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Biochem > Test 2 > Flashcards

Test 2 Flashcards

1
Q

what are all living organisms made from

A

a set of some of the 20 amino acids

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2
Q

how are amino acids joined

A

in linear sequences through amide or peptide bonds

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3
Q

what qualities allow a protein to be separated

A

differences in chemical and functional properties based on their amino acid sequence

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4
Q

what are the primary building blocks of proteins

A

amino acids

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5
Q

what is a zwitter ion

A

in pH range of 3-10, neutral because one is protonated and one is not

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6
Q

what conformation are amino acids in nature

A

L

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7
Q

what is an amino acid residue

A

when it looses and H2O to form a peptide bond

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8
Q

what is the N-Calpha bond called

A

phi

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9
Q

what is the Calpha-C bond called

A

psi

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10
Q

what is the C-N (peptide bond called)

A

omega

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11
Q

what is a dihedral angle in terms of amino acids

A

angle between planes formed by the backbone

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12
Q

what is pI

A

ph when charge on molecule is zero, in between buffering zones

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13
Q

what are the nonpolar amino acids

A

glycine, alanine, proline, valine, leucine, isoleucine, methionine

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14
Q

what are the polar uncharged amino acids

A

serine, threonine, cysteine, asparagine, glutamine

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15
Q

aromatic amino acids

A

phenylalanine, tyrosine, tryptophan

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16
Q

positvely charged amino acids

A

lysine, arginine, histidine

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17
Q

negatively charged amino acids

A

aspartate, glutamate

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18
Q

what many buffering zones does each amino acid have

A

at least 2

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19
Q

what are the modification for amino acids

A

methylation and acetylation

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20
Q

equation for estimating weight of an amino acid

A

of residues x 110 Da

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21
Q

how can you purify proteins

A

charge, size and tags

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22
Q

ion exchange chromatography

A

cation and anion exchanges, column runs with buffers, the affinity for the analytes to the column is affected by the pH and salt concentration

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23
Q

cation exchange

A

cations stick (resin is negative)

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24
Q

anion exchnage

A

anions stick (resin is positive)

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25
Q

what do you do if positive proteins get stuck to the positive column

A

add more concetrated salt water, it will block resin negative allowing protein to come free

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26
Q

The concentrated salt water increases the pH in the column, how does this allow the protein to be unstuck

A

increasing the pH so will make the protein no longer positive so it wont stick to column but this is not ideal

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27
Q

what moves quicker in size exclusion chromatography

A

large proteins

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28
Q

how does size exclusion chromatography work

A

small proteins go through beads, large ones will go through 1st because they wont get lost in the beads

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29
Q

what is a con to size exclusion chromatography

A

it has to run slowly, if you run it too fast by adding concentration it will increase the pressure which can crush/break the beads

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30
Q

common tags in affinity chromatography

A

His, GST, ATP-binding domain

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31
Q

how to proteins move in an SDS-PAGE gel

A

smaller proteins move further, larger proteins don’t move as far, you look for a single band at the right size to confirm a purified protein

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32
Q

what happend for isoelectric focusing and proteome analysis via 2D gels

A

inject protein sample with pH gradient, inject the proteins you want to move, neutral charge means pH=pI

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33
Q

what is modern sequencing with MS-MS

A

how proteins are sequences with mass spec, need a small sample size

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34
Q

which proteins are hard to tell apart for mass spec

A

leucine and isoleucine because same molar mass

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35
Q

what is solid phase protein synthesis

A

synthesis chemically from c terminal

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36
Q

what are the steps for solid phase protein synthesis

A
  1. link first amio acid at C term
  2. need protecting group
  3. F molecule linked to N term as protecting group
  4. remove protecting gourp
  5. add next amino acid with protecting group
  6. remove protecting group
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37
Q

visual representation of protein sequences

A

sequence logo

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38
Q

what is a signature sequence

A

insertions found only in specific taxonomic groups

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39
Q

homolog

A

refers to shared origin (derived from a common ancestor)

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40
Q

homologs (homologous protiens)

