Midterm

Question 1

What was the “one gene hypothesis,” and does it apply to humans

Answer 1

• one gene hypothesis: one gene = one protein (1980’s); once we are able to match the gene with the protein, the DNA itself will tell you how humans are built
• No, this does not apply to humans; The problems is that there are over 300,000 human proteins, so for this hypothesis to be accurate, there must be over 300,000 genes, and one human gene must code for at least 10 different proteins

Question 2

SNPs, and other mutations, were thought to be the sole cause of human variation, was this assumption correct?

Answer 2

No, this is not accurate. Compared to other mammalian species, humans have the least genetic variation from one another but greater phenotypic expression. This means that SNPs by themselves are not responsible for our large variation in phenotypic expression - it must be largely a result of both gene regulation and the epigenome. This suggests that above all other mammals, we have the ability to adapt faster and with more varied responses.

Question 3

How much of the Human Genome is protein coding? How much is RVS?

Answer 3

• 4% of genome is protein coding; most of the rest regulates this 4% (no junk DNA!)
• RVS = 9% but 10% if what he means is actually ERV

Question 4

here does (what country) most of the variability in the genome still reside?

Answer 4

90% of diversity is in the San Bushmen of Africa

Question 5

How are mitochondrial DNA and Y chromosome DNA different, and how are they used in migration studies?

Answer 5

-mtDNA dates a species - changes at a fairly constant rate over time and allows for geneticists to estimate the age of a species; only females can pass down mtDNA
-SNPs in Y chromosome DNA trace migration - SNP’s occur in a sequential manner throughout generations, allowing geneticists to trace human migration patterns and determine when ppl move into an area. Only boys get Y. Father passes Y on to son so this path of SNP can be studied (single nucleotide polymorphism: single base pair substitution. MC in non-coded gene regions.)
-comparing the mtDNA “age” w/ # of mutations on the Y chromosome, the timeframe & direction of
migration was determined

Question 6

What did Koko and her kitty cat suggest about human behavior?

Answer 6

Behaviors like deception are likely inherited traits from the animal kingdom

Question 7

What are the three main problems with trying to determine the cause vs. correlation in genetic disease
with genetic studies like the GWAS (slide 27 lecture 1)

Answer 7

• The variant may be important in disease causation OR:
• The association has been found by random chance
• The assoc is a result of bias in the study (linkage disequilibrium - where the variant is situated close to the dz-causing segment, but does nothing in and of itself)
• Population stratification - an ethnic group has a concentration of the variant, and the dz, though the two aren’t linked

Question 8

5 points of control of gene expression

Answer 8

1. Chromatin
2. Transcriptional
3. Translational
4. Post-translational control into cytoplasm
5. Post-translational modification

Question 9

Chromatin stage (DNA tightly wound up)

Answer 9

-Histone methylation - methylation of Cytidine residues (dinucleotode CG aka CpG) regulates transcription
-Histone acetylation - stops DNA from becoming further condensed
Other types of histone modification = ubiquination, sumoylation, phosphorylation

Question 10

Transcriptional stage (first step of gene expression - DNA segment copied onto RNA by RNA poly)

Answer 10

-Promoters - located 40 base papers from start site (eg TATA and CCAAT boxes)
-Exon Shuffling - exons exit the nucleus (introns stay in the nucleus) —> this is how 1 gene can code for 3 different proteins
-Enhancers - transcription factors bind to enhancer regions —> transcription of DNA to RNA
starts

Question 11

Translational stage

Answer 11

-Addition of 5’ cap and 3’ poly(A) tail
Poly(A)-binding protein (BABP) interacts w/translation initiation factor, brings 5’cap and poly(A) tail together —> enhancement of translation
-Removal of introns (non-coding regions)
-Splicing of exons (coding regions)

Question 12

Post-translational control into cytoplasm

Answer 12

-only some RNAs fxn within the nucleus - all others meant for protein synthesis have to be transported to the cytoplasm through nuclear pores
-entry/exit of large molecules from the nucleus is tightly controlled by nuclear pore complexes (NPCs)
-small molecules can enter nucleus without regulation, but macromolecules like RNA and proteins require association w/karyopherins called importins to enter the nucleus
and exportins to exit
-importins and exportins transport activity is regulated by Ran (small GTPase proteins)

Question 13

Post-translational modification

Answer 13

protein is modified by folding, cutting, or other processes like adding functional groups or
phosphorylation

Question 14

TATA and CCAAT boxes are examples of what?

