briefly describe the body folding that occurs during weeks 3-6 of development and what drives it.

Body folding is driven by differential growth in different areas of the embryo.
Occurs in two planes
1 Caudal and Cranial folding where the caudal and cranial aspects fold in together to form the normal embryonic position
2 Lateral folding- the lateral edges of the embryo fold ventrally until they come together and the 3 layers fuse with the same layer from the other side turning the embryo from a disc shape into a cylinder shape


What is the main cause of mortality in diabetes patients?

Cardiovascular complications


What 2 disorders result from a failure of the neural tube to close completely?

1 Spina bifida - caudal NEUROPORE
2 anencephaly- cranial NEUROPORE


Name some of the risk factors for diabetes that can and cannot be controlled by lifestyle changes.

Family history
Higher birth weight
Advancing age
High blood pressure
Sedentary lifestyle
Sleep patterns


Plot the stages of diabetes and indicate where primary, secondary and tertiary prevention takes place.

Normal -> Prediabetes -> Diabetes -> Complications -> Disability/death

Primary takes place in Normal and prediabetes to prevent onset of diabetes
Secondary takes place during diabetes but before the onset of complications in order to prevent/delay onset of complications
Tertiary takes place after complications have begun to slow the progression of complications toward disability and death


Describe the results of the diabetes prevention program study in primary prevention of diabetes.

Recruited a group of patients at high risk of type 2 diabetes based on being prediabetic and overweight or obese
They were randomized into 1 of 3 groups
1 Lifestyle intervention- received nutrition/health classes and were helped to achieve the goal of 7% weight loss to be achieved by calorie restriction 1200-1800 Calories per day with less than 25% coming from fat and exercise (150 minutes per week)
2 Metformin group
3 Placebo
Metformin group = 31% reduction in risk of T2DM
Lifestyle group = 58%
Further, metformin was only effective in patients with stage 3 obesity all other BMI categories were not helped by metformin but were significantly aided by lifestyle change
Even after 10 years and although many lifestyle participants gained back much of the weight they still had lower risk of T2DM or delayed onset by 4 years


What effect does losing 1 kg of weight have on the risk of T2DM for someone with prediabetes?

16% reduction in risk


Describe the methods and results of the look AHEAD study on secondary prevention of diabetes.

Recruited overweight and obese patients with T2DM to be randomized into a lifestyle intervention group or usual care group
The lifestyle intervention group received meal replacements for calorie restriction, 75 minutes per week of exercise and optional pharmacotherapy to lose 7-10% of body weight
Lifestyle intervention group showed lower a1c lower blood pressure but no change in LDL cholesterol. Overall CV risk factor score was reduced.
In long term assessments, many participants gained weight back and raised a1c’s somewhat but improvements remained in blood pressure, a1c and HDL cholesterol after 4 years


Can lifestyle changes lead to lowering of medication need in patients with T2DM? Site the evidence presented in class

One study reported that 73.5% of patients lowered mediations in lifestyle group compared to 26.4 in standard care group


What are the 4 components of therapeutic lifestyle change?

1 Dietary consultation-Medical nutrition therapy (nutrition prescriptions)
2 Behavioral modification
3 Increased physical activity
4 weight loss


What is the best diet/macronutrient composition for a patient with diabetes?

There isn’t enough evidence to suggest that one diet is best
What works for the individual is best. In general low saturated fats and complex carbohydrates are good things along with avoidance of added sugar. The most important part is total energy intake


Differentiate between compliance and adherence.

Compliance = how well a person’s behavior matches a medical advice
Adherence = how well behavior corresponds to recommendations from provider BASED ON SHARED DECISION MAKING


What are the 5 main types of non adherence?

1 Intentional
2 Unintentional-often caused by forgetfulness or carelessness or confusion
3 Chronic
5 Cost-related- includes lowering doses to ration expensive medications


What types of non adherence exist in diabetes?

Overuse, underuse, misuse or erratic use of insulin
Infrequent blood glucose testing
Failure to attend medical appointments
Poor tracking or record keeping


Which age group is most likely to be nonadherent and what factors cause this?

They are seeking independence and rebelling against authority often
They have more short term goals
Peer influences and less parental involvement in their lives


What are some forms of intentional non-adherence in diabetes?

Overuse of insulin to allow increased eating
Skipping meals to avoid insulin administration
Diabulimia- avoiding insulin to lose weight


Describe the health belief model of non adherence and how it can be used to design an intervention.

Five factors affecting adherence
1 Susceptibility- what do they believe about risk of the illness
2 Severity- how serious are the consequences of the illness or of non-adherence
3 Benefits- are there immediate benefits
4 barriers
5 Cues- things that prompt action

Intervention should be based on which of these factors is most prominent in causing non-adherence


Describe the social cognitive theory in adherence and how it could be used to craft an intervention for non-adherence.

Interaction between behavior, personal factors and external environment come together to influence adherence

Intervention should involve skill building and self-advocacy


Describe the theory of planned behavior in adherence and how it could be used to design an intervention to non-adherence.

Factors affecting adherence:
1 Attitude
2 Subjective norm- someone else would like this to happen
3 motivation
4 perceived behavioral control

Assess and address motivation and perceived control for intervention


Describe the transtheoretical or “stages of change” model of adherence and how it could be used to design an intervention for non-adherence.

