Glossary of Biochem II Exam
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- What is the function of pyridoxine?
- B6 involved in all transamination reactions, most decarboxylations and deaminations
- How does pyridoxine work?
- Forms a schiff base with E-amino group of lysine in the active site of the enzyme.
- What is an aldimine linkage?
- Same thing as Schiff base
- Function of glutamate in cells?
- Takes NH3 group off other aa's during transamination and drops it off in the mitochondria for conversion to urea
- How does the alanine glucose cycle work?
- Breakdown of muscle aa's for energy yields NH3, this is transferred to pyruvate with ALT to form alanine. The alanine is transferred to the liver where it is converted back to pyruvate and the NH3 is given to glutamate to be disposed of. The pyruvate is converted by the liver back to glucose
- Functions of glutamine in the body?
- Glutamine is used in pyrimidine synthesis and as the primary carrier of NH3 in the blood.
- What do you need to make carbamoyl phosphate?
- CO2 and NH3 which comes from glutamate. The enzyme is carbamoyl phosphate synthase 1. You also need 2ATP - 2ADP
- What do you need to make urea?
- Carbamoyl phosphate is converted to citrulline which then accepts aspartate and uses another ATP - AMP. The urea is released from arginine to ornithine.
- How many phosphates are needed to make urea?
- 2ATP - ADP (carbamoyl phosphate formation). ATP - AMP to form argininosuccinate.
- What enzyme is needed to make N-Acetylglutamate?
- N-acetylglutamate synthetase (Acetyl CoA and glutamate)
- Why do you need N-acetylglutamate?
- N-acetylglutamate is a cofactor required for carbamoyl phosphate synthetase 1 (CPS1)
- What controls the urea cycle and how?
- Arginine because it controls the formation of N-acetylglutamate which is a cofactor required for carbamoyl phosphate synthetase 1 (CPS1)
- What is the problem with adding aspartate into the urea cycle? What is the solution?
- Aspartate is made from oxaloacetate with AST and this reduces the TCA cycle quantities of OAA. Solution: Fumarate is a byproduct of the conversion of argininosuccinate to arginine, this replaces the OAA in the TCA cycle
- Which enzyme is deficient in: Citrullinemia, Argininosuccinic aciduria and Arginemia
- Argininosuccinate synthetase, Argininosuccinate lyase and Arginase
- What additional compound is needed for these 3 enzymes: Glutamate dehydrogenase, Glutamine synthetase and Glutaminase?
- GluDH: NADPH or NADH
- How do sulfur drugs work?
- They contain sulfanilamide which is an analogue of PABA and prevent bacterial production of folic acid.
- 2 drugs that block dihydrofolate reductase?
What does a deficiency in folic acid cause?
- Aminopterin and methotrexate.
Neural tube defects and megaloblastic anemia.
- 3 uses of THF carbon transfer?
- 1) Production of methionine from homocysteine. 2) Purine production. 3) Conversion of dUMP to dTTP.
- What is the precursor to serine? How does serine relate to THF? What cofactor is required?
- 3-Phosphoglycerate. Serine is able to donate a carbon group to THF to form 5,10 methylene THF. In the process, glycine is formed. Pyridoxine
- What is the precursor to glycine? Name 2 ways that glycine relates to THF? What cofactor is required?
- Serine. 1)Glycine can add a carbon group to THF to form 5,10 methylene-THF like serine did. This results in complete breakdown of glycine. Cofactor: NAD. 2) Glycine can be deaminated to formic acid which can donate to THF.
- How is histidine related to THF?
- The breakdown of His yields a compound called N-formimino-L-glutamate (FIGLU). This releases glutamate, and FIGLU transfers a 1 carbon unit to THF to form 5-formimino-THF
- Why is histidine glucogenic?
- Because when it is converted into FIGLU, glutamate is released
- How does the FIGLU test work?
- When folic acid is deficient, if you provide the individual with histidine FIGLU will build up and be excreted because there is no THF to accept the carbon group
- Name the 5 compounds that can add carbons to THF
- Serine, glycine, purines, histidine and formic acid.
- What are the oxidation states of THF?
- 5-methyl (CH3). 5,10 Methylene (CH2). 5,10 Methenyl (CH alkene). 10-Formyl (C=O)
- How do we make Methionine?
- We use 5-Methyl THF and add a carbon to homocysteine. B12 IS REQUIRED FOR THIS REACTION!
- What is the relationship between B12 and folic acid? What happens with B12 deficiency?
- Both B12 and 5-methyl THF are required to convert homocysteine into methionine.
The formation of 5-methyl THF from 5,10 Methylene THF is irreversible. If B12 is deficient then 5-methyl THF cannot be converted back to THF. The THF is trapped as 5-methyl THF (called the methyl trap)
- Why is methionine an essential aa?
- Although we can synthesize Met from homocysteine, there isn't a net increase. The homocysteine comes from met and makes met.
- How do we form SAM? What are the byproducts after SAM has donated carbons?
- Hydrolyze ATP-AMP and add AMP to methionine. SAM loses a carbon and the AMP and so homocysteine is released.
- Why is cysteine a non-essential aa?
- Because it can be made by adding homocysteine to serine.
- Name 3 functions of methionine?