Answer 14

Promoters

Question 15

What is exon shuffling, and which part (exon or intron) remains as a section of the mRNA?

Answer 15

• exons exit the cytoplasm and can be shuffled around, which is how 1 gene can code for 3 different proteins
• introns are spliced out
• Exon shuffling is a molecular mechanism for the formation of new genes. It is a process through which two or more exons from different genes can be brought together ectopically, or the same exon can be duplicated, to create a new exon-intron structure. (Wikipedia)

Question 16

What is the role of enhancers?

Answer 16

they bind activators to increase the rate of transcription

Question 17

What are the 3 major types of molecular groups that modify histones and cause epigenetic effects?

Answer 17

Methyl, Acetyl, Phosphate, (also ubiquinone, sumo protein)

Question 18

When looking at a cartoon of a chromosome, how can you tell which is the locus, and which is the gene? (slide 7 lecture 3)

Answer 18

• locus = exact physical location of a gene on a chromosome; marked by “p” or “q”, followed by a number; same for everyone
• genes are usu acronyms given by their discoverer

Question 19

What are DNA Marker Alleles?

Answer 19

• don’t necessarily have any fxn but can be detected in lab by southern blotting or PCR
• there may be different variations of these DNA marker allele in a population (could be different sizes)

Question 20

What is the difference between the Genotype and the Phenotype?

Answer 20

• Genotype = particular combination of alleles that a person has
• Phenotype = reflection of the genotype i.e. any observable trait; refers to presence or absence of physical or behavioral characteristics of the disease

Question 21

Mendelian traits =

Answer 21

single gene disorders

Question 22

Autosomal effect on M/F

Answer 22

both M and F affected equally

Question 23

X-linked effect on M/F

Answer 23

M and F NOT affected equally

Question 24

Autosomal dominant

Answer 24

• the locus is on an autosomal chromosome (1-22)
• only one mutant allele is required for expression of the phenotype
• typically observed in sequential generations; expressed in every generation (M=F) -Heterozygous/homozygous parents - recurrence risk is 50%, so 1/2 the children will be affected; however, if both parents are heterozygous, the recurrence risk is 75% (rare but severe)
• Eg - familial hypercholesterolemia (mainly LDL receptor deficiency), Huntington dz, neurofibromatosis Type 1, Marfan syndrome, acute intermittent porphyria

Question 25

Autosomal recessive

Answer 25

• the locus is on an autosomal chromosome (1-22)
• BOTH alleles must be mutant to express the phenotype
• typically observed in only one generation of a pedigree (skips generations); (M=F)
• Eg - sickle cell anemia, cystic fibrosis, PKU, Tay-Sachs

Question 26

X-linked dominant

Answer 26

• the locus is on the X chromosome
• only one mutant allele is required for expression of the phenotype (in females) –affects multiple generations
• seen about 2x more in females than males

Question 27

X-linked recessive

Answer 27

• the locus is on the X chromosome
• BOTH alleles must be mutant to express the phenotype in females
• males can get this with only one X chromosome, bc they only have one
• females are carriers - rare for them to inherit 2 mutant chromosomes
• skips generations

Question 28

Mitochondrial

Answer 28

• the locus is on the mitochondrial “chromosome”
• only passed on through females - ALL offspring of a female are affected males can get the dz from mom but will NOT pass it on
• these generally cause myopathies and neuropathies (affects small motor muscles first!) many of the d/o caused by mutations in mtDNA affect tissues w/high energy demand, such as CNS, heart, muscle
• males can be affected but cannot pass the mutation on to their children

Question 29

Why can males get X-linked recessive diseases when two disease alleles are usually needed to manifest
any recessive disease? (slide 13 lecture 3)

