Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

MCAT-BIOCHEMISTRY > Amino Acids & Proteins > Flashcards

Amino Acids & Proteins Flashcards

You may prefer our related Brainscape-certified flashcards:
MCAT flashcards
1
Q

what gives each amino acid its unique identity/physical & chemical properties?

A

it’s side chain or variable R group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

what are the acidic amino acids that are deprotonated at physiological pH (negative charge)?

A

glutamic acid Glu E

aspartic acid Asp D

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

what are the 3 basic amino acids?

A

lysine Lys K
arginine Arg R
histidine His H

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

what distinguishes histidine from the other basic amino acids?

A

it has a pH of 6.5, very close to physiological pH so could be protonated or deprotonated (although 90% deprotonated)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

what are the hydrophobic, nonpolar, aliphatic amino acids (5)?

A 
glyince Gly G
alanine Ala A
valine Val V
Leucine Leu L
Isoleucine Ile I
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

what are the hydrophobic, nonpolar, aromatic amino acids? (2)

A

tryptophan Trp W

phenylalanine Phe F

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

what are the five polar amino acids (uncharged)?

A 
serine Ser S
threonine Thr T
tyrosine Tyr Y
asparagine Asn N
glutamine Gln Q
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

what are the two sulphur containing amino acids?

A

cysteine Cys C

methionine Met M

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

what’s the main difference between Cys and Met?

A

Cys is polar while Met is nonpolar, and Cys can form disulfide bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

what class does proline Pro P belong to?

A

nonpolar side chain, although it has unique consequences due to its bonding and ring structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

what are the 9 essential amino acids

A 
Histidine 
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Threonine
Tryptophan
Valine
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

how are amino acids are amphoteric?

A

amino acids can act as acids or bases due to acidic carboxylic acid group and basic amino group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

what is the state of the acidic group when the pH of the solution is less than the pKa of the acidic group?

A

the acidic group will be mostly in its protonated form

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

what is the state of the acidic group when the pH of the solution is greater than the pKa of the acidic group?

A

the acidic group will mostly be in its deprotonated form

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

ammonium group

A

when the amine is protonated or in its acidic group, NH3+ with a pKa between 9-10

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

zwitterion

A

a molecule with positive and negative charges in balance

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

isoelectric point (pI)

A

the pH at which a molecule is uncharged (zwitterionic)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

how do you find the pI (isoelectric point) of an amino acid?

A

average the pKa’s of the two functional groups

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

peptide bond

A

the covalent bond that links amino acids together into polypeptide chains

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

disulfide bridges

A

covalent bonds between cysteine R-groups

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

what is the polypeptide backbone?

A

N-C-C-N-C-C

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

residue

A

an individual amino acid that is part of a polypeptide chain

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

thermodynamics states that free energy must decrease for a reaction to proceed spontaneously and that such a reaction will spontaneously move toward:

A

equilibrium

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

proteolysis/proteolytic cleavage

A

hydrolysis of a protein by another protein (cutting)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

proteolytic enzyme/protease

A

the enzyme that does the cutting

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

proteolytic cleavage is a specific means of cleaving:

A

peptide bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

where is the reducing environment?

A

inside of cells because cells possess antioxidants (chemicals that prevent oxidation reactions)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

denatured

A

improperly folded proteins, usually non-functional

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

denaturation

A

the disruption of a protein’s shape without breaking peptide bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

primary structure

A

the same as sequence

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

what are the results of the unique side chain or proline in a polypeptide chain?

A

1) the formation of a peptide bond with proline eliminates the only hydrogen atom on the nitrogen atom of proline, the absence of the NH bond disrupts the backbone hydrogen bonding the polypeptide chain
2) the unique structure of proline forces it to kink the polypeptide chain

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

due to the broken hydrogen bonding pattern, in which secondary structure is proline always absent?

A

alpha-helix

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

which secondary structure is favourable for a hydrophobic transmembrane region?

A

alpha-helix because all polar NH and CO groups in the backbone are hydrogen-bonded to each other and on the inside of the helix, nonpolar R groups can interact with the hydrophobic membrane interior. good for integral transmembrane proteins the lipid bilayer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

are are beta-pleated sheets stabilized?

A

by hydrogen bonding between NH and CO groups in the polypeptide backbone, unlike in the alpha-helix, hydrogen bonding can occur between residues distance from each other in the chain or even on separate polypeptide chains

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

what drives the formation of tertiary structures?

A

interactions of R groups with each other and with the solvent (water)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

hydrophobic effect

A

hydrophobic R groups tend to fold into the interior of the protein and hydrophilic R groups tend to be exposed to water on the surface of the protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

hydrolase

A

hydrolyzes chemical bonds (includes ATPases, proteases, and others)

38
Q

isomerase

A

rearranges bonds within a molecule to form an isomer

39
Q

ligase

A

forms a chemical bond (eg. DNA ligase)

40
Q

lyase

A

breaks chemical bonds by means other than oxidation or hydrolysis (ex. pyruvate decarboxylase)

41
Q

kinase

A

transfers a phosphate group to a molecule from a high energy carrier, such as ATP

42
Q

oxidoreductase

A

runs redox reactions

43
Q

polymerase

A

polymerization

44
Q

phosphatase

A

removes a phosphate group from a molecule

45
Q

phosphorylase

A

transfers a phosphate group to a molecule from inorganic phosphate

46
Q

protease

A

hydrolyzes peptide bonds

47
Q

reaction coupling

A

one very favourable reaction is used to drive an unfavourable one

48
Q

how can ATP hydrolysis drive unfavourable reactions?

A

1) cause a conformational change in a protein

2) transfer a phosphate group from ATP to a substrate

49
Q

how can enzyme catalyze unfavourable reactions?

