Test 2 Flashcards
(140 cards)
1
Q
what are all living organisms made from
A
a set of some of the 20 amino acids
2
Q
how are amino acids joined
A
in linear sequences through amide or peptide bonds
3
Q
what qualities allow a protein to be separated
A
differences in chemical and functional properties based on their amino acid sequence
4
Q
what are the primary building blocks of proteins
A
amino acids
5
Q
what is a zwitter ion
A
in pH range of 3-10, neutral because one is protonated and one is not
6
Q
what conformation are amino acids in nature
A
L
7
Q
what is an amino acid residue
A
when it looses and H2O to form a peptide bond
8
Q
what is the N-Calpha bond called
A
phi
9
Q
what is the Calpha-C bond called
A
psi
10
Q
what is the C-N (peptide bond called)
A
omega
11
Q
what is a dihedral angle in terms of amino acids
A
angle between planes formed by the backbone
12
Q
what is pI
A
ph when charge on molecule is zero, in between buffering zones
13
Q
what are the nonpolar amino acids
A
glycine, alanine, proline, valine, leucine, isoleucine, methionine
14
Q
what are the polar uncharged amino acids
A
serine, threonine, cysteine, asparagine, glutamine
15
Q
aromatic amino acids
A
phenylalanine, tyrosine, tryptophan
16
Q
positvely charged amino acids
A
lysine, arginine, histidine
17
Q
negatively charged amino acids
A
aspartate, glutamate
18
Q
what many buffering zones does each amino acid have
A
at least 2
19
Q
what are the modification for amino acids
A
methylation and acetylation
20
Q
equation for estimating weight of an amino acid
A
of residues x 110 Da
21
Q
how can you purify proteins
A
charge, size and tags
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
23
Q
cation exchange
A
cations stick (resin is negative)
24
Q
anion exchnage
A
anions stick (resin is positive)
25
what do you do if positive proteins get stuck to the positive column
add more concetrated salt water, it will block resin negative allowing protein to come free
26
The concentrated salt water increases the pH in the column, how does this allow the protein to be unstuck
increasing the pH so will make the protein no longer positive so it wont stick to column but this is not ideal
27
what moves quicker in size exclusion chromatography
large proteins
28
how does size exclusion chromatography work
small proteins go through beads, large ones will go through 1st because they wont get lost in the beads
29
what is a con to size exclusion chromatography
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
30
common tags in affinity chromatography
His, GST, ATP-binding domain
31
how to proteins move in an SDS-PAGE gel
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
32
what happend for isoelectric focusing and proteome analysis via 2D gels
inject protein sample with pH gradient, inject the proteins you want to move, neutral charge means pH=pI
33
what is modern sequencing with MS-MS
how proteins are sequences with mass spec, need a small sample size
34
which proteins are hard to tell apart for mass spec
leucine and isoleucine because same molar mass
35
what is solid phase protein synthesis
synthesis chemically from c terminal
36
what are the steps for solid phase protein synthesis
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
37
visual representation of protein sequences
sequence logo
38
what is a signature sequence
insertions found only in specific taxonomic groups
39
homolog
refers to shared origin (derived from a common ancestor)
40
homologs (homologous protiens)
in different species are called orthologs
41
homologs in same species
paralog
42
paralog
gene where an isoform refers to the protein
43
what is the pauling scale
discovered by Linus Pauling, concept of electrons being shared
44
what can be used for determining protein structure of small proteins
2D NMR
45
what is used for determining structure of large proteins
cyro electron microscopy
46
what will not form crystals
non polar, hydrophobic membrane proteins, and big floppy ones (more disordered)
47
levels of protein structure
primary, secondary, tertiary, quaternary
48
primary structure
amino acid residues are connected via covalent bonds (peptide bonds) and disulfide bridges (Cys-Cys)
49
secondary structure
common protein folding structure, held together by hydrogen bonds between functional groups
50
tertiary structure
folded 3D structure of a single chain, H bonds and other weak interaction between backbone and side chains
51
quaternary structure
final folded structure with multiple chains
52
degrees in a trans angle
180 degrees
53
what are the secondary structures
alpha helicies and beta sheets
54
how are alpha helcies held together
by hydorgen bonds between functional groups on backbone
55
what is the orientation of the hydrogen bonds in alpha helices
parallel to axis of helix
56
range of length of h bonds on alpha helix
2.8-3.1A
57
is a short hydrogen bond strong or weak
strong
58
how long is one turn of the helix
5.4A
59
how many amino acids is one turn of the helix
3.6 amino acids
60
how big is the rise per amino acid in the helix
1.5 A per residue
61
how many residues in 40A helix
27
62
diameter of a helix made of all alanine
5.6A
63
diameter of helix with a mix of side chains
8-10 A
64
perfect alpha helix degrees
ɸ=-57° Ѱ=-47°
65
why does an alpha helix form
1. certain amino acids perfer alpha helix formation
2. complementary residues at i, i+3, i+4
66
what percent of amino acids are alpha helices
25%
67
which amino acids favor alpha helix formation
