Week 2 Flashcards
(194 cards)
1
Q
- Why is the oxidation of fructose not controlled by insulin, when glucose oxidation is controlled by insulin?
A
: The carbons from fructose oxidation enter the glycolytic pathway as DHAP and glyceraldehyde-3-P, after the step in glycolysis catalyzed by PFK-1, the enzyme that is regulated by insulin and glucagon.
2
Q
- Why are several of the glycolytic enzymes present as different isozymes in different tissues?
A
Each tissue has different energy and synthetic requirements. Isozymes are frequently regulated differently, so the activity of a particular pathway will depend on which isozymes are expressed in a given tissue.
3
Q
- Why are glycolysis and gluconeogenesis counter-regulated at specific steps in the pathways?
A
Metabolic pathways are usually regulated at the key control steps in the pathway. By regulating the key enzymes in each pathway, the cell can rapidly switch between synthetic and degradative pathways.
4
Q
- Why would heart failure result in hyperlactatemia?
A
Answer: During heart failure, not enough oxygen will be delivered to the cardiac muscle cells (and other tissues) due to decreased blood flow. The lack of oxygen will slow the rate of ATP production by the mitochondria, and the cells will have to upregulate glycolysis to produce ATP. Since the reduced NADH produced by glycolysis will not be adequately oxidized by the mitochondria, lactate dehydrogenase will convert pyruvate to lactate, which will be secreted causing hyperlactatemia.
5
Q
- How do the dynamic assembly/disassembly properties of microtubules affect spindle formation?
A
Microtubules add subunits at the plus for the microtubule to extend. The plus ends switch between growing and shrinking. The shrking phase is also called catastrophe, which is the rapid loss of tublin subunits. Kinetochores remain bound to the shrinking end of the microtubule, draggin the chromosome along with it. Coupling the chromosome to the microtubule undergoing catstrophe provides the force to pull the chromosome apart in the first part of anahase (anaphase A). Motor proteins that “walk” along microtubules push the spindle poles apart in the second part of anaphase (anaphase B).
6
Q
- How are chromosome segregation errors sensed in the cell?
A
The mitotic (or spindle assembly) checkpoint is the major cell cycle checkpoint that ensures accurate chromosome segregation. The checkpoint will halt the cell cycle until all kinetochores of the chromosomes are attached to the microtubule spindle. Kinetochore acts as a signaling center that produce a “wait” singal, until the kinetochore is bio-oriented on the microtubule spindle. 3. How will acentric chromosomes segregate at mitosis? Acentric chromosomes are chromosome fragements that lack centromeres due to chromosome breakage. Because they cannot attach to the microtubule spindle, these acentric chromosomes will be randomly distributed between daughter cells.
7
Q
- How will acentric chromosomes segregate at mitosis?
A
Acentric chromosomes are chromosome fragements that lack centromeres due to chromosome breakage. Because they cannot attach to the microtubule spindle, these acentric chromosomes will be randomly distributed between daughter cells.
8
Q
- How are chromosome organized during mitosis relative to interphase?
A
The function of chromosome organization in mitosis and interphase is very different. Interphase chromatin must be accessible for transcription. In contrast, chromosomes must betightly packaged and paired in preparation for efficient segregation into daughts cells. Cohesin proteins bind sister chromosomes together at the centromere until anaphase onset. Condensin complexes are used to compatect the chromatin and organize them so they can be easitly moved and segregated.
9
Q
- Why does the loss of Rb expression or mutation of the protein promote cancer?
A
Rb is the major regulator of the S-phase transition. Rb inhibits cell cycle progression in the absence of phosphorylation. Rb receives input from several sources. These include growth factor signaling which promote cyclinD stability and Cdk4/6 activity towards Rb to promote cell cycle progression. Without Rb function cells no long require growth factor-stimulation to proliferate which leads to the unregulated growth of cancer cells.
10
Q
- What is the advantage of a cell becoming senescent due to excessive DNA damage?
A
Senescence means that the cells stop dividing and thus proliferating. Senescence in response to DNA damage (no matter where it is in the genome) helps the cells avoid accumulating DNA mutations that could eventually lead to unregulated cell proliferation. This is also why mutations in P53 are so prevalent in cancer, because they bypass an important DNA damage checkpoint and allow damaged cells to continue to proliferate.
11
Q
- Why is Cdk/cyclin activity regulated by post-translational modification in addition to cyclin expression?
A
The process of moving the cell cycle forward depends on the irreversible degradation of cyclin proteins. This process is driven by the ubiquitylation of cyclins. In contrast, phosphorylation—which can be removed by phosphatases—is used to provide reversible control of the cell cycle machinery.
