Amino acids ch. 6 and 7 Flashcards
1
Q
All amino acids except _____ have L forms
A
Glycine
2
Q
What two things bind to peptide bonds bond
A
O- of one amino acid to NH3+ of another one
3
Q
Zwitterion
A
Amino group is positively charged and carboxyl group is negatively charged
4
Q
Cysteine forms what bonds
A
Disulfide
5
Q
MM form
A
Skeletal muscle
6
Q
BB form
A
Brain
7
Q
MB form
A
Cardiac muscle
8
Q
What protein will be leaked during a myocardial infarction
A
Troponin
9
Q
Posttranslational modifications
A
Occur after the protein has folded into into a 3D structure
10
Q
Primary structure
A
Covalent sequence of amino acid residues
11
Q
Secondary structure
A
Regular, repeating noncovalent structure resulting from H bonding
12
Q
Tertiary structure
A
Determined by R group interactions, includes hydrogen binding
13
Q
Quartenary structure
A
Multiple subunits binded through noncovalent interactions
14
Q
Side chains are ____ to each other and alternate above and below peptide chain
A
Trans
15
Q
What forms a series of rigid planes in a protein
A
C and N of peptide bonds
16
Q
What translates mRNA into protein
A
Ribosomes
17
Q
mRNA is translated in which direction
A
5’ to 3’
N terminal to C terminal
18
Q
What do the coils and folds from the secondary structure result from
A
Hydrogen bonds
19
Q
Coiled
A
a-helix
20
Q
Folded
A
b-pleated sheet
21
Q
What AA is a helix breaker
A
Proline
22
Q
Structure of secondary structure
A
Each O of carbonyl attaches to H from NH group,
determined by backbone interaction, Hydrogen bonded
23
Q
What determines tertiary structure
A
Interactions between R groups, NOT backbone components
24
Q
What are strong covalent bonds called
A
Disulfide bridges
25
What do chaperone proteins do
Prevent misfolding of protein by shielding the hydrophobic surfaces
26
Hsp70 proteins
Bind to polypeptides that are synthesized on ribosomes
Shields hydrophobic forces to prevent misfolding
27
Hsp60 proteins (chaperonins)
Assist Hsp70 and have ATPase activity
28
AGEs
Advanced glycosylation end products
29
Denaturants
Heat
lower than a pH of 3
Urea
30
Removal of denaturants can lead to
Protein renaturations
31
Prions
Proteins that induce bad conformation of protein
32
Myoglobin
Monomer of globin
33
Heme has how many rings
4 pyrole rings
34
Proximal histidine blinds to what on heme
Fe2+ on side of poryphyrin ring
35
T state
Tense state with LOW affinity for O2
36
R state
Relaxed state with HIGH affinity for O2
37
Nonpolar, aliphatic amino acids
Glycine, Alanine, proline, valine, leucine, isoleucine, METHIONINE, TRYPTOPHAN, PHENYLALINE
38
Aromatic amino acids
Phenylaline, tyrosine, tryptophan
39
Polar, uncharged amino acids
asparagine, glutamine, serine, threonine, CYSTEINE, TYROSINE
40
Negative charge (acidic)
Asparate, glutamate
41
Positive charge (basic)
Arginine, lysine, histidine
42
Variant region
Noncritical region
43
Hypervariable region
Many different amino acid residues tolerated at that region
44
Conservative substitutions
Replace one AA with another one with a similar structure
45
Invariant region
Forms binding sites, same AA sequence between individuals or species
46
polymorphism
Variants of an allele that occurs with a significant frequency
47
What is PI points
Isoelectric point
the pH at which the charge is 0
48
Superfamily
Very large families of homologous proteins
49
Isozymes
Catalyze the same reactions
50
Isoforms
Have same function, but different properties and sequence structures
51
What hormone is highly conserved between species with no amino acid substitutions
Insulin
52
Structure of insulin
One long polypeptide chain, cleaved by protease after disulfide bonds form
53
What are the invariant residues in insulin
cysteine residues
54
When do posttranslational modifications occur
After protein folded into 3D form
55
What is altered in a posttranslational modification
A specific amino acid
56
What is the B-turn?