- 1) It is part of proteins
2) It can be converted into cysteine via homocysteine + serine
3) It can donate carbons as SAM.
- What is the enzyme defect in homocystinuria? What is it's normal function?
- Cystathionine B-synthase. It adds homocysteine to cysteine to form L-cystathionine which is then converted into cysteine.
- Why is homocysteine both glucogenic and ketogenic?
- The breakdown of homocysteine with CBS produces cysteine (glucogenic) and propionyl-CoA (ketogenic)
- 2 compounds we must know that SAM methylates?
- Nepi - Epi
Choline - Phosphatidylcholine
- How would you treat homocystinuria?
- Betaine adds to homocysteine to form methionine thus reducing the pools of homocysteine. Betaine actually comes from the breakdown of choline
- Name 2 ways to make methionine?
- 1) Use 5-methyl THF to add carbons to homocysteine.
2) Use betaine + homocysteine
- Why is Phe essential but Tyr non-essential? When does Tyr become essential?
- Tyrosine is made from Phe with Phenylalanine Hydroxylase. When someone has PKU, they are unable to convert Phe-Tyr and it becomes essential.
- What is the molecular difference btw Phe and Tyr? What enzyme and cofactor caused this?
- Tyr has an additional OH on the benzene ring. Phenylalanine hydroxylase used tetrahydrobiopterin to add OH group to tyrosine.
- What causes classic PKU? What about malignant PKU?
- Classic PKU is caused by a deficiency in phe hydroxylase converting Phe-Tyr. Malignant PKU is caused by a deficiency in BH4 which is the cofactor required for this reaction and others.
- Why is tyrosine both glucogenic and ketogenic?
- Because it's final breakdown products are fumarate (glucogenic) and acetoacetate (ketogenic)
- What causes alkaptonuria? Discuss reaction and enzyme deficiency?
- Alkaptonuria is caused by a deficiency in homogentisic acid oxidase which breaks down homogentisate an intermediate in tyrosine metabolism. Alkaptonuria is black urine due to increased amounts of homogentisic acid.
- What can you make with tyrosine?
- Dopa, Nepi, Epi, Melanin, T3 and T4.
- What enzyme deficiency causes albinism?
- Tyrosinase which converts tyrosine into dopa quinone which is then converted into melanin.
- What can you make with Tryptophan? Why is it glucogenic and ketogenic?
- Serotonin and Nicotinamide.
Alanine (glucogenic) and acetyl-CoA (ketogenic).
- What is the rate limiting enzyme of catecholamine synthesis?
- Tyrosine hydroxylase which converts tyrosine into L-DOPA.
- What is the molecular difference between all the compounds of catecholamine synthesis?
- 1) Tyrosine to LDOPA add an OH on the phenol ring
2) LDOPA to DOPA take the COO off the amino acid terminal
3) DOPA to NEPI add OH to the carbon off the phenol ring
4) NEPI to EPI add CH3 to amino end.
- Name the sequence of enzymes in catecholamine synthesis
- Tyrosine hydroxylase, DOPA decarboxylase, dopamine hydroxylase and phenyl-ethanolamine-N-methyl transferase
- What coenzymes does dopamine hydroxylase require?
- Cu2+ and ascorbate. The function of the ascorbate is to reduce the Cu2+ back to Cu+
- Name 2 things different about the conversion of Nepi to Epi
- 1) The enzyme which does the conversion (phenylethanolamine N-methyl transferase) is only found in the cytoplasm so the Nepi has be taken out of the vesicle and converted into Epi and then repackaged.
2) SAM is involved in adding a methyl group to Epi.
- What does MAO do? What coenzyme does it need?
- It breaks down Nepi/Epi into 3,4-Dihydroxymandelaldehyde. FADH2.
- What COMT do? What coenzyme does it use?
- Catechol-O-methyl transferase adds methyl groups to the OH on Nepi/Epi for excretion. It uses SAM the methyl donor man and the end product is vanillyl mandellic acid.
- How do you make serotonin?
- Convert tryptophan into 5-hydroxy-1-tryptophan with trp hydroxylase and then convert 5-hydroxy-1-tryptophan into 5-hydroxy-1-tryptamine with aa decarboxylase.
- What is similar between tyr,phe and trp hydroxylases?
- They all use BH4, NADPH and O2. They are all affected in malignant PKU
- How is serotonin broken down?
- Using MAO, serotonin is oxidized and then aldehyde dehydrogenase (replaces COMT) produces the final product 5-hydroxyindole-acetic acid.
- Where does 5-hydroxy-indole-acetic acid come from?
- It is the final product in the breakdown of serotonin.
- What does melatonin come from? What cofactor is used in the process? What reactions take place?
- Melatonin comes from serotonin and SAM is used in the reactions. Serotonin is acetylated and methylated.
- How do you make GABA? How is it broken down?
- Use glutamate decarboxylase and convert glutamate into GABA. It is broken down into succinate which feeds into the TCA cycle.
- What is different about glutamate decarboxylase compared to the other decarboxylase enzymes?
- It requires B6
- How do you make histamine? How it is broken down?
- Use histidine decarboxylase to convert histidine into histamine. By MAO and DAO (diamine oxidase)
- Which Vitamin can be synthesized from an aa precursor?
