David

Front 1

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

Back 1

van der Waals interaction

(heads up people, VDW interaction and VDW force are the same thing, so you can say whatever)

Front 2

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

Back 2

quaternary structure (becareful, don't spell it as quarternary)

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 events.

Back 6

hydrogen bond

Front 7

A __________ induces denaturation of proteins by disturbing the hydrophobic effect

Back 7

chaotropic agent

Front 8

Name the following protein structure:

R1-CH2-S-S-CH2-R2

Back 8

disulfide bond

Front 9

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

Back 9

Ramachandran plot (You have to use a capital "R", I think?)

Front 10

A __________ has 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 an enzyme and lowers the transition state free energy of the associated reaction.

Back 13

catalysis

Front 14

The __________ of an enzymatic catalysis 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 V0=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

_____(1)_____ of enzyme catalysis occurs when an inhibitor binds to the active site of the enzyme.

_____(2)_____ of enzyme catalysis occurs when the inhibitor only binds to the active site of the enzyme-substrate complex.

Back 19

(1) Competitive inhibition

(2) Uncompetitive inhibition

Front 20

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

Back 20

steady state approximation

Front 21

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

Back 21

hydrophobic effect

H-bonding

disulfide bonds

van der Waals forces

ionic bonds (salt bridges)

dipole-dipole interactions

Front 22

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

Back 22

pH

solvent polarity

temperature

salt concentration(s) and types

presence of chaotropes

osmolytes

Front 23

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

Back 23

serine and hydroxylate

Front 24

Pyridine aldoximine methiodide (PAP) reactivates acetylcholine esterase, functioning as a __________.

Back 24

Nerve gas antidote

Front 25

Hey people,

Just a heads up if you're using my flashcards and you didn't get the memo - The final exam questions are in the same order as we learned the material. So the first quarter will be test 1, second quarter test 2, the latter half will be test 3 & 4, etc. The question bank on pp. 291 (this question bank will make up ~80% of our final, according to Nate dog). Use this to your advantage. Good luck!

-I love you,

David

Back 25

These flashcards do not have the following questions (it requires an image, I don't have time to upload them): 1, 5, and 8. The final exam has fill in the blank questions so that hardin can have his assistants grade it faster. Also, the back of the book has abbreviated answers. However, we aren't allowed to put abbreviated answers on the test! No abbreviations, period.

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 progessively binding substrates.

Back 27

ping-pong

Front 28

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

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 glycolysis and the Krebs cycle.

Back 32

Kinase & phosphatase

Front 33

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

Back 33

Cyclin kinase

Front 34

Which two amino acids are modified in the reactions catalyzed by the enzyme in question 35 (i dont know what this question is asking because this question is question 35 in the book and there's no rxn. just memorize the answer - david)

Back 34

tyrosine & threonine

Front 35

Two examples of reversible factors that control the catalytic capability of an enzyme are: __________, __________.

Back 35

noncovalent modifications

pH and pKa changes

[salt] changes

possibly others

Front 36

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

Back 36

Arrhenius equation

Front 37

List the two "chemical modes of catalysis"

Back 37

acid-base

covalent

Front 38

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

Back 38

histidine

Front 39

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

Back 39

serine proteases

Front 40

The amino acids collaborate to accomplish __________.

Back 40

acid-base catalysis

Front 41

The most typically cited currency of energy in metabolism is (abbreviation)

Back 41

ATP

Front 42

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

Back 42

Mg2+

Front 43

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

Back 43

prosthetic group

Front 44

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

Back 44

xanthine oxidase

Front 45

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

Back 45

pyrophosphate

Front 46

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

Back 46

nicotinamide

Front 47

The other key redox coenzyme is abbreviated __________.

Back 47

FAD

Front 48

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

Back 48

pyridoxal phosphate

Front 49

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

Back 49

acetate

Front 50

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

Back 50

biotin

Front 51

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

Back 51

N5,N10 methylenetetrahydrofolate

Front 52

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

Back 52

anticancer chemotherapy

Front 53

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

Back 53

UDP-galactose

Front 54

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

Back 54

transducing

Front 55

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

Back 55

ketose

aldose

Front 56

The two important ring forms of carbohydrates are the __________ and __________.

Back 56

pyranose

furanose

Front 57

The two important ring conformations of B-D-glucopyranose are the __________ and __________.

Back 57

chair

boat

Front 58

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

Back 58

inositol triphosphate

Front 59

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

Back 59

N-acetyl glucosamine

Front 60

The key polysaccharide in starch is __________.

Back 60

amylopectin

Front 61

The key polysaccharide in the liver is __________.

Back 61

glycogen

Front 62

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

Back 62

penicillin

Front 63

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

Back 63

carbohydrates

Front 64

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

Back 64

diacylglycerol

Front 65

The compound chondroitin sulfate __________ cartilage and skeletal joints.

Back 65

lubricates

Front 66

Saturated/unsaturated (circle one) fatty acids of the same length have a lower melting temperature (Tm).

Back 66

unsaturated

Front 67

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

Back 67

liquid crystal

Front 68

Lipid __________ are composed of two face-toface monolayers while lipid __________ form a biphasic sphere.