12
Q
- How does telomere length limit cell proliferation?
A
Telomeres are shortened during each round of DNA replication. In contrast to germ cells, somatic cells that do not need to proliferate turn off expression of the telomerase enzyme that lengthens telomeres. If somatic cells proliferate too much they shorten their telomeres beyond the telomere sequences present at the ends of chromosomes. This leads to activation of the DNA damage pathway, turns on P53 and arrests the cell cycle.
13
Q
- What thermodynamic property of the TCA cycle reactions drives the cycle?
A
The reactions catalyzed by the dehydrogenases of the TCA cycle have large negative free energy changes, so the equilibrium for the reactions lies strongly toward the formation of product. Also, because of their sequential arrangement in the cycle, the products of one reaction are quickly used as substrates for the next reaction and they never accumulate to high levels.
14
Q
- What are the four direct metabolic fates of pyruvate?
A
1) conversion to acetylCoA by pyruvate dehydrogenase, 2) conversion to oxaloacetate by pyruvate carboxylase, 3) synthesis of alanine by alanine aminotransferase, 4) reduction to lactate by lactate dehydrogenase.
15
Q
- Why do cells lacking mitochondria not utilize the TCA cycle for energy production?
A
The dehydrogenases of the TCA cycle donate electrons to NAD and FAD. These reduced coenzymes must be oxidized by the OXPHOS enzymes in the mitochondrial matrix. Cells lacking mitochondria are unable to oxidize the large number of reduced coenzymes that would be produced by the TCA cycle.
16
Q
- Why are fatty acids a more energy rich fuel source than carbohydrates?
A
Fatty acids are more highly reduced, and therefore contain more electrons that can be utilized in oxidative metabolism.
17
Q
- What effect would high ethanol consumption have on fatty acid oxidation?
A
The oxidation of ethanol produces reduced NADH. Increasing the NADH/NAD ratio inhibits the dehydrogenases that catalyze the oxidation of fatty acids.
18
Q
- Why are the carbons from glucose not used to synthesize ketone bodies?
A
During ketogenesis, liver pyruvate dehydrogenase is inhibited so pyruvate cannot be oxidized to acetylCoA. Also, ketogenesis occurs when glucose levels are low, so most available glucose is utilized by primarily the brain and RBCs, neither tissue can synthesize ketone bodies.
19
Q
- What are the only two reactions in humans that require vitamin B12?
A
The synthesis of methionine from homocysteine and rearrangement of L-methylmalonyl CoA to form succinyl CoA during the degradation of branched amino acids or the last three carbons of odd chain fatty acids.
20
Q
- What form of tetrahydrofolate is required for the synthesis of methionine from homocysteine?
A
methyl tetrahydrofolate
21
Q
- Methylation of histones and DNA is an important epigenetic modification for the regulation of gene expression. What is the methyl donor for these modifications?
A
S-adenosylmethionine
22
Q
- Why are membrane transporters needed to move small molecules into and out of the mitochondria?
A
The inner mitochondrial membrane is highly impermeable to ions, more so than other membranes, due to the membranes high protein composition and the presence of a unique diphosphatidylglycerol lipid called cardiolipin. The only place this lipid is found is in mitochondria and bacterial membranes.
23
Q
- What benefits could a cell derive from uncoupling electron transport from oxidative phosphorylation?
A
The energy lost during electron transport is converted to heat energy to warm the organism. This is the mechanism used by brown fat mitochondria to produce heat.
24
Q
- How can mitochondria maintain a proton gradient in the absence of electron transport?
A
The ATP synthase complex can pump protons out of the matrix coupled to the hydrolysis of ATP. This is the opposite to what occurs when electron transport is coupled to oxidative phosphorylation to generate ATP.
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4. Why would mitochondria require attachment to the cytoskeleton?
Mitochondria are too large to diffuse through the cytoplasm so they require motors for movement. Mitochondrial fission and fusion require mitochondrial movement. Attachment to the cytoskeleton can also position mitochondria at places in the cell with high ATP requirements.
26
1. Why don’t erythrocytes utilize fatty acids as an energy source?
1. They do not contain mitochondria and therefore cannot carry out oxidative metabolism.
27
2. Why doesn’t the liver use fatty acids to produce glucose during starvation?
2. The pyruvate dehydrogenase reaction that converts pyruvate to acetylCoA is irreversible. Therefore, for acetyl CoA to produce glucose, it must enter the TCA cycle. Since 2 carbons are lost for every turn of the cycle, there is no net gain of carbons that can be used for glucose synthesis.
28
3. Why would high concentrations of ketone bodies in the blood lower the pH of the blood?
The ketone bodies acetoacetate and β-hydroxybutyrate are acids.