- Trp can be converted into niacin (B3)
- What is the difference btw a porphyrin and a porphyrinogen?
- Porphyrins are colored because they have unsaturated carbon bridges. Porphyrinogens are not colored because they have saturated bridges. Think heme is colored and it has porphyrins
- Which is saturated methene bridges on porphyrin or methylene bridges on porphyrinogen. Which are formed first?
- Methene is same as methenyl these are alkenes so unsaturated. Methylene is not an alkene so saturated? Porphyrinogens with saturated bonds are formed first.
- What is the difference btw uroporphyrinogen, coproporphyrinogen and protoporphyrinogen? What is the order they are made?
- Uro has 4 AP groups (acetyl-proprionyl). Copro has 4 MP groups (methyl-proprionyl) and Proto has 2MP and 2MV (methyl-proprionyl and methyl-vinyl)
Uro, then copro then proto.
- Which isomer in heme synthesis is active, Type I or Type III? What is the difference?
- Type III is the active compound, type I is inactive. The difference is the reversal of side groups around gamma bridge.
- Which cause photodamage porphyrins or ogens? When would this happen? How does it happen? How does it present?
- The porphyrins can absorb light because they are colored, these are the ones that cause damage.
If you have porphyrias which is a deficiency in enzymes.
Porphyrins damage cell membranes and lysosomal membranes.
Presents with itching, edema, erythema and ulceration.
- What is the rate limiting step in heme synthesis? Where is this enzyme found?
What coenzyme does it need?
- ALA synthase joining glycine to succinyl-CoA to form Aminolevulinic acid.
ALA synthase is found in the mitochondria but ALA is transported into the cytosol.
- Where is aminolevulinic acid found and what do we do with it?
- ALA is found in the cytosol. 2 ALA are added together to form porphobilinogen
- What is Porphobilinogen and what do we need to make it? What do we do with it?
- PBG is 1 pyrrole ring made from 2 ALA's. We need the enzyme ALA dehydratase
We add 4PBG's together to form hydroxymethylbilane with the enzyme PBG deaminase
- What is hydroxymethylbilane?
- It is 4 PBG pyrrole rings attached together to form a linear precursor to heme.
- What do the following enzymes do?
- ALA synthase makes ALA from glycine and succinyl-CoA. ALA dehydratase makes PBG out of 2 ALA.
PBG deaminase makes hydroxymethylbilane out of 4 PBGs.
- What does uroporphyrinogen III cosynthase do?
What happens if it is deficient?
- Uro'gen III cosynthase converts hydromethylbilane into uro'gen III. W/o it hydroxymethylbilane is converted into uro'gen Type I which is inactive.
- How do I make coproporphyrinogen?
- Use Uro'gen decarboxylase to convert all acetic groups into methyl groups (AP to MP)
- When do the ogen's in heme synthesis make it back into mitochondria?
- Going from coproporphyrinogens to protoporphyrinogens using the enzyme copro'ogen oxidase moves them into mitochondria.
- What is the first step in heme synthesis when the bridge carbons change saturation? Where does this happen? What's the significance?
- Going from proto'ogen IX to protoporphyrin IX with the enzyme proto'ogen oxidase.
In the mitochondria.
Protoporphyrin IX is now colorful and can cause damage.
- What is hemin and what is it's function? Name 3 ways that it performs this function?
- Hemin is the auto-oxidation product of free heme and it controls ALA synthase and therefore heme synthesis in normal cells. NOT IN RBC's
1) It is an allosteric inhibitor of ALA synthase
2) It decreases transcription of ALA synthase
3) It prevents ALA from being transported into the mitochondria where it does it's job.
- How do drugs like phenobarbitol affect the liver?
- They increase the enzymes which produce heme thereby revving up the Cp450 system.
- How is ALA synthase different in RBC's?
- It is not the rate limiting enzyme. It is not inhibited by hemin. It's activity is tied in with cell maturation and division.
- Why do normal people not have porphyrin deposits in the skin?
- Porphyrin is normally transported bound to albumin but if levels are increased then it becomes free and deposits in the skin.
- How does lead poisoning work? Treatment? What is it specific for?
- Lead poisoning inhibits ALA dehydratase and ferrochelatase. This increases ALA, proto IX and copro III. You treat with EDTA-Ca2+, lead replaces the Ca2+ on the drug and is excreted. LEAD POISONING AFFECTS RBC'S MORE THAN THE LIVER.
- How is heme broken down to indirect bilirubin? (enzymes, coenzymes etc)
- Using heme oxygenase, the a-bridge carbon is hydroxylated. This step uses NADPH and O2. This a-bridge then spontaneously forms two ketones, this is biliverdin. Biliverdin reductase then uses NADH to reduce the Y-bridge to a saturated methylene, this is indirect bilirubin.
- What is the rate limiting step in heme breakdown?
- Heme oxygenase converting heme into biliverdin.
- How does aspirin affect free bilirubin levels?
- Aspirin bumps indirect bilirubin off of albumin
- What was the point of leaving 2 proprionyl side groups on protoporphyrinogen?
- When you go to conjugated bilirubin during excretion, it is these side groups that allow for attachment of UDP-gluronic acid.
