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CHM 432 > Exam Two > Flashcards

Exam Two Flashcards

1
Q

What level structure is the amino acid sequence?

A

Primary

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2
Q

What level structure is alpha helices and beta sheets?

A

Secondary

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3
Q

What level structure is 3D folding?

A

Tertiary

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4
Q

What level structure do subunits comprise?

A

Quaternary

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5
Q

What is the structure level that is not necessarily applicable to every protein?

A

Quaternary

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6
Q

What changes electron distribution within a peptide bond?

A

differences in electronegativity

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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

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8
Q

Why do secondary structures form?

A

to satisfy hydrogen bonding requirement and minimize steric strain

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9
Q

What secondary structure is a single strand twisted?

A

Alpha Helix

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10
Q

Are right or left handed alpha helices more favorable?

A

right

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11
Q

Why are right handed alpha helices more favorable?

A

There is minimized steric strain between the side chains and the main chain

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12
Q

How many residues ahead does the carbonyl form a hydrogen bond with N-H?

A

approximately 4

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13
Q

What is the backbone of an alpha helix/what drives hydrogen bonding?

A

Van der Waals forces

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14
Q

Do the side groups on an alpha helix extend inward or outward?

A

outward

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15
Q

What secondary structure is comprised of several strands arranged to be flat?

A

Beta Sheet

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16
Q

How is the Hydrogen Bond requirement met for beta sheets?

A

bonding between neighboring strands

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17
Q

Do the side chains on a beta sheet extend on one face or on both faces?

A

both faces

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18
Q

Are fibrous proteins soluble or insoluble?

A

insoluble

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19
Q

What fibrous protein is a triple helix?

A

collagen

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20
Q

What fibrous protein is comprised of stacked beta sheets?

A

silk

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21
Q

What fibrous protein is comprised of alpha helices that are cross-linked by disulfide bonds?

A

alpha-keratin

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22
Q

What structural protein forms a coiled-coil structure?

A

keratin

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23
Q

What structural protein is the most abundant in mammals?

A

Collagen

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24
Q

What structural protein is rich in proline?

A

Collagen

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25
Q

What are the three amino acids that primarily repeat to form the collagen triple helix?

A

Gly-Pro-Hyp

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26
Q

What is the most common secondary structure? Alpha helices or beta sheets?

A

Alpha helices?

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27
Q

How much of secondary structure is irregular? i.e. not alpha helix or beta sheet?

A

46%

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28
Q

what is the driving force of secondary structure?

A

hydrogen bonds among peptide groups

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29
Q

What is a domain?

A

Single structural unit with several secondary structures within

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30
Q

Is the hydrophobic effect or hydrogen bonding more important for domain stability and tertiary folding?

A

hydrophobic effect

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31
Q

How is a protein’s 3D structure mainly formed?

A

tucking hydrophobic side groups in

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32
Q

Which shape of domain has an open middle?

A

beta barrel

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33
Q

Which shape of domain has a pretty crowded middle?

A

saddle

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34
Q

What are three other stabilizing factors in the tertiary structure of a protein?

A

disulfide bonds, ion pairs, zinc fingers

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35
Q

What kind of environment are disulfide bonds normally found in?

A

oxidizing (extracellular)

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36
Q

Where is folding information stored in a protein?

A

Within the protein’s primary sequence

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37
Q

Is structure or sequence more conserved?

A

structure

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38
Q

What are the two ways to denature proteins?

A

heating, adding salt or urea

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39
Q

What does adding salt or urea do to denature proteins?

A

interfere with structure of water (solvent) and disrupt the hydrogen bonds

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40
Q

What are proteins that prevent misfolding and aggregation of unfolded peptides?

A

chaperones

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41
Q

How many hydrophobic cores are in a tertiary structure?

A

One

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42
Q

What is the prosthetic group that contains the iron where O2 binds?

A

heme

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43
Q

What is the single peptide chain that carries O2 in muscles via diffusion?

A

Myoglobin

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44
Q

What is the tetramer that carries O2 from lungs to tissue through the bloodstream?

A

Hemoglobin

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45
Q

Why is hemoglobin so much more sophisticatd?

A

It knows when to grab O2 and when to release it

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46
Q

Oxygen binding to Mb or Hb is _________.

A

Transient

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47
Q

How do ligands bind?

A

Via the same noncovalent interactions that dictate protein structure

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48
Q

What allows Hb and Mb binding to Oxygen to be transient?

