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BMS > RNA to Protein > Flashcards

RNA to Protein Flashcards

1
Q

The study of the mechanisms of transcription and translation

A

Molecular biology

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2
Q

Protein synthesis is very important in part because it is the last opportunity for

A

Regulating gene expression

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3
Q

The genetic code is degenerate, with the exception that

A

The UGA stop codon encodes selenocysteine in humans

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4
Q

Mutation that changes the codon to a termination codon

A

Nonsense mutation

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5
Q

Mutation that changes the codon to another sequence coding the same amino acid

A

Silent muttion

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6
Q

Mutation that changes the codon to a sequence that encodes an entirely different amino acid

A

Missense mutation

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7
Q

What are the six features of a typical mammalian mRNA?

A
  1. ) 5’ Cap
  2. ) 5’ UTR
  3. ) Start codon (AUG)
  4. ) Stop codon (UAA)
  5. ) 3’ UTR
  6. ) Poly A tail
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8
Q

The region between the start and stop codon

A

Coding region

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9
Q

Specialized nucleotide (7-methyl-GMP) that is required for binding of initiation factors

A

5’ cap

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10
Q

The start codon AUG codes for

A

Methionine

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11
Q

What are the three stop codons

A

UGA, UAG, and UAA

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12
Q

The sequence between the stop codon and the poly(A) tail, and the site of key regulatory sequences

A

3’ UTR

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13
Q

Protects mRNA from degredation and increases translational efficiency

-Un-templted

A

Poly(A) tail

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14
Q

Deletion of a base can be disastrous because it will change the

A

Reading frame

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15
Q

The 3’ CCA end of tRNA is not trancribed, but is added after processing and it

A

Attaches to amino acids

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16
Q

Recognize tRNAs and add the appropriate amino acid to them

A

aminoacyl tRNA synthetases

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17
Q

Aminoacylation requires

A

ATP

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18
Q

Recognize the anticodon as well as other structural features in the tRNA

A

aminoacyl tRNA synthetases

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19
Q

The eukaryotic ribosome (80S) is made up of

A
  1. ) A large subunit (60S)

2. ) A small subunit (40S)

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20
Q

The ribosome is mostly RNA. Peptide bond formation occurs without the contribution of any protein, meaning the ribosome is a

A

ribozyme

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21
Q

Fill the gap between the large and small subunits of the ribosome

A

tRNAs

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22
Q

What are the three tRNA binding sites in a ribosome?

A
  1. ) A (aminoacyl) site: initial tRNA binding site for next codon
  2. ) P (peptidyl) site: where peptide bond is formed
  3. ) E (exit) site: tRNA is released
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23
Q

Initiation and elongation occur simutaneously, yielding multiple ribosomes on a single mRNA molecule. This very large mRNA/ribosome complex is called a

A

Polysome

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24
Q

Encompasses the assembly of the ribosome and mRNA and the positioning of the ribosome on the start codon

A

Initiation

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25
Q

The first step of initiation is the formation of the

A

Pre-initiation complex (made up of elongation factors like GTP dependant elF2)

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26
Q

The second step of initiation is the pre-initiation complex

A

Sans the mrNA for the AUG codon

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27
Q

Part of the initiation complex that binds to the 5’ cap

A

elF4E

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28
Q

Part of the initiation complex the binds and delivers initiator Met-tRNA

-requires GTP

A

elF2

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29
Q

PArt of initiation complex that serves as a scaffold protein that binds elF4E required for assembly of the pre-initiation complex

A

elF4G

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30
Q

The initiator tRNA is special in that it is not used during

A

Elongation or to incorporate Met

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31
Q

The initiator tRNA moves along the RNA searching for the first start codon. During this process, it utilizes

A

Helicase activity and ATP hydrolysis

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32
Q

The third step of initiation is that after the start codon has been located, the

A

Large subunit joins the complex

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33
Q

Causes elF2 release, signalling the large ribosomal subunit to bind

A

GTP hydrolysis

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34
Q

A common theme in many steps of translation. It often provides a signal for the next step (i.e. the binding of the 60S subunit)

A

GTP-dependent release of factors

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35
Q

The movement of the ribosome down the mRNA, coordinated with aminoacyl tRNA delivery

A

Elongation

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36
Q

During initiation, the very first tRNA is bound in the P site. All subsequent tRNAs first bind to the

A

A site

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37
Q

What is step one of elongation

A

Delivery of aa-tRNA to the A site and E site release

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38
Q

The incoming tRNA is bound to the GTP-dependent factor

A

eEF1A

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39
Q

What is step two of elongation?

A

GTP hydrolysis and eEF1A release, followed by proofreading

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40
Q

What is step three of elongation?

A

eEF2 (w/ GTP) binding to catalyze translocation

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41
Q

What is step four of elongation?

A

GTP hydrolysis and eEF2 release (completion of cycle)

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42
Q

Binds to all canonical tRNA’s (i.e. all tRNAs except the initiator tRNA and the selenocysteine tRNA

A

eEF1A

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43
Q

A G-protein that is required for ribosome translocation

44
Q

Occurs in the ribosomal A-site, where codon/anticodon pairs are “checked” by ribosome conformation

A

Proofreading

45
Q

Is there a terminator tRNA?

46
Q

A tRNA mimetic that catalyzes the release of the completed peptide, signalling termination

A

eRF1 (enzyme release factor 1)

47
Q

Unlike in eukaryotes, bacterial transcription and translation are

48
Q

Bacterial mRNAs are different from eukaryotic mRNAs in that they are

A

Polycystronic (a single code encodes multiple proteins)

49
Q

In bacteria, initiation is dictated by a sequence upstream of the start codon, which directly base pairs to the ribosomal RNA. This is called the

A

Shine-Dalgarno sequence

50
Q

Bacterial ribosomes are smaller and sufficiently divergent from mammalian ribosomes, to allow

A

Selective inhibition by the ribosome inhibitor class of antibiotics

51
Q

Typically do have residual toxicity due to their effects on mitochondrial ribosomes, which are more similar to bacterial ribosomes

A

Ribosome inhibitors

52
Q

What are the sedimentation coefficients for the large and small ribosomal subunits of the prokaryotic ribosome?

A

30S and 50S for a 70S ribosome

53
Q

What are the prokaryotic counterparts for the following eukaryotic enzymes?

  1. ) eIF2
  2. ) eEF1A
  3. ) eEF2
A
  1. ) IF2
  2. ) EFTu
  3. ) EFG
54
Q

Post transcriptional, but pre-translational, regulation

A

mRNA editing

55
Q

The apolipoprotein B is made in the liver and intestine. However, the intestine requires a shorter version. Thus

A

apoB mRNA is edited to induce a premature stop codon for the intestinal apoB

56
Q

Short RNA molecules that base pair with mRNAs and regulate translation

A

micro RNAs (miRNAs)

57
Q

miRNAs usually bind to the 3’ UTR and

A

inhibit translation

58
Q

A protein complex thought to physically impede translation initiation

59
Q

Many miRNAs are correlated with

60
Q

Iron homeostasis is regulated by an

-binds the iron regulatory element (IRE) and prevents translation

A

Iron sensing protein (IRP)

61
Q

The IRP can not bind the IRE if it is bound to

62
Q

Some mRNAs encoding proteins that regulate iron homeostasis contain an “iron response element (IRE)” that binds to an iron-sensing protein (IRP) that regulates

A

Translation or mRNA stability depending on cellular ion concentrations

63
Q

Nutritional status regulates

A

Translation

64
Q

Phosphorylation of an initiation factor (eIF2) causes translation inhibition in response to

A
  1. ) Low amino acid concentration
  2. ) Cellular stress (e.g. oxidative stress)
  3. ) Immune response
  4. ) Unfolded proteins
65
Q

To assist in re-binding GTP after hydrolysis, the G-protein eIF2 requires a

A

Guanine Nucleotide Exchange Factor (GEF) (which for eIF2 is eIF2B)

66
Q

GEFs are required because the

A

Affinity for GDP is much higher than that for GTP

67
Q

Under normal conditions, GDP is echanged for GTP by the action of eIF2B. However, poor nutrition (i.e. reduced amino acid concentrations) causes eIF2 phosphorylation, which

A

Causes eIF2 to bind eIF2B as an inactive complex.

68
Q

What happens to protein synthesis when phosphorylated eIF2 binds eIF2B?

A

There will be an excess of inactive eIF2 (the GDP bound form), and protein synthesis slows dramatically

69
Q

Hypoxia regulates

A

translation

70
Q

The mTOR (mammalian Target Of Rapamycin) signaling pathway represses translation in response tohypoxia by regulating the function of

71
Q

Is like a cellular rheostat - it upregulates
translation during growth and downregulates
during stress. It is constitutively in an
active state in order to keep growth in check.

A

The mTOR pathway

72
Q

Normoxia (growth conditions) induces

A

mTOR signaling

73
Q

Proteins that bind to eIF4E and inhibit translation

74
Q

When 4EBPs are phosphorylated, they are

A

Released from eIF4E (ending inhibition)

75
Q

The mTOR pathway is a key regulator of

A

4EBP phosphorylation

76
Q

Activation of mTOR (during growth) causes

A

4EBP phosphorylation and increased translation

77
Q

Inhibits mTOR, and thus allows 4EBP dephosphorylation and binding to eIF4E, causing decreased translation

78
Q

What is often called the 21st amino acid?

deficiency causes hyperthyroidism

A

Selenocysteine (Sec)

79
Q

Selenocysteine incorporation requires alternative usage of the

A

UAG stop codon

80
Q

The deiodinases are required for TH synthesis, thus among other things, selenium is essential for

A

Proper thyroid function

81
Q

Selenocysteine incorporation requires a unique set of

A

Translation factors

82
Q

A specialized elongation factor, similar to eEF1A,

that binds to the Sec-tRNA

83
Q

A specialized tRNA that recognizes UGA codons and carries the selenocysteine amino acid

A

Sec-tRNA^Sec

84
Q

An RNA element in the 3’ UTR required for Sec incorporation

A

SECIS element

85
Q

Binds to the SECIS element and assists in getting eEFSec ternary complex to the ribosome at UGA Sec codons

A

SECIS binding protein 2 (SBP2)

86
Q

Encoded by a UGA stop codon that has been “re-coded” to allow Sec-tRNA binding

A

Selenocystein

87
Q

Required for the “re-coding” of the stop codon

88
Q

Caused by SBP2 mutations in humans because reduced Sec incorporation leads to reduced production of the deiodinases

A

Some rare forms of hypothyroidism

89
Q

Creating more than one protein from a single mRNA

-Utilized by viruses like HIV

A

Ribosomal frameshifting

90
Q

A single mRNA can encode more than one protein product if the ribosomes are signaled to

A

Frameshift

91
Q

Frameshift signals include the

A

RNA pseudoknot, and an RNA sequence called the “slippery site”

92
Q

The efficiency of frameshifting determines the amount of each protein that is

93
Q

Targets translation by modifying the elongation factor responsible for translocation (eEF2)

A

Diptheria toxin

94
Q

Transcriptional regulation sometimes takes too long, for a faster response, we want

A

Translational regulation

95
Q

Typically, a frame shift mutation will result in

A

Premature termination (Stop codon formation)

96
Q

Typically, a ribozyme is an enzyme that can cleave

97
Q

Place where you maintain the registry of the mRNA and maintain the reading frame. The actual function of the is still debated

98
Q

Most proteins in the translation process are

-Act as switches to sequence the events of translation

A

G-proteins (GTP dependent)

99
Q

The pre-initiation complex comes across a lot of secondary structural motifs. In order to break these structures up, it relies on a

A

Helicase (Only step in protein synthesis that requires ATP)

100
Q

Occurs in step 2 of elongation. If there are no errors, then we will get GTP hydrolysis and eEF1A release

A

Proofreading

101
Q

Uses GTP hydrolysis to catalyzes the translocation mechanism that moves the new peptide from the A site to the P site

102
Q

eEF2 binds into the A site, which forces the A site tRNAs to move into the P site. GTP hydrolysis allows the release of eEF2 from the A site and the ribosome shifts by

103
Q

Feedback on the initiation complex and physically block translation

A

RISC complex

104
Q

Can not bind the IRE and thus, translation is normal and we produce ferratin

A

Iron-bound iron regulatory protein

105
Q

Bind and inhibit eIF4E, the protein which binds to the cap to allow translation to occur

A

4E Binding Proteins (4EBP)

106
Q

In children, deficiencies in selenium present as

A

Hypothyroidism

107
Q

caused by SBP2 mutations in humans because reduced Sec incorporation leads to reduced production of the deiodinases

A

Some rare forms of hypothyroidism

BMS (62 decks)

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