A

in different species are called orthologs

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41
Q

homologs in same species

A

paralog

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42
Q

paralog

A

gene where an isoform refers to the protein

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43
Q

what is the pauling scale

A

discovered by Linus Pauling, concept of electrons being shared

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44
Q

what can be used for determining protein structure of small proteins

A

2D NMR

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45
Q

what is used for determining structure of large proteins

A

cyro electron microscopy

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46
Q

what will not form crystals

A

non polar, hydrophobic membrane proteins, and big floppy ones (more disordered)

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47
Q

levels of protein structure

A

primary, secondary, tertiary, quaternary

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48
Q

primary structure

A

amino acid residues are connected via covalent bonds (peptide bonds) and disulfide bridges (Cys-Cys)

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49
Q

secondary structure

A

common protein folding structure, held together by hydrogen bonds between functional groups

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50
Q

tertiary structure

A

folded 3D structure of a single chain, H bonds and other weak interaction between backbone and side chains

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51
Q

quaternary structure

A

final folded structure with multiple chains

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52
Q

degrees in a trans angle

A

180 degrees

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53
Q

what are the secondary structures

A

alpha helicies and beta sheets

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54
Q

how are alpha helcies held together

A

by hydorgen bonds between functional groups on backbone

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55
Q

what is the orientation of the hydrogen bonds in alpha helices

A

parallel to axis of helix

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56
Q

range of length of h bonds on alpha helix

A

2.8-3.1A

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57
Q

is a short hydrogen bond strong or weak

A

strong

58
Q

how long is one turn of the helix

A

5.4A

59
Q

how many amino acids is one turn of the helix

A

3.6 amino acids

60
Q

how big is the rise per amino acid in the helix

A

1.5 A per residue

61
Q

how many residues in 40A helix

A

27

62
Q

diameter of a helix made of all alanine

A

5.6A

63
Q

diameter of helix with a mix of side chains

A

8-10 A

64
Q

perfect alpha helix degrees

A

ɸ=-57° Ѱ=-47°

65
Q

why does an alpha helix form

A
  1. certain amino acids perfer alpha helix formation
  2. complementary residues at i, i+3, i+4
66
Q

what percent of amino acids are alpha helices

A

25%

67
Q

which amino acids favor alpha helix formation

A

ala, arg, leu, gly, met, iso

68
Q

what are the bad residues

A

gly, pro

69
Q

why is glycine a bad amino acid

A

too flexible

70
Q

why is proline a bad amino acid

A

too rigid

71
Q

what stabilizes the n terminus

A

negative residues

72
Q

what stabilizes the C terminus

A

positive residues

73
Q

what are the 2 types of beta sheets

A

parallel and antiparallel

74
Q

parallel beta sheet

A

bent hydrogen bonds

75
Q

antiparallel beta sheets

A

stronger hydrogen bonds, more stable and more common

76
Q

length of a beta sheet per amino acid

A

3.5A for antiiparallel
3.25 A for parallel

77
Q

globular protein

A

discrete unit, mixture of secondary structure

78
Q

fibrous protein

A

structural role form long dimers

79
Q

examples of fibrous proteins

A

keratin and silk

80
Q

how many amino acids are in the smallest turn of a beta sheet

A

4

81
Q

what holds amino acids together in a beta turn

A

hydrogen bond between 1st and 4th residue

82
Q

what is a type 1 turn

A

residue 2 is a proline in cys conformatgion

83
Q

what is a type 2 turn

A

residue 2 is a glycine that can rotate easily

84
Q

how to measure secondary structure

A

circular dichorism (CD spechtrosocpy) MR

85
Q

how does CD spechtrosocpy work

A

peptide will absorb left and right plane polarized light differently

86
Q

what is ketatin made up of

A

alpha helix

87
Q

what is composed on keratin

A

skin, hair, nails, horns, calws, wool

88
Q

special keratine strucutre

A

2 alpha helices wrapped around each other (right handed)

89
Q

what are the amino acids in alpha keratin

A

ala, val, leu, met, phe, cys

90
Q

how many amino acids make up a collagen turn

A

3 residues per turn

91
Q

what is in collagen that needs vitamin C to make it

A

hypohydroxyproline

92
Q

what happens with lack of hypohyroxyproline

A

breakdown of collagen

93
Q

what are packed outside of collagen

A

pro and hyp

94
Q

what is packed on the middle of collagen

A

gly

95
Q

special strucutre of collagen

A

3 left handed alpha helices wrapped togehter to become right handed

96
Q

what is silk made of

A

layers of antiparallel sheets

97
Q

amino acid residues in silk

A

ala, gly (small, pack together with no cross linking)