Answer 29

because males only have 1 X chromosome

Question 30

What is a missense mutation

Answer 30

• single base change in the gene that leads to a change in the codon that encodes for one amino acid (SNP)
• because the codon has changed, it substitutes for a different amino acids than the one originally intended for a specific protein
• everything else about the protein states the same, but this can drastically alter its folding or conformation, and therefore its function
• eg leucine to isoleucine may not have a large effect, maybe only slight decline in protein fxn, but glutamate to lysine would change a positive charge to a negative charge - if this occurred in the enzyme active site, the enzyme would be completely dead, resulting in complete loss of function and more severe sx

Question 31

Nonsense mutation

Answer 31

• creates a “stop” codon
• when the ribosome comes to the stop codon, it stops and the mRNA drops off and releases a partially completed protein
• this results in a short and completely inactive protein or enzyme
• ppl with these are likely to have severe dz as they have complete absence of a functional enzyme or structural protein
• genetic fluctuation depends on where the stop codon is present - close to the beginning or farther towards the end

Question 32

What is the difference between a gain-of-function and a loss-of-function mutation, and is one necessarily less troublesome than the other?

Answer 32

• Gain-of-function mutation = occur when either a completely new enzyme is produced in a cell, or more commonly when the enzyme is overproduced (eg porto-oncogenes become oncogenes)
• Loss-of-function mutation = causes a vital or protective protein to become non-functional (eg loss of tumor suppressors, PKU, Tay-Sachs dz, sickle cell dz)

Question 33

Why is consanguinity important in clinical medicine, even though it is rare amongst Americans?

Answer 33

-“kissing cousins” = individuals whose parents are related are expected to have an increased proportion of their autosomal genome that is homozygous
consanguinity is almost always an autosomal recessive dz
-higher probability of same mutations —> higher likelihood of some genetic disease

Question 34

Why is it called fragile X syndrome, and what determines its severity?

Answer 34

-called “Fragile X” because a portion of the chromosome is dangling by a thread
-most common inherited form of mental retardation
-caused by unstable CGG repeat
severity correlates with the number of CGG repeats
-Characteristics = broad forehead, elongated face, large prominent ears, strabismus (crossed eyes), highly arched palate, hyper extensible joints, hand calluses (from self-abuse), pectus excavatum, MVP, enlarged testicles, hypotonia, soft/fleshy skin, flat feet, seizures

Question 35

What is the epigenetic significance of X Chromosome Inactivation, and what is a barr body. Do barr bodies form when autosomal chromosomes are imprinted (as in for instance, AS and PWS?)

Answer 35

-Epigenetic significance of X chromosome inactivation = females are a combination of 2 different cell types; in half her cells, dad’s X chromosome is working, in the other half her mom’s X is working
-Barr body = X chromosome condensed by methylation into an inactive form - occurs in ALL females early in fetal development
-Imprinting = a small number of genes are transcriptionally active only when transmitted by one of 2 sexes (eg Angelman Syndrome and Prader-Willi Syndrome)
No, barr bodies do not form when autosomal chromosomes are imprinted

Question 36

What is the general clinical characteristic of inherited mitochondrial disease?

Answer 36

neuropathies and/or myopathies

Question 37

What is the difference between penetrance, incomplete penetrance, and variability?

Answer 37

• Penetrance = how many ppl who have the genotype actually manifest the phenotype (the disease)
• Incomplete penetrance = when some individuals with a disease-causing mutation (genotype) do not display the disease phenotype
• Variability = refers to how bad the disease is going to be when it is expressed

Question 38

How is recurrence risk calculated?

Answer 38

• RR = how many ppl will get the disease

- Multiply the penetrance by either 25% or 50% depending upon if the disease is AR or AD respectively

Question 39

What is pleiotropy? Is Marfan syndrome an example?

Answer 39

• Pleiotropy = when a single disease causing mutation affects multiple organs systems
• Example: Marfan Syndrome (caused by a mutation in the gene that encodes fibrillin) very long hands, excessive tall body height, arm span exceeds body height

Question 40

What is anticipation, that is, what does it mean for each subsequent generation with a disease characterized by anticipation?

