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Cell Biology > Ch.10 - Protein Synthesis, Processing, and Regulation > Flashcards

Ch.10 - Protein Synthesis, Processing, and Regulation Flashcards

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1
Q

Where does mRNA translation occur?

A

in the cytoplasm

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2
Q

what is mRNA translation directed by?

A

mRNA templates

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3
Q

How are proteins synthesized?

A

from mRNA templates

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4
Q

Polypeptide chains are synthesized from what to what terminus?

A

amino (N) to the carboxy (C)

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5
Q

codon definition

A

3 nucleotides long translated region

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6
Q

What makes mRNA?

A

RNA polymerase II

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7
Q

What is the tRNA sequence?

A

3’ CCA

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8
Q

What is the small eukaryotic ribosomal subunit?

A

40S

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9
Q

What is the large eukaryotic ribosomal subunit?

A

60S

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10
Q

The editing site of Aminoacyl tRNA synthetases only bind to what amino acid?

A

the wrong one

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11
Q

What do aminoacyl tRNA synthetases do?

A

attach tRNA to appropriate amino acid

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12
Q

How is the tRNA attached to the appropriate amino acid (2 steps)?

A

1) amino acid is joined to AMP –> forms aminoacyl AMP
2) amino acid is transferred to the 3’ CCA end of the tRNA and AMP is released

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13
Q

When is AMP released?

A

when the amino acid is transferred to the 3’ CCA end of the tRNA

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14
Q

What eukaryotic rRNAs are part of the large ribosomal subunit?

A

28S, 5.8S, and 5S

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15
Q

What eukaryotic rRNAs are part of the small ribosomal subunit?

A

18S

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16
Q

What is the large PROKARYOTIC ribosomal subunit?

A

50S

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17
Q

What is the small PROKARYOTIC ribosomal subunit?

A

30S

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18
Q

What rRNAs are part of the prokaryotic small ribosomal subunit?

A

16S

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19
Q

What rRNAs are part of the prokaryotic large ribosomal subunit?

A

23S and 5S

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20
Q

What are the 3 tRNA binding sites in ribosomes?

A

EPA

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21
Q

What are the 3 stages of translation?

A

initiation, elongation, and termination

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22
Q

What is the initiator of translation?

A

methionyl tRNA

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23
Q

What do methionyl tRNA and mRNA bind to?

A

the small ribosomal subunit (40S)

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24
Q

What joins last to form a functional ribosome?

A

large ribosomal subunit (60S)

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25
Q

What eukaryotic transcription factors are required for initiation (that we will be focusing on)?

A

eIF1A, eIF2, eIF4E, eIF4G

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26
Q

What eukaryotic transcription factors are required for elongation?

A

eEF1a (alpha), eEF1By (beta, gamma), eEF2

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27
Q

What eukaryotic transcription factors are required for termination?

A

eRF1, eRF3

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28
Q

What 3 components are part of the initiation ternary complex?

A

eIF2, met-tRNA, and GTP

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29
Q

eIF2 is what?

A

a small GTPase (that breaks down GTP to GDP)

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30
Q

What does GAP stand for? (in the CAP-dependent translation initiation)

A

G - GTPase
A - Activating
P - Proteins

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31
Q

What does GAP do?

A

tells GTP to be “done”

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32
Q

What does GEF stand for? (in the CAP-dependent translation initiation)

A

G - Guanine nucleotide
E - Exchange
F - Factor

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33
Q

eIF4E only binds to the 5’ cap if also bound to what?

A

eIF4G

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34
Q

What binds to the 5’ cap in the CAP-dependent translation initiation?

A

eIF4E

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35
Q

What happens when all 12 proteins are bound to the mRNA?

A

ATP —> ADP + P

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36
Q

Once you hit the start site in the CAP-dependent translation initiation, what is broken down + then released?

A

GTP

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37
Q

When are the 12 proteins in the CAP-dependent released?

A

when it hits the start site

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38
Q

Why can some viral and cellular eukaryotic mRNAs be CAP-Independent?

A

they have internal ribosome entry sites (IRESs)

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39
Q

What first happens in CAP-Independent Translation Initiation?

A

eIF4G binds to IRES

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40
Q

When do the 12 proteins and the met-tRNA bind to the mRNA (in cap-independent)?

A

after eIF4G binds to IRES

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41
Q

In initiation, tRNA brings methionine to what site?

A

P

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42
Q

In elongation, tRNA brings amino acids to what site?

A

A

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43
Q

What 3 things are part of the elongation ternary complex?

A

tRNA, amino acid, and eEF1a (alpha)

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44
Q

In what step does the large subunit shift?

A

elongation

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45
Q

Why is there a translocation in elongation?

A

eEF2 breaks down GTP —> GDP

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46
Q

Which ribosomal subunit works as a decoding center for mismatches?

A

small ribosomal subunit

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47
Q

what codons does elongation stop at?

A

UAA, UAG, or UGA

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48
Q

what do release (eRFs) do?

A

recognize stop codons

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49
Q

How do release factors work?

A

recognize stop codons in the P site and then bind to the A site to terminate translation

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50
Q

what are polysomes?

A

when multiple ribosomes translate mRNAs simulatneously

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51
Q

What type of CAP dependency is global translational activity?

A

CAP-dependent

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52
Q

what does global translational activity respond to?

A

stress, nutrient availability, and growth factor stimulation

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53
Q

Regulation of ferritin translation by _____ proteins.

A

repressor

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54
Q

If there is no iron in the translational regulation of ferritin process, then what happens?

A

iron regulatory protein (IRP) binds to the iron response element (IRE) in the 5’ UTR, blocking translation

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55
Q

When there is an adequate amount of iron for the translational regulation of ferritin, what binds to the IRE?

A

40S ribosomal subunit (which allows more eukaryotic proteins to bind)

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56
Q

What is the repressor that binds to IRE (in translational regulation of ferritin) that blocks 40S ribosomal subunit from binding to IRE?

A

IRP (iron regulatory protein)

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57
Q

In the translation of mRNA, a translational repressor binds to what 3’ codon to inhibit translation?

A

UTR

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58
Q

Why is translation inhibited when a translational repressor binds to 3’ UTR?

A

the initiation factor eIF4E can no longer bind eIF4G

59
Q

Phosphorylation of eIF2 and eIF2B by regulatory protein kinases blocks what?

A

the exchange of bound GDP for GTP, inhibiting initiation of translation

60
Q

What do growth factors activate in the regulation of eIF4E?

A

protein kinases that phosphorylate regulatory proteins (such as eIF4E binding proteins and 4E-BPs)

61
Q

mRNA translation cannot occur when what is hypophosphorylated?

A

mTORC1 or 4E-BP1

62
Q

What are folded and modified to become functional proteins?

A

polypeptide chains

63
Q

3-D conformation (tertiary) is due to what?

A

side chains and amino sequence

64
Q

chaperone protein functions

A

1) facilitate protein folding
2) assist the self-assembly process
3) bind to and stabilize unfolded or partially folded polypeptides

65
Q

____ binds to polypeptide chains that are still being translated on ribosomes.

A

chaperones

66
Q

Why do chaperones bind to polypeptide chains that are still being translated on ribosomes?

A

to protect the chain from improper folding or aggregation with other proteins until synthesis of an entire domain is complete

67
Q

What stabilizes unfolded polypeptide chains during transport into organelles?

A

chaperones

68
Q

what were the first types of chaperones identified?

A

heat shock proteins (Hsp)

69
Q

heat shock proteins (Hsp) are expressed in what cells?

A

cells subjected to high temperatures

70
Q

Hsp70 do what?

A

1) stabilize polypeptide chains during translation
2) transport by binding to short hydrophobic segments

71
Q

chaperonins are what Hsp?

A

Hsp60

72
Q

chaperones are what Hsp?

A

Hsp70

73
Q

When a polypeptide is transferred to a chaperonin, what takes place?

A

folding

74
Q

chaperonins are what?

A

subunits in two stacked rings that form a double-chambered structure

75
Q

Defects in protein folding are responsible for what?

A

protein misfolding diseases

76
Q

What neurodegenerative disease has the Amyloid-B aggregating protein?

A

alzheimer’s disease

77
Q

What neurodegenerative disease has the alpha-Synuclein aggregating protein?

A

Parkinson’s disease

78
Q

What neurodegenerative disease has the Huntingtin aggregating protein?

A

Huntington’s disease

79
Q

What neurodegenerative disease has the superoxide dismutase aggregating protein?

A

amyotrophic lateral sclerosis

80
Q

What neurodegenerative disease has the prion protein aggregating protein?

A

spongiform encephalopathies

81
Q

What non-neurodegenerative disease has the amylin aggregating protein?

A

type 2 diabetes

82
Q

What non-neurodegenerative disease has the crystallins aggregating protein?

A

cataracts

83
Q

What non-neurodegenerative disease has the insulin aggregating protein?

A

injection-localized amloidosis

84
Q

What systemic disease has the immunoglobulin light chain aggregating protein?

A

amyloid light-chain amyloidosis

85
Q

What systemic disease has the serum amyloid A protein aggregating protein?

A

amyloid A amyloidosis

86
Q

What systemic disease has the transthyretin aggregating protein?

A

senile systemic amylodisis

87
Q

When 2 enzymes act as chaperones by catalyzing protein folding…

A

protein disulfide isomerase (PDI)

88
Q

protein disulfide isomerase (PDI) is abundant where in the cell?

A

ER

89
Q

what does protein disulfide isomerase (PDI) catalyze?

A

catalyzes disulfide bond formation

90
Q

Oxidizing environments allow _____ linkages

A

disulfide

91
Q

what does peptidyl prolyl isomerase do?

A

catalyzes isomerization of peptide bonds that involve proline residues

92
Q

If the isomerization between the cis and trans configurations of prolyl-peptide bonds did not have peptidyl prolyl isomerase, what would happen?

A

would be a rate-limiting step in protein folding

93
Q

proteolysis does what?

A

cleavage of a polypeptide chain

94
Q

signal sequences do what?

A

target protein for transport to a specific destination

95
Q

how does the signal sequence work?

A

inserted into a membrane channel as it emerges from the ribosome and the polypeptide chain passes through as translation proceeds

96
Q

What is the signal sequence cleaved by?

A

signal peptidase (a membrane protease)

97
Q

what is proteolytic processing?

A

formation of active enzymes or hormones by cleavage or larger precursors

98
Q

what is an example of proteolytic processing?

A

insulin

99
Q

Insulin is synthesized as what?

A

a precursor polypeptide (2 cleavages produce the mature insulin)

100
Q

what happens in glycosylation?

A

carbohydrate chains are added to proteins (glycoproteins)

101
Q

What important roles do the carbohydrate moieties play?

A

1) protein folding in the ER
2) targeting proteins for transport
3) recognition sites in cell-cell interactions

102
Q

N-linked glycoproteins

A

the carbohydrate is attached to the nitrogen atom in the side chain of asparagine

103
Q

O-linked glycoproteins

A

the carbohydrate is attached to the oxygen atom in the side chain or serine or threonine

104
Q

glycosylation starts where during translation?

A

ER

105
Q

O-linked oligosaccharides are added in the ____.

A

golgi

106
Q

How are O-linked oligosaccharides formed?

A

by addition of one sugar at a time in the golgi

107
Q

Many cytoplasmic, nuclear proteins, and transcription factors are modified by addition of one what?

A

O-linked N-acetylglucosamine residue

108
Q

What are 2 fatty acids that are lipid anchors that modify some eukaryotic proteins?

A

1) myristic acid
2) palmitic acid

109
Q

What are 2 prenyl groups that are lipid anchors that modify some eukaryotic proteins?

A

1) farnesyl
2) geranylgeranyl

110
Q

N-myristoylation is a type of what?

A

lipid anchor

111
Q

In N-myristoylation, what is attached to what?

A

myristic acid is attached to an N-terminal glycine

112
Q

Prenyl groups attach to sulfur in the _______

A

side chains of cysteine near the C terminus in prenylation.

113
Q

Many of the prenylation proteins are involved in what?

A

1) control of the cell growth
2) differentiation including the Ras oncogene proteins

114
Q

In palmitoylation, palmitic acid is added to sulfur in the ___________.

A

side chains of internal cysteine residues

115
Q

Palmitoylation is important in what?

A

association of some proteins with the cytosolic face of the plasma membrane

116
Q

glycolipids are lipids that are linked to what?

A

oligosaccharides

117
Q

Glycolipids are added to ___-terminus ____ groups

A

1) C
2) carboxyl

118
Q

what anchors some proteins to the external plasma membrane?

A

glycolipids

119
Q

what are the anchors in glycolipids?

A

glycophosphatidylinositol (GPI) anchors

120
Q

What are the 3 mechanisms that regulate the amounts/activities of their proteins?

A

1) regulation by small molecules
2) phosphorylation
3) protein-protein interactions

121
Q

What is allosteric inhibition?

A

the end product inhibits the production of more products by binding to the other site on the site where it was first produced

122
Q

what is a common regulation?

A

GTP or GDP binding

123
Q

What happens when there are subtle conformational differences in the inactive GDP-bound formation?

A

cannot work

124
Q

What interacts with its target molecule signaling cell division?

A

Ras-GTP

125
Q

25% of human cancers are from mutations in ____ genes.

A

ras

126
Q

Ras protein is locked in the ______________, which always allows signaling of cell division.

A

GTP-bound conformation

127
Q

What is the reversibility of phosphorylation?

A

reversible

128
Q

what does phosphorylation do in terms of regulation of protein function?

A

activates or inhibits proteins due to environmental signals

129
Q

protein kinases do what?

A

transfer phosphate groups from ATP to amino acids

130
Q

What are the 2 most common amino acids that protein kinases transfer phosphate groups to?

A

1) Serine
2) Threonine

131
Q

The protein-tyrosine kinase was discovered when?

A

1980

132
Q

How was protein-tyrosine kinase discovered?

A

studies of Rous sarcoma virus

133
Q

What are 4 other covalent modifications?

A

1) acetylation of lysine
2) methylation of lysine and arginine
3) nitrosylation (addition of NO groups) to cysteine
4) glycosylation of serine and threonine

134
Q

What is an example of protein-protein interactions?

A

cAMP-dependent protein kinase (PKA)

135
Q

How are protein levels determined?

A

by rates of synthesis and rates of degradation

136
Q

Half-lives (t1/2) of proteins are what?

A

differential rates of degradation that are important in cell regulation

137
Q

What is short t1/2?

A

many regulatory proteins; allows levels to change quickly in response to external stimuli

138
Q

What is the Ubiquitin-proteasome pathway?

A

a major pathway of protein degradation in eukaryotes

139
Q

Ubiquitin is what?

A

1) highly conserved in all eukaryotes
2) added to the amino group of the side chain of a lysine residue (more are added to form chain)

140
Q

What does a proteasome do?

A

recognizes and degrades polyubiquinated proteins

141
Q

Ubiquitination is a multistep process involving what enzymes?

A

E1, E2, E3

142
Q

Which enzyme, in Ubiquitination, selectively targets proteins for degradation?

A

E3

143
Q

What are targets for regulated ubiquitylation and proteolysis?

A

many proteins that control fundamental cellular processes

Cell Biology (8 decks)

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