29
how does ATP produce energy
high energy bonds are hydrolyzed to form energy (ATP --> ADP + P)
30
what is creatine phosphate
high energy compound that stores energy to be converted into ATP, it has high P bonds, serves as a energy bank, if a lot of ATP is being hydrolyzed, then use this
31
more reduced a molecule is (gain of electrons), the more ____ can be obtained
energy
32
what is gibbs free energy
the energy that can be obtained from a reaction
33
if gibbs is < 0, then at equilibrium, ___ > _____
Products >>> Reactants (exergonic)
34
what is gaucher disease
Gaucher disease is a lysosomal storage disease, in which a macromolecule, glucocerebroside, accumulates in the lysosomes because of deficiency of the lysosomal enzyme that is critical for its degradation (acid β-glucosidase, AKA glucocerebrosidase).
35
symptoms of gaucher?
enlarged spleen and liver, pain in bones; enlarged spleen means hyperactive --> removes healthy red blood cells from circulation --> anemia (low RBC) and low platelet
36
what is treatment
enzyme replacement every 2 weeks
37
Sources of acetyl CoA for TCA cycle
oxidation of FA, KB, monosaccharides, amino acids, ethanol
38
How is Pyruvate --> Acetyl CoA? What are the other products, where is pyruvate coming from?
Pyruvate (from glycolysis of glucose and AA like alanine); pyruvate dehydrogenase complex used; CO2 and NADH are other products
39
How is PDC (pyruvate dehyrogenase used to make pyruvate --> acetyl CoA) regulated? In well fed vs starvation states!
PD Kinase (inactivates) and PD Phosphatase (activates); in high energy states (high ADP inactivate the kinase, increasing PDC activity; Ca activate phosphatase, increasing PDC activity) vs. during starvation, the kinase is transcribed more, in order to decrease PDC so that pyruvate is not oxidized. During starvation, metabolism shifts towards FAT utilization, and other tissues are prevented from catabolizing glucose.
40
1. What makes citrate in TCA cycle?
Acetyl CoA + OAA + Citrate Synthase
41
Citrate, Isocitrate, A-Ketoglutarate, Succinyl CoA, Succinate, Fumarate, Malate, OAA. When is NADH produced? (3 SPOTS) When is CO2 made (2 spots)
1. Isocitrate ----> A-KG, (CO2)
2. A-KG --> Succinyl CoA (CO2)
3. Malate ---> OAA
42
Citrate, Isocitrate, A-Ketoglutarate, Succinyl CoA, Succinate, Fumarate, Malate, OAA. When is GTP produced?
Succinyl CoA --> Succinate
43
Citrate, Isocitrate, A-Ketoglutarate, Succinyl CoA, Succinate, Fumarate, Malate, OAA. When is FADH made?
Succinate --> Fumarate
44
How is isocitrate dehydrogenase regulated?
Rate limiting, allosterically, ADP and Ca2 upregulate, NADH downregulate
45
How is A-KG Dehydrogenase regulated?
Downregulated with NADH, upregulated with Ca2
46
How is malate dehydrogenase regulated
Downregulated with NADH
47
In well fed, low energy consumption state, the TCA cycle can be used to synthesize AA, glucose, FA, heme, NT. This depletes C from the cycle. Needs carbons to continue oxidizing acetyl CoA. How is that restored?
Anaplerotic reactions. Amino Acids to Pyruvate (and then Pyruvate Carboxylase used to catalyze Pyruvate --> OAA.) Fatty Acid to Propionyl CoA (and then to Succinyl CoA)
48
What is glutaminolysis? Related to tumor cells?
Use of glutamine in cell; active in proliferating cells/tumor cells. Tumor cells are high in ROS which inhibit the TCA cycle; glutamine generates antioxidants to remove ROS. Glutamine used in synthesis of other biomolecules from TCA cycle through alpha keto glutarate.
49
what are the phases of the cell cycle and what do they do
Interphase (G0 arrest, G1 growth, S synthesis, G2 growth) and Mitosis
50
characteristics of cyclin and CDK
cyclins change in activity and availability throughout the cycle, and bind to the CDK activating them. CDK are constant throughout the cycles but can only function when cyclin is bound to them. these complexes are regulated by their availability (express/degrade cyclin) and their activity (cki inhibit, and phosphorylation can activate or inactivate them)
51
G1 cyclin/cdk?
D-4, 5
52
G1/S transition cyclin?
E-2
53
S cyclin?
A-1,2
54
G2 cyclin?
A-1,2
55
Mitosis cyclin?
