Biochemistry Final Exam Review

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 with hydrogen and constitutes one of the important 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 denaturation of proteins by disturbing the hydrophobic effect.

Back 8

chaotropic agent

Front 9

Name the following protein structure:

R1 --- CH2 --- S --- S --- CH2 --- R2

Back 9

disulfide bond

Front 10

A _____________ is a graph of the conformational torsion angles for the residues in a protein or peptide. A map of the structure of the polypeptide backbone (alpha helices and beta sheets etc.)

Back 10

Ramachandran plot

Front 11

A _____________ has two charges which neutralize each other.

Back 11

zwitterion

Front 12

The _____________ is the primary "force" of protein structural stabilization.

Back 12

hydrophobic effect

Front 13

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 13

initial rate

Front 14

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

Back 14

catalysis

Front 15

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

Back 15

maximum velocity

Front 16

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

Back 16

Lineweaver-Burk

Front 17

Km is the substrate concentration when Vo = Vmax / 2, or _____________.

Back 17

Michaelis-Menten constant

Front 18

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

Back 18

Michaelis complex

Front 19

The catalytic rate constant of an enzyme is abbreviated as:

Back 19

k_cat

Front 20

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

Back 20

Competitive inhibition

Front 21

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

Back 21

Uncompetitive inhibition

Front 22

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

Back 22

steady state approximation

Front 23

Internal factors that limit the velocity of an enzymatic reaction:

Back 23

- hydrophobic effect

- hydrogen bonding

- disulfide bonds

- van der Waals forces

- ionic bonds (salt bridges)

- dipole-dipole interactions

Front 24

External factors that limit the velocity of an enzymatic reaction:

Back 24

- pH

- solvent polarity

- temperature

- salt concentration(s) and types

- presence of chaotropes

- osmolytes

Front 25

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

Back 25

Amino acid : Serine

Functional group : hydroxylate

Front 26

Pyridine aldoximine methiodide (PAM) reactivates acetylcholine esterase, functioning as a _____________.

Back 26

nerve gas antidote

Front 27

What kind of reaction produces the reactivated enzyme?

Back 27

nucleophilic substitution

Front 28

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 28

ping-pong

Front 29

An _____________ works by amplifying an initial signal via several linked protease cleavage reaction stages. (e.g., blood clotting)

Back 29

enzyme cascade

Front 30

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

Back 30

zymogen

Front 31

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 31

feedback inhibition

Front 32

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

Back 32

Allosterism

Front 33

_____________ and _____________ reactions, involving phosphate addition and removal respectively, regulate both glycolysis and the Krebs cycle.

Back 33

Kinase ; phosphatase

Front 34

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

Back 34

Cyclin kinase

Front 35

Which two amino acids are phosphorylated in cyclin kinase?

Back 35

tyrosine and threonine

Front 36

Examples of reversible factors that control the catalytic capability of an enzyme:

Back 36

- noncovalent modifications

- pH and pKa changes

- salt concentration changes

Front 37

Examples of irreversible factors that control the catalytic capability of an enzyme:

Back 37

- covalent modification

- proteolysis

- irreversible inhibitors

Front 38

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

Back 38

Arrhenius equation

Front 39

List the two "chemical modes of catalysis"

Back 39

- acid-base

- covalent

Front 40

List the two "binding modes of catalysis"

Back 40

- proximity effect

- transition-state stabilization

Front 41

A _____________ attacks an electropositive site in its role in a chemical (enzymatic) reaction.

Back 41

nucleophile

Front 42

A common process used to produce a nucleophile is:

Back 42

acid-base catalysis

Front 43

The most common amino acids used by enzymes to carry out acid-base catalysis is _____________.

Back 43

histidine

Front 44

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

Back 44

serine proteases

Front 45

The amino acids collaborate to accomplish _____________.

Back 45

acid-base catalysis

Front 46

The most typically cited currency of energy in metabolism is:

Back 46

ATP

Front 47

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

Back 47

Mg2+

Front 48

A coenzyme is either a loosely bound cosubstrate or a strongly bound _____________.

Back 48

prosthetic group

Front 49

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

Back 49

xanthine oxidase

Front 50

When ATP is used in some biochemical applications it yields AMP and _____________.

Back 50

pyrophosphate

Front 51

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

Back 51

nicotinamide

Front 52

The other key redox coenzyme is abbreviated _____.

Back 52

FAD

Front 53

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

Back 53

pyridoxal phosphate

Front 54

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

Back 54

acetate

Front 55

The _______-avidin noncovalent binding interaction is used to capture ligand-binding entities in the "affinity capture" technique.

Back 55

biotin

Front 56

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

Back 56

N5, N10 methylenetetrahydrofolate

Front 57

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

Back 57

anticancer chemotherapy

Front 58

The coenzyme bound carbohydrates _____________ and glucose are required to synthesize lactose.

Back 58

UDP-galactose

Front 59

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

Back 59

transducing

Front 60

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

Back 60

ketose ; aldose

Front 61

The two important ring forms of carbohydates are the ________ and _________.

Back 61

pyranose and furanose

Front 62

The two important ring conformation of beta-D-glucopyranose are the _______ and _________.

Back 62

chair and boat

Front 63

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

Back 63

inositol triphosphate

Front 64

The acronym NAG is used to abbreviate the name of the compound:

Back 64

N-acetyl-glucosamine

Front 65

The key polysaccharide in starch is:

Back 65

amylopectin

Front 66

The key polysaccharide in the liver is:

Back 66

glycogen

Front 67

The antibiotic _____________ selectively inhibits cell wall peptidylglycan synthesis in bacteria.