ala, arg, leu, gly, met, iso
68
what are the bad residues
gly, pro
69
why is glycine a bad amino acid
too flexible
70
why is proline a bad amino acid
too rigid
71
what stabilizes the n terminus
negative residues
72
what stabilizes the C terminus
positive residues
73
what are the 2 types of beta sheets
parallel and antiparallel
74
parallel beta sheet
bent hydrogen bonds
75
antiparallel beta sheets
stronger hydrogen bonds, more stable and more common
76
length of a beta sheet per amino acid
3.5A for antiiparallel
3.25 A for parallel
77
globular protein
discrete unit, mixture of secondary structure
78
fibrous protein
structural role form long dimers
79
examples of fibrous proteins
keratin and silk
80
how many amino acids are in the smallest turn of a beta sheet
4
81
what holds amino acids together in a beta turn
hydrogen bond between 1st and 4th residue
82
what is a type 1 turn
residue 2 is a proline in cys conformatgion
83
what is a type 2 turn
residue 2 is a glycine that can rotate easily
84
how to measure secondary structure
circular dichorism (CD spechtrosocpy) MR
85
how does CD spechtrosocpy work
peptide will absorb left and right plane polarized light differently
86
what is ketatin made up of
alpha helix
87
what is composed on keratin
skin, hair, nails, horns, calws, wool
88
special keratine strucutre
2 alpha helices wrapped around each other (right handed)
89
what are the amino acids in alpha keratin
ala, val, leu, met, phe, cys
90
how many amino acids make up a collagen turn
3 residues per turn
91
what is in collagen that needs vitamin C to make it
hypohydroxyproline
92
what happens with lack of hypohyroxyproline
breakdown of collagen
93
what are packed outside of collagen
pro and hyp
94
what is packed on the middle of collagen
gly
95
special strucutre of collagen
3 left handed alpha helices wrapped togehter to become right handed
96
what is silk made of
layers of antiparallel sheets
97
amino acid residues in silk
ala, gly (small, pack together with no cross linking)
98
what does myoglobin do
in muscles and holds oxygen
99
characteristics of unfolded globular proteins
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
TIM barrel structure
alpha outside, beta insude
has a B-a-B loop motif, a/B barral
101
motif
it repeats over and over again, recognizes structure with 2 or morw secondary strucutres (2a, a and B) and the connection between them
102
a/b barrel
alternates back and forth
103
domain
recognizable independently stable
104
what kinds of proteins have lots of domains
large one
105
functions of a protein domain
catalytic or regulatory
106
will a protein close together in primary sequence be close in 3D space and why or why not
yes, because it folds as it is synthesized
107
hemoglobin structure
quaternary
2 alpha helices
2 beta sheets
108
what must be true of a quaternary structure
must have multiple chains, 2 fold symetry, cannot have mirror images becuase no D amino acids
109
what does a homo quaternary structure mean
same peptide bond
110
what does a hetero quaternary structure mean
different subunits
111
how to unfold a protein
1. add head
2. adjust pH
3. add chemicals
112
how does adding heat unfold a protein
breaks disulfide linkages
113
what chemicals can be used to unfold proteins
urea, guanidinium, hydrochlrodie
114
what do unfolded proteins do
aggregate and form large fibrils
115
what is needed to get an aggregated protein back to its correct shape
chaperones
116
how can we monitor unfolding
CD spechtroscopy, tryptophan flouresence
117
what is needed for CD spech
secondary structure
118
what is needed for tryptophan fluresence
sensitive to their environment
often are inside (not exposed to H2O), need tryptophan and if it doesnt have it then we modify it
119
what happens when favorable hydrogen bonds lead to a stable structure
will refold to its lowest energy state called the native state
120
what is the point where a protein unfolds
melting temp
121
what are chaperones that assist in folding
heat shock proteins
122
what can we do to prevent fibrils
degrade the misfolded proteins right away so it doesnt have the chance to form, send to proteosome
123
how many alpha helcies in myoglobin
8
124
what group is in myoglobin
heme group sequestered deep in the core of the protein, preventing oxidation of Fe2+ tp Fe3+
125
what is myoglobins prothestic group
heme
126
what is myoglobins ligand
oxygen gas
127
where is the iron held
in the perforin ring
128
what connects the iron
proximal hist residue
129
what does the 6th position around the iron do
picks up oxygen
130
at what concentrations does oxygen bind myoglobin
high concentrations
131
what does a lower Kd mean
better at binding to protein
132
what is the kd equal to
concentration fo ligand needed for 50% of biding sites to be occupied
133
what two proteins are structured similarly
myoglobin and hemoglobin
134
what is sequence similarity
the amino acid sequence is different but they have similar properties
135
how much sequence identity is needed to get similar folds among different proteins
20-25%
136
T state
perfers low oxyegn concentration so it does not favor oxygen binding
137
R state
prefers high oxygen concentration so it favors oxygen binidng
138
what must happen between the T and R groups
they must be able to switch from R state in the lungs to T state in the tissues
139
at what pH is O2 delievred most effectively
lower
140
does t state drop off more oxygen in basic or acidic environments
acidic