A

the fact that you bind with the same interactions that dictate protein structure

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49
Q

What are the 6 binding sites on the central Fe (II) atom of the heme group bound to?

A

4 Nitrogen atoms, protein at His, and O2

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50
Q

Why is heme not an effective oxygen carrier by itself/not bound to Hb or Mb?

A

By itself, Fe (II) is easily oxidized to Fe(III), which cannot bind O2.

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51
Q

Would a lower or higher p50 indicate better affinity for Ow?

A

Lower

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52
Q

Does myoglobin or hemoglobin have a higher p50?

A

Hemoglobin

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53
Q

Why does myoglobin bind oxygen better than hemoglobin?

A

the allosteric effect of quaternary structure that hemoglobin experiences

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54
Q

Does the T or R state have a higher affinity for Oxygen?

A

R = relaxed state

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55
Q

What does O2 binding trigger in hemoglobin?

A

a T to R conformational change

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56
Q

Does Hb bind oxygen better at lower or higher pH?

A

Higher pH

57
Q

Is Oxygen released at low or high pH?

A

Low pH

58
Q

Lung or tissue: CO2 rich and therefore has a low pH

A

Tissue

59
Q

Lung or tissue: CO2 expired and therefore has a high pH

A

Lung

60
Q

Do lungs or tissue bind oxygen better?

A

lungs

61
Q

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

A

respiring

62
Q

What does BPG do?

A

stabilize the deoxy form of Hb

63
Q

What occurs in the absence of BPG?

A

too tight binding

64
Q

What is the amino acid change in fetal Hb that causes a lower affinity for BPG and thus a higher affinity for O2?

A

His to Ser

65
Q

Is BPG neutral, negatively charged, or positively charged?

A

negatively charged

66
Q

What cells produce antibodies?

A

B cells

67
Q

How does antibodies binding to antigens affect cellular response?

A

binding will mark the antigen for destruction or interfere with its function

68
Q

where does an antibody bind to the antigen?

A

epitope of the antigen

69
Q

What are antigens typically made of?

A

macromolecules

70
Q

Is Fab made up of constant, variable, or both domains?

A

both

71
Q

Is Fc made up of constant, variable, or both domains?

A

Constant

72
Q

Where does the antigen bind to the antibody? Fab or Fc?

A

Fab

73
Q

Is Fab made up of heavy, light, or both chains?

A

Both

74
Q

Is Fc made up of heavy, light, or both chains?

A

Heavy

75
Q

How do antigens bind?

A

induced fit

76
Q

What does antibody specificity detect?

A

a protein/antigen of interest

77
Q

What does ELISA detect?

A

the presence/amount of antibodies

78
Q

What does Western blot/immunoblot detect?

A

a specific protein within a mixture

79
Q

What is the covid antibody test?

A

ELISA

80
Q

what is the covid antigen test?

A

rapid test

81
Q

What does a catalyst do?

A

accelerates the reaction rate by lowering the energy of activation

82
Q

What kind of enzyme catalyzes the transfer of electrons?

A

oxidoreductase

83
Q

What kind of enzyme catalyzes group transfer reactions

A

transferases

84
Q

What kind of enzyme catalyzes hydrolysis reactions

A

hydrolases

85
Q

What kind of enzyme catalyzes cleavage of C-C, C-O, or C-N by elimination, leaving double bonds or rings?

A

Lyases

86
Q

What kind of enzyme catalyzes transfer of groups within molecules to yield isomeric forms?

A

Isomerases

87
Q

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?

A

Ligases

88
Q

Where is the active site usually found?

A

At the interface of 2 domains

89
Q

What is the equation of S to P with the presence of an enzyme?

A

E+S —> ES —> EP —> E+P

90
Q

How does an enzyme lower the activation energy?

A

by forming the ES complex

91
Q

What are transition state analogs?

A

transition state lookalikes that bind to the enzyme better than the substrate

92
Q

What are non-protein substances that turn on inactive enzymes?

A

Cofactors

93
Q

How is acid base catalysis pH dependent?

A

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
Q

What are the amino acids commonly used in general acid-base catalysis?

A

Glu, Asp, Lys, Arg, Cys, His, Ser, Tyr

95
Q

What are the stages of covalent catalysis?

A
  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
Q

What is a sure sign of covalent catalysis?

A

Schiff base formation

97
Q

What amino acids would form a Schiff base?

A

Asn, Gln, Lys, Arg, His

98
Q

What are some of the metals that are not catalytic and therefore would not participate in metal catalysis?

A

Na+, K+, Ca2+

99
Q

What is the most common way that metal catalysis works?

A

metals facilitate ionization of water to help form a nucleophilic OH

100
Q

Where does chymotrypsin cleave?

A

after Phe, Trp, and Tyr residues

101
Q

What kind of catalysis does chymotrypsin participate in?

A

Acid/Base AND covalent

102
Q

What is the catalytic triad of serine proteases?

A

3 important amino acid residues in its catalytic site

103
Q

What is the catalytic triad made up of in all serine proteases?

A

His 57, Asp 102, Ser 195

104
Q

How can chymotrypsin’s catalytic triad be so far away from each other on their chain and still interact?

A

They are close in the 3D structure

105
Q

What kind of molecule does chymotrypsin accept into the specificity pocket, and therefore, what is important about the structure of the specificity pocket itself?

A

bulky, aromatic molecules so the pocket has lots of space

106
Q

What kind of molecule does trypsin accept into the specificity pocket, and therefore, what is important about the structure of the specificity pocket itself?

A

positively charged molecules so the pocket has a negatively charged molecule

107
Q

What kind of molecule does elastase accept into the specificity pocket, and therefore, what is important about the structure of the specificity pocket itself?

A

small, non-charged molecules so the pocket is crowded and non-charged

108
Q

What are the 2 important mechanisms for transition state stabilization in chymotrypsin?

A

Oxyanion hole and low barrier hydrogen bonds between Asp 102 and His 57

109
Q

What kind of catalysis does RNAse participate in?

A

Acid/Base

110
Q

Why does RNAse have two different His residues with DIFFERENT pKas?

A

One works as an acid, one works as a base

111
Q

Why doesn’t RNAse work on DNA?

A

the OH in the mechanism that is found only on RNA and not DNA is very important

112
Q

What enzyme breaks up bacterial cell wall’s polysaccharides (peptidoglycan)

A

lysozyme

113
Q

What does the binding of peptidoglycan to lysozyme do to the structure?

A

Changes the conformation of the D ring so the bond to be cut will align

114
Q

is NAG or NAM recognized in the peptidoglycan

A

NAM

115
Q

What is an inhibitor of transpeptidase

A

penicillin

116
Q

What breaks open the beta-lactam ring of penicillin and thus inactivates it?

A

beta-lactamase

117
Q

What is an inhibitor of beta-lactamase

A

clavulanic acid (augmentin)

118
Q

How is chymotrypsin activated?

A

By removal of 2 dipeptides

119
Q

How does activation affect the catalytic activity of an enzyme?

A

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
Q

What do protease inhibitors do?

A

Act as a safety backup; inhibit proteases in the case of premature activation

121
Q

How do protease inhibitors work?

A

Once they are bound, the complex is too tight so that the leaving group can’t leave and water can’t enter

122
Q

What is an example of a REVERSIBLE covalent modification?

A

phosphorylation

123
Q

What enzyme adds phosphate groups onto a substrate?

A

kinase

124
Q

What enzyme removes phosphate groups from a substrate?

A

Phosphatase

125
Q

What is an example of a noncovalent modification?

A

allosteric regulators

126
Q

How does modulator binding affect the enzyme?

A

It changes the conformation of the entire enzyme so that the substrate can bind better

127
Q

Does the modulator bind to the catalytic subunit or the regulatory subunit?

A

regulatory

128
Q

Which amino acids do kinases transfer phosphates to?

A

Ser, Thr, and Tyr

129
Q

What does a curved arrow in a reaction represent?

A

the movement of an electron pair

130
Q

How many oxygen atoms can Hb bind at once?

A

4

131
Q

How many oxygen atoms can Mb bind at once?

A

1

132
Q

What is the shape of the hemoglobin-oxygen binding curve?

A

sigmoidal

133
Q

Which test has proteins in their native state?

A

ELISA

134
Q

Which test has proteins with no higher order structure?

A

western blotting

135
Q

Which test are proteins transferred to a membrane or a sheet?

A

western blotting

136
Q

What fragments of an antibody crystallize readily?

A

Fc

137
Q

What fragments of an antibody are recognized by macrophage surface receptors?

A

Fc

138
Q

What fragments of an antibody often undergo conformational changes?

A

Fab

139
Q

What fragments of an antibody contain the immunoglobulin fold?

A

Both Fab and Fc

CHM 432 (4 decks)

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