Week 2 Flashcards
- Why is the oxidation of fructose not controlled by insulin, when glucose oxidation is controlled by insulin?
: 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.
- Why are several of the glycolytic enzymes present as different isozymes in different tissues?
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.
- Why are glycolysis and gluconeogenesis counter-regulated at specific steps in the pathways?
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.
- Why would heart failure result in hyperlactatemia?
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.
- How do the dynamic assembly/disassembly properties of microtubules affect spindle formation?
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).
- How are chromosome segregation errors sensed in the cell?
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.
- 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.
- How are chromosome organized during mitosis relative to interphase?
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.
- Why does the loss of Rb expression or mutation of the protein promote cancer?
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.
- What is the advantage of a cell becoming senescent due to excessive DNA damage?
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.
- Why is Cdk/cyclin activity regulated by post-translational modification in addition to cyclin expression?
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.
- How does telomere length limit cell proliferation?
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.
- What thermodynamic property of the TCA cycle reactions drives the cycle?
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.
- What are the four direct metabolic fates of pyruvate?
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.
- Why do cells lacking mitochondria not utilize the TCA cycle for energy production?
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.
- Why are fatty acids a more energy rich fuel source than carbohydrates?
Fatty acids are more highly reduced, and therefore contain more electrons that can be utilized in oxidative metabolism.
- What effect would high ethanol consumption have on fatty acid oxidation?
The oxidation of ethanol produces reduced NADH. Increasing the NADH/NAD ratio inhibits the dehydrogenases that catalyze the oxidation of fatty acids.
- Why are the carbons from glucose not used to synthesize ketone bodies?
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.
- What are the only two reactions in humans that require vitamin B12?
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.
- What form of tetrahydrofolate is required for the synthesis of methionine from homocysteine?
methyl tetrahydrofolate
- Methylation of histones and DNA is an important epigenetic modification for the regulation of gene expression. What is the methyl donor for these modifications?
S-adenosylmethionine
- Why are membrane transporters needed to move small molecules into and out of the mitochondria?
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.
- What benefits could a cell derive from uncoupling electron transport from oxidative phosphorylation?
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.
- How can mitochondria maintain a proton gradient in the absence of electron transport?
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.
- 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.
- Why don’t erythrocytes utilize fatty acids as an energy source?
- They do not contain mitochondria and therefore cannot carry out oxidative metabolism.
- Why doesn’t the liver use fatty acids to produce glucose during starvation?
- 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.
- 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.
how does ATP produce energy
high energy bonds are hydrolyzed to form energy (ATP –> ADP + P)
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
more reduced a molecule is (gain of electrons), the more ____ can be obtained
energy
what is gibbs free energy
the energy that can be obtained from a reaction
if gibbs is < 0, then at equilibrium, ___ > _____
Products»_space;> Reactants (exergonic)
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).
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
what is treatment
enzyme replacement every 2 weeks
Sources of acetyl CoA for TCA cycle
oxidation of FA, KB, monosaccharides, amino acids, ethanol
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
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.
- What makes citrate in TCA cycle?
Acetyl CoA + OAA + Citrate Synthase
Citrate, Isocitrate, A-Ketoglutarate, Succinyl CoA, Succinate, Fumarate, Malate, OAA. When is NADH produced? (3 SPOTS) When is CO2 made (2 spots)
- Isocitrate —-> A-KG, (CO2)
- A-KG –> Succinyl CoA (CO2)
- Malate —> OAA
Citrate, Isocitrate, A-Ketoglutarate, Succinyl CoA, Succinate, Fumarate, Malate, OAA. When is GTP produced?
Succinyl CoA –> Succinate
Citrate, Isocitrate, A-Ketoglutarate, Succinyl CoA, Succinate, Fumarate, Malate, OAA. When is FADH made?
Succinate –> Fumarate
How is isocitrate dehydrogenase regulated?
Rate limiting, allosterically, ADP and Ca2 upregulate, NADH downregulate
How is A-KG Dehydrogenase regulated?
Downregulated with NADH, upregulated with Ca2
How is malate dehydrogenase regulated
Downregulated with NADH
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)
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.
what are the phases of the cell cycle and what do they do
Interphase (G0 arrest, G1 growth, S synthesis, G2 growth) and Mitosis
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)
G1 cyclin/cdk?
D-4, 5
G1/S transition cyclin?
E-2
S cyclin?
A-1,2
G2 cyclin?
A-1,2
Mitosis cyclin?
B-1
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
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
What keeps cell at the G1 checkpoint?
Rb, INK 4
How do we move past G1 checkpoint?
Mitogen signals from growth facts which stabilize and increase cyclin D; allowing it to remove Rb
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.
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.
What is senescence and how does it happen?
Permanent cell cycle arrest in response to stress and damaged cells. P21 mediated.
How are telomeres affected by replication?
Shorten over time; shelterin protects ends; telomerase extends ends
prophase?
chromosomes condense, MT spindle develops, cyclin B increases, nuclear lamin breaks down so MT access chromosomes, condensins condense
what is kinetochore/where
between chromosome and MT spindle, mediate attachment
metaphase?
chromosomes at middle, metaphase plate
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
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
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
condensin vs cohesin?
condensin – compacts chromosome, uses ATP; cohesin – keeps sister chromosomes together from S phase to mitosis, dissolved in anaphase
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
Telophase?
nucleus envelope and lamin reforms
Cytokinesis?
ECT2 helps with cytokinesis by activating actin and myosin; it is inhibited by cyclins so can’t happen until APC degrades cyclins
structure of chromosomes?
packaged around histones – forming nucleosomes; packaged into solenoid (nucleosome and linker DNA) and chromatin loops
metacentric
centromere in middle; p=q
submetacentric
centromere leaning on one side
acrocentric
centromere on an end