B-1
56
what are the cyclin kinase inhibitor proteins and when do they function
INK 4 -- inhibits G1 by inactivating cyclin D; KIP works at different parts
57
how is G1 regulated? G1 checkpoint?
G1 only occurs when cell cycle is big and nutrition and mitogens present. INK 4 inhibits cyclin D. Rb binds to E2F inactivating it. Mitogens however, increase cyclin D, degrade CKI, and increase E2F. Cyclin D and E phosphorylate Rb removing it! Thus E2F is activated and can make genes needed for S phase
58
What keeps cell at the G1 checkpoint?
Rb, INK 4
59
How do we move past G1 checkpoint?
Mitogen signals from growth facts which stabilize and increase cyclin D; allowing it to remove Rb
60
Role of p53?
When damage is sensed, P53 is transcribed, it transcribes P21 which inhibits S phase cyclins (A and E). P53 can also lead to apoptosis.
61
What is quiescence and how does it occur?
Programmed temporary inactivity. G0 stage. In stems cell/differentiated types. Induced by low mitogen. INK 4 inhibits cyclin D. Rb stays on E2F inhibiting it. P27 (KIP) inhibits cyclin E.
62
What is senescence and how does it happen?
Permanent cell cycle arrest in response to stress and damaged cells. P21 mediated.
63
How are telomeres affected by replication?
Shorten over time; shelterin protects ends; telomerase extends ends
64
prophase?
chromosomes condense, MT spindle develops, cyclin B increases, nuclear lamin breaks down so MT access chromosomes, condensins condense
65
what is kinetochore/where
between chromosome and MT spindle, mediate attachment
66
metaphase?
chromosomes at middle, metaphase plate
67
what happens at the metaphase checkpoint?
important to make sure all the chromosomes are all lined up and connected before anaphase. unattached chromosome sends signal to the MCC (mitotic checkpoint complex) which will tell the APC to wait (anaphase promoting complex) -- this is a way to make sure metaphase is done and ready
68
what does APC do
anaphase promoting complex -- when activated it targets securin and cyclin B through ubiquitinylation; it degrades M cyclin, which leads to next steps; loss of coheision; sister chromatids separate
69
what are the 2 ways G2/M damage checkpoint
ATM kinase activates p53 which transcribes p21 which inhibit G2/M cyclins. OR ATR phosphorylates ChK 1 (Checkpoint Kinase 1) which inactivates cdc25
70
condensin vs cohesin?
condensin -- compacts chromosome, uses ATP; cohesin -- keeps sister chromosomes together from S phase to mitosis, dissolved in anaphase
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anaphase? A and B?
A : kinetochore MT shortens, chromatids pulled apart, dynamic instability. B: motor forces pull and push poles so that poles separate. when APC increases, securin and cyclin decreases, so separase increases and chromatids separate
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Telophase?
nucleus envelope and lamin reforms
73
Cytokinesis?
ECT2 helps with cytokinesis by activating actin and myosin; it is inhibited by cyclins so can't happen until APC degrades cyclins
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structure of chromosomes?
packaged around histones -- forming nucleosomes; packaged into solenoid (nucleosome and linker DNA) and chromatin loops
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metacentric
centromere in middle; p=q
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submetacentric
centromere leaning on one side
77
acrocentric
centromere on an end
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ideograms
representation of the regions, bands, sub-bands; used as models
79
preparing for cytogenetics test? karyotype
inhibit anaphase, low salt solution so water enters cell and swells; harden cell with fixative solution; cell suspended on microscope slide, chromosome dried and spread, stained
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euploid
exact multiple of haploid set (a whole set different)
81
aneuploid
a number different than 46 but not a whole haploid set different
82
para inversion?