- What enzyme conjugates bilirubin? How does it do this?
- UDP-glucuronyl transferase (UGT) takes UDP-glucuronic acid (derived from glycolysis) and attaches it to the proprionyl side groups of unconjugated bilirubin one at a time. This bilirubin diglucuronide is soluble and is referred to as direct bilirubin.
- Where do urobilin and stercobilin come from?
- Bacteria act on the sugar residues of conj. bilirubin in the gut and convert it into urobilin which is reabsorbed and excreted by the kidney. Sterobilin is the same as urobilin except it is excreted in the feces.
- Why are they called direct and indirect bilirubin? What is the name of the reaction?
- The Van Den Bergh reaction is a dye which reacts with bilirubin. It reacts directly with conj. bilirubin because it isn't bound to albumin. Methanol must be added for the dye to react with unconj. to remove the albumin. Therefore, unconj is indirect bilirubin.
- What is cholestasis?
- Increased levels of direct bilirubin in the plasma
- Why do infants get jaundice?
- Immature UGT to conjugate bilirubin and increased RBC hemolysis. They also do not have ligandin (initially) which is required for the liver to take up bilirubin.
- What hepatotoxic drugs cause jaundice?
- Carbon tetrachloride, iproniazid and halothane
- What drugs increase conjugated bilirubin?
- Oral contraceptives, steroids and chlorpromazine
- Why don't you give sulfur drugs or aspirin to newborns?
- Both drugs displace bilirubin from albumin causing kernicterus.
- What is wrong in patients with Crigler-Najjar and what is the difference between I and II?
- Crigler-Najjar I is a complete lack of UGT preventing the conjugation of bilirubin. II is a partial deficiency which prevents diglucuronide from forming.
- What is Gilbert's disease?
- Caused by a mutation in the promoter region of the UGT1 gene causing decreased expression. Mild jaundice
- What is Dubin-Johnson?
- Conjugate hyperbilirubinemia, mild jaundice
- What is ELSI?
- Ethical, Legal, Social Implications of the Human Genome Project. 5% of HGP budget set up for this program.
- What is law of segregation? What is law of independant assortment?
- Segregation: Two alleles of the same gene will separate into 2 separate gametes. Independent: These two alleles will separate independantly of one another.
- What is sex-influenced inheritance? Example
- When a phenotype presents more in one sex than the other. Hemachromatosis presents more in men because they don't menstruate
- What is a male pseudohermaphrodite? Example
- An XY individual with female external genitalia. Example: Testicular feminization in individuals with a testosterone receptor deficiency.
- What is a female pseudohermaphrodite? Example
- XX individual with male external genitalia. Example: CAH increases the production of androgens from the adrenal cortex.
- 4 reasons why women present with an X-linked recessive disorder when dad seems to be normal?
- Xo Turner's
Mother is homozygote diseased
Mutation in the normal X allele
It's not the dad
- 4 types of genetic mutations
- Chromosomal abnormalities
Single gene deletions
- Which one includes the centromere, peri or paracentric inversions?
- Pericentric includes the centromere, paracentric does not.
- What is a Robertsonian Translocation?
- Fusion of the centromeres of two acrocentric chromosomes.
- Which is the most common chromosome abnormality, aneuploidy or euploidy?
- Aneuploidy and most often results from non-disjunction.
- 2 Assumptions of Hardy-Weinberg law. What does the law state?
- Random mating and equal viability of 3 genotypes (no natural selection, no inbreeding).
Given those assumptions, the frequency of alleles will remain the same through generations.
- What are the consequences of inbreeding?
- Increased frequency of AR diseases, birth defects, stillbirths, metabolic disorders and miscarriages.
- What genetic inheritance patterns do inborn errors of metabolism all follow?
- Autosomal recessive.
- Name the 3 reasons why we began screening for PKU?
- We understood the nature of the disease and how to treat.
We had the analytical ability to screen a lot of people.
Economics drove it (cheaper to screen than to deal with affected individuals)
- Name the 4 justifications for newborn screenings?
- The disease is serious
We are able to diagnose it with a test
Economics favor the screening
We are able to offer them treatment options
- What is TMS? Name 4 things it does better
- Tandem mass spectroscopy allows us to screen a very large number of individuals compared to previously.
It is automated, highly specific, measure aa and acylcarnitines from single blood spot. It can also detect inborn errors of metabolism of aa's, fatty acids and organic acids.
- Name 1 disorder that brought TMS to the forefront?
- MCAD - Medium chain acyl dehydrogenase
- Example of a polygenic trait?
- Examples of multifactorial congenital disorders
- Cleft lip/palate, cardiac defects, neural tube defects, pyloric stenosis.
- Examples of multifactorial pediatric onset disorders
- Asthma, epilepsy, obesity
- Examples of adult onset multifactorial disease
- Coronary artery disease, hypertension, obesity, diabetes mellitus etc.
- Compare the incidence of multifactorial traits with other disorders?
- Multifactorial traits tend to show an incidence higher than normal population but lower than single gene disorder.
- Name the 3 types of cancer genes?
- Tumor suppressor gene (need 2 mutations for cancer).
