Exam Two Flashcards
1
Q
What level structure is the amino acid sequence?
A
Primary
2
Q
What level structure is alpha helices and beta sheets?
A
Secondary
3
Q
What level structure is 3D folding?
A
Tertiary
4
Q
What level structure do subunits comprise?
A
Quaternary
5
Q
What is the structure level that is not necessarily applicable to every protein?
A
Quaternary
6
Q
What changes electron distribution within a peptide bond?
A
differences in electronegativity
7
Q
What makes the peptide bond so rigid that it can only rotate around C-alpha?
A
the resonance double bond between the C and N termini
8
Q
Why do secondary structures form?
A
to satisfy hydrogen bonding requirement and minimize steric strain
9
Q
What secondary structure is a single strand twisted?
A
Alpha Helix
10
Q
Are right or left handed alpha helices more favorable?
A
right
11
Q
Why are right handed alpha helices more favorable?
A
There is minimized steric strain between the side chains and the main chain
12
Q
How many residues ahead does the carbonyl form a hydrogen bond with N-H?
A
approximately 4
13
Q
What is the backbone of an alpha helix/what drives hydrogen bonding?
A
Van der Waals forces
14
Q
Do the side groups on an alpha helix extend inward or outward?
A
outward
15
Q
What secondary structure is comprised of several strands arranged to be flat?
A
Beta Sheet
16
Q
How is the Hydrogen Bond requirement met for beta sheets?
A
bonding between neighboring strands
17
Q
Do the side chains on a beta sheet extend on one face or on both faces?
A
both faces
18
Q
Are fibrous proteins soluble or insoluble?
A
insoluble
19
Q
What fibrous protein is a triple helix?
A
collagen
20
Q
What fibrous protein is comprised of stacked beta sheets?
A
silk
21
Q
What fibrous protein is comprised of alpha helices that are cross-linked by disulfide bonds?
A
alpha-keratin
22
Q
What structural protein forms a coiled-coil structure?
A
keratin
23
Q
What structural protein is the most abundant in mammals?
A
Collagen
24
Q
What structural protein is rich in proline?
A
Collagen
25
What are the three amino acids that primarily repeat to form the collagen triple helix?
Gly-Pro-Hyp
26
What is the most common secondary structure? Alpha helices or beta sheets?
Alpha helices?
27
How much of secondary structure is irregular? i.e. not alpha helix or beta sheet?
46%
28
what is the driving force of secondary structure?
hydrogen bonds among peptide groups
29
What is a domain?
Single structural unit with several secondary structures within
30
Is the hydrophobic effect or hydrogen bonding more important for domain stability and tertiary folding?
hydrophobic effect
31
How is a protein's 3D structure mainly formed?
tucking hydrophobic side groups in
32
Which shape of domain has an open middle?
beta barrel
33
Which shape of domain has a pretty crowded middle?
saddle
34
What are three other stabilizing factors in the tertiary structure of a protein?
disulfide bonds, ion pairs, zinc fingers
35
What kind of environment are disulfide bonds normally found in?
oxidizing (extracellular)
36
Where is folding information stored in a protein?
Within the protein's primary sequence
37
Is structure or sequence more conserved?
structure
38
What are the two ways to denature proteins?
heating, adding salt or urea
39
What does adding salt or urea do to denature proteins?
interfere with structure of water (solvent) and disrupt the hydrogen bonds
40
What are proteins that prevent misfolding and aggregation of unfolded peptides?
chaperones
41
How many hydrophobic cores are in a tertiary structure?
One
42
What is the prosthetic group that contains the iron where O2 binds?
heme
43
What is the single peptide chain that carries O2 in muscles via diffusion?
Myoglobin
44
What is the tetramer that carries O2 from lungs to tissue through the bloodstream?
Hemoglobin
45
Why is hemoglobin so much more sophisticatd?
It knows when to grab O2 and when to release it
46
Oxygen binding to Mb or Hb is _________.
Transient
47
How do ligands bind?
Via the same noncovalent interactions that dictate protein structure
48
What allows Hb and Mb binding to Oxygen to be transient?
the fact that you bind with the same interactions that dictate protein structure
49
What are the 6 binding sites on the central Fe (II) atom of the heme group bound to?
