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Capstone > Midterm > Flashcards

Midterm Flashcards

1
Q

name the greek letters in order for the additional carbons in an amino acid

A

alpha, beta, gamma, delta, epsilon, zeta, eta, theta, phi, chi, psi, omega

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2
Q

what is a zwitterionic

A

charged form ion but charges make atom neutral

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3
Q

what determines the charged forms of aa

A

sidechain properties and pH of medium

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4
Q

what is the L form of aa

A

co, r, n

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5
Q

what is the d form of aa

A

n, r, co

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6
Q

what form of aa is almost found exclusively in naturally occurring proteins

A

L-form

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7
Q

is glycine chiral

A

no due to no side chain

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8
Q

what are some functions of proteins

A

enzymes, motor proteins, structural or cytoskeletal proteins, transport proteins, electron transfer, cell signaling, chaperones, storage proteins

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9
Q

proteins are diversified with what type of interactions

A

covalent and non covalent

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10
Q

what is primary structure

A

the linear amino acid sequence of the polypeptide chain

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11
Q

what is the secondary structure

A

the local structure of linear segments of the polypeptide backbone atoms without regard to conformation of the side chains

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12
Q

what is tertiary structure

A

the overall 3D arrangement of all atoms in a single polypeptide chain

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13
Q

what is quaternary structure

A

the arrangement of separate polypeptide chains (subunits) into the functional protein

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14
Q

what creates the peptide bond

A

condensation of the carboxyl group of aa 1 and amino group aa 2 which form an amide bond

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15
Q

what are some factors of the peptide bond

A

resonance, partial double bond, shorter than single bond but longer than double bond

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16
Q

where is the partial dipole in peptide bond

A

N in amino group and O in carboxyl group

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17
Q

polarity is important for the blank of a folded protein

A

stability

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18
Q

the peptide plane is

A

planar

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19
Q

what are the six atoms in the peptide plane

A

C alpha, carbon, O, N, H and C alpha

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20
Q

where is the limited rotation in the primary structure

A

around the peptide bond, due to resonance

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21
Q

what bonds are single and free to rotate

A

N-Ca and Ca-C

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22
Q

what atoms are in the psi angle

A

Ca-C

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23
Q

what atoms are in the phi angle

A

N-Ca

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24
Q

what are dihedral angles

A

phi and psi

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25
Q

omega angle directs what

A

the orientation of the sidechains between two consecutive aa in a peptide

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26
Q

180 degree for omega

A

trans

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27
Q

0 degree for omega

A

cis

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28
Q

which is more energetically favorable, trans or cis

A

trans due to less steric henderance

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29
Q

when do you see cis

A

when proline involved

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30
Q

what is ramachandran plot based on

A

close contacts between atoms based on their van der waals radii

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31
Q

the ramachandran plot shows

A

conformations of phi and psi that are sterically favorable or unfavorable

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32
Q

how do secondary structures form

A

repetition of similar phi and psi angles

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33
Q

what are the three common types of secondary structures found in proteins

A

alpha helices, beta strands, beta sheets

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34
Q

what is the other category of secondary structures

A

turns, loops and connections

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35
Q

what is a common element of secondary structures

A

h bonds

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36
Q

what is the basis of secondary structure

A

get as many carbonyl O and amide NH to b paired

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37
Q

what is the most prevalent type of secondary structure

A

alpha helice

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38
Q

how many residues per turn in alpha helice

A

3.6

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39
Q

dihedral angles are what in alpha helices

A

same or similar

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40
Q

what is the pitch of the alpha helix

A

5.4 A per turn of helix

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41
Q

what is the angstrom per residue of 100 degree rotation in alpha helice

A

1.5

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42
Q

how are the side chains viewed in the alpha helix

A

staggered, outside of helix

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43
Q

carbonyl oxygens point to what is alpha helix

A

to c terminus

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44
Q

R groups point to what in the alpha helix

A

N terminus

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45
Q

what aa are good helix formers

A

A, E, L , M

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46
Q

what aa are bad helix formers

A

P, G, Y, S

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47
Q

alpha helical structures are stabilized by

A

h-bonding within the main chain atoms

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48
Q

what makes the alpha helix the most stable secondary structure

A

repetitive H-bonding pattern

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49
Q

how do the H bond in the alpha helix

A

carbonyl O, h bonded with H of NH four residues away

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50
Q

how many atoms are joined in H bond of main chain in alpha helix

A

13

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51
Q

what is helix propensity

A

tendency of aa to be in a helix

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52
Q

what determines helix propensity

A

H-bond, hydrophobic interactions, sidechain interactions with helix, lower energy value indicates higher probability

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53
Q

what causes dipole in single peptide

A

polarity of NH and CO

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54
Q

what aligns the dipole of each peptide approximately parallel to the helical axis

A

H-bonds

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55
Q

what s the degree that aa residues are plotted around the spiral of alpha helix

A

100 degree

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56
Q

where are helices located and why

A

outer surface of globular proteins with hydrophobic inside and hydrophillic outside

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57
Q

what part of helix can bind to DNA

A

n term

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58
Q

a number of enzymes have their active site close to what on helix

A

N term of helix

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59
Q

explain helix capping

A

the n and c ends that have un-bound due to H bond only binding every four

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60
Q

so if you have 12 residues how many h bonds in main chain of alph

A

4 h bond but leaves four empty at both c and n term

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61
Q

what do you call the last unoccupied N and C term with helix capping

A

C1, C2, and very end is Ccap and Ncap

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62
Q

in alpha helix how many aa for one spiral

A

3.6

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63
Q

describe aa distribution in spiral of helix

A

hydrophobic on one side and charged on the other

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64
Q

what are the different types of alpha helices

A

alpha (3.6), 3.10, pi (4.4)

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65
Q

feature of 3.10 helix

A

narrower in diameter, longer in length, tighter turn

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66
Q

feature of pi helix

A

wider in diameter, shorter in length, wider turn

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67
Q

describe h bonds in 3.10 helix

A

between i and i+3

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68
Q

where can you see 3.10 helix

A

beginning or end of alpha helix with a single turn

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69
Q

what leads to potential steric interference in 3.10 helix

A

side chain

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70
Q

collagen contains what secondary structure

A

alpha helix, (3), twist around each other

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71
Q

how is collagen alpha helix stabilized

A

inter-chain H bonding

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72
Q

what is PPII

A

poly-proline helices

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73
Q

feature of PPII

A

4-8 residues long, more flexible, more exposed to solvent

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74
Q

what is a beta strand

A

a continuous stretch of aa residues in Beta conformation

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75
Q

features of beta strand

A

peptide bonds of adjacent residues point in opposite directions, alternate side chain point in opposite directions

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76
Q

beta strands associate with

A

beta sheet

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77
Q

average length of beta strand

A

6 residues

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78
Q

what are the three perpendicular features in beta strands

A

direction of backbone, direction of h bond bw strand, direction of side chain above and below plane sheet

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79
Q

where does the h bond go in beta sheets

A

c=o and h-n

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80
Q

why can beta sheets contain strands that are not local

A

h-bond between different segment of a polypeptide

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81
Q

what are the different types of h bond in beta sheets

A

antiparallel, parallel, mixed

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82
Q

feature of parallel beta sheet

A

h bond not parallel, not perpendicular to strand, 3.2 A per residue translation, less stable than anti, must have more than 4 strands to improve stability, equal space of h bond

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83
Q

what are the side chains like in parallel beta sheet

A

hydrophobic, buried in protein

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84
Q

since h bonds angled in parallel beta sheet, what happens to dipole

A

only 1/3 of peptide dipole aligns parallel to strand

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85
Q

Features of H bond of antiparallel beta sheet

A

shorter connection bw adjacent strands and connection is on same side, H bonds parallel and perpendicular to strand but not equally spaced

86
Q

features of antiparallel beta sheet

A

3.5 A residue translation, uneven spaced h bond pattern, narrowly spaced bond pairs alternate with widely spaced bond pairs, stable even with two strands

87
Q

what is an example of beta sheets that have different morphology

A

beta barrel

88
Q

example of beta barrel protein

A

GFP, green fluorescent protein

89
Q

hairpin

A

backbone enters the same end of the sheet that is left, small,

90
Q

crossover

A

the backbone enters the opposite end, longer,

91
Q

different types of crossover

A

right vs left

92
Q

which crossover is more prevalent

A

right

93
Q

feature of beta bulge

A

h bonds between two residues on one strand opposite a single residue on the other strand, slight bend in beta sheet

94
Q

when does beta bulge happen

A

between antiparallel strands, between a narrow pair of hydrogen bonds

95
Q

function of beta bulge

A

compensating for the effects of a single residue insertion or deletion within beta structure, providing the strong local twist required for form closed beta barrel structures

96
Q

a turn causes direction change of polypep by what degree

A

180

97
Q

where do turns occur

A

surface of the molecule

98
Q

loops between anti parallel beta strands referred to

A

beta hairpins, hairpin bends, beta turns

99
Q

turns contain about how many residues

A

2

100
Q

in a turn what are the residues

A

i and i+3

101
Q

feature of type 1 turn

A

antiparallel beta sheet, pro is second residue

102
Q

feature of type 2 turn

A

antiparallel beta sheet, residue three glycine

103
Q

difference between type one and two

A

180 flip in residue two

104
Q

feature of gamma turn

A

only 3 residues

105
Q

feature of omega turn

A

main chain to side chain h bond, cause chain reversal, found in metal binding locations

106
Q

what is the main driving force of protein folding

A

pack hydrophobic side chain in the inside and hydrophilic surface

107
Q

how to create hydrophobic core

A

main chain should be neutralized by forming H bonds between the amide N and carbonyl O

108
Q

super secondary structures are also known as

A

motifs

109
Q

motifs contain

A

more than one secondary structural element, 2 or 3 consecutive secondary structures and arrange themselves with specific geometry even with completely different sequences

110
Q

motifs can have what type of roles

A

structural or functional

111
Q

examples of super secondary structures

A

alpha-alpha, beta-beta, beta-alpha-beta

112
Q

example of alpha-alpha unit

A

helix-turn-helix

113
Q

feature of helix turn helix

A

two helices, lie antiparallel connected by short loop, helices are roughly perpendicular to each other, sequence specific interactions with DNA

114
Q

how does helix turn helix work with DNA

A

second helix binds to major groove of DNA (recognition helix) and first helix stabilizes the interaction (stabilization helix), interact with H bond and hydrophobic of protein sidechain and DNA bases

115
Q

feature of helix turn helix with three helices

A

regulate developmental gene expression, third helix interacts directly with DNA, stabilized by salt bridges and H bonds

116
Q

describe winged helix turn helix

A

dna binding motif, wings are small beta sheets, 3 helices and 3 beta, H1S1S2H2H3S3S4H4

117
Q

feature of winged HTH

A

3rd helix makes contact with the major groove of DNA, wings bind to minor groove

118
Q

features of helix hairpain helix (HhH)

A

contain two alpha helices with hydrophobic residues in helix that pack the two helices, gly and pro in the hairpin

119
Q

binding DNA and HhH

A

non-sequence specific DNA interaction, binds to DNA with hairpin, positive charge on loop bind to phosphate backbone

120
Q

describe EF hand

A

loop has 12 residues and has polar and hydrophobic aa for binding with metal ion

121
Q

how does metal bind in EF hand

A

carboxyl side chain, main chain groups and bound solvent

122
Q

describe three helix bundle

A

helix 2 and 3 antiparallel to each other, helix 1 tilted at 30 degree angle, hydrophobic residues are buried in interior

123
Q

describe four helix bundles

A

interfaces consist of hydrophobic residues and polar side chains are present on the exposed surfaces

124
Q

coiled coils function as

A

oligomerization domains

125
Q

coiled coils typically consist of

A

two or more alpha helices that wrap around each other with a superhelical twist

126
Q

coiled coils may interact with each other to form

A

homotypic oligomers

127
Q

coiled coils may interact with other coiled coil domains to form

A

heterotypic oligomers

128
Q

coiled coil structures are characterized by the

A

heptad repeat pattern (7 pattern)

129
Q

coiled coil motif features

A

hydrophobic residues inside and interact with different helices

130
Q

example of coiled coil

A

leucine zipper

131
Q

how does leucine zipper work

A

monomers held together in a dimer in the zipper region, basic region bind to DNA in major groove

132
Q

where are globin folds found

A

myoglobin, hemoglobin, phycocyanins

133
Q

feature of globin fold

A

eight alpha helices, helices form pocket for active site which binds to heme group, the last two helices are antiparallel

134
Q

what is a lone helix

A

small proteins (peptides) often consist of a single structural element, can form pores in the membrane, similar to 3.10 helix, amphipathic helix

135
Q

beta hairpin motifs contain

A

antiparallel beta strands connected by a loop

136
Q

what is in a propeller blade

A

six motifs made up of 4 stranded anti parallel sheet connected by a loop from strand 4 to first motif to strand one of second motif

137
Q

feature of greek key motif

A

folding of 4 adjacent antiparallel beta strands

138
Q

what is the topology of a greek key

A

-1,-1, +3 or +1,+1, -3

139
Q

do all four beta stands have to fall within the same beta sheet of greek key

A

no could be 4,0 or 3,1

only up to two beta sheets though

140
Q

describe jelly roll barrel

A

nonlocal structure in which four pairs of antiparallel beta strands are wrapped in 3d to form a barrel shape

141
Q

feature of jelly roll

A

loops crossing over on top and bottom of barrel, antiparallel when strands next to each other, consecutive greek key motifs wrapped around barrel

142
Q

feature of beta barrel

A

antiparallel, last strand joined by H bond with first strand closing barrel, has one open end and one close end, hydrophobic inside

143
Q

feature of beta sandwhich

A

two separate beta sheets pack together face to face, end strands of each sheet not H bonded to one another

144
Q

feature of orthogonal beta sandwhich

A

beta sheets are folded on themselves, two sheets make an angle of 90 degree

145
Q

feature of aligned beta sandwhich

A

antiparallel beta strands, sheets surround a central hydrophobic core, single disulfide bond bridges the two sheets, angles vary from 20 to 50 degree

146
Q

feature of beta helix

A

beta strands wind around the structure forming a helical topology, 2 or 3 sheets

147
Q

how many coils for 2 sheet beta helix

A

3 complete coils, 2 parallel beta sheets

148
Q

how many residues in the loop of beta helix

A

2

149
Q

membrane proteins contain what secondary structure

A

either all alpha or beta structures

150
Q

what secondary structure are more common for membrane proteins

A

alpha helices due to intra strand H bonds

151
Q

feature of beta alpha beta

A

parallel beta strands connected by alpha helix

152
Q

why b-a-b composed of parallel or mixed sheets

A

parallel sheets create longer region of chain which cross over and the cross over create alpha helix, usually right which go above plane

153
Q

b-a-b aka

A

a/b fold

154
Q

what are the three types of b-a-b

A

TIM barrel, rossman fold, horseshoe fold

155
Q

feature of packing helice and sheet of b-a-b

A

hydrophobic core, alpha pack up against beta shield hydrophob inside, loop regions vary in length

156
Q

the loop linking the c terminal end of the 1st beta strand to the N tem end of helix is involved in

A

binding of ligands or substrates

157
Q

binding crevices of a/b motif are formed by

A

loop regions that do not contribute to structural stability

158
Q

feature of a/b barrel

A

alpha helices outside, hydrophobic side chains inside, +1x, +1x…

159
Q

feature of TIM barrel

A

closed a/b barrel, 8 beta strands and 8 helices, beta inside and alpha outside, parallel beta sheet

160
Q

what does TIM barrel stand for

A

triose isomerase

161
Q

TIM barrel is always associated with

A

an enzymatic function

162
Q

where is the active site in the TIM barrel

A

C-term end of the eight parallel beta strands of the barrel

163
Q

feature of double wound a/b folds

A

open twisted sheet, not closed, central twisted wall of parallel or mixed b sheet, start in middle then go from one side to other

164
Q

what are the types of double wound a/b folds

A

classic and reverse

165
Q

what is a classic doubly wound a/b fold

A

starts in the middle

166
Q

what is a reverse doubly wound a/b fold

A

starts on one end

167
Q

function of doubly wound a/b folds

A

bind nucleotides

168
Q

feature of rossman fold

A

a/b open twisted sheet, parallel or mixed b sheet with a helices on both sides, b strands vary from 4 to 10, BABAB motif, involves two motifs

169
Q

rossman fold binds what dinucleotides

A

NAD/NADP, FAD

170
Q

feature of a/b horseshoe fold

A

tandem repeats of 20 to 30 aa, no closing in structure, one side of sheet faces helices (hydrophobic) and other side exposed to solvent

171
Q

a/b horseshoe fold used in

A

proteins involved in cell adhesion, virulence, DNA repair, RNA splicing

172
Q

what amino acid present in horseshoe

A

leucine,

173
Q

features of Zn finger motif

A

30 residues, 4 ligands bind Zn atom, antiparallel beta hairpin motif followed by helix and loop region which bind to DNA seq and non seq specifically

174
Q

finger region in zinc finger motif consist of

A

linker region between last cys and the first his is 12 aa long

175
Q

classic zing fingers bind to DNA in tandem along

A

the major groove

176
Q

feature of a+b folds

A

folds include alpha and beta secondary structure but are mixed

177
Q

3D structure is stabilized by

A

multitude of specific interactions b/w various chemical groups

178
Q

can different primary sequences give rise to similar tertiary folds

A

yes

179
Q

3D structure is more highly conserved than

A

primary structure

180
Q

can a protein by composed of single or multiple domains

A

both

181
Q

can a domain fold independently of rest of protein

A

yes

182
Q

for multi domain proteins, tertiary structure describes the

A

association of the polypeptide within each domain

183
Q

feature of domains

A

all or mostly alpha, all or mostly beta, can be alpha/beta, alpha + beta

184
Q

mosaic proteins

A

different domains in same polypeptide

185
Q

how are domains attached

A

covalently through loops of varying length

186
Q

disulfide bonds or metal ligands (S-M) features

A

single domain and monomeric, distorted helix clusters, distorted beta barrels

187
Q

oligomer

A

protein assemblies with more than one polypeptide

188
Q

subunit/ monomer

A

single polypeptide in oligomer

189
Q

how do monomers assembly

A

spontaneously and specific

190
Q

homomultimers

A

copies of same polypeptide chain associate non-covalently, symmetric, subunit coded by same gene

191
Q

heteromultimers

A

different polypeptide chains, each subunit coded by different gene, each subunit can have a similar/different fold

192
Q

similar fold despite sequence differences hints what

A

gene duplication event

193
Q

oligomers form through what interactions

A

H bonds, van der waals, salt bridges, disulfides, metal ion binding, buried water molecules

194
Q

what indicates the strength of binding in oligomer

A

the amount of surface area buried

195
Q

an assembly with more area and a predominance of hydrophobic interactions indicate

A

tight binding assemblies

196
Q

a smaller buried area and polar interactions indicate

A

weaker complexes that have to dissociate often for biological function

197
Q

why is oligomerization important

A

for optimized biological performance, higher order structures can facilitate the allosteric cooperativity resulting in increased catalytic efficiency

198
Q

can each subunit of oligomer have independent reactions

A

yes

199
Q

active sites can be formed from

A

two monomers

200
Q

assembly of biomolecules into quarternary structures provide

A

enhanced, multiple, or novel functional and structural roles

201
Q

protein folding structure determined by

A

primary sequence

202
Q

what else can stabilize protein structures

A

post translational modifications

203
Q

3D structure is stabilized by

A

efficiently packing atoms into the protein interior

204
Q

what are some chemical interactions that stabilize polypeptides

A

covalent bond, disulfide bond, salt bridge, h-bond, van der waals, long-range electrostatic interactions

205
Q

what chemical interaction has the smallest distance that stabilizes polypeptides

A

covalent

206
Q

what chemical interaction has the largest distance that stabilizes polypeptides

A

van der waals

207
Q

post translational modification increases the

A

functional diversity of the proteome

208
Q

what are the different types of post translational mods

A

phosphorylation, glycosylation, ubiquitination, s-nitrosylation, methylation, n-acetylation, lipidation, proteolysis

209
Q

phosphorylation

A

protein kinase on aa with OH, protein folding

210
Q

glycosylation

A

covalent addition of sugar, cell attachment to extracellular matrix and protein ligand interactions

211
Q

methylation

A

add methyl group on arg or lys

212
Q

acetylation

A

lys residues within n term tail are acetylated for regulating gene expression

Capstone (1 decks)

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