Proto-oncogene (need 1 mutation)
DNA repair gene (need 2 mutations)
- How did the mutations in Burkitt's Lymphoma and Chronic Myelogenous Leukemia occur?
- Both are examples of translocations
Burkitt's - myc IgH
CML - abl/bcr
- What does the protein product of bcr/abl do?
- It is a tyrosine kinase which constitutively phosphorylates proteins to stimulate cell growth
- What is Imatinib? How does it work and why would you use it?
- Imatinib is a drug to treat CML. It replaces ATP on the bcr/abl protein and thereby suppresses it.
- What usually causes a Hereditary oncogene syndrome?
- It is usually a base pair change as opposed to a translocation.
- Name 4 things different between sporadic cancers and those caused by BRCA1 and BRCA2
- 1)BRCA1/2 present < 45yrs. Sporadic is later.
2)1/2 are bilateral. Sporadic is unilateral
3)1/2 have increased risk for ovarian cancer (slight in 2). Sporadic does not
4) 1/2 positive family history. Sporadic not
- Which chromosomes are BRCA1 and 2 on?
- BRCA1 on 17. BRCA2 on 13
- Which cancers does the Regional Hereditary Cancer Evaluation Program test for?
- Breast, ovarian, colon, medullary thyroid cancers and others.
- Name 6 features that suggest hereditary cancer
- Early onset, autosomal dominant presentation, several affected relatives, rare cancers, bilateral or multifocal and multiple primary cancers.
- When should genetic testing be considered? (4 things)
- When the test is available
When it looks like there is an inheritance pattern
When you can help the patient if diagnosed
When they want the test
- When would you do a nuchal translucency test? What can it detect?
- You would do it during the first trimester. It can detect 91% of down syndrome, 97% of trisomy 18, aneuploidy and cardiac defects
- What do the levels of PAPP-A and BHCG look like with down syndrome and trisomy 18?
- BHCG is increased with Down syndrome and PAPP-A is decreased. Both are decreased with trisomy 18
- What markers are measured in a second trimester screen? What should you adjust these markers for? What is the most common reason for a positive test?
- BHCG, estriol and AFP. Maternal age, race and ethnicity.
Mis-dated pregnancy is the most common reason for a positive test.
- What do the levels of estriol, BHCG and AFP look like with: Open neural tube defects, trisomy 18, down syndrome?
- Open NT defects have increased AFP but normal other markers.
Down has increased BHCG but decreased other markers.
Trisomy 18 has all the markers decreased.
- What is the quad test? Which disorder does it detect for better?
- Estriol, BHCG, AFP are the normal markers. Quad test adds inhibin-A and it is more specific for Down syndrome.
- What is Chorionic villus sampling? When would you do it and what could it detect?
- It is taking a biopsy of the chorionic villus to detect for fetal aneuploidy. It is done in the first trimester 12 weeks.
- When would you do an amnio and what would it detect?
- At 15 weeks and it will detect fetal aneuploidy
- What is the difference btw the molecular structure of phoshodiester and phosphoanhydride bonds?
- Phosphodiesters have a carbon on either side of the phosphate attached to the oxygen. Phosphoanhydrides are phosphates with oxygens in between.
- Give 3 examples of compounds that have acyl-phosphoanhydride bonds
- Creatine phosphate, phosphoenolpyruvate and 1,3-BPG.
- What are 4 things different btw NAD and FAD
- 1) NAD can transfer 2e, FAD both 1 and 2e
2) NAD let's go of enzyme, FAD is tightly bound
3)NAD yields 2.5ATP, FAD 1.5ATP
4) NAD converts alcohols to aldehydes or ketones. FAD converts alkanes to alkenes.
- What type of ring does glucose form? Which carbons are involved?
- A pyranose ring with carbons 1 and 5 involved. Carbon 1 is the aldehyde.
- What type of ring does fructose form? Which carbons are involved?
- Furanose ring between 2nd and 5th carbon. 2nd carbon is ketone.
- What is the difference btw the alpha and beta forms of glucose?
- The alpha form has the 2' OH on the opposite side of the 6'C. The beta form is the same side.
- What is the difference btw a reducing sugar and a non-reducing sugar?
- Reducing sugar has a free anomeric carbon to react with additional monomers. Non-reducing sugar has both anomeric carbons tied up in a bond.
- Name 3 carbohydrate derivatives and their functions
- Sugar acid: Glucuronic acid used to conjugate bilirubin
Sugar alcohol: Sorbitol/glucitol causes osmotic damage
Sugar amine: Used in glycoproteins.
- What is the difference between GA3P and DHAP?
- The ketone is located on the end of the molecule with GA3P whereas it is in the middle of the molecule with DHAP
- When are the ATP used in glycolysis?
- Going from glucose to G6P and from F6P to F1,6BP
- Where is the NADH generated in glycolysis and what enzyme is involved?
- Going from GA3P to 1,3BPG. The enzyme involved is glyceraldehyde-3-phosphate dehydrogenase.
- Where are the ATP generated in glycolysis?
- Going from 1,3BPG to 3PG and going from PEP to pyruvate
- What helps the thermodynamically unfavorable reaction of GA3P to 1,3BPG move?
- Mass action because the next reaction in the series (1,3BPG to 3PG) is very favorable
- Why does PEP have such high energy?