Answer 40

-pattern of inheritance in which individuals in the most recent generations of a pedigree develop a dz at an earlier age or with greater severity than those in the earlier generations
-this can be attributed to the gradual expansion of trinucleotide repeat polymorphisms within or near a coding gene
-some individuals may then transmit an expanded number of repeats to their offspring
-Eg Huntington Dz - an expanded number of repeats may be transmitted to their offspring, where >39
is where sx are seen

Question 41

How are the bands of a chromosome stained for a karyotype, and how many BPs have to be involved in
a deletion or duplication to be detectable under the microscope without special stains? If the deletion is smaller than this, can a FISH study be used to detect it?

Answer 41

• metaphase chromosomes are treated with trypsin to remove associated proteins and then Giemsa stained
• greater than 4 Mb have to be involved to be seen under the microscope
• less than 4 Mb requires a FISH study

Question 42

What is the main cause of NUMERICAL chromosome abnormalities?

Answer 42

• poor meiotic nondisjunction - “spindles behaving badly”

- causes gain or loss of a chromosome

Question 43

trisomy 21

Answer 43

Trisomy 21 (Down Syndrome)
-MC autosomal trisomy
-growth failure, mental retardation, flat back of head, abnormal ears, congenital
heart defects, broad flat face and nose, slanting eyes, single palmar crease, widely separated first and 2nd toes

Question 44

Trisomy 18

Answer 44

Edward Syndrome

• very poor prognosis - most don’t live past birth
• hand and foot malformations, low set ears, micrognathia, prominent occiput, malformed ears, small mouth and jaw, short neck, short and prominent sternum, wide-set nipples, flexed big toe, prominent heels

Question 45

Trisomy 13

Answer 45

Patau Syndrome

• very poor prognosis
• polydactyly, cleft lip, cleft palate, microphthalmia (small eyes), microcephaly, cardiac and renal defects, undescended or abnormal testes

Question 46

Why aren’t there any autosomal Monosomies listed in the slides?

Answer 46

all autosomal monosomies are inconsistent with a live birth

Question 47

Turner Syndrome

Answer 47

• only monosomy consistent with life (bc it is not autosomal but X-linked)
• 50% are 45,X; the rest are 46,XX and 47,XXX occurring in different cells
• short stature, ovarian dysgenesis, neurocognitive pbms, infertility, osteoporosis

Question 48

Klinefelter’s Syndrome 47,XXY

Answer 48

• aka Hermaphrodite Disorder
• occurs in meiosis 1
• hypogonadism - more likely low testosterone and elevated LH:FSH levels than testicular atrophy
• appears over time and not at birth - physical traits become more evident during puberty dt lower testosterone levels - less muscular body, less facial and body hair, broader hips, larger breasts, weaker bones, lower energy
• weaker muscles, reduced strength, taller than average as they grow older, infertility

Question 49

Aliens 3 Syndrome - 47,XYY

Answer 49

• occurs in meiosis 2

- clinical phenotype is normal (other than tall stature)

Question 50

By what process is the Philadelphia chromosome formed? What is its significance?

Answer 50

• formed by reciprocal translocation - 2 non-homologous chromosomes break and exchange fragments
• involves only a single cell and genetic material is balanced, so often no consequence
• rarely - may alter expression or structure of an oncogene or a tumor suppressor gene, conferring an abnormal growth advantage to the cell - alters genetic control of cellular proliferation
• if this occurs in hematopoietic cells, it can results in CML

Question 51

Can partial Monosomies occur? What would the karyotype of down syndrome by translocation read?

Answer 51

• Yes

- 95%: 47,XX,+21 or 47,XY,+21

Question 52

Cri-du-chat results from what abnormality? Does the patients voice improve as they age?

Answer 52

• gene deletion: 46,XX or 46,XY, del(5p)

- causes abnormal larynx development - voice improves and by age 2, it is much less noticeable

Question 53

Know how Angelman Syndrome (AS) and Prader-Willi Syndrome (PWS) work, and their significance in
the development of the field of epigenetics.