4 Nitrogen atoms, protein at His, and O2
50
Why is heme not an effective oxygen carrier by itself/not bound to Hb or Mb?
By itself, Fe (II) is easily oxidized to Fe(III), which cannot bind O2.
51
Would a lower or higher p50 indicate better affinity for Ow?
Lower
52
Does myoglobin or hemoglobin have a higher p50?
Hemoglobin
53
Why does myoglobin bind oxygen better than hemoglobin?
the allosteric effect of quaternary structure that hemoglobin experiences
54
Does the T or R state have a higher affinity for Oxygen?
R = relaxed state
55
What does O2 binding trigger in hemoglobin?
a T to R conformational change
56
Does Hb bind oxygen better at lower or higher pH?
Higher pH
57
Is Oxygen released at low or high pH?
Low pH
58
Lung or tissue: CO2 rich and therefore has a low pH
Tissue
59
Lung or tissue: CO2 expired and therefore has a high pH
Lung
60
Do lungs or tissue bind oxygen better?
lungs
61
What kind of tissue is being described?
1. CO2 produced decreases pH (increases H+)
2. lactic acid produced by active muscle also decreases pH
3. Hb releases more O2
respiring
62
What does BPG do?
stabilize the deoxy form of Hb
63
What occurs in the absence of BPG?
too tight binding
64
What is the amino acid change in fetal Hb that causes a lower affinity for BPG and thus a higher affinity for O2?
His to Ser
65
Is BPG neutral, negatively charged, or positively charged?
negatively charged
66
What cells produce antibodies?
B cells
67
How does antibodies binding to antigens affect cellular response?
binding will mark the antigen for destruction or interfere with its function
68
where does an antibody bind to the antigen?
epitope of the antigen
69
What are antigens typically made of?
macromolecules
70
Is Fab made up of constant, variable, or both domains?
both
71
Is Fc made up of constant, variable, or both domains?
Constant
72
Where does the antigen bind to the antibody? Fab or Fc?
Fab
73
Is Fab made up of heavy, light, or both chains?
Both
74
Is Fc made up of heavy, light, or both chains?
Heavy
75
How do antigens bind?
induced fit
76
What does antibody specificity detect?
a protein/antigen of interest
77
What does ELISA detect?
the presence/amount of antibodies
78
What does Western blot/immunoblot detect?
a specific protein within a mixture
79
What is the covid antibody test?
ELISA
80
what is the covid antigen test?
rapid test
81
What does a catalyst do?
accelerates the reaction rate by lowering the energy of activation
82
What kind of enzyme catalyzes the transfer of electrons?
oxidoreductase
83
What kind of enzyme catalyzes group transfer reactions
transferases
84
What kind of enzyme catalyzes hydrolysis reactions
hydrolases
85
What kind of enzyme catalyzes cleavage of C-C, C-O, or C-N by elimination, leaving double bonds or rings?
Lyases
86
What kind of enzyme catalyzes transfer of groups within molecules to yield isomeric forms?
Isomerases
87
What kind of enzyme catalyzes formation of C-C, C-S, C-O, and C-N bonds by condensation reactions coupled to cleavage of ATP?
Ligases
88
Where is the active site usually found?
At the interface of 2 domains
89
What is the equation of S to P with the presence of an enzyme?
E+S ---> ES ---> EP ---> E+P
90
How does an enzyme lower the activation energy?
by forming the ES complex
91
What are transition state analogs?
transition state lookalikes that bind to the enzyme better than the substrate
92
What are non-protein substances that turn on inactive enzymes?
Cofactors
93
How is acid base catalysis pH dependent?
if pH of the enzyme < pKa then enzyme will act as an acid
if pH of the enzyme > pKa then enzyme will act as a base
94
What are the amino acids commonly used in general acid-base catalysis?
Glu, Asp, Lys, Arg, Cys, His, Ser, Tyr
95
What are the stages of covalent catalysis?
1. nucleophilic enzyme attacks electrophilic substrate
2. temporary covalent bond formed between the nucleophile and electrophile
3. rearrangement of electrons
4. removal of enzyme: rearrangement of electrons into the product
96
What is a sure sign of covalent catalysis?
