Biochemistry Practice Final Exam

Front 1

The _____ describes the relation between interatomic distances, electronic charge, solution dielectric and free energies.

Back 1

Van der Waals interaction

Front 2

Protein _____ defines the relation among subunits in a multisubunit lattice.

Back 2

Quaternary structure

Front 3

Protein _____ defines the amino acid sequence.

Back 3

Primary structure

Front 4

Protein _____ defines the packing of helices, sheets, turns, etc.

Back 4

Tertiary structure

Front 5

Protein _____ defines the motifs formed by short-range interactions between amino acids.

Back 5

Secondary structure

Front 6

A _____ interaction involves polar O, N, or both and the atom for which it is named, and constitutes one of the important protein stabilization elements.

Back 6

Hydrogen bond.

Front 7

_____ is used to determine the sequence of a protein based on sequential chemical reactivity.

Back 7

Edman degradation

Front 8

A _____ induces denatration of proteins by disturbing the hydrophobic effect.

Back 8

Chaotrophic agent

Front 9

A _____ is a graph of a conformational torsion angles phi psi for the residues in a protein or peptide, a map of the structure of the polypeptide backbone.

Back 9

Rachamandran plot

Front 10

A _____ had two charges which neutralize each other.

Back 10

zwitterion

Front 11

The _____ is the primary “force” of protein structural stabilization.

Back 11

Hydrophobic effect

Front 12

The _____ is the characteristic speed of an enzyme’s kinetics extrapolated to the time when a defined amount of substrate is added to the enzyme solution.

Back 12

Initial rate

Front 13

An act of _____ does not change the enzyme and lowers the transition state free energy of the associated reaction.

Back 13

Catalysis

Front 14

The _____ of an enzymatic reaction is the rate achieved when it is saturated with substrate.

Back 14

Maximum velocity

Front 15

The _____ (or double reciprocal) equation defines parameters that are used to characterize the kinetics of an enzyme.

Back 15

Lineweaver-Burk

Front 16

Km is the substrate concentration when vo=vmax/2, or _____

Back 16

Michaelis-Menten constant

Front 17

A _____ is the enzyme-substrate combination formed during an enzyme catalysis event.

Back 17

Michaelis complex

Front 18

The catalytic rate constant of an enzyme is abbreviated as _____

Back 18

Kcat

Front 19

_____ of enzyme catalysis occurs when an inhibitor binds to the active site of an enzyme.

Back 19

Competitive inhibition

Front 20

_____ of enzyme catalysis occurs when an inhibitor only binds to the enzyme-substrate complex.

Back 20

Uncompetitive inhibition.

Front 21

The _____ postulates that a constant input feed of substrate is supplied whose rate equals that of product formation.

Back 21

Steady state approximation

Front 22

Two internal factors that limit the velocity of and enzymatic reaction are _____ and _____.

Back 22

Hydrophobic effect and H-bonding

Front 23

Two external factors that limit the velocity of an enzymatic reaction are _____ and _____.

Back 23

pH and temperature

Front 24

What amino acid and functional group in the esterase site of acetylcholine esterase reacts with the substrate”

Back 24

Serine, hydroxylate

Front 25

PAM reactivates acetylcholine esterase, functioning as a _____.

Back 25

Nerve gas antidote

Front 26

What kind of reaction produces the reactivated enzyme?

Back 26

Nucleophilic substitution

Front 27

The bisubstrate-enzyme _____ reaction is used by transaminases in the exchange of an amino group for a carbonyl group between two progressively binding substrates.

Back 27

Ping-pong

Front 28

An _____ works by amplifying the initial signal via several linked protease cleavage reaction stages.

Back 28

Enzyme cascade

Front 29

A _____ is a protein that is converted from inactive to active forms by a covalent modification, typically protease cleavage.

Back 29

Zymogen

Front 30

A decrease in the activity of an enzyme as a result of binding of a product from the reaction in question or subsequent reactions is referred to as _____.

Back 30

Feedback inhibition

Front 31

_____ involves binding of a regulatory molecule at a site other than the active site.

Back 31

Allosterism

Front 32

_____ and _____ reactions, involving phosphate addition and removal respectively, regulate both qlycolysis and the Krebs cycle.

Back 32

Kinase and phosphatase

Front 33

_____ regulates entry and exit from mitosis by catalyzing a covalent modification reaction.

Back 33

Cyclin kinase

Front 34

What two amino acids are modified in the reactions catalyzed by cyclin kinase?

Back 34

Tyrosine and threonine

Front 35

Two example of reversible factors that control the catalytic capability of an enzyme are:

Back 35

Noncovalent modifications, and pH changes

Front 36

Two examples of irreversible factors that control the catalytic capability of an enzyme are:

Back 36

Covalent modification, and irreversible inhibitors

Front 37

The _____ accounts for the temperature dependence of the rate of a reaction.

Back 37

Arrhenius equation

Front 38

List two “chemical modes of catalysis”

Back 38

Acid-base, and covalent

Front 39

List two “binding modes of catalysis”

Back 39

Proximity effect, and transition-state stabilization

Front 40

A _____ attacks an electropositive site in i’s role in a chemical (enzymatic) reaction.

