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BMS109 Cell & Molecular > Protein structure, function, & mutations > Flashcards

Protein structure, function, & mutations Flashcards

1
Q

Which part of the amino acid has a positive charge?

A

amino group

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2
Q

Which part of the amino acid has a negative charge?

A

carboxyl group

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3
Q

Which amino acids have a negative charge?

A

aspartic and glutamic acid

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4
Q

What amino acids have a positive charge?

A

arginine, lysine and histidine

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5
Q

Which amino acid has a phenol ring?

A

Tyrosine

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6
Q

How is the hydrophobic core formed during folding?

A

from non polar side chains

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7
Q

How are polar side chains exhibited on proteins after folding?

A

Project outwards to form hydrogen bonds with water

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8
Q

polar molecule meaning

A

molecule with partial positive and negative charges - charged

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9
Q

non-polar meaning

A

no charge

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10
Q

Describe the effect of urea on proteins

A

Urea can denature proteins by direct interaction

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11
Q

is the effect of urea on proteins reversible or irreversible?

A

reversible

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12
Q

Describe Van der Waals

A

short range weak electrical attraction and repulsion

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13
Q

Describe non-covalent interactions

A

electrostatic attraction between positively and negatively charged ions

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14
Q

Types of secondary structure

A

alpha helix, beta sheet, random coil

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15
Q

Which type of beta sheets has a continuous structure

A

anti-parallel

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16
Q

describe the characteristics of protein domains

A

compact, stable, hydrophobic core

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17
Q

Describe Green Fluorescent protein as a domain

A

very stable, formed from beta sheet structure

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18
Q

What are the functions of GFP

A

biological research, labels specific proteins

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19
Q

What is the PDZ domain

A

common structural domain found in signalling proteins of bacteria, yeast, animals etc

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20
Q

Where is PDZ abundant?

A

brain and synapses

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21
Q

What is the function of PDZ

A

mediate protein-protein interactions, and act as protein scaffolds

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22
Q

Where does the PDZ mainly act as a protein scaffold

A

post synaptically

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23
Q

Describe src tyrosine kinase

A

multi protein domain

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24
Q

What are SH2 and SH3

A

Src tyrosine domains

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25
Q

What is the function of SH2

A

adds specificity to kinase

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26
Q

What does SH2 bind to

A

phosphorylated tyrosine residues

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27
Q

What is the function of SH3

A

adds specificity to kinase

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28
Q

What does SH3 bind to

A

proline rich regions in proteins

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29
Q

Describe quaternary structure

A

proteins in a multi protein complex

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30
Q

What do common structures in proteins indicate?

A

Common functions

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31
Q

What do tubulin subunits form

A

microtubules

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32
Q

What are the different structures of microtubules?

A

filaments, sheets, rings and tubes

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33
Q

What do protein-protein interactions require?

A

complementary surfaces

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34
Q

What drives coiled coil packing

A

hydrophobic interactions

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35
Q

Examples of proteins as molecular motors

A

myosin on actin, kinesin on microtubules, polymerases on DNA

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36
Q

What type of amino acids are in membrane spanning domains

A

non-polar

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37
Q

Describe the the terminals in single pass type 1 membrane proteins

A

N terminus is extracellular, C terminus is intracellular

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38
Q

Which domain is largest in single pass type 1 membrane proteins

A

Extracellular domain

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39
Q

Describe the relationship of tumour necrosis factor with the membrane

A

tethered to membrane by lipid modifications

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40
Q

Examples of post-translational modifications

A

phosphorylation, glycosylation, palmitoylation, ubiquitination and acetylation

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41
Q

Where do post-translational modifications occur?

A

on reactive side chains

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42
Q

Describe lipid modifications

A

variety of lipophilic covalent attachments

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43
Q

Examples of lipid modifications

A

Acylation, Prenylation, GPI anchors

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44
Q

Describe acylation

A

intracellular addition of long chain fatty acids to cysteine residues

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45
Q

Describe prenylation

A

intracellular addition of farnesyl groups

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46
Q

Where do GPI anchors occur

A

extracellularly

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47
Q

Is acylation reversible?

A

YES

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48
Q

Describe palmitoylation

A

covalent attachment of fatty acids usually to cysteine

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49
Q

TRUE or FALSE, palmitoylation is irreversible

A

FALSE

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50
Q

Describe the bonding in a farnesyl anchor

A

thioether linkage between cysteine and prenyl groups

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51
Q

Describe the bonding in palmitoyl anchors

A

thioester linkage between cysteine and palmitic group

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52
Q

What is the general function of lipid anchors?

A

target and stabilise association of proteins with the membrane

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53
Q

What is the function of GTPase Ras

A

transmit signals within cells

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54
Q

What lipid modifications can be performed on ras?

A

farnesylation and palmitoylation

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55
Q

What is the function of lipid modifications on RAS

A

regulate cycling of Ras between membranes

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56
Q

What is the function of depalmitoylation of Ras

A

allows cycling back to endomembranes

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57
Q

What is the function of GTP

A

signalling molecule

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58
Q

what is synaptosomal-associated protein 25

A

t-SNARE protein

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59
Q

How is synaptosomal associated protein 25 modified

A

palmitoylation

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60
Q

what is the function of palmitoylation on synaptosomal associated protein 25

A

allows recycling between PM, endosomes and golgi

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61
Q

Where are disulphide bonds typically found?

A

secreted proteins like anti-bodies

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62
Q

Describe proteolytic processing

A

active hormone or enzyme is post-translationally cleaved

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63
Q

what is the outcome of proteolytic processing

A

mature functional molecule

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64
Q

What does glycosylation modify

A

extracellular proteins (generally)

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65
Q

What are the two types of glycosylation

A

N-linked and O-linked

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66
Q

What is the function of N-linked glycosylation

A

cellular protection

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67
Q

example of N-linked glycosylation

A

mucins in mucous

68
Q

describe O-linked glycosylation

A

attachment via hydroxyl group of serine

69
Q

What type of proteins does O-linked glycosylation modify?

A

intracellular proteins

70
Q

Example of glycosylation patterns

A

blood groups

71
Q

What is released from the kinase following protein phosphorylation

A

ADP

72
Q

What amino acids does protein phosphorylation usually occur on

A

serine, threonine and tyrosine

73
Q

What does protein phosphorylation do

A

converts a hydroxyl group into negatively charged phosphate groups

74
Q

Where on proteins does phosphorylation occur?

A

binding surface

75
Q

What does protein phosphorylation prevent/promote?

A

protein interactions

76
Q

What type of change is phosphorylation to the protein

A

conformational change can alters nature of binding surface

77
Q

Describe GTP binding proteins

A

heterotrimers

78
Q

What is the function of GTP binding proteins

A

Bind guanine nucleotides GDP and GTP

79
Q

Where are GTP binding proteins located

A

inner surface of plasma membrane and transmembrane receptors

80
Q

Describe ubiquitination

A

attachment of new protein by addition of chain of ubiquitin to lysine residues

81
Q

What are the types of ubiquitination

A

mono-ubiquitylation, multi-ubiquitylation, and poly-ubiquitylation

82
Q

Which type of ubiquitination is the most common?

A

poly-ubiquitylation

83
Q

What is the function of mono-ubiquitylation

A

histone regulation

84
Q

what is the function of multi-ubiquitylation

A

endocytosis

85
Q

what is the function of poly-ubiquitylation

A

proteasomal degradation, DNA repair, and further modification

86
Q

What is the function of sorting siganls

A

direct target proteins to correct destination

87
Q

What happens if a protein has NO sorting signal

A

remains in the cytosol

88
Q

What is a signal peptidase?

A

protease that chops off signal peptide

89
Q

What is the function of a signal peptidase

A

allows release of mature protein into ER lumen

90
Q

What type of proteins can cross the ER

A

water soluble proteins

91
Q

What happens to transmembrane proteins in the ER

A

partially cross the ER and become embedded in the membrane

92
Q

When does protein folding occur

A

translocation

93
Q

What influences protein folding

A

primary structure of the protein

94
Q

What type of bonding stabilises protein folding

A

covalent bonding

95
Q

What type of bonding is mainly involved with protein folding

A

non-covalent bonding

96
Q

What is the function of disulphide bonds in protein folding

A

aid folding and stabilisation of final structure

97
Q

What is the function of molecular chaperones?

A

assist protein folding

98
Q

What do molecular chaperones bind to

A

misfolded exposed hydrophobic regions

99
Q

How do heat shock proteins assist protein folding?

A

hydrolyse ATP

100
Q

When is protein misfolding common

A

at high temperatures

101
Q

What is the difference between Hsp70 and Hsp60

A

Hsp60 acts on fully synthesised proteins, Hsp70 works during protein synthesis

102
Q

How does Hsp70 work?

A

binds to regions of hydrophobic amino acids, applies mechanical force to aid correct folding

103
Q

How does Hsp60 work?

A

Acts as an isolation chamber, applies mechanical force

104
Q

Describe the Hsp60 chamber

A

lining that prevents protein binding

105
Q

What can misfolding lead to

A

aggregation

106
Q

Where do protein aggregations accumulate

A

extracellular matrix

107
Q

Diseases associated with protein aggregations

A

Alzheimer’s and prion diseases

108
Q

What is the effect of aggregation on neurons

A

neurons cant regenerate, so detrimental to brain function

109
Q

Example of stable beta sheet aggregates

A

amyloid fibrils

110
Q

what causes amyloid fibrils to aggregate

A

cross linking

111
Q

What is the function of amyloid fibrils

A

store peptide hormones in secretory granules

112
Q

Give examples of prion diseases

A

Creutzfeldt-jakob disease, bovine spongiform encephalopathy

113
Q

Where are prion proteins located?

A

outside of PM, mainly in neurons

114
Q

What is the function of prion proteins?

A

maintaining myelination of peripheral nervous system

115
Q

What is different about abnormal prion proteins?

A

resist protease action, so aren’t degraded

116
Q

Where does protein destruction occur?

A

proteasome

117
Q

What proteins are targeted for destruction?

A

old and damaged, incorrectly assembled, proteins whose concentrations change depending on cell state

118
Q

How are proteins marked for destruction?

A

covalent attachment of ubiquitin

119
Q

What binds to ubiquitylated proteins

A

proteasome cap

120
Q

What is the effect of proteases on proteins targeted for destruction?

A

cleave the protein into short peptides

121
Q

What is ubiquitination mediated by?

A

ubiquitin conjugating enzymes and ubiquitin ligases (E2 & E3)

122
Q

What is the function of ubiquitin ligases (E3)?

A

bind to degradation signals on proteins

123
Q

What does ubiquitin ligases E3 enable ubiquitin conjugating enzymes E2 to do

A

Enables E2 to link a polyubiquitin chain to lysine on target protein

124
Q

What type of DNA is conserved? (introns or exons)

A

Exons

125
Q

Mutations in which cell type are inherited?

A

Germline

126
Q

What type of mutations are dominant

A

gain of function

127
Q

What type of mutations are recessive

A

loss of function

128
Q

Describe an amorphic mutation

A

complete loss of function

129
Q

Describe hypo-morphic mutations

A

reduction of function

130
Q

Describe a hyper morphic mutation

A

increase in protein function

131
Q

Describe an antimorphic mutation

A

Protein interferes with function of wild type protein

132
Q

Describe a neo morphic mutation

A

acquisition of a new function or ectopic expression or function

133
Q

Describe a synonymous mutation

A

does not disturb the protein sequence

134
Q

Describe a non-synonymous mutation

A

structural change of protein

135
Q

What is an indel

A

insertions of deletions of sequence

136
Q

What is the effect of an indel

A

adds residues into protein sequences

137
Q

What are the types of mutation (non-sense) etc

A

transition, transversion, mis-sense, non-sense, neutral, silent, frameshift

138
Q

Describe a transition mutation

A

change of base from purine to purine

139
Q

Describe a transversion mutation

A

substitution of purine to pyrimidine

140
Q

Describe a missense mutation

A

change in amino acid

141
Q

describe a non-sense mutation

A

change to code for a stop codon

142
Q

What is the effect of a non-sense mutation

A

premature termination of translocation, incomplete polypeptide

143
Q

What is a neutral mutation

A

changes from one AA to another with non functional effect

144
Q

What does wobble base pairing cause

A

spontaneous mutation

145
Q

describe deamination

A

chemical change - cytosine is deaminated into uracil

146
Q

describe depurination

A

chemical change - adenine or guanine is lost from DNA backbone

147
Q

What type of mutations do X-rays and gamma rays induce?

A

point mutations

148
Q

Why does ionising radiation (x-rays) induce point mutations

A

high energy

149
Q

What is the effect of UV on DNA

A

replication problems

150
Q

Why does UV cause DNA replication problems

A

low energy so causes photochemical changes in DNA

151
Q

What are the types of chemical induced mutations

A

base analogues, base modifiers, intercalating reagents

152
Q

Example of a base analogue

A

5-bromouracil

153
Q

What type of mutations do base analogues cause

A

transition mutations

154
Q

What is the effect of base modifiers

A

chemically modify structure of bases

155
Q

what is the effect of intercalating agents

A

insert themselves in-between bases in DNA

156
Q

what type of mutations do base modifiers cause

A

transition mutations

157
Q

What type of mutations do intercalating agents cause?

A

frameshift or deletion

158
Q

What causes sickle cell anaemia?

A

recessive mutation

159
Q

what mutation causes sickle cell anaemia

A

single point missense mutation at residue 6 in the beta chain

160
Q

how can sickle cell anaemia mutation be identified?

A

electrophoresis

161
Q

What is an advantage of being a heterozygous carrier for malaria

A

tolerance to malaria

162
Q

what is the function of the cystic fibrosis transmembrane conductance regulator

A

transport chloride, regulate ion concentration in extracellular fluid

163
Q

where are mutations in GTPase Ras normally found

A

cancer cells

164
Q

What is the effect of mutations on ras

A

impairs the intrinsic GTPase activity

165
Q

What are the types of chromosomal mutations

A

deletion, inversion, duplication, translocation

166
Q

Describe the Philadelphia chromsome

A

translocation of a piece of chromosome 22 to chromosome 9 causing fusion of 2 genes

167
Q

What is the function of lipid modifications

A

help to bind proteins to membranes

BMS109 Cell & Molecular (26 decks)

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