a region is flipped, does not include centromere
83
peri inversion
region is flipped, includes centromere
84
translocation
non homologous chromosomes, regions are swapped between 2 chromosomes
85
ring
ends of chromosome fuse
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nomenclature for abnormal DNA
46 (XY), t (1:13) (p36.1; q12) -- number of chromosomes, sex chromosomes, characteristics
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what is lyon hypothesis about x chromosomes
that in XX, 1 is inactive (condensed) and only 1 is active
88
explain meiosis I and II
MEIOSIS I: start with diploid cell of single; replicate, line up homologous chromosomes; split homologs and divide cells forming two haploid daughter cells; MEIOSIS II; line up chromosomes, split sister chromatids forming four haploid daughter cells
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prophase I meiosis -- what is leptotene
chromosomes condense
90
prophase I meiosis what is zygotene
homologs align and held together
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prophase I meiosis what is pachytene
each pair of homologs coils tightly and crossing over occurs
92
prophase I meiosis what is diplotene
homologs begin to separate but stay attached at crossing over points
93
prophase I meiosis what is diakinesis --
separation of homolog pairs, chromosomes are condensed
94
characteristics of recombination -- where does it happen most and to what gender
most at telomeres, more in females
95
what makes female meiosis different
starts early (in embryo vs puberty), lasts longer (10 years vs 2 months), about 20-30 mitoses in gamete production (vs 30-500), 1 ovum per cycle (vs 100-200 per ejaculation)
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signs of constitutional chromosome abnormalities
advanced maternal age, family history. post natal: congenital problems, retardation, lack of puberty
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what is non disjunction
failure of homologs (during M1) or sister chromatids (during M2) to separatey. leads to trisomy and monosomy
98
what is maternal age
greater than 35 you have risk of chromosomal abnormality
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translocation offspring? what is balanced translocation
balanced -- no genetic material lost. forms tetravalent instead of bivalent in meiosis --> can lead to many different segregation patterns. results in normal, balanced translocation, or unbalanced (the monosomy/trisomy could be not viable) depending on chromosome gene content and size
100
robertsonian translocation what is it
a translocation between 2 acrocentric chromosmoes (13, 14, 15, 21, 22) that results in loss of the short arms for both chromosomes, doesnt affect DNA content of long arms. 2 types -- whole arm translocation and fusion of centromeres
101
what is the only viable monosomy
sex
102
what is the only viable trisomy
13, 10, 21
103
what is trisomy 21
downs
104
what does paracentric inversion and recombination lead to
paracentric doesnt include centromere. when recombination occurs within the inversion loop, offspring won't be viable. leads to acentric (no centromere) and dicentric (2 centromeres). carriers of paracentric could have miscarriages or normal offspring
105
what is pericentric inversion and what does it lead to
crossing over leads to chromosomes with only 1 centromere. recombination can occur in loop -- but the abnormality depends on which chromosome and the extent. can result in deletion and duplication of some genes
106
what is microdeletion syndrome? how common? what happens to it during meiosis?
deletion of small regions that can be detected through cytogenetics, low incidence, phenotypically and genetically characterized syndrome, sporadic not inherited usually, during meiosis can lead to duplication/deletion or endjoining
107
how does FISH work
denature DNA, add probe targeted for gene of interest, probe anneals to patient DNA sequence, visualize/quantify probe
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how does microarray work
add green flourescent to patient dna, combine with red control dna, put in microarray, if they both are present then it will look yellow on digital imaging. if more green, than more patient. if more red, than it is less
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pros and cons of karyotyping
visualize whole genome, not limited; low resolution, must be done during metaphase when chromsomes are condensed; different levels of condensation results in different resolution
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FISH pros and cons
can be done at any stage, molecular level resolution; you need to know what youre looking for, cant tell you the difference between deleted and condensed band
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array pros and cons
can be done at any time, molecular level, can look for multiple deletions, can look at entire DNA; can't detect structural abnormalities (like rearrangement), many copy number variants can be benign, can't distinguish mechanism
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locus
specific place in the genome
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variant
single specific difference between genetic sequence of 2 ppl
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reference genome
variant described relative to reference
115
tandem duplication
copy next to it
116
interspersed duplication
copy elsewhere
117
copy number variant
multiple copies in a row, varies in length
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synonymous
AA does not change
119
nonsynomous
a single AA is changed
120
nonsense
early stop codon
121
splice variant
disrupts splicing motif, severe but variable effects, cuases various splice errors like exon skipping on intron retention
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loss of function
partial or total reduction of protein levels
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gain of function
allele causes protein to function in a new way instead of the normal way (eg. TF activates wrong gene, or a signalling protein is always on)
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exome
the entire protein coding of the genome, aka all the exons, only 1% of the human genome
125
what is the classification for variants
benign, likely benign, uncertain significance, likely pathogenic, pathogenic
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1. Why are genotypes described using 2 letters (i.e. C/C or C/G)?
Genotypes are described always using 2 letters because humans have 2 copies of every chromosome, one maternal and one paternal (another word for this is ‘diploid’). The 2 genotype denotes whether a variant is homozygous (both alleles the same) or heterozygous (one of each allele).
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2. What kinds of variants are most likely to result in a Loss of Function?
Loss of Function means an allele that is not able to make any protein of any function. This is usually caused by deletions (whole gene or large segments are missing from genome), or variants that result in a premature stop codon (nonsense, frameshift, some splice variants). These variants are sometimes referred to as ‘truncating’ variants.