Back 40

Nucleophile

Front 41

A common process used to produce a nucleophile is _____.

Back 41

Acid-base catalysis

Front 42

Probably the most common amino acid used by enzymes to carry out acid-base catalysis is _____.

Back 42

Histidine

Front 43

A “catalytic triad” of amino acids is typically present in (enzyme class name) _____

Back 43

Serine proteases

Front 44

The amino acids “collaborate” to accomplish _____.

Back 44

Acid-base catalysis (or protein cleavage)

Front 45

The most typically cited currency of energy in metabolism is

Back 45

ATP

Front 46

_____ is typically required to achieve optimal activity with ATP-cosubstrate enzyme reactions.

Back 46

Mg2+

Front 47

A coenzyme is either a loosely bound cosubstrate of a tightly bound _____.

Back 47

Cofactor

Front 48

He heavy metal molybdenum is used to facilitate the biochemical reaction in _____, a key enzyme in purine catabolism.

Back 48

Xanthine oxidase

Front 49

When ATP is used I some biochemical applications it yields AMP and _____.

Back 49

pyrophosphate

Front 50

The (vitamin) _____ is required to synthesize coenzyme NAD+ for use in metabolic redox reactions.

Back 50

Nicotinamide

Front 51

The other key redox coenzyme is abbreviated _____

Back 51

FAD

Front 52

The coenzyme _____ often forms a Schiff base with the ε-amino group of a lysine residue in the enzyme.

Back 52

Pyroidoxal phosphate

Front 53

What chemical group does CoA typically carry in the course of its biochemical function?

Back 53

Acetate

Front 54

The _____-avidin noncovalent binding interaction is used to capture ligand-binding entities in the “affinity capture” technique.

Back 54

Biotin

Front 55

The coenzyme _____ is required to incorporate the methyl group into thymidine, a necessary prerequisite for the production of DNA.

Back 55

N5, N10 tetrahydrofolate

Front 56

Our understanding of this function can be used in a strategy for (treatment technique) _____.

Back 56

Anti-cancer chemotherapy

Front 57

The coenzyme-bound carbohydrate _____ and glucose are required to synthesize lactose.

Back 57

UDP-galactose

Front 58

Cis-retinal functions in _____ the signal of a photon of light into a chemically recognizable form.

Back 58

Transducing

Front 59

The two important straight-chain forms of carbohydrate structure are the _____ and _____.

Back 59

Ketose and aldose

Front 60

The two important ring forms of carbohydrate are the _____ and _____.

Back 60

Pyranose and furanose

Front 61

The two important ring conformations of β-D-glucopyranose are the _____ and _____.

Back 61

Chair and boat

Front 62

The cyclohexane ring containing compound _____ is released by phospholipase C in the phospholipids signal transduction mechanism.

Back 62

Inositol triphosphate

Front 63

The acronym NAG is used to abbreviate the name of the compound _____.

Back 63

N-acetyl galactosamine

Front 64

The key polysaccharide in starch is _____.

Back 64

Amylopectin

Front 65

The key polysaccharide in the liver is _____.

Back 65

Glycogen

Front 66

The antibiotic_____ selectively inhibits cell wall peptidylglycan synthesis in bacteria.

Back 66

penicillin

Front 67

Extra-cellular surface _____ regulate the osmotic pressure around cells.

Back 67

Carbohydrates

Front 68

Phospholipase C produce two second messengers in the phospholipids signal transduction pathway. The lipid-containing second messenger is _____.

Back 68

Diacylglycerol

Front 69

The compound chondroitin sulfate _____ cartilage and skeletal joints.

Back 69

Lubricates

Front 70

_____ fatty acids of the same length have a lower melting temperature (Tm).

Back 70

Unsaturated

Front 71

Lipid Tm values monitor the transformation from _____ to dispersed forms.

Back 71

Liquid crystal

Front 72

The most popular model for a biological membrane is called the _____ model.

Back 72

Fluid mosaic

Front 73

Liquid _____ are composed of two face-to-face monolayers while lipid _____ form a biphasic sphere.

Back 73

Bilayers, micelles

Front 74

The four nucleic acid bases in RNA are _____, _____, _____, and _____.

Back 74

Adenine, guanine, cytosine, and uracil

Front 75

The normal base pairs in DNA and RNA are called _____ base pairs.

Back 75

Watson-Crick

Front 76

The _____ bond in a nucleoside connects the base to the sugar.

Back 76

Glycosidic

Front 77

The _____ can be used to determine if a double helix forms from 2 single strands of DNA or RNA.

Back 77

Absorbance at 260nm

Front 78

The face-to-face interaction between nucleic acid bases is called______.

Back 78

Base stacking

Front 79

Counterions bind all nucleic acids and are required to neutralize the _____.

Back 79

Phosphodiester phosphates.

Front 80

The proteins called _____ serve this function in the case of most chromosomal DNA’s.

