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Life Science 3 > Lecture 5 > Flashcards

Lecture 5 Flashcards

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Biology 101 flashcards
1
Q

general formula of an amino acid

A 
alpha carbon in center
amino group
carboxyl group
(20) side chain
hydrogen
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2
Q

at pH 7 the amino acid is a

A

zwitterion

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3
Q

all amino acids have a stereoisomer except

A

glycine

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4
Q

only – amino acids are found in proteins

A

L

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5
Q

stereoisomers have same – but different –

A

same physical characteristics but different biological characteristics

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6
Q

Basic side chains (+)

A

lysine, arginine, histidine

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7
Q

Acidic side chains (-)

A

aspartic acid, glutamic acid

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8
Q

Nonpolar side chains

A

alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan glycine, proline, cysteine

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9
Q

uncharged polar side chains

A

asparagine, glutamine, serine, threonine, tyrosine

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10
Q

a polypeptide is a polymer of –

A

amino acids

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11
Q

the primary structure of a protein is the –

A

specific linear sequence of AA

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12
Q

the – of AA makes each protein different

A

arrangement

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13
Q

AA are linked by –

A

covalent peptide bonds

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14
Q

backbone of a peptide chain has directionality

A

N-terminus –> C-terminus

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15
Q

What makes up the peptide backbone?

A

N of amino group, alpha carbon, C of carboxyl group

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16
Q

– determine the properties of the protein

A

side chains

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17
Q

a – in the primary sequence can cause devastating results in the structure and function of a protein

A

single change

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18
Q

secondary structure is determined by the –

A

peptide backbone interactions

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19
Q

the polypeptide backbone provides many sites for –

A

H-bond formation

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20
Q

Where can hydrogen bonds of the peptide backbone be found?

A

O of carboxyl and H of amino group

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21
Q

hydrogen bonds are between – residues in the backbone

A

nearly adjacent

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22
Q

How many residues per turn?

A

3.6

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23
Q

in an alpha helix, H bonds are – to the axis

A

almost perfectly parallel

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24
Q

alpha helices are abundant in –

A

transmembrane proteins

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25
Q

in B sheet the hydrogen bonds between backbone atoms in –

A

neighboring chains

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26
Q

the – contain extensive regions of B sheet

A

core of proteins

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27
Q

B-sheet produce – structures

A

rigid

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28
Q

H bonds are perpendicular to the backbone in – B sheet

A

anti-parallel

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29
Q

fixed bond angles in the backbone produce

A

a pleated contour

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30
Q

change the direction of a polypeptide

A

B turns

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31
Q

Most common residues in a turn

A
  • glycine (small) can squeeze in small places

- proline bends the backbone

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32
Q

final folding of a single polypeptide

A

tertiary structure

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33
Q

proteins fold into a conformation with the

A

lowest energy state

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34
Q

Oil drop model of protein folding in a water environment

A

hydrophobic core and hydrophilic surface

35
Q

a protein’s conformation (3D structure) is determined solely by

A

its linear sequence

36
Q

protein domain

A

a substructure produced by any part of a polypeptide chain that can fold independently into a compact, stable strucutre

37
Q

a domain usually contains

A

40-350 residues

38
Q

different domains of a polypeptides are usually associated with –

A

different functions

39
Q

motifs is often a signature for a –

A

specific function

40
Q

small structural domains

A

structural motifs

41
Q

motifs are – structures composed of a defined arrangement of alpha helices and/or beta sheets

A

tertiary

42
Q

structural motif

A

same structure but different sequence

43
Q

sequence motif

A

same sequence and same structure

44
Q

helix-loop-helix contains

A

2 alpha helices connected by a short loop

45
Q

the loop is made up of

A

glutamate and aspartate

46
Q

What would happen to the helix-loop-helix motif if the [Ca2+] decreases in the cytoplasm?

A

it will straighten out

47
Q

coiled-coil structural motif

A

2 alpha helices wound around each other to form a rod-shaped protein

48
Q

coiled-coil motif is composed of

A

repeats of 7 AA

49
Q

coiled-coil is stabilized by the interaction of

A

the hydrophobic side chains of the 1st and 4th amino acids

50
Q

protein domains are – from which larger proteins are built

A

modular units

51
Q

at least 40% of human protein-coding gene can be assigned to – by sequence comparison

A

500 protein families

52
Q

many large proteins have evolved through the joining of preexisting domains

A

domain shuffling

53
Q

domain shuffling during vertebrate evolution has given rise to many – of protein domains

A

novel combinations

54
Q

binding site

A

reacts with another molecule through non-covalent interaction

55
Q

dimerization region

A

where two different polypeptides interact with one another

56
Q

active site

A

region where catalysis takes place

57
Q

regulatory site

A

binding site for molecule which may increase or decreases the activity of an enzyme through allosteric regulation

58
Q

interactions between two or more protein subunits

A

quaternary structure

59
Q

quaternary structure describes the – in multi metric proteins

A

number and relative positions of the subunits

60
Q

2 identical protein subunits

A

homodimer

61
Q

2 different protein subunits

A

heterodimer

62
Q

protein subunit

A

one polypeptide chain

63
Q

the most common covalent cross-linkage in proteins

A

disulfide bond

64
Q

interchain disulfide bond

A

quaternary structure

65
Q

intrachain disulfide bond

A

tertiary structure

66
Q

the cysteine n side chain contains a – which can form a covalent disulfide bond to a second cysteine

A

reactive sulfhydryl group

67
Q

disulfide bond usually exists

A

outside the cell (oxidizing environment)

68
Q

protein molecules often serve as subunits for the assembly of large structures by –

A

non-covalent interactions

69
Q

T/F: all structures held together by noncovalent bonds self-assemble

A

false

70
Q

the special protein aggregate that cause prion diseases

A

amyloid fibril

71
Q

normal functions fro – amyloid fibril

A

reversible

72
Q

primary structure stabilized by

A

peptide bonds

73
Q

secondary structure stabilized by

A

H bonds between groups along the peptide-bonded backbone

74
Q

interaction between R-groups or between R-groups and the backbone stabilizes

A

tertiary structure

75
Q

interactions beween R-groups, and between backbones of different polypeptides stabilizes

A

quaternary structure

76
Q

steric limitation of – restrict the possible 3D conformations of atoms

A

planar peptide bonds

77
Q

rotations around alpha carbon and N

A

phi

78
Q

rotations around alpha carbon and C

A

psi

79
Q

partially double bonded peptide created by –

A

resonance

80
Q

folding of protein in vivo is promoted by

A

molecular chaperones

81
Q

bind and stabilize newly synthesized or unfolded proteins thereby preventing these proteins to interact with other proteins and become degraded

A

molecular chaperone (Hsp 70)

82
Q

form a small folding chamber into which an unfolded protein can be sequestered, giving it time and environment to fold properly

A

chpaeronin (hsp-60-like)

83
Q

information directing a protein’s folding is encoded in its

A

amino acid sequence

Life Science 3 (20 decks)

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