Answer 53

• depends on whether the micro deletion is on the paternal chromosome 15 (PWS) or maternal chromosome 15 (AS)
• AS = very happy kids, developmental delays, ataxia, strabismus, tongue thrusting
• PWS = kids have intense craving for food —> weight gain/obesity; small/floppy newborn

Question 54

What is a ring chromosome, and what is its significance?

Answer 54

• can form when a deletion occurs on both tips of a chromosome and the remaining chromosome ends fuse together
• ring chromosomes are often list, resulting in a monosomy

Question 55

What are isochromosomes, and are they seen in the autosomes in live patients?

Answer 55

• occurs when a chromosome divides along the axis perpendicular to its normal axis of division -results in 2 copies of one but no copy of the other
• autosomal isochromosomes are lethal - most that have been observed in live births involve the X chromosome

Question 56

In the Overkalix studies, it was found that nutritional influences could effect subsequent generations. When is it thought that these epigenetic effects are imprinted onto the fetuses of women, and when can the influence be acquired for transmission by the males. Also, is this the only time that epigenetic

effects can potentially be acquired by a person, and subsequently transmitted to future generations?

Answer 56

• Females are imprinted when grandma is pregnant (when her daughter’s eggs are formed) paternal line of inheritance
• Males are imprinted when dad is in puberty (sperm formation)
• No, this is not the only time epigenetic effects can be acquired

Question 57

Did mouse studies at the world renown and prestigious Washington State University show that the
cancer causing inherited factors in mice were not coming from a change in the DNA sequence itself? Were these mice pregnant or pregnant and in the 3rd trimester when sprayed with pesticides?

Answer 57

• No - epigenetic marks in affected DNA, which modify gene activation but not DNA sequence; epigenetic changes are preserved when cells divide
• Mice were not pregnant when sprayed - they were bred afterwards

Question 58

Know the major reasons gene therapy did not work out well

Answer 58

short-lived nature of gene therapy - therapeutic DNA must remain functional and cells containing the therapeutic DNA must be long-lived and stable

it is difficult to introduce long dsRNA strands into mammalian cells

dsRNA are rapidly degraded and evoke an immune response eventually
-immune response will attack the therapeutic DNA and may reduce gene therapy effectiveness; additionally the enhanced response to invaders it has seen before can make it difficult for gene therapy to be repeated

pbms with viral vectors

• viruses are the carrier of choice but can lead to toxicity, immune and inflammatory responses, and gene control and targeting issues
• once inside the pt, the viral vector may recover its ability to cause dz

dsRNA have to artificially make their way into every target cell

pts have to undergo multiple rounds of gene therapy

you must overwhelm the system, and continue to do so in the face of host antibodies targeted to it multigene or

multifactorial disorders are hard to treat effectively using gene therapy
-best candidates for gene therapy are single gene mutation disorders, but some of the
most commonly occurring disorders are caused by the combined effects of variations in many genes

Question 59

Can iRNA be passed to subsequent generations? Would this make it an epigenetic mechanism?

Answer 59

Yes and yes

Question 60

What are knock-down studies? Why are they unlikely to be as effective in the study of human genetics, as they are in simpler organisms?

Answer 60

• knock down studies are when each gene in a cell is systematically shut down in order to identify what the gene normally does
• some genetic loci have been proven very difficult to knock out, some may be lethal or fail to produce an observable change

Question 61

Know the primary differences between single gene disorders and common diseases

Answer 61

Single gene disorder = disease caused by alteration in a single gene or in a specific chromosome

• can be dx via lab test - person either has dz or does not
• MOA is understood
• recurrence risk (RR) can be derived based on known principles of inheritance

Common diseases (heart dz, DM, etc) tend to cluster in families but do not conform to Mendelian pedigree patterns

• many variants of small effect contribute to dz risk, along w/many environmental factors (causation is complex)
• don’t conform to Mendelian pedigree patterns
• cannot be dx via lab test, have to use diagnostic criteria
• underlying multifactorial traits have not been identified specifically
• empirical recurrence risks (RR) must be derived based on direct observation of data

Question 62

Recurrence risk is calculated differently from AR and AD diseases than it is in common diseases. How is it calculated in common diseases?