nonrepetitive, hairpin loop
Found on protein surface
57
What protein structure is flexible and dynamic
Tertiary
58
What main interaction is in tertiary proteins
Hydrophobic interactions
59
G-actin fold
ATP is bound to middle of cleft
Antiparallel
60
NAD+ fold
Parallel, domain 1 forms NAD+ bond
61
B-andrenergic structure
a-helix goes through membrane in loops
62
cis-trans-prolyl isomerases
Converts peptide bond in proline from trans to cis
Makes hairpin turns
63
Protein disulfide isomerases
Breaks and reforms disulfide bonds between 2 cysteines
64
Hsp70
Shield hydrophobic surfaces to prevent aggregation, prevents it from folding prematurely
65
Hsp60
serves as a template for folding, unfolded protein fits into barrel
Has ATPase activity
66
Nonenzymatic glycosylation
glucose binds to exposed amino group
leads to irriversible glycosylated protein
67
What causes AGEs
Large protein aggregates of glycosylated proteins
68
PrPsc structure
More B-sheets
69
Prpc structure
No B-sheets, all a-helices
70
What does PrPsc do
Lowers activation energy, makes it easier for proteins to refold into PrPsc, leads to multimeric assembly which is RESISTANT to protealytic digestion
71
Multimeric complexes from Prpsc are resistant to
Protealytic digestions
72
Prion infections
mad cow disease, doctor-induced CJD, Kuru
73
Sporadic or inherited prions
Familial CJD
74
Holoprotein
With prosthetic group
75
Apopoprotein
Without prosthetic group
76
What is heme
Prosthetic group
77
Myoglobin
Monomeric, globular
78
Hemoglobin structure
Tetramer
79
What is the function of heme
Oxygen binding site
80
The 4 monomers of hemoglobin are held together by
Noncovalent forces
81
Tertiary structure of myoglobin
Globulin fold
8 a-helices connected by short coils
82
how many poryphyrin rings in heme
4
83
Where does proximal histidine bind to in hemoglobin
Fe2+ on one side of porphyrin ring
84
How does oxygen binding in hemoglobin work
Proximal histidine binds to Fe2+ on one side of porphyrin ring, causes fe2+ to be pulled above plane
O2 binds to Fe2+ on the other side
O2 causes Fe2+ to be pulled back into plane of ring
85
What causes cooperativity of O2 binding in hemoglobin
Conformational change of tertiary structure when O2 binds
86
Curve for myoglobin
Hyperbolic
87
Curve for hemoglobin
Sigmoidal
88
P50
Half saturated with O2
89
Ligand for NAD+
LDH domain
90
Ligand for ATP
G-actin
91
Ligand for b2-agrenergic receptor
Adrenaline
92
Ka
Association constant
93
Ka is what to Kd
1/kd or inverse
94
what does high affinity mean
Less of the ligand is required to fully occupy the binding site
Tighter binding
95
What is the shape of the curve of the sigmoidal graph
S shape
96
Does myoglobin or hemoglobin have a higher affinity for oxygen
Myoglobin
97
Why is the P50 of myoglobin so low?
It has a high affinity for O2, so it takes less O2 to saturate it halfway
98
At lower levels of PO2, what binds to oxygen better
Myoglobin
99
what is the p50 of a high affinity
Low p50
100
what does Km tell
concentration of substrate required for enzyme to achieve 50% of velocity
101
p50 equals
Kd (inverse of Ka)
102
What end defines the beginning of a polypeptide
N-terminal
103
What 3 amino acids can be phosphorylated
Serine, threonine, tyrosine
104
Nonconservative substitution
Replace one AA with one that has a completely different structure
Ex. nonpolar replaced with polar
105
What does the left side of the hemoglobin graph show
High affinity
106
What does the right side of the hemoglobin graph mean
Low affinity
107
As pH decreases, affinity...
Decreases
108
Co2 forms carbamates with the ____ of the b-chain of hemoglobin (Hb)
N terminal
109
Strongest bond
Covalent bonds
110
Hydrogen bonds are the strongest when
Molecules are in a straight line
111
Hydrophobic amino acids
Leucine and isoleucine
112
What does hydrophobic regions do when they interact
Reduces the size of hydration layer
113
How do polypeptides fold if they have hydrophobic molecules
The hydrophobic molecules move towards the inside (hydrophilic stays outside) to avoid contact with the water surrounding
114
What change in amino acids causes sickle cell
Glutamic acid to valine
115
Does fetal hemoglobin or adult hemoglobin have a higher affinity
Fetal hemoglobin
116
Does fetal hemoglobin or adult hemoglobin have a mutation that can cause sickle cell anemia
Adult hemoglobin
117
Higher pH means ___ Co2
Lower
118
Lower pH means ____ CO2
Higher CO2, more protons
119
acidic pH does what to affinity
Decreases
120
What movement does oxygen binding to heme cause
It causes conformational change to the subunit that it's bonded to ionically. The loss of the ionic bond will induce conformational change in the rest of the subunits.
121
Heme group with oxygen does what
Pulls Fe into plane of ring
122
Disulfide bridges are required to
Maintain the function of insulin
123
Prosthetic group
Organic ligand that does not dissociate until protein is degraded (NOT an amino acid)
124
Soluble vs. transmembrane proteins
Transmembrane: found in hydrophobic lipid layer
Soluble: found in hydrophilic, water environments
125
What does L form mean
NH3+ is on left side of carbon, H is on right
126
What does D form mean
H is on left side of carbon, NH3+ is on the right
127
There are 9 different isoforms of what
Adenylate cyclase
128
What does adenylate cyclase respond to
Adrenaline
129
What type of protein causes prions
Anti parallel b-pleated sheets
130
Nonpolar amino acids are also
Hydrophobic
131
What structure is the end product of hemoglobin with O2 binding
Quartenary
132