Back 68

bilayers

micelles

Front 69

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

Back 69

fluid mosaic

Front 70

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

Back 70

adenine

guanine

cytosine

uracil

(For these, I put out the shortest word. For example, adenine is shorter than adenosine. This works for 3 of the 4 because cytosine and cytidine both have 8 letters)

Front 71

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

Back 71

Watson-Crick

Front 72

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

Back 72

glycosidic

Front 73

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

Back 73

absorbance at 260 nm

Front 74

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

Back 74

base stacking

Front 75

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

Back 75

phosphodiester phosphates

Front 76

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

Back 76

histones

Front 77

G*C/A*T (or A*U) (circle one) base pairs are less stable than G*C/A*T (or A*U) (circle one) base pairs.

Back 77

A*T (or A*U) base pairs are less stable than G*C base pairs.

Front 78

Two differences between A and B forms of DNA are

Back 78

A-form:

3' endo sugar conformation

base pairs tilted 20 degrees from helix axis

central axial cavity in the helix

shorter, squatter helix

B-form:

2' endo sugar

bp's perpendicular to helix axis

base pairs cross center of helix

longer, narrower helix

Front 79

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

Back 79

alkaline hydrolysis

Front 80

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 80

tRNA anticodon

Front 81

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

Back 81

ribosomal RNA

transfer RNA

Front 82

Two distinctive features of most eukaryotic mRNA are

Back 82

m7G+ (5'-5') cap (the 7 and the + should be superscripted)

monocistronic

contains introns and exons

poly(A) tail

Front 83

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

Back 83

DNA probe

Front 84

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

Back 84

Restriction endonucleases

Front 85

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

Back 85

amino acid acceptor

Front 86

The three most central catabolic pathways of intermediary metabolism are

Back 86

glycolysis

Krebs cycle

electron transport/oxidative phosphorylation

Front 87

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

Back 87

ATP

NADH

FADH2

Coenzyme QH2

Front 88

The __________ (Q) corrects for deviations from standard state concentrations (1 M).

Back 88

mass action ratio

Front 89

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

What do these reactions have in common? They are __________

Back 89

three

metabolically irreversible

Front 90

In contrast, the rest of the reactions are __________.

Back 90

near equilibrium

Front 91

The kinetics of an enzyme reaction are most easily controlled when KM is the approximately equal to __________.

Back 91

the actual concentration of the reactant

Front 92

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

Back 92

dihydroxyacetone phosphate

Front 93

When citrate negatively regulates (discourage) the phosphofructokinase-1 reaction, the general name for this phenomenon is __________.

Back 93

feedback inhibition

Front 94

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

Back 94

feed-forward activation

Front 95

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

Back 95

acetyl CoA

ethanol

lactate

Front 96

The enzyme alcohol dehydrogenase converts __________ to ethanol

Back 96

acetaldehyde

Front 97

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

Back 97

Dihydrolipoamide acetyl transferase

Front 98

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

Back 98

pyruvate translocase

Front 99

The two oxidative decarboxylatoin reactions of the Krebs Cycle are catalyzed by __________ and __________.

Back 99

isocitrate dehydrogenase

a-ketoglutarate dehydrogenase

Front 100

List the reactions, coenzyme(s), cofactor(s), and enzymes involved in the "substrate-level phosphorylation" reaction of the Krebs Cycle.

Back 100

Succinyl CoA synthetase

Front 101

the enzymes __________ and malate dehydrogenase "fix" a carbonyl group on succinate in the production of oxaloacetate.

Back 101

fumarase

Front 102

What crucial 2 carbon compound is then "fixed" to OAA?

Back 102

acetate

Front 103

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

Back 103

alanine

lactate

Front 104

What energy sources are used to produce the protonmotive force?

Back 104

NADH

CoQH2

FADH2 (indirectly)

Front 105

What enzyme complex uses this phenomenon as the driving energy for ATP synthesis in oxidative phosphorylation?

Back 105

f0f1 ATP synthase

Front 106

How does electron transport drive production of the protomotive force?

Back 106

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

Front 107

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

Back 107

four

Front 108

What are the products of one round of B-oxidation and what's the tally in terms of ATP equivalents of energy conserving products?

Back 108

1 CoQH2

1 NADH

1 H+

1 Acetyl CoA

1 Fatty acid (which lost 2 carbons)

Front 109

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 step of fatty acid B-oxidation. Write down the names of the four cofactors involved in this siphon.

Back 109

CoA

FAD/FADH2

Fe-S2+/3+ (2+/3+ is superscripted)

CoQ/CoQH2

Front 110

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

Back 110

succinate dehydrogenase

fumarase

malate dehydrogenase

Front 111

The __________ enlarges at an increasing propensity when it is subjected to an active site which then induces a conformational change of the active site and in the process, releases E7,A4-diethyl-3-methylacetate (NDMA) into the inner membrane space. NDMA becomes protonated through a series of redox reactions releasing a byproduct that activates 3,5-diacetylfructokinase-2 further fueling the production of pyruvate in glycolysis.

Back 111

big black cock