Describes the stages individuals go through in the process of changing a behavior
1 Precontemplation- no awareness or desire to change
2 Contemplation- beginning to think about changing
3 Preparation- makes a plan
4 Action
5 Maintenance

For an intervention assess which stage they are in and give them resources to help them in that stage and toward the next one


What are some general things that can be done to improve adherence? (3)

1 Education- helpful initially but usually not enough on its own
2 Organizational- simplify regimens, change the way care is delivered, improve patient doctor relationship
3 Behavioral- assess barriers and encourage incentives


What is collaborative/co-managed care?

A model where the patient is more responsible and empowered over their own care with the provider as a guide who receives input from the patient in order to help them design a daily management plan
Requires providers to not blame patients, avoid showing frustration and seek to build rapport with the patient

Research suggests this is the best form of care


Describe the role of free fatty acids in hyperglycemia.

FFA’s go to the liver and the skeletal muscle generally
Cause increased fatty acid oxidation leading to increased gluconeogenesis
Increased fatty acid oxidation results in decreased glucose utilization
These factors along with the fact that FFA’s can lead to insulin resistance mean that higher FFA’s makes hyperglycemia more likely


What are the clinical features of insulin resistance? (4)

1 Central obesity
2 Acanthosis Nigerians (darkened, thickening of skin)
3 Hypertension and dyslipidemia
4 Metabolic Syndrome

Metabolic syndrome = central obesity + 2 or more of the following:

Raised triglyceride levels
Reduced HDL
High BP
Raised Fasting glucose


Describe the progression from insulin resistance to diabetes.

Insulin resistance begins in prediabetes but early on, the body responds by just making more insulin to counteract. Eventually insulin secretory defects progress to a state of inadequate secretion.

By the time of diabetes diagnosis, 50% of beta cell mass is lost
Amyloid (co-secreted with insulin) deposits in islet cells)
Elevation of FFA’s worsens beta cell function


What are some other things that could lead to diabetes besides insulin sensitivity?

1 MODY- genetic defects of insulin secretion
2 Genetic disorders of insulin action
3 Pancreatic disorders- ex pancreatitis
4 Endocrinopathies- ex- cushing’s hyperthyroidism
5 Drug-chemical induced- ex glucocorticoids
6 Infections
7 Gestational
8 Immune mechanisms
9 Other genetic syndromes- Down syndrome, klinefelter’s etc.


Describe the cause of gestational diabetes.

Placental hormones such as human placenta lactogen promote insulin resistance in order to increase nutrient supply to the fetus

Patients are at higher risk for T2DM afterwards


What is stress diabetes?

Hyperglycemia associated with critical illness in patients who have not been diagnosed with diabetes prior. Examples: trauma and burns. May be a result of factors such as cortisol, epinephrine, glucagon, growth hormone, gluconeogenesis and glycogenolysis being more common in these patients. SHould be treated acutely and may or may not be reversible after critical illness


What enzyme is responsible for converting proinsulin to insulin?

Prohormone convertase


What would be the effect of low Zn or lack of Zn ion transporters on insulin secretion?

Zn allows hexamer formation of insulin in storage granules allowing higher concentration within granules. Without Zn in granules, there would be lower insulin concentrations and therefore lower secretion levels


Define pathology, etiology and Pathogenesis.

Pathology = study of morphological, biochemical and functional changes in cells, tissues and organs that underlie disease
Etiology = initiating event or agent of a disease
Pathogenesis = sequence of cellular, biochemical or molecular events that follow exposure of a cell/tissue/organ to an injury


What are the 4 adaptive responses of cells to stress/injury?

1 Hypertrophy- cells grow in size
2 Hyperplasia- increase in cell number
3 Metaplasia- cells change from one cell type to another
4 Atrophy- cells decrease in size and/or number


Give an example of hyperplasia and hypertrophy simultaneously and another where only hypertrophy occurs.

Hyperplasia and hypertrophy often occur simultaneously
Example: Uterus in response to pregnancy
Hypertrophy occurs by itself whenever hyperplasia is not possible
Ex: cardiac muscle in response to high blood pressure


By what cellular mechanisms does atrophy occur?

Degradation of proteins/other components that are no longer required by Ubiquitin/proteasome system and autophagy


What is Barrett’s esophagus?

Metaplasia where non-keratinized squamous epithelium of the esophagus is converted to non ciliated mucin producing epithelium to cope with reflux of stomach acid into esophagus


What is dysplasia?

Disordered cell growth that can occur in long-standing hyperplasia or Metaplasia. Often a proliferation of pre-cancerous cells and it is believed to be reversible if stress is removed


What 4 factors determine a cell’s response to injury?

1 Cell physiology/type- certain cells are more sensitive to some stresses than others
2 Type of injurious stimulus
3 Strength/intensity of injurious stimulus
4 Duration of injurious stimulus


What are the 2 morphologies of reversible cell injury?

1 Cell swelling- occurs when ATP is low and cell can’t maintain ion/water homeostasis by active transport
2 Fatty change- lipid vacuoles appear in the cytoplasm if cells that depend on lipid metabolism as a result of toxic, metabolic or hypoxic injury