Back 67

penicillin

Front 68

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

Back 68

carbohydrates

Front 69

Phospholipase C produces two different second messengers in the phospholipid signal transduction pathway. The lipid-containing second messenger is _____________.

Back 69

diacylglycerol

Front 70

The compound chondroitin sulfate _____________ cartilage and skeletal joints.

Back 70

lubricates

Front 71

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

Back 71

Unsaturated

Front 72

Lipid Tm values monitor the transformation form _____________ to dispersed forms.

Back 72

liquid crystal

Front 73

Lipid _____________ are composed of two face-to-face monolayers while lipid _____________ form a biphasic sphere.

Back 73

bilayers ; micelles

Front 74

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

Back 74

fluid mosaic

Front 75

The four nucleic acid bases in RNA:

Back 75

adenosine, uracil, guanine, cytosine

Front 76

The two normal base pairs in DNA and RNA are called _____________ base pairs.

Back 76

Watson-Crick

Front 77

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

Back 77

glycosidic

Front 78

The _____________ can be used to determine if 2 single strands of DNA or RNA form a double helix.

Back 78

absorbance at 260nm

Front 79

The face-to-face interaction between nucleic acid bases is called _____________.

Back 79

base stacking

Front 80

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

Back 80

phosphodiester phosphates

Front 81

Protein complexes called _____________ serve this counterion function in the case of most chromosomal DNAs.

Back 81

histones

Front 82

________ base pairs are less stable than _____ base pairs.

Back 82

A & T

G & C

Front 83

Differences between A and B forms of DNA:

Back 83

A form: 3' endo sugar conformation, base pairs tilted 20 degrees from helix axis, shorter central axial cavity, "fatter helices"

B form: 2' endo sugar conformation. Base pairs' perpendicular to helix axis, base pairs cross center of helix.

Front 84

The 2' hydoxyl group catalyzes _____________ of RNA, a good example of anchiomeric assistance in a non-protein biomolecular mechanism.

Back 84

alkaline hydrolysis

Front 85

An antisense oligonucleotide functionally inactivate a mRNA for use in translation by a ribosome by forming a double helix with it and precluding _____________ binding.

Back 85

tRNA anticodon

Front 86

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

Back 86

ribosomal RNA and transfer RNA

Front 87

Some distinctive features of most eukaryotic mRNAs are:

Back 87

- m7G+ 5'-5' cap

- monocistronic

- contains introns and exons

- poly(A) tail

Front 88

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

Back 88

DNA probe

Front 89

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

Back 89

Restriction endonucleases

Front 90

The two functional ends of transfer RNA are the anticodon and _____________.

Back 90

amino acid acceptor

Front 91

The three most central catabolic pathways of intermediary metabolism are:

Back 91

- glycolysis
- Krebs cycle
- electron transport chain / oxidative phosphorylation

Front 92

The four major compounds in which energy is captured in a chemically usable form by metabolic reaction pathways are:

Back 92

- ATP

- NADH

- FADH2

- Coenzyme QH2

Front 93

The _____________ (Q) corrects or deviations from standard state concentrations (1M).

Back 93

mass action ratio

Front 94

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

Back 94

Three

Front 95

What do those three reactions in glycolysis have in common?

Back 95

They are metabolically irreversible

Front 96

Most of the reactions in glycolysis are:

Back 96

Near equilibrium

Front 97

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

Back 97

the actual concentration of the reactant

Front 98

The enzyme triose phosphate isomerase converts _____________ into glyceraldehyde-3-phosphate.

Back 98

dihydroxyacetone phosphate

Front 99

When citrate negatively regulates the phosphofructokinase-1 reaction, the general name for this phenomenon is _____________.

Back 99

feedback inhibition

Front 100

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

Back 100

feed-forward activation

Front 101

The three possible catabolic fates of pyruvate:

Back 101

- acetyl CoA

- ethanol

- lactate

Front 102

The enzyme alcohol dehydrogenase converts _____________ to ethanol

Back 102

acetaldehyde

Front 103

_____________ uses the coenzyme lipoic acid in fueling the Krebs Cycle.

Back 103

Dihydrolipoamide acetyl transfease (DHP acetyl)

Front 104

What symport reaction accompanies import of pyruvate into the mitochondrion and what enzyme catalyzes the reaction?

Back 104

pyruvate translocase

Front 105

The two oxidative decarboxylation reactions of the Krebs Cycle are catalyzed by _____________ and _____________.

Back 105

isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase

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 compounds is 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 protonmotive force?

Back 109

NADH, CoQH2, FADH2

Front 110

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

Back 110

ATPase

Front 111

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

Back 111

exports H+ from mitochondrion, creating a gradient

Front 112

How many reactions does each round of beta oxidation of a fatty acid require?

Back 112

FOUR (oxidation, hydration, oxidation, thiolysis)

Front 113

What are the products of one round of beta oxidation?

Back 113

- 1 CoQH2
- 1 NADH
- H+
- 1 acetyl CoA
- 1 fatty acid (minus 2 Cs)

Front 114

Which three steps of the Krebs Cycle do the first three steps of the fatty acid beta-oxidation cycle resemble?

Back 114

- succinate dehydrogenase

- fumarase

- malate dehydrogenase