128
3. How might a single missense variant cause disease?
? A single missense variant might cause disease through a Gain of Function – for example, causing a protein to misfold, which distorts the structure of the cell, which causes disease (this is what happens in Sickle Cell Disease). A single missense variant could also cause disease through Loss of Function – for example, a variant in a critical protein region that prevents a protein from binding to any partner (this happens in some forms of Hereditary Breast/Ovarian Cancer
129
how does glucose enter the cell
facilitated diffusion through membrane transporters (GLUT) and then phosphorylated to G6P by hexokinase
130
where does glycolysis occur and why
to make ATP, in cytoplasm
131
what are the products of glycolysis
2 pyruvate, 2 ATP, 4 e (as NADH)
132
when is ATP used during glycolysis
to go from glucose to glucose 6 phosphate using hexokinase AND from f6b to f16b using PFK-1
133
what happens to F16bp
it cleaves into DHAP and GA3P
134
when are the 2 ATP released during glycolysis
when 1,3 bisphosphateglycerate goes to 3phosphoglycerate and when PEP is phosphorylated to pyruvate using pyruvate kinase
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NAD+ is used during GA3P to 1,3BPG. How is more of this NAD+ made?
aerobic pathway -- GA3P shuttle or malate aspartate shuttle that moves NADH to mitochondrial where it is reoxidized; or anaerobic pathway where pyruvate converts into lactate, making NADH into NAD
136
what is the rate limiting enzyme in glycolysis
PFK 1 which goes from Fructose 6 P to Fructose 1,6 bis P.
137
How is PFK 1 regulated
AMP upregulates it. ATP downregulates it. Citrate downregulates it. F-2,6,bisP upregulates it, which increases when insulin is high in a well fed state, so then glycolysis increases.
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how does fatty acid oxidation differ than glycolysis
its a source of energy between meals, higher energy than glucose because it is more reduced, in mitocondrial matrix, stored as TAG in cytoplasm or as free FA taken up by tissues
139
how do long chain FA enter the mito
fatty acid and acyl coA combine (ATP required) and travel through outer membrane (CPI 1 needed). then CoA switches to Carmatine. Fatty acid carmatine travels across inner membrane (using CPI 2) into the matrix. it switches back to fatty acyl coA.
140
how about short chain FA entering mito
transporters
141
what are the 4 steps of Beta oxidation and final product?
oxidation to a double bond, hydration to an alcohol, oxidation to ketone, cleavage into fatty acyl coA (-2 C) and acetyl coA
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how do levels of NADH and FAD2H affect beta oxidation
high NADH inhibits B oxidation because no more oxidized NAD+ to accept electrons. basically high ATP, means ETC decreases, so NADH builds up and inhibits B oxidation
143
role of malonyl CoA in oxidation of fatty acids?
inhibits CPI I -- keeps FA from entering mitochondria. makes sense because malonyl CoA is involved in synthesis so you wouldn't want oxidation happening at the same time
144
what is an alternative to beta oxidation of fatty acids
when beta doesnt work. peroxisomes -- oxidate very long FA. O2 used to oxidize instead of dehydrogenase, producing H202. then it goes into mitochondria
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what is w oxidation in ER
w methyl --> alcohol --> carboxylic acid (forming a dicarboxylic acid), it is more soluble, common if defect in beta oxidation
146
where are ketone bodies
in peripheral tissues
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how are KB oxidized to acetyl CoA
oxidized (NAD), then succ. CoA (from TCA cycle) adds CoA group. CoASH used to make 2 acetyl CoA
148
how does alcohol become metabolized into acetyl coA
oxidized using dehydrogenase (NAD --> NADH) into acetaldehyde, enters mito, oxidized again, CoASH/AMP --> acetyl CoA
149
Fatty Acid Synthesis. How is acetyl coA made and moved out of the mitochondria to be used?
Pyruvate --> acetyl CoA using dehydrogenase. and Pyruvate --> OAA using carboxylase. Acetyl CoA and OAA combine with citrate synthase to make Citrate!! Citrate can now move out of the mitochondria. A lyase breaks it back down into Acetyl CoA and OAA
150
Now that acetyl CoA is in cytoplasm. How is fatty acid synthesis initiated? What is needed to convert it into malonyl coA?
Acetyl CoA --> Malonyl coA. Using Acetyl CoA Carboxylase, Co2 and ATP.
151
how is acetyl coA carboxylase used to go from acetyl coA to malonyl coA for FA synthesis regulated?
Citrate upregulates it. AMP downregulates it by inactivating the carboxylase. AMP works in low energy conditions. Because in low energy, we want to oxidize FA not synthesize it.
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how does FA synthase work?
dimeric enzyme with 7 active sites. acetyl CoA adds on acyl carrier protein side. Moves over to condensing side. Malonyl CoA attaches on first site. Electrophilic reaction, Malonyl CoA attacks, lose a CO2 and Malonyl+Acetyl are on the first site. Reduction (NADPH), Dehydration (lose H20), Reduction (NADPH) and then all is repeated.