Back 80

Histones

Front 81

_____ base pairs are less stable than _____ base pairs.

Back 81

A-T (or A-U), G-C

Front 82

Two differences between A and B forms of DNA are:

Back 82

A= 3’endo sugar confirmation, shorter, fatter helix

Front 83

The 2’-hydroxyl group catalyzes _____ of RNA, a good example of anchiomeric assistance in a non-protein bimolecular mechanism.

Back 83

Alkaline hydrolysis

Front 84

An antisence oligonucleotide functionally inactivates an mRNA for use in translation by a ribosome by forming a double helix with it and precluding _____ binding.

Back 84

tRNA anticodon

Front 85

Name the two most prevalent of the 4 classes of RNA.

Back 85

Ribosomal RNA and transfer RNA

Front 86

Two distinctive features of most eukaryotic mRNAs are _____ and _____.

Back 86

7-Methyl G cap, poly A tail

Front 87

A _____ is used to detect the presence of a specific complementary nucleic acid sequence.

Back 87

DNA probe

Front 88

_____ are required to produce, manipulate, and clone specific pieces of DNA.

Back 88

Restriction endonucleases

Front 89

Two functional ends of transfer RNA are the anticodon and _____.

Back 89

Amino acid acceptor

Front 90

The three most central catabolic pathways of intermediary metabolism are _____, _____, and _____.

Back 90

Glycolysis, Kreb’s cycle, and electron transport/oxidative phosphorylation

Front 91

The four major compounds in which energy is captured in a chemically usable form by metallic reaction pathways are _____, _____, _____, and _____.

Back 91

ATP, NADH, FADH2, and coenzyme Q

Front 92

The _____ (Q) corrects for deviations from standard stat concentrations (1M)

Back 92

Mass action ratio

Front 93

_____ (number) steps in glycolysis control most of the flux through the pathway under actual cellular conditions.

Back 93

3

Front 94

What do the 3 reactions that control most of glycolysis have in common?

Back 94

They are metabolically irreversible

Front 95

What do the reactions other than the 3 controlling reactions in glycolysis have in common?

Back 95

They are near equilibrium

Front 96

The kinetics of an enzyme reaction are most easily controlled when Km is approximately equal to _____.

Back 96

The actual concentration of the reactant

Front 97

The enzyme Triose phosphate isomerase converts ______ into glyceraldehydes-3-phosphate.

Back 97

Dihydroxyacetone phosphate

Front 98

When citrate negatively regulates (discourages) the phosphofructosekinase-1 reaction, the general name for this phenomenon is _____

Back 98

Feedback inhibition

Front 99

When fructose-1,6-bisphosphate stimulates the pyruvate kinase reaction, the general name for this phenomenon is _____.

Back 99

Feedforward activation

Front 100

The three possible catabolic fates of pyruvate are _____, _____, and _____.

Back 100

Acetyl CoA, lactate, and ethanol

Front 101

The enzyme alcohol dehydrogenase converts _____ to ethanol.

Back 101

acetaldehyde

Front 102

_____ uses the coenzyme lipoic acid in “fueling” the Kreb’s Cycle.

Back 102

Dihydrolipoamide acetyl transferase

Front 103

What “synport” reaction accompanies import of pyruvate into the mitochondrion and what enzyme catalyzes the reaction? (enzyme name)

Back 103

Pyruvate translocase

Front 104

The two “oxidative decarboxylation” reaction of the Krebs Cycle are catalyzed by _____ and _____.

Back 104

Isocitrate dehydrogenase and α-ketogluterate dehydrogenase

Front 105

List the reactions, coenzymes, cofactors, and enzymes involved in the “substrate-level phosphorylation” reaction of the Krebs Cycle.

Back 105

Succinyl CoA synthetase

Front 106

The enzymes _____ and malate dehydrogenase “fix” a carbonyl group on succinate in the production of oxaloacetate.

Back 106

fumarase

Front 107

What crucial 2 carbon compound is then “fixed” to OAA?

Back 107

acetate

Front 108

What amino acid and what product of pyruvate metabolism are the principle substrates for gluconeogenesis in mammals?

Back 108

Alanine and lactate

Front 109

What energy sources are used to produce the “proton motive force”?

Back 109

NADH, FADH2, CoQH2

Front 110

What enzyme complex uses proton motive force as the driving energy for ATP synthesis in oxidative phosphorylation?

Back 110

F0F1ATPase

Front 111

How does electron transport drive production of the proton motive force?

Back 111

Exports H+ from mitochondrion (which creates a gradient, making them predisposed to flowing back in)

Front 112

How many reactions of each round of β-oxidation of a fatty acid require?

Back 112

4

Front 113

A set of coupled cofactor regeneration cycles siphon off reducing equivalents then fix them into coenzyme Q in reactions that are coupled to the first oxidative steps of fatty acid β-oxidation. Name the four cofactors involved in this “siphon.”

Back 113

CoA, FAD/FADH2, Fe-S, CoQ/CoQH2

Front 114

Which three steps of the Krebs Cycle do the first three steps of β-oxidation resemble?

Back 114

Succinate dehydrogenase, fumarase, malate dehydrogenase