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Life Science 3 > Lecture 6 > Flashcards

Lecture 6 Flashcards

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Biology 101 flashcards
1
Q

the function of nearly all proteins depend on their ability to bind to molecules (ligands or substrates) with a

A

high degree of specificity

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2
Q

region of a protein that associates with a ligand

A

binding ste

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3
Q

protein-ligand interaction is mediated by

A

noncovalent bonds

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4
Q

protein-ligand interaction can be measured by

A

velocity, affinity (binding strength), and specificity (binding preference)

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5
Q

level of affinity and specificity depends on –

A

molecular complementaries

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6
Q

– identify crucial ligand-binding sites

A

evolutionary tracing method

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7
Q

most common way two proteins bind with each other

A

surface-surface

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8
Q

antibodies can directly – or mark it for destruction

A

inactivate target protein

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9
Q

T/F: antibodies can distinguish between proteins that differ by only one AA

A

true

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10
Q

foreign substance that elicits production of an antibody

A

antigen

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11
Q

subunits/polypeptides of an antibody

A

2 heavy chains and 2 light chains

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12
Q

the chains of an antibody are held together by

A

disulfide bonds

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13
Q

each polypeptide chain of an antibody can be divided into 2 domains

A

variable and constant

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14
Q

the – domains interact with the antigen

A

variable

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15
Q

ligand binding site in antibodies

A

hypervariable loop

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16
Q

interaction between antibody and epitope of antigen is

A

complementary

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17
Q

enzymes binds 2 molecules and – them to encourage a reaction to occur between them

A

precisely orients

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18
Q

binding of substrate to enzyme rearranges electrons in the substrate that –

A

favor a reaction

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19
Q

enzymes strains the bound substrate molecule, forcing it toward a – to favor a reaction

A

transition state

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20
Q

enzyme that catalyze a hydrolytic cleavage

A

hydrolase

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21
Q

break down nucleic acids by hydrolyzing bonds between nucleotides

A

nucleases

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22
Q

break down proteins by hydrolyzing bonds between AA

A

proteases

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23
Q

synthesize molecules in anabolic reactions by condensing two smaller molecules together

A

synthase

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24
Q

join together two molecules in an energy-dependent process

A

ligase

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25
Q

catalyze rearrangement of bonds within a single molecule

A

iosmerase

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26
Q

catalyze polymerization reactions such as synthesis of DNA and RNA

A

polymerases

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27
Q

catalyze the addition of phosphate groups to molecules

A

kinases

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28
Q

hydrolyze ATP

A

ATPases

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29
Q

GTPase

A

hydrolyze GTP

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30
Q

dissociation rate

A

Koff * [AB]

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31
Q

association rate

A

Kon * [A][B]

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32
Q

dissociation rate = association rate at

A

equilibrium

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33
Q

Vmax

A

all enzymes are used

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34
Q

Km

A

substrate concentration at 0.5 Vmax

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35
Q

low Km

A

enzyme binds to substrate very tightly

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36
Q

enzyme’s active site is made up of

A

catalytic site and binding pocket

37
Q

trypsin-like serene proteases’ catalytic site

A

serine, histidine, aspartate, oxyanion hole

38
Q

trypsin-like serene proteases’ catalytic site - serine

A

break peptide bond

39
Q

trypsin-like serene proteases’ catalytic site - histidine

A

stabilize (accept proton)

40
Q

trypsin-like serene proteases’ catalytic site - aspartate

A

orient histidine at right location by H bonding

41
Q

trypsin-like serene proteases’ catalytic site - oxyanion hole

A

stabilize intermediates

42
Q

trypsin-like serene proteases’ catalytic site - the binding site

A

is general

43
Q

trypsin-like serine proteases’ catalytic site - has a – binding pocket

A

side chain specificity

44
Q

Trypsin (Asp)

A

Arg and Lys (positive side chains)

45
Q

Chymotrypsin (Ser)

A

Phe, Tyr, Trp (large hydrophobic side chains)