- Because it contains an acyl phosphate and it is able to tautomerize when the phosphate is cleaved.
- Which enzymes of glycolysis are controlled?
- Hexokinase (glucose - G6P)
Phosphofructokinase (F6P - F1,6BP)
Pyruvate kinase (pep - pyruvate)
- What glut transporter is found on liver and kidney? How is it different?
- GLUT2. It transports glucose both ways and it not insulin dependent.
- What glut transporter is found on muscle and other cells? How is it different?
- GLUT4 and it only transports glucose into cells. It is insulin dependent.
- List 5 things different btw hexokinase and glucokinase
- 1) Hexokinase is found in most cells, glucokinase only in liver/pancreas
2) Hex has a low Km so it functions at low BGL but doesn't steal glucose at high BGL. Glucokinase has high Km so when BGL increases, it responds exponentially.
3) Hexokinase is inhibited by G6P, Gluco is not.
4) Hexokinase will phosphorylate any 6C sugars, glucokinase is specific for glucose
5)Can induce transcription of glucokinase with insulin, not so with Hex.
- What is metabolic cycling? What enzymes are involved?
- The reaction of F6P to F1,6BP is running in both directions all the time to keep the pathway ready to go.
Enzymes involved are PFK and F1,6BPASE
- What 5 cofactors are needed by pyruvate dehydrogenase? What type of reaction is it?
- Thiamine, FADH2, NADH, CoASH and Lipoic acid. Oxidative decarboxylation.
- What is the function of the right side of the TCA cycle? Reversible or irreversible?
- It is oxidative decarboxylation. It cuts off the 2CO2 added by acetyl-CoA and generates 2NADH by oxidizing citrate.
- Which enzyme of the TCA cycle is identical to pyruvate dehydrogenase?
- α-ketoglutarate dehydrogenase
- Which enzyme catalyzes the only substrate level phosphorylation of the TCA cycle?
- Succinyl-CoA synthetase generates GTP converting succinyl-CoA to succinate.
- What is unique about succinyl-CoA synthetase?
- It generates GTP from substrate level phosphorylation (converts succinyl-CoA into succinate). More importantly, it is the only step on the right side of the TCA not the same as fatty acid synthesis.
- Name 4 things special about succinate dehydrogenase
- 1) It is the only enzyme of the TCA cycle that uses FAD.
2) It is bound to the inner mitochondrial membrane
3) It is bound to FAD
4) It is in both the TCA cycle and oxidative phosphorylation
- List the types of reactions of the TCA cycle in order
- Isomerization, oxidative decarboxylation, oxidative decarboxylation, substrate level phosphorylation, oxidation, hydration, oxidation
- What are the controls on pyruvate dehydrogenase?
- Acetyl-CoA and NADH allosterically inhibit it. Ca2+ activates PDH phosphatase which activates PDH by dephosphorylation. Ca2+, ADP and pyruvate all inhibit PDH kinase which activates PDH.
- What are allosteric control on pyruvate dehydrogenase?
- Acetyl CoA and NADH
- What are phosphorylation controls on pyruvate dehydrogenase?
- Ca2+ stimulates PDH phosphatase to dephosphorylate. Ca2+, ADP and pyruvate all inhibit PDH kinase to allow dephosphorylation.
- What reactions are points of control for the TCA cycle?
- Citrate synthase, isocitrate dehydrogenase and α-ketoglutarate dehydrogenase.
- How does NADH control the malate dehydrogenase reaction? What do the levels of OAA look like compared to malate?
- Malate + NAD --- OAA + NADH.
It controls the equilibrium, if NADH increases then this reaction goes back to malate.
The levels of OAA are low and malate are high, to make reaction favorable.
- How do the levels of OAA control the citrate synthase reaction?
- OAA + Acetyl-CoA ---- Citrate
At equilibrium, there are very low levels of OAA, slight increases in OAA are rapidly pushed to citrate.
- What controls the citrate synthase reaction?
- Succinyl-CoA and citrate (feedback inhibition)
- Which enzymes in TCA cycle does NADH control?
- Citrate synthase, isocitrate dehydrogenase and α-ketoglutarate dehydrogenase
- What are the controls of isocitrate dehydrogenase?
- ADP and Ca2+ stimulate it. NADH and ATP (from GTP succinyl-CoA reaction) inhibit it
- What are the controls on α-ketoglutarate dehydrogenase?
- Ca2+ stimulates it. Succinyl-CoA inhibits it.
- Which reactions in the TCA cycle does Ca2+ control?
- It stimulates α-ketoglutarate dehydrogenase and isocitrate dehydrogenase
- Which reactions in the TCA cycle does Succinyl-CoA control?
- α-ketoglutarate dehydrogenase and citrate synthase
- Which reaction in the TCA cycle does ATP from GTP substrate level phosphorylation control?
- Isocitrate dehydrogenase
- What enzymes can acetyl-CoA inhibit?
- It inhibits pyruvate dehydrogenase and exits the mitochondria through citrate to inhibit pyruvate kinase.
- What enzyme is required for acetyl-CoA to inhibit pyruvate kinase?
- In order for Acetyl-CoA to exit the mitochondria, it is converted to citrate. Citrate leaves the mitochondria to the cytosol where ATP-citrate lyase cuts it up into OAA and citrate.