Answer 62

RR = (incidence in exposed)/(incidence in non-exposed)

RR increases when:
-# of affected relatives increases
-severity of dz expression increases
-# of affected children in a family increases
presence of multiple affected individuals indicates that the family is located higher on
the liability distribution
-the affected individual is a member of the less commonly affected sex
eg - pyloric stenosis is more common in males, so if a female gets it, she has more genetic/environmental risk factors —> her relatives are more likely to be affected than a male’s would
-the prevalence of the dz increases in a population (RR for single-gene disorder remains the same regardless of prevalence)
populations w/higher prevalence rates will have more genetic/environmental risk
factors
-the parent is more severely affected
-there is consanguinity

If the 2 sexes have a different probability of being affected, the least likely sex, if affected, is the most
likely sex to produce an affected offspring

Question 63

Know the difference between twin types and how adoption studies are used to tease out the genetic
contribution vs the epigenetic contribution in common diseases.

Answer 63

twins = 2 offspring produced in same pregnancy

• monozygotic (“identical”) = 1 egg, 1 sperm —> embryo splits
• dizygotic (“fraternal”) = 2 eggs, 2 sperm

if one wishes to gauge the relative effect of genetic inheritance on a trait, we can compare the
-concordance of the trait in monozygotic vs dizygotic twins
concordant = share same trait
-discordant = do not share the same trait
somatic mutations may occur in MZ after the cleavage event —> causing them to be somewhat genetically different

adoption = measures prevalence of trait in ppl who had one biologic parent w/ the trait, but who are adopted by parents who do not have the trait (individual receives predisposing genes from affected parent, but adopted individual does not share environmental factors with the affected biologic parent)
-supports gene involvement in schizophrenia (10% risk for twin raised by schiz parent, 8% risk
for twin raised by non-schiz parent)

for a trait that is determined strictly by genes, one would expect:

• 100% concordance in MZ twins (they share all of their genes)
• 50% concordance in MZ twins (they share 50% of their genes)

for a trait that is determined strictly by environment, one would expect:
-equal concordance in MZ & DZ twins (assuming they were raised together) (no genetic influence)
problem = MZ twins often tx’d differently than DZ twins (develop
heritability plots based on #’s of actual concordance in DZ vs MZ)

Question 64

Related to question #46, what does the CMZ-CDZ/1-CDZ equation do?

Answer 64

• used to calculate heritability by using the data from twin studies (though no instance in which a trait is strictly genetically or strictly environmentally determined - all are multifactorial)
• ex: psoriasis (genes play a large role, environment play a minor role) & OA (environment has a larger role than genes)

Question 65

What does p53 do, and what happens if it is mutated?

Answer 65

• p53 is a tumor suppressor gene that stops a cell w/damaged DNA from entering S phase
• if it is mutated —> increased risk/liability for cancer (90% chance)
• they don’t necessarily have cancer, but their liability is extremely high
• double hit = if they incur a loss-of-function somatic mutation in a cell, it will lead to cancer
• eg Li-Fraumeni Syndrome

Question 66

What is genetic liability?

Answer 66

• the summation of genetic and environmental factors (risk factors)
• distribution in the population represented as a Gaussian curve (bell curve)

Question 67

Who was George Price and what was his contribution to genetics?

Answer 67

Price’s ‘mathematical’ theory of altruism reasons that organisms are more likely to show altruism toward each other as they become more genetically similar to each other. As such, in a species that requires two parents to reproduce, an organism is most likely to show altruistic behavior to a biological parent, full sibling, or direct offspring. The theory then holds that the further genetically removed two organisms are from each other the less likely they are to show altruism to each other. If true, then altruistic (kind) behavior is not truly selfless and is instead an adaptation that organisms have in order to promote their own genetic heritage. (Wikipedia)