153
how is FA elongated?
condensation reduction dehydration reduction reaction
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how are FA desaturated (double bond added)
with fatty acid coA desaturase, can add at C5, 6, or 9. uses O2 as electron acceptor to reduce
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when are KB synthesized and where
fasting, carb restriction, in the mitochondria in the liver; when fatty acid levels are elevated due to starvation or a low carb/high fat diet so increased FA oxidation so acetyl CoA is being made. acetyl coA is accumulated so KB is made.
156
when fat is gone, how is ketone made?
from AA (proteins) during starvation
157
relationship between ATP and beta oxidation
high ATP inhibits more B oxidation from happening
158
how are TAG (triacylglycerides) synthesized? what are the two options for sources/locations and when?
1. from glycerol, in liver, at any time
| 2. from glucose, in liver or tissue, must be well fed state bc glucose
159
how is glycerol 3 P made into TAG
fatty acyl CoA activated molecules are added
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where does TAG go (2 options)
into adipose stores or into blood
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how are membrane phospholipids formed
phosphatidic acid and head groups combined through activated intermediates --> glycero-phospholipid. intermediate is either CDP+headgroup added to a diacylglycerol OR a CDP-diacylglycerol added to the head group
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how is cholesterol synthesized
from acetyl CoA supplied from glucose through glycolysis. acetyl CoA and acetoacetyl CoA made into HMG-CoA intermediate.
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what is 1 carbon pool
groups that contain 1 carbon atom in different reduced states
164
what does tetrahydrofolate do and how is it produced
enzyme that accepts 1 carbon groups, transferred to liver, produced by folate --> dihydrofolate --> THF. reduced by two NADPH
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roles of vitamin B12
rearrangement of methyl in methylmalonyl CoA to Succinyl CoA; transfer of methyl from homocysteine to methionine
166
explain what happens to THF, and carbon metabolism
THF-CH3 active forms (formyl, methyl, methylene THF) can go on to purine/thymidine and DNA and RNA cell division; reduced CH3 THF goes back to THF. CH3 THF and B12 --> B12 THF. B12 THF and homocysteine --> Methionine. Methionine + ATP --> S-AMP --> releases CH3+product (methylates a precursor), SAH --> Homocysteine.
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what does S-AMP do
major donor of methyl groups, can methylate many reactions, comes from diet or from homocysteine+CH3
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what happens when B12 is or methionine synthase is down
methyl FH4 (THF CH3) accumulates, folate is trapped, leading to folate deficiency --> disease
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excess homocysteine leads to heart and brain disease. how does homocysteine accumulate?
1. defect in methionine synthase
2. methylene FH4 reductase decreases, then methylene FH4 cant be remade --> prevents conversion of homocysteine to methionine
3. homocysteine converts to cysteine through a synthase, which if mutated will lead to accumulation
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difference between outer and inner membranes?
outer is lipid based and highly permeable because it has voltage dependent anion channels which allows diffusion across outer membrane (eg. pyruvate, citrate, phosphate). inner is protein rich and highly impermeable to nucleotides and ions, but permeable to uncharged small molecules and monocarboxylic acids, so needs transporters.
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where is inner space? where is matrix?
inner space between the 2 membranes. matrix is the space fully in the mitochondria, in between the cistae
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how do NADH and FADH2 enter
use transporters. they carry electrons which are harvested by the ETC. then made into ATP with ATP synthase
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In aerobic glycolysis, reducing equivalents (NADH and FADH) are transferred by shuttle mechanisms into the mitochondria. NADH produced in the cytosol cannot penetrate the inner membrane. Two shuttle mechanisms exist to transfer electrons (reducing equivalents) from the cytoplasm to the mitochondrial matrix. explain the glucose 3 phosphate shuttle
cystolic G3P dehydrogenase transfers the electrons from NADH to DHAP --> making it into glycerol 3 P. (NADH makes DHAP --> G3P) Glycerol 3-phosphate donates the electrons to an inner membrane bound FAD-dependent glycerol-3-phosphate dehydrogenase to regenerate DHAP. This enzyme transfers electron to CoQ. This is the major shuttle in most tissues.
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how does malate aspartate shuttle work
Cytosolic NADH is used to reduce cytosolic oxaloacetate (OAA) to malate. (electrons from NADH make OAA --> Malate) Malate is transported across the inner membrane in exchange for α-ketoglutarate by a specific translocase. In the matrix, malate is oxidized back to OAA by mitochondrial malate dehydrogenase regenerating NADH. The newly formed OAA is transaminated to aspartate that is then transported to the cytoplasm in exchange for glutamate, where it is then deaminated to for OAA.