A

by reaction coupling (a selective process)

50
Q

active site

A

the region in an enzyme’s three-dimensional structure that is directly involved in catalysis (generally globular)

51
Q

substrates

A

the reactants in an enzyme-catalyzed reaction

52
Q

active site model

A

“lock and key” : substrate and active site are perfectly complementary

53
Q

induced fit model

A

substrate and active site differ slightly in structure and the binding of the substrate induces a conformational change in the enzyme

54
Q

how do enzymes accelerate the rate of a given reaction?

A

by helping to stabilize the transition state

55
Q

recognition pocket

A

a pocket in the enzyme’s structure which attracts certain residues on substrate polypeptides

56
Q

what is the nature of amino acids in the active site of enzymes that act on hydrophobic substrates?

A

the amino acid in the active site is also hydrophobic

57
Q

what is the nature of amino acids in the active site of enzymes that act on hydrophilic substrates?

A

the amino acid in the active site is also hydrophilic

58
Q

how does temperature influence enzymatic function?

A

as temperature increases, the thermal motion of the peptide and surrounding solution destabilizes its structure. if the protein denatures, it will lose its orderly structure and not be able to bind to the enzyme

59
Q

how does pH influence enzymatic function

A

ionizable R groups can change charge depending on pH, this can decrease the affinity of a substrate for the active site, and if the pH deviates sufficiently, the protein can denature

60
Q

cofactors

A

metal ions or small molecules that are required for the activity in many enzymes

61
Q

coenzyme

A

when a cofactor is an organic molecule, these often bind to the substrate during the catalyzed reaction

62
Q

covalent modification

A

groups that are covalently attached to proteins can regulate their activity, lifespan in the cell, or cellular location ex. kinase (activate or inactivate the enzyme), phosphorylase, phosphatase

63
Q

proteolytic cleavage

A

many enzymes and other proteins are synthesized in inactive forms that are activated by cleavage by a protease

64
Q

association with other polypeptides

A

some enzymes have catalytic activity in one polypeptide subunit that is regulated by association with a separate regulatory subunit

65
Q

constitutive activity

A

means continuous or unregulated activity

66
Q

allosteric regulation

A

the modification of active-site activity through interactions of molecules with allosteric sites on the enzyme

67
Q

how can enzyme activity be regulated?

A

1) covalent modification
2) proteolytic cleavage
3) association with other polypeptides
4) allosteric regulation

68
Q

what kind of bond binds the allosteric regulator to the allosteric site?

A

generally a noncovalent and reversible bond

69
Q

enzyme kinetics

A

the study of the rate of formation of products from substrates in the presence of an enzyme

70
Q

reaction rate V

A

the amount of product formed per unit time (mol/s)

71
Q

what does reaction rate depend on?

A

concentration of substrate [S] and enzyme

72
Q

if there is only a little bit of substrate, what is V proportional to?

A

the amount of substrate added

73
Q

saturated

A

the point at which there is so much substrate, every active site is continuously occupied and adding more substrate doesn’t increase the reaction rate at all (V max)

74
Q

what is V max a property of?

A

V max is specific to each enzyme at a particular concentration of that enzyme

75
Q

Michaelis constant Km

A

the substrate concentration at which the reaction velocity is half of V max, it is unique for each enzyme-substrate pair and gives information on the affinity of the enzyme for its substrate

76
Q

what does it mean if enzymes are said to bind substrates cooperatively?

A

it means that in such enzymes, the binding of substrate to one subunit modulates the affinity of other subunits for substrate

77
Q

positive cooperativity

A

binding of a substrate to one subunit increases the affinity of the other subunits for substrate

78
Q

negative cooperativity

A

the binding of a substrate to one subunit reduces the affinity of the other subunits for substrate

79
Q

what is a quality all cooperative enzymes must have?

A

more than one active site

80
Q

what kind of curve results from positive cooperative binding?

A

a sigmoidal curve

81
Q

tense state

A

enzyme complex has a low affinity for substrate

82
Q

relaxed state

A

when enzyme has grater affinity for substrate

83
Q

what kind of interaction is cooperativity?

A

a special kind of allosteric interaction, but instead of an allosteric site, an active site acts like an allosteric regulatory site for the other active sites

84
Q

competitive inhibitors

A

molecules that compete with substrate for binding at the active site

85
Q

how can one overcome competitive inhibition?

A

by adding more substrate

86
Q

describe the curve for competitive inhibitor

A

V max does not change, Km increases

87
Q

noncompetitive inhibitors

A

bind to an allosteric site, no matter how much substrate you add, the inhibitor will not be displaced from its site of action

88
Q

describe the curve for noncompetitive inhibitors

A

V max diminishes, does not alter Km; substrate can still bind to active site, but inhibitor prevents catalytic activity

89
Q

uncompetitive inhibitor

A

binds to the allosteric site on the enzyme-substrate complex, and cannot bind before the substrate has been bound

90
Q

describe the curve for uncompetitive inhibitor

A

decreases V max (limits the amount of available enzyme-substrate complex which can be converted to product) and decreases Km (enzymes and substrate cannot readily dissociate)

91
Q

mixed-type inhibition

A

inhibitor can bind to either the unoccupied enzyme or the enzyme-substrate complex,

1) if enzyme has greater affinity for the inhibitor in its free form, the enzyme will have a lower affinity or the substrate (Km increases)
2) if enzyme-substrate complex has greater affinity for the inhibitor, the enzyme will have greater affinity for the substrate (Km decreases)
3) if enzyme has equal affinity towards inhibitor in both forms, it would actually be a noncompetitive inhibitor
* in each situation, V max decreases because inhibitor binds to an allosteric site and additional substrate cannot overcome inhibition

MCAT-BIOCHEMISTRY (3 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions