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Introduction to Biochemistry > Lecture 2 > Flashcards

Lecture 2 Flashcards

1
Q

what is the operating system for nearly all biological functions?

A

the proteome

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2
Q

what are 4 things common to all amino acids?

A

-alpha carbon
-Carboxyl group
-Amino group
-Variable R group

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3
Q

The R groups in amino acids differ by what two things?

A

size and charge

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4
Q

how many standard amino acids are there?

A

20

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5
Q

what are the four types of R groups that categorize amino acids?

A

-nonpolar R groups
-polar R groups
-polar charged R groups
-aromatic R groups

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6
Q

where are nonpolar R groups located?

A

the intertior of proteins where they don’t interact with water

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7
Q

what were the 7 molecules shown in class with nonpolar R groups?

A

Glycine, alanine, proline, valine, leucine, isoleucine, methionine

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8
Q

what were the 5 compounds shown in class with uncharged polar R groups?

A

serine, threonine, cysteine, asparagine, glutamine

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9
Q

what are the 3 molecules shown in class with positively charged polar R groups?

A

lysine, arginine, histidine

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10
Q

what are the 3 molecules shown in class with negatively charged polar R groups?

A

aspartate, glutamate

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11
Q

true or false? if false, correct statement

polar charged R groups are (almost) always charged under
physiological conditions

A

true

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12
Q

true or false? if false, correct statement

polar charged R groups can be either positively or negatively charged

A

true

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13
Q

what are the 3 compounds shown in class with aromatic R groups?

A

phenylalanine, tyrosine, tryptophan

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14
Q

true or false? if false, correct statement

Certain polar-uncharged amino acids can become charged
depending on the environment

A

true

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15
Q

what compound is very versatile in catalyzing chemical reactions?

A

Histidine

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16
Q

true or false? if false, correct statement

Histidine can act only as a base

A

false; Histidine can act as an acid and a base

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17
Q

true or false? if false, correct statement

The position of an AA relative to its neighbors
DOES NOT affect stability of helix

A

false; The position of an AA relative to its neighbors
DOES affects stability of helix

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18
Q

true or false? if false, correct statement

the microenviroment of the active site does not affect the protonation state of amino acids

A

false; the microenviroment of the active site DOES affect the protonation state of amino acids

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19
Q

true or false? if false, correct statement

Proteins have diverse properties and an incredible
number of functions

A

true

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20
Q

true or false? if false, correct statement

alpha helix and beta sheets meet the requirements of a secondary structure

A

true

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21
Q

what is something that is very important for protein structure?

A

covalent links between polypeptide chains and subunits

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22
Q

what configuration are all AA residues in proteins?

A

L-configuration

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23
Q

are amino acids chiral or achiral?

A

chiral

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24
Q

all AA are chiral except for what compound? what atom is repeated?

A

glycine; H

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25
Q

every AA has at least how many ionizable groups?

A

2

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26
Q

what is a compound?

A

a substance formed by two or more different types of elements chemically combined in a fixed proportion

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27
Q

what is a molecule?

A

a group of two or more atoms held together by chemical bonds

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28
Q

define zwitterion and at what pH does it occur?

A

a molecule that has both a positive and negative charge, but has a net charge of zero, making it electrically neutral; occurs at neutral pH

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29
Q

AA with ionizable R groups will have how many ionizable groups?

A

3

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30
Q

what are two things each ionizable group will have?

A
  1. pKa
    2.region of buffering capacity
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31
Q

what does pKa meassure?

A

it measures the tendency to lose s proton

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32
Q

how do ionizable groups act?

A

they act as acids with increasing pH (give up protons)

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33
Q

what type of environment stabilizes the protonated form?

A

a hydrophobic environment

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34
Q

what causes repulsion and can affect protonation state?

A

proximate amino acids of similar charged

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35
Q

the point at which the pH of a molecule has no net electrical charge is the …

A

isoelectric point

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36
Q

how does the buffer zone on a titration curve look? what happens in these zones?

A

the relatively flat section of the curve where the pH changes very little with the addition of titrant

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37
Q

what are comprised of a wide variety of amino acid monomers with varied charge distribution?

A

proteins

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38
Q

what are four types of proteins?

A

-structural
-enzymatic
-carrier
-regulatory

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39
Q

where are structural proteins found?

A

hair, skin, eyes, muscle, silk

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40
Q

what do carrier proteins help with?

A

respiration and metabolism

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41
Q

what do enzymatic proteins help with?

A

digestion, blood clotting, replication, transcription, translation

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42
Q

what do regulatory proteins do?

A

coordinate events within and between cells

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43
Q

protein 3D structure depends on the …

A

primary sequence of AAs

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44
Q

what happens if you change a single amino acid in the primary sequence?

A

small changes at the amino acids level can affect structure which can lead to sickness and disease

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45
Q

what is an example (shown in class) of changing a protein at the amino acid level? what is the outcome?

A

hemoglobin at 6 position changing from a Glu to Val can cause sickle cell anemia

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46
Q

what type of bonds link amino acids to make proteins?

A

peptide bonds

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47
Q

what are the 3 things to keep in mind about the polarity of peptides?

A

-it goes from left tor right
-free amino group is on the left - N Terminus
-Free carboxyl group is on the right – C Terminus

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48
Q

what property of the polypeptide depends on the R groups?

A

electrostatic property

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49
Q

what are the four levels of protein structure?

A

primary
secondary
tertiary
quaternary

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50
Q

name the protein structure:

Sequence of AAs

A

primary

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51
Q

name the protein structure:

Conformation of backbone
(main chain atoms only –no regard to side chains) (arrangement of
adjacent AAs)
-alpha helix or beta sheet-

A

secondary

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52
Q

name the protein structure:

How multiple secondary structures are arranged relative to each other in one polypeptide (arrangement of adjacent and distant AAs)

A

tertiary

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53
Q

name the protein structure:

Multiple polypeptides arranged
relative to each other to form
a protein with different subunits

A

quaternary

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54
Q

name the protein structure:

A

primary

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55
Q

name the protein structure:

A

secondary

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56
Q

name the protein structure:

A

tertiary

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57
Q

name the protein structure:

A

quaternary

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58
Q

what are peptide bond characteristics?

A

-Partial sharing of electrons between the carbonyl oxygen
and the amide nitrogen
-partial double bond character across the peptide bond
-no rotation around the C-N

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59
Q

phi and psi angles are influenced by …

A

steric interference of R
groups

60
Q

fill in the blank:
Atoms of the peptide bond are ____ and tend to form __________

A

polar; H-bonds

61
Q

what are 3 requirements of secondary structures?

A
  1. H-bond requirements of the polar peptide bond
  2. minimizes steric strain
    (limited movement of bonds due to rotation)
  3. positioning of side chains to minimize interference
62
Q

if a person has acidemia (increased [H+] in blood), what is the appropriate treatment?

A

hyperventilating

63
Q

what does the bicarbonate system maintain?

A

blood pH

64
Q

what is Le Chatelier’s principle?

A

if a dynamic equilibrium is disturbed (change of conditions), then the position of equilibrium will shift to counteract the change to reestablish an equilibrium

65
Q

is the tyrosine R- group:

a.hydrophobic
b.hydrophilic
c. amphiphilic

A

C. amphiphilic

66
Q

what compounds have hydrophobic R-groups (shown in class)?

A

phenylalanine and tryptophan

67
Q

Enantiomers:

a. are only associated with amino acids
b. can be specific types of diastereomers
c. are never mirror images of each other
d. can exist for molecules with more than one chiral carbon

A

d. can exist for molecules with more than one chiral carbon

68
Q

what are asymmetric carbons called?

A

chiral center

69
Q

if a molecule has n number of chiral carbons, how many stereoisomers will it have?

A

2^n

70
Q

can enantiomers exist for molecules that have more than one chiral carbon?

A

yes

71
Q

One turn of the helix = ____ A along
the axis
(____ amino acid residues)

A

5.4; 3.6

72
Q

what type of contact do atoms in the core of the helix have?

A

Van der Waals

73
Q

Do AA side chains point inward or outward from the helix in secondary structures?

A

outward

74
Q

what two compounds (shown in class) are least likely to form a alpha helix?

A

Proline and glycine

75
Q

why is proline least likely to form an alpha helix?

A

-No rotation around C-N bond
-Results in destabilizing kink

76
Q

why is glycine least likely to form an alpha helix?

A

Too much
conformational flexibility

77
Q

what are the two ways beta sheets can form?

A

parallel and antiparallel

78
Q

what types of bonds are formed between neighboring strands in beta sheets?

A

H-bonds

79
Q

in parallel beta sheets, strands run in ____ direction

A

same

80
Q

in antiparallel beta sheets, strands run in ____ direction

A

opposite

81
Q

what is the average number of strans per beta sheet?

A

6

82
Q

what are two small compounds (shown in class) that are common in beta sheets?

A

glycine and alanine

83
Q

what kind of linkage links antiparallel beta sheets?

A

beta-turns

84
Q

what kind of linkage links parallel beta sheets?

A

beta loops

85
Q

what two compounds (shown in class) are common to have beta-turns?

A

proline and glycine

86
Q

the hydrophobic core houses what kind of amino acids?

A

hydrophobic

87
Q

the hydrophobic core allows polar residues to participate in what kind of bonding?

A

H-bonding

88
Q

the hydrophobic core allows charged residues to participate in what kind of bonding?

A

ionic-bonding

89
Q

what are the three examples of folding possibilities shown in class?

A

beta-alpha-beta
beta-hairpin
alpha-alpha

90
Q

a hydrophilic surface has what two things?

A
  • charged amino acids
    -polar residues
91
Q

what is the part of a peptide chain that is independently stable or can undergo
movement as a single entity with respect to the entire protein called?

A

domain

92
Q

will domains retain their individual structure if separated?

A

yes

93
Q

what are polypeptide subunits associated with each other to form a multisubunit protein called?

A

oligomers

94
Q

a homo-oligomer has ____ subunits

A

identical

95
Q

a hetero-oligomer has ____ subunits

A

different

96
Q

Associations between the different subunits are ____

A

noncovalent

97
Q

What factors drive and stabilize the folding of proteins?

A

Proteins fold into the conformation that is the most thermodynamically stable - lowest Gibbs free energy

98
Q

label:

A
  1. denatured
  2. native
99
Q

what effect drives protein folding?

A

the hydrophobic effect

100
Q

what will nonpolar groups do to minimize their contact with water?

A

aggregate to displace water molecules surrounding the protein

101
Q

what are 3 weak noncovalent interactions that stabilize protein structures?

A

Van der Waals forces
hydrogen bonds
ionic interactions

102
Q

what is a covalent interactions that stabilize protein structures?

A

disulfide bonds

103
Q

describe the hydrophobic collapse into molten globule

A

Spontaneous collapse of the polypeptide into a
compact state (molten globule)

104
Q

what are 4 things that drive protein folding?

A
  1. Hydrophobic Effect (lowest Gibbs free energy)
  2. Ionic Bonds (Salt Bridges) - Charged Amino Acids
  3. Hydrogen Bonds*
  4. Disulfide Bonds * *Stabilizing (After Folding)
105
Q

protein folding in vivo often requires what?

A

chaperones

106
Q

name the 1, 3 letter code and property of R groups for: glycine

A

Gly G; nonpolar r group

107
Q

name the 1, 3 letter code and property of R groups for: alanine

A

Ala A; nonpolar r group

108
Q

name the 1, 3 letter code and property of R groups for: proline

A

Pro P ; nonpolar r group

109
Q

name the 1, 3 letter code and property of R groups for: valine

A

Val V; nonpolar r group

110
Q

name the 1, 3 letter code and property of R groups for: leucine

A

Leu L; nonpolar r group

111
Q

name the 1, 3 letter code and property of R groups for: isoleucine

A

Ile I ; nonpolar r group

112
Q

name the 1, 3 letter code and property of R groups for: methionine

A

Met M ; nonpolar r group

113
Q

name the 1, 3 letter code and property of R groups for: phenylalanine

A

Phe F; aromatic r group

114
Q

name the 1, 3 letter code and property of R groups for: tryosine

A

Tyr Y ; aromatic r group

115
Q

name the 1, 3 letter code and property of R groups for: tryptophan

A

Trp W ; aromatic r group

116
Q

name the 1, 3 letter code and property of R groups for: serine

A

Ser S; uncharged polar r group

117
Q

name the 1, 3 letter code and property of R groups for:threonine

A

Thr T ; uncharged polar r group

118
Q

name the 1, 3 letter code and property of R groups for: glutamine

A

Gln Q ; uncharged polar r group

118
Q

name the 1, 3 letter code and property of R groups for: asparagine

A

Asn N ; uncharged polar r group

119
Q

name the 1, 3 letter code and property of R groups for: cysteine

A

Cys C ; uncharged polar r group

120
Q

name the 1, 3 letter code and property of R groups for: lysine

A

Lys K ; positively charged r group

121
Q

name the 1, 3 letter code and property of R groups for: histidine

A

His H; positively charged r group

122
Q

name the 1, 3 letter code and property of R groups for: arginine

A

Arg R ; positively charged r group

123
Q

name the 1, 3 letter code and property of R groups for: aspartate

A

Asp D; negatively charged r group

124
Q

name the 1, 3 letter code and property of R groups for: glutamate

A

Glu E; negatively charged r group

125
Q

name the compound:

A

glycine

126
Q

name the compound:

A

alanine

127
Q

name the compound:

A

proline

128
Q

name the compound:

A

valine

129
Q

name the compound:

A

leucine

130
Q

name the compound:

A

isoleucine

130
Q

name the compound:

A

methionine

131
Q

name the compound:

A

serine

131
Q

name the compound:

A

threonine

131
Q

name the compound:

A

cysteine

132
Q

name the compound:

A

asparagine

133
Q

name the compound:

A

glutamine

133
Q

name the compound:

A

lysine

134
Q

name the compound:

A

arginine

135
Q

name the compound:

A

histidine

136
Q

name the compound:

A

aspartate

137
Q

name the compound:

A

glutamate

138
Q

name the compound:

A

phenylalanine

139
Q

name the compound:

A

tyrosine

140
Q

name the compound:

A

tryptophan

Introduction to Biochemistry (4 decks)

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