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overview of ETC and ATP synthase?
4 complexes, each oxidizes electron carriers to generate energy to pump H+ from matrix into inner membrane space. each successive complex has more reducing potential, the energy of each electron decreases as it passes through the complexes. then there is an electrochemical gradient and so the ATP synthase transports H back out into matrix. the energy generated from the flow of H+ converts ADP into ATP.
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What does complex I do
it is a NADH Dehydrogenase complex. Removes H from NADH and passes e along. Uses FMN and Fe-S binding proteins
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Complex II
Does not span the membrane. Succinate dehydrogenase from TCA cycle. ETF CoQ transfers e from B oxidation. Glycerol 3 Phosphate takes e from the G3P shuttle for re-oxidizing cystolic NADH from glycolysis.
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Coenzyme Q
Mobile carrier that accepts electrons from Complex I and II and donates to complex III.
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Complex III
Cytochrome C Complex. Cytochrome proteins have a bound heme with an iron atom. The electrons are transferred to cytochrome C.
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Cytochrome C
In the intermembrane space. Heme ring, iron atom to bind and release electrons, iron sulfur cluster
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Complex IV
Cytochrome C Oxidase. Complex passes electrons from Cytochrome C to the final electron acceptor, O2. Contains copper ions.
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Chemiosmotic theory
Lower pH (more acidic) and more positive in the innermembrane space, where all the H is pumped into. Creates the proton motive force or PMF because it represents the potential energy driving protons to return to the more negatively charged alkaline matrix.
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ATP synthase
makes energy from transfer of H across membrane into energy in ATP bonds
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How is ETC regulated
Matrix ADP. If there isn't a lot of ADP, rate of proton flux through ATP synthase slows, overall rate of ETC slows, then TCA slows because NADH isn't reoxidized. Basically if lots of ATP is being hydrolyzed into ADP, then ETC is needed and increased
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What do UCP Uncouplers do
Uncouple protein flow and ATP generation. So energy is released as heat instead. Doesn't do the generation of ATP. Present in newborn babies.
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examples of membrane transport systems
phosphate and pyruvate transport; calcium uniport so that mito is known as calcium sink. ANT exchanges ATP and ADP.
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how does mitochondrial permeability transition pore work
associated with ANT and VDAC. regulates apoptosis. if Ca, phosphate or reactive oxygen increases, pore opens, mitochondria swells and apoptosis
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ROS and NOS
Reactive oxygen and reactive nitrogen species. When O2 accepts single electrons, it forms highly reactive oxygen radicals that can damage cellular lipids, proteins and DNA. ROS also a result of enzymatic and non enzymatic reaction. NOS from environmental and bacteria. Antioxidants protect against damage.
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brain preferred fuel sources
high requirement for oxgen and glucole, can source some glycogen
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liver energy sources
glucose, synthesis and export of cholesterol and TAG, FA metabolism, glycogen storage, produces urea
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muscle energy source
uses glucose, stores glycogen a little, in low oxygen lactic acid is metabolized, AA used, can metabolize fatty acids, creatine phosphate, cardiac muscle uses mostly fatty acids
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what happens in a fed state
A. Carbohydrates (mainly glucose) oxidized by various tissues for energy or stored as glycogen in the liver and muscle cells. Glucose is also the major source of carbons for biosynthetic reactions. Excess glucose is converted to triacylglycerols in the liver.
B. Proteins are digested to amino acids or dipeptides and taken up by tissues for protein synthesis or other biosynthetic reactions. Some can also be oxidized for energy or converted to glucose.
C. Lipids are converted to triacylglycerols by the intestinal epithelial cells and transported through the blood to adipose tissue.
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fasted state
A. Stored fuel release regulated by levels of insulin and glucagon.
B. Liver glycogen is degraded (glycogenolysis) and glucose released.
C. Adipose triacylglycerols mobilized by lipolysis to release fatty acids.
D. Use of fatty acids as fuel increases with length of fast.
E. Glucose used primarily by brain and erythrocytes, muscle and other tissue use mainly fatty acids.
F. Liver begins to oxidize fatty acids to ketone bodies for use by muscle and kidney.
G. As glycogen stores are depleted, liver switches to gluconeogenesis using lactate, glycerol and amino acids.
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what happens in starvation
A. Muscle continues to use fatty acids as fuel, but decreases its use of ketone bodies.
B. As ketone body levels in the blood rise, the brain begins to use them for energy.
C. The liver decreases gluconeogenesis decreasing the need for muscle amino acids to preserve vital functions (aka conserve cardiac muscle).