ATP-CITRATE LYASE IS NEEDED.
- What are the 3 uses of the enzyme ATP-CITRATE lyase?
- It cuts citrate into Acetyl-CoA for inhibition of pyruvate kinase and for fatty acid synthesis. It also produces OAA in the cytosol for gluconeogenesis. This enzyme basically switches the cell to store glucose and fats when energy is high.
- What is the bifunctional enzyme? What's it's function?
- Phosphofructokinase 2 and F2,6Bisphosphatase.
It creates and breaks down F2,6BP which is an allosteric controller of PFK1 and F1,6BPase
- How is the bifunctional enzyme controlled?
- F6P activates PFK2 to make more F2,6BP and inhibits the F2,6BPASE.
cAMP dependent kinases phosphorylate the enzyme thereby inhibiting PFK2 and activating F2,6BPASE. This pushes the cell to production of glucose.
- What controls PFK1?
- F2,6BP activates it.
AMP activates it.
Citrate and ATP inhibit it.
- What controls F1,6BPASE?
- F2,6BP inhibits it and AMP inhibits it.
- True/False: The bifunctional enzyme in muscle responds to phosphorylation/dephosporylation?
- FALSE. Only the liver isoform responds.
- What do glucagon and epi do to the bifunctional enzyme? Do they work in all cells?
- Glucagon and Epi increase cAMP which phosphorylates the enzyme. This activates F2,6BPASE to make more glucose and inhibits PFK2.
Glucagon only works on the liver. Epi stimulates glycolysis in normal cells but gluconeogenesis in the liver.
- BIG PICTURE, what controls the PFK reaction step?
- Citrate controls glycolysis here. The ATP/AMP ratio controls this step and the bifunctional enzyme controls this step.
- What does anaplerotic mean?
- It means using other pathways to replenish TCA cycle intermediates
- What 3 reactions do we need to reverse in order for gluconeogenesis to occur?
- Hexokinase --- Glucose-6-Phosphatase
Phosphofructokinase --- F1,6BPASE
Pyruvate kinase --- Pyruvate carboxylase and phosphoenolpyruvate carboxykinase (PEPCK)
- What enzyme is needed to convert pyruvate into OAA? What else is used? Where is it found?
- Pyruvate carboxylase.
It uses 1ATP and CO2
It is found in the mitochondria (LIVER ONLY)
- What coenzyme does pyruvate carboxylase require?
- What enzyme is needed to convert OAA into PEP? Where is it found? What else is used?
- Phosphoenolpyruvate carboxykinase (PEPCK).
It is found in both mitochondria and cytosol but only in the liver.
USES 1 GTP
- Name 2 enzymes that acetyl-CoA stimulates?
- Pyruvate carboxylase to convert pyruvate into OAA
Citrate synthase (through equilibrium)
- Where are all the NTP consumed when making glucose?
- 1 ATP pyr --- OAA
1 GTP OAA --- PEP
1 ATP 3PG --- 1,3BPG
This is all x2
- Where is NADH used in gluconeogenesis?
- 1 NADH 1,3BPG --- GA3P
This is x2
- How many NTP and NADH are used for gluconeogenesis from pyruvate? What about from PEP?
- 6 NTP and 2 NADH from pyruvate
2 ATP and 2NADH from PEP.
- How can insulin and glucagon control gluconeogenesis through gene transcription?
- Insulin downregulates the expression of PEPCK. Glucagon upregulates it's expression.
- What is the Cori cycle?
- It is a way to get glucose out of muscle in the form of lactate so it can be transported to the liver for gluconeogenesis.
- What is the control of hexokinase? What about glucokinase?
- Low G6P stimulates it
High G6P activates it
THESE DO NOT AFFECT GLUCOKINASE
- What controls pyruvate kinase (6 things)?
- F1,6BP activates it
AMP activates it
Acetyl-CoA inhibits it
ATP inhibits it
Alanine inhibits it
cAMP dependant kinases phosphorylate it to inhibit
- What is the point of the malate/aspartate shuttle?
- To move NADH/NAD in and out of the mitochondria for oxphos and move OAA out of the mitochondria for gluconeogenesis.
- Which way does the malate/aspartate shuttle go during glycolysis? (malate to OAA in cytosol or reverse)
- In cytosol, it will go from OAA to malate. The malate will be transported in and then converted back to OAA. This will generate NADH inside mitochondria. NOTE: Aspartate can be used instead if you like
- Which way does the malate/aspartate shuttle go during gluconeogenesis? (malate to OAA in cytosol or reverse)
- During gluconeogenesis, OAA will go to malate in the mitochondria, the malate will be transported out and converted back to OAA. This will generate NADH in cytosol. NOTE: Aspartate can be used instead if you like. JUST THINK, YOU NEED MORE OAA IN CYTOSOL FOR GLUCONEOGENESIS
- What are the similarities between succinate dehydrogenase and glycerol-3-phosphate dehydrogenase?
- Both use FAD as a cofactor
Both are bound to the mitochondrial membrane
Both take part in oxphos.
- Which way does the G3P shuttle run during glycolysis? (G3P to DHAP in the cytosol or reverse)
- It goes from DHAP to G3P in the cytosol to regenerate NAD for glycolysis. The G3P is flipped into the mitochondria where it is converted back into DHAP and FADH2 is generated.
- What is the problem with the glycerol-3-phosphate shuttle?
- You lose 1 ATP getting the hydrogens transferred from NADH into the mitochondria because G3P dehydrogenase uses FADH2
- Name 2 things the pentose phosphate shunt is used for?
- The pentose phosphate shunt generates R5P for pyrimidine synthesis. It also generates NADPH which will reduce glutathione once it has been oxidized.
- What is the rate limiting enzyme for the pentose-phosphate shunt? What does it catalyze?
- Glucose-6-Phosphate dehydrogenase.
It converts glucose-6-P into R5P and generates 2NADPH.
- What is the main point of the pentose phosphate shunt?
- To generate NADPH so that glutathione can be regenerated
- What does glutathione do? What helps it do this job?
In what form is it most helpful?
- It is an antioxidant. It has cysteine residues which are oxidized when exposed to harmful cellular oxidants.
GSH form --- GSSG when it reacts.
- What enzyme allows glutathione and NADPH to interact?
- Glutathione reductase oxidizes NADPH and reduces GSSG back to GSH.
- Why is the pentose phosphate shunt not a dead end?
- Because R5P can be converted into F6P and GA3P which can feed back into glycolysis.
- What is the point of having branches in glycogen? Which are branched bonds, which are straight bonds?
- To allow for rapid degradation.
- What is glycogenin? What does it do?
- Glycogenin is a self-glycosylating protein which begins the synthesis of glycogen by creating a-1,4 bonds
- What do the following enzymes do?
- Glycogen synthase forms α-1,4-glycosidic bonds.
Glycogen phosphorylase breaks down α-1,4-glycosidic bonds
Branching enzyme forms α-1,6-glycosidic bonds
Debranching enzyme breaks down α-1,6-glycosidic bonds
- What is the difference between phosporylytic cleavage and hydrolytic cleavage? Which enzyme does which in glycogen breakdown?
- Phosphorylytic cleavage uses phosphoric acid, yields G1P and it catalyzed by glycogen phosphorylase.
Hydrolytic cleavage uses water, yield FREE glucose and is catalyzed by debranching enzyme.
- What molecule is actually added to glycogen? Where does it come from? What enzyme is involved?
G1P + UTP --- UDP-glucose
- Where do the 2 phosphate in UDP glucose come from?
- One comes from G1P, the other comes from UMP
- How does glycogen branching work? How many residues are between branches? How many is the minimum? What percentage of glycogen is branched?
- Branching enzyme takes a 7 residue piece from the main chain and attaches it to a 6'OH group on the main chain.
8-14 residues between the branches usually but minimum is 4. About 10% of glycogen is in the α-1,6 form.
- Which end of the glycogen molecule is glucose added?
- Non-reducing end
- How does debranching of glycogen work?
- Glycogen phosphorylase cuts down the branch to about 5 units left. Debranching enzyme then transfers 4 residues to the main chain and cuts the α-1,6-glycosidic bond to yield FREE GLUCOSE
- How much of glycogen breakdown is free glucose and how much is G1P?
- 10% free
- What are the allosteric controls of glycogen synthase?
- ATP, G6P and free glucose stimulate this enzyme
- What are the allosteric controls of glycogen phosphorylase?
- ATP, G6P and free glucose inhibit this enzyme. AMP stimulates it.
- How do cAMP dependant kinases affect glycogen metabolism?
- 1) Glucagon binds, cAMP dependant kinases become active
2) CADK's phosphorylate phosphorylase kinase, phosphoprotein phosphatase I (PPPI) inhibitor
3) Active phosphorylase kinase phosphorylates glycogen phosphorylase and activates it. It also phosphorylates glycogen synthase and inhibits it.
4) PPPI inhibitor binds PPPI and prevents it from dephosphorylating stuff.
- What are the control mechanisms of phosphorylase kinase?
- Ca2+ and AMP allosterically activate it to phosphorylate glycogen phosphorylase and break it down.
Phosphorylation by CADK's of phosphorylase kinase activates it
- How does insulin affect glycogen metabolism?
- 1) It activates phosphodiesterase which decreases cAMP levels.
2) It activates phosphoprotein phosphatase I (PPPI). PPPI dephosphorylates glycogen synthase (active), glycogen phosphorylase (inactive), phosphorylase kinase (inactive) and it's own inhibitor PPPI inhibitor (inactive)
- What targets do cAMP dependant protein kinases have? (5)
- Pyruvate kinase
- Name 5 things glucagon does to the cell?
- Activates gene transcription of PEPCK.
Inhibits transcription of pyruvate kinase
Breaks down glycogen
Stimulates gluconeogenesis in liver and glycolysis in muscle
- Name 5 things insulin does to the cell?
- Activates glut4 on muscle and adipose
Decreases transcription of PEPCK
Activates transcription of glucokinase in liver
Activates phosphodiesterase to decrease cAMP
Increases glycogen production
- Which inversions, paracentric or pericentric cause centromere problems?
- Although pericentric include the centromere, it is actually paracentric that cause additional centromeres or non at all.
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