Schiff base formation
97
What amino acids would form a Schiff base?
Asn, Gln, Lys, Arg, His
98
What are some of the metals that are not catalytic and therefore would not participate in metal catalysis?
Na+, K+, Ca2+
99
What is the most common way that metal catalysis works?
metals facilitate ionization of water to help form a nucleophilic OH
100
Where does chymotrypsin cleave?
after Phe, Trp, and Tyr residues
101
What kind of catalysis does chymotrypsin participate in?
Acid/Base AND covalent
102
What is the catalytic triad of serine proteases?
3 important amino acid residues in its catalytic site
103
What is the catalytic triad made up of in all serine proteases?
His 57, Asp 102, Ser 195
104
How can chymotrypsin's catalytic triad be so far away from each other on their chain and still interact?
They are close in the 3D structure
105
What kind of molecule does chymotrypsin accept into the specificity pocket, and therefore, what is important about the structure of the specificity pocket itself?
bulky, aromatic molecules so the pocket has lots of space
106
What kind of molecule does trypsin accept into the specificity pocket, and therefore, what is important about the structure of the specificity pocket itself?
positively charged molecules so the pocket has a negatively charged molecule
107
What kind of molecule does elastase accept into the specificity pocket, and therefore, what is important about the structure of the specificity pocket itself?
small, non-charged molecules so the pocket is crowded and non-charged
108
What are the 2 important mechanisms for transition state stabilization in chymotrypsin?
Oxyanion hole and low barrier hydrogen bonds between Asp 102 and His 57
109
What kind of catalysis does RNAse participate in?
Acid/Base
110
Why does RNAse have two different His residues with DIFFERENT pKas?
One works as an acid, one works as a base
111
Why doesn't RNAse work on DNA?
the OH in the mechanism that is found only on RNA and not DNA is very important
112
What enzyme breaks up bacterial cell wall's polysaccharides (peptidoglycan)
lysozyme
113
What does the binding of peptidoglycan to lysozyme do to the structure?
Changes the conformation of the D ring so the bond to be cut will align
114
is NAG or NAM recognized in the peptidoglycan
NAM
115
What is an inhibitor of transpeptidase
penicillin
116
What breaks open the beta-lactam ring of penicillin and thus inactivates it?
beta-lactamase
117
What is an inhibitor of beta-lactamase
clavulanic acid (augmentin)
118
How is chymotrypsin activated?
By removal of 2 dipeptides
119
How does activation affect the catalytic activity of an enzyme?
There isn't that much change, but it does open up the specificity pocket so that it is more accessible to the substrate and open up the oxyanion hole
120
What do protease inhibitors do?
Act as a safety backup; inhibit proteases in the case of premature activation
121
How do protease inhibitors work?
Once they are bound, the complex is too tight so that the leaving group can't leave and water can't enter
122
What is an example of a REVERSIBLE covalent modification?
phosphorylation
123
What enzyme adds phosphate groups onto a substrate?
kinase
124
What enzyme removes phosphate groups from a substrate?
Phosphatase
125
What is an example of a noncovalent modification?
allosteric regulators
126
How does modulator binding affect the enzyme?
It changes the conformation of the entire enzyme so that the substrate can bind better
127
Does the modulator bind to the catalytic subunit or the regulatory subunit?
regulatory
128
Which amino acids do kinases transfer phosphates to?
Ser, Thr, and Tyr
129
What does a curved arrow in a reaction represent?
the movement of an electron pair
130
How many oxygen atoms can Hb bind at once?
4
131
How many oxygen atoms can Mb bind at once?
1
132
What is the shape of the hemoglobin-oxygen binding curve?
sigmoidal
133
Which test has proteins in their native state?
ELISA
134
Which test has proteins with no higher order structure?
western blotting
135
Which test are proteins transferred to a membrane or a sheet?
western blotting
136
What fragments of an antibody crystallize readily?
Fc
137
What fragments of an antibody are recognized by macrophage surface receptors?
Fc
138
What fragments of an antibody often undergo conformational changes?
Fab
139
What fragments of an antibody contain the immunoglobulin fold?
Both Fab and Fc
