ACS biochemistry

question

Describe the structural changes in hemoglobin that allow for cooperative binding of O2
answer

Binding of O2 in one subunit causes a conformational change in an adjacent subunit allowing O2 to bind
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Which amino acids in “a” would be charged at pH 7?
answer

Asp, Glu, Arg, His, Lys
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Which amino acids are negatively charged?
answer

Asp, Glu
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which amino acids are positively charged?
answer

Arg, His, Lys
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How are beta sheets stabilized in proteins?
answer

Hydrogen bonding between peptide backbone groups
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Does myoglobin show cooperativity in O2 binding? If not, what structural differences account for this?
answer

Myoglobin does not show cooperativity because it is monomeric
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What is a transition state inhibitor (how does its structure compare to the enzyme stubstrate?) how does its affinity for the enzyme compare to the enzyme’s substrate?
answer

Similar to the substrate; binds to the active site with greater affinity than the substrate
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would it be advantageous for these potential drugs to covalently bind to the enzyme? why or why not?
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Not advantageous because the urea cycle would shut down
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From a practical standpoint, would it be advantageous for these potential drugs to be less chemically stable than the substrate?
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No, because of shelf life and time to reach target
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In DNA, which bases hydrogen bond?
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A-T; G-C
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In each base pair, how many hydrogen bonds are there?
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A-T=2; G-C=3
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Which base-pair would require a higher temperature to destroy the hydrogen bonds?
answer

G-C
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Based on the mechanism of alkaline hydrolysis of RNA, why is DNA less susceptible to alkaline hydrolysis?
answer

DNA lacks the 2′ hydroxyl group
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What is the difference between a reducing and nonreducing sugar?
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Reducing sugars have a free anomeric carbon that in the linear form can reduce an oxidizing agent.
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what is a reducing monosaccharide?
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fructose or glucose
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what is a reducing disaccharide?
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lactose
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what is a nonreducing dissacharide?
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sucrose
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what is a nonreducing monosaccharide?
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all monosaccharides are nonreducing
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Why can’t the peptide WYLVP be glycosylated in a glycoprotein?
answer

because it does not contain N, S, or T which are sites of glycosation (attachment of a carbohydrate)
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Name three secondary messengers and what class of biomolecules they are derived from
answer

cAMP-nucleotide; IP3-lipid; DAG-lipid
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What reactions occur during stage one of glycolysis?
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aldolase, F6P
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What reactions occur during stage two of glycolysis?
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NADH formed, 3PG formed
question

name an allosteric regulator that can decrease glycolysis by inhibiting PFK
answer

ATP
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What enzymes are unique to glycolysis?
answer

hexokinase, PFK, pyruvate kinase
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what enzymes are unique to gluconeogenesis?
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glucose-6-phosphatase, fructose 1,6-biphosphatase, PEPCK carboxylase
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what are the corresponding enzymes in glycolysis and gluconeogenesis
answer

pyruvate kinase is the corresponding enzyme in glycolysis for PEPCK and pyruvate carboxylase
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what metabolic conditions can activate gluconeogenesis?
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low F6BP; high citrate; epinephrine/glucagon
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what are the products of the pentose phosphate pathway?
answer

NADPH, ribose
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List all the enzymes that use OAA as a substrate
answer

Pyruvate carboxylase, citrate synthase, malate dehydrogenase
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what reaction is catalyzed by the coenzyme TPP (thiamine/B1)?
answer

Oxidative decarboxylation
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What reaction is catalyzed by the coenzyme tetrahydrofolate (folic acid)?
answer

One carbon group transfer
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what reaction is catalyzed by the coenzyme pyridoxal-5-phosphate (b6)
answer

Amino group transfer
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what reaction is catalyzed by the coenzyme Cobalamin )B12)
answer

Alkylation
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What reaction is catalyzed by the coenzyme lipoamide
answer

Transfer of an acetyl group to CoA
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What is the chemiosmotic theory?
answer

Electron transport generates a proton gradient across the inner membrane due to H+ being pumped out; the energy released (proton motive force) when H+ returns to the matrix is used to power ATP synthesis
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What are ketogenic substrates degraded to?
answer

acetyl CoA or ketone bodies
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What are glucogenic substrates degraded to?
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pyruvate, alphaketoglutarate, succinyl CoA, fumarate, OAA
question

what is the equation to determine the number of cycles of B-oxidation of a saturated fatty acid?
answer

n/2-1
question

Describe what metabolic processes occur in the muscle and liver in the glucose-alanine cyvles during branched chain amino acid catabolism
answer

branched chain amino acids are degraded in the muscle and the NH3 is transported to the liver in the form of Ala. The liver uses the Ala for gluconeogenesis and the glucose is transported to the muscle for glycolysis.
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what is an antagonist?
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binds to a receptor and prevents a response by keeping agonist from binding
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what is an antagonist
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binds a receptor and causes a response
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Is transverse or lateral diffusion in a lipid bilayer least likely to occur?
answer

transverse
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If triglycerides and phospholipids are separated using TLC, what spot is more soluble (will be at the top)?
answer

tryglyceride; phospholipid will be less soluble so will not travel as far
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In a gel filtration column, what proteins elute the quickest?
answer

the larger proteins that have a higher kDa elute first
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what amino acid sequence is most likely to be in the core of a globular protein? why?
answer

ITFWLI; no charged amino acids and highest percent nonpolar
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an example of a sticky restriction enzyme?
answer

A CGTGA
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an example of a blunt restriction enzyme?
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ACG TGA
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What is the function of TPP in the pyruvate dehydrogenase component of the pyruvate dehydrogenase complex?
answer

oxidative decarboxylation of pyruvate
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what is the function of lipoamide in the dihydrolipoyl transacetylase portion of the pyruvate dehydrogenase complex?
answer

transfer of acetyl group to CoA
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what is the function of FAD in the dihydrolipoyl portion of the pyruvate dehydrogenase complex
answer

regeneration of the oxidized form of lipoamide

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