98
Q

what does myoglobin do

A

in muscles and holds oxygen

99
Q

characteristics of unfolded globular proteins

A

hydrophobic effect favors 2 layers, beta and alpha segments are seperate, follow N-C folding (no knots), no crossover or right handed connections, favors twisted beta sheets, beta sheets will never be fully flat

100
Q

TIM barrel structure

A

alpha outside, beta insude
has a B-a-B loop motif, a/B barral

101
Q

motif

A

it repeats over and over again, recognizes structure with 2 or morw secondary strucutres (2a, a and B) and the connection between them

102
Q

a/b barrel

A

alternates back and forth

103
Q

domain

A

recognizable independently stable

104
Q

what kinds of proteins have lots of domains

A

large one

105
Q

functions of a protein domain

A

catalytic or regulatory

106
Q

will a protein close together in primary sequence be close in 3D space and why or why not

A

yes, because it folds as it is synthesized

107
Q

hemoglobin structure

A

quaternary
2 alpha helices
2 beta sheets

108
Q

what must be true of a quaternary structure

A

must have multiple chains, 2 fold symetry, cannot have mirror images becuase no D amino acids

109
Q

what does a homo quaternary structure mean

A

same peptide bond

110
Q

what does a hetero quaternary structure mean

A

different subunits

111
Q

how to unfold a protein

A
  1. add head
  2. adjust pH
  3. add chemicals
112
Q

how does adding heat unfold a protein

A

breaks disulfide linkages

113
Q

what chemicals can be used to unfold proteins

A

urea, guanidinium, hydrochlrodie

114
Q

what do unfolded proteins do

A

aggregate and form large fibrils

115
Q

what is needed to get an aggregated protein back to its correct shape

A

chaperones

116
Q

how can we monitor unfolding

A

CD spechtroscopy, tryptophan flouresence

117
Q

what is needed for CD spech

A

secondary structure

118
Q

what is needed for tryptophan fluresence

A

sensitive to their environment
often are inside (not exposed to H2O), need tryptophan and if it doesnt have it then we modify it

119
Q

what happens when favorable hydrogen bonds lead to a stable structure

A

will refold to its lowest energy state called the native state

120
Q

what is the point where a protein unfolds

A

melting temp

121
Q

what are chaperones that assist in folding

A

heat shock proteins

122
Q

what can we do to prevent fibrils

A

degrade the misfolded proteins right away so it doesnt have the chance to form, send to proteosome

123
Q

how many alpha helcies in myoglobin

A

8

124
Q

what group is in myoglobin

A

heme group sequestered deep in the core of the protein, preventing oxidation of Fe2+ tp Fe3+

125
Q

what is myoglobins prothestic group

A

heme

126
Q

what is myoglobins ligand

A

oxygen gas

127
Q

where is the iron held

A

in the perforin ring

128
Q

what connects the iron

A

proximal hist residue

129
Q

what does the 6th position around the iron do

A

picks up oxygen

130
Q

at what concentrations does oxygen bind myoglobin

A

high concentrations

131
Q

what does a lower Kd mean

A

better at binding to protein

132
Q

what is the kd equal to

A

concentration fo ligand needed for 50% of biding sites to be occupied

133
Q

what two proteins are structured similarly

A

myoglobin and hemoglobin

134
Q

what is sequence similarity

A

the amino acid sequence is different but they have similar properties

135
Q

how much sequence identity is needed to get similar folds among different proteins

A

20-25%

136
Q

T state

A

perfers low oxyegn concentration so it does not favor oxygen binding

137
Q

R state

A

prefers high oxygen concentration so it favors oxygen binidng

138
Q

what must happen between the T and R groups

A

they must be able to switch from R state in the lungs to T state in the tissues

139
Q

at what pH is O2 delievred most effectively

A

lower

140
Q

does t state drop off more oxygen in basic or acidic environments

A

acidic

Biochem (4 decks)

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