46
Q

Elastase (Val)

A

Gly and Ala (small side chains)

47
Q

substrate of lysozyme

A

6-sugar oligosaccharide

48
Q

lysozyme breaks uses – to break between the 4th and 5th sugar

A

glutamate and aspartate

49
Q

final products of lysozyme are

A

4-sugar oligosaccharide and a disaccharide

50
Q

proteins often use – to carry functions that would be difficult using AA alone

A

small non-protein molecules

51
Q

change conformation –> change function examples

A

allosteric walking and ABC transporter

52
Q

enzymes in a common pathway are often –

A

physically associated with one another

53
Q

– hold related enzymes

A

scaffold

54
Q

regulation of protein activity by kinase/phosphatase switch is an example of – protein modification

A

covalent

55
Q

T/F: kinase can only turn on proteins

A

false

56
Q

Which amino acids are used in the kinase/phosphatase switch?

A

serine, threonine, tyrosine (hydroxyl group)

57
Q

receptro tyrosine kinase is activated by –

A

dimerization

58
Q

once RTK is active, they –

A

phosphorylate each other

59
Q

Src-type kinase as –

A

signal-integrating device

60
Q

refers to the changes of protein conformation and activity upon binding to a ligand

A

allosteric regulation

61
Q

allosteric regulation is an example of – protein modification

A

noncovalent

62
Q

T/F: allosteric regulation can be positive or negative

A

true

63
Q

active PKA has lost its

A

catalytic site

64
Q

in allosteric regulation, the activity of an enzyme is either inhibited to activated by a regulatory molecule that binds to the allosteric site that is – from the active site

A

distinct

65
Q

the binding to the allosteric site produces a – of the active site either simulating or inhibiting the enzyme to catalyze a reaction

A

conformational change

66
Q

the binding of tryptophan changes the conformation of the –

A

repressor

67
Q

allosteric switch of calmodulin is

A

noncovalent

68
Q

GTP bound

A

ON

69
Q

GDP bound

A

OFF

70
Q

GAP (GTPases Activating Protein)

A

help turn off faster

71
Q

GEF (Guanine Exchange Factor)

A

help turn on faster

72
Q

when the amount of the – is high it inhibits an enzyme that functions early in the reaction pathway

A

end product

73
Q

three conformations of the acetylcholine receptor

A

unoccupied and closed
occupied and open
occupied and closed

74
Q

most stable form of the acetylcholine receptor

A

occupied and closed (inactivated)

75
Q

tryptophan repressor is an examples of – modification

A

noncovalent

76
Q

when there’s a lot of tryptophan, it will bind to the – which binds to the DNA and turns it off

A

tryptophan repressor

77
Q

enzymatic cleavage of a backbone peptide bond, resulting in the removal of residues from the polypeptide chain

A

proteolytic cleavage

78
Q

proteolytic cleavage is a common mechanism for activating enzymes that function in

A

programmed cell death

79
Q

proteolysis also generates active peptide hormones such as – from larger precursor polypeptides

A

insulin

80
Q

proteolytic cleavage – inactivates or activates proteins

A

irreversibly

81
Q

Ubiquitin is a – amino acid polypeptide that marks proteins for degradation

A

76

82
Q

ubiquitin can be covalently linked to other proteins via a covalent bonds between an internal – and its C-terminal

A

lysine on the substrate protein

83
Q

monoubiquitylation

A

histone regulation

84
Q

multiubiquitylation

A

endocytosis

85
Q

polyubiquitylation (Lys 48)

A

proteosomal degradation

86
Q

polyubiquitylation (Lys 63)

A

DNA repair

87
Q

ubiquitin activating enzyme (E1) uses – to attach ubiquitin to itself via a high energy thioester bond

A

ATP hydrolysis

88
Q

E1 passes activated ubiquitin to –

A

E2 ubiquitin-conjugating enzymes

89
Q

E2 works with E3 (ubiquitin ligases) which has the – for the target protein

A

binding site

Life Science 3 (20 decks)

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