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BS209: Molecular Biology > Chapter 11: Translation > Flashcards

Chapter 11: Translation Flashcards

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1
Q

production of a protein from the information in an mRNA

A

translation

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2
Q

provides the physical link that decodes mRNA into protein

A

tRNA (transfer RNA)

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3
Q

tRNAs read the mRNA by base-pairing 3 nucleotides: region in tRNA is the (1), while the region on the mRNA is the (2)

A
  1. anticodon
  2. codon
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4
Q

amino acids are attached to tRNAs by ()

A

aminoacyl-tRNA synthetases

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5
Q

Protein synthesis is carried out by a large molecular machine ()

A

ribosome

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6
Q

ribosomes have ()

A

2/3 RNA (rRNA) + 1/3 protein (r-proteins)

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7
Q

the (1) subunit of the ribosome deciphers the mRNA and the (2) subunit mediates the chemical bond formation

A
  1. small
  2. large
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8
Q

ribosomes move () along an mRNA molecule

A

processively (5’ to 3’)

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9
Q

Proteins are synthesized at a rate of about (1) amino acids per second, with
an error rate of about (2) per residue

A
  1. 15
  2. 10-3 to 10-4
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10
Q

translation factors are often () that use the energy of () hydrolysis

A

GTPases, GTP

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11
Q

4 main stages of translation

A
  1. initiation
  2. elongation
  3. termination
  4. ribosome recycling
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12
Q

two essential processes of transfer RNAs (tRNAs)

A
  1. decipher mRNAs
  2. carry amino acids
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13
Q

(): tRNA structure has four regions of double-stranded RNA, including 3 stem-loops

A

clover-leaf pattern

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14
Q

2D structure of tRNA: 5’ and 3’ ends base pair and form the (1), with a conserved (2), which is the attachment point of the amino acid

A
  1. acceptor stem
  2. 3’ CCA tail
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15
Q

2D structure of tRNA: the () has 3 nucleotides that base pair with the codon in mRNA in an antiparallel fashion

A

anticodon loop

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16
Q

a folded tRNA has an () structure (3D)

A

L-shape

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17
Q

the bases in a tRNA anticodon (position 34-36) are typically stacked on top of each other in a structure called a () -> anticodon loop positions the nucleotides to effectively base pair with mRNA

A

U-turn

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18
Q

A () (e.g. base Y) occurs just after the anticodon (typically position 37, found in anticodon loop), to prevent this from base-pairing with the codon in mRNA.

A

hypermodified purine

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19
Q

hypermodified purine after the anticodon aligns the codon and anticodon properly -> critical for ensuring high fidelity of ()

A

decoding

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20
Q

in tRNA, () is typically in position 34 (in anticodon loop) is important for wobble pairing

A

inosine

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21
Q

the DHU (D) loop in tRNA is named after the () in the loop

A

dihydrouridine (D)

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22
Q

the TpsiC (T) loop has (1) and (2) in the T loop

A
  1. ribothymidine (T)
  2. pseudouridine (psi)
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23
Q

Each triplet codon specifies a single amino acid (1) or no amino acid (2).

A
  1. sense codon
  2. stop codon; nonsense codon
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24
Q

() codons signal the end of the protein-coding region of the mRNA

A

stop

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25
Q

Different tRNAs that carry the same amino acids are called ()

A

isoacceptors

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26
Q

the first 2 positions on the mRNA (reading 5’ to 3’) are read by () with positions 2 and 3 of the anticodon

A

strict Watson-Crick base pairing

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27
Q

in the 3rd position of the codon (interacts with position 1 of the anticodon) pairing deviations are allowed -> called ()

A

wobble pairing

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28
Q

consequences of wobble pairing

A
  1. allows some non-Watson-Crick interactions
  2. same tRNA can interpret both CUC and CUU
  3. not each codon needs its own tRNA
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29
Q

some codons are used more infrequently than others -> called (); tend to be decoded by rarer tRNAs

A

rare codons

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30
Q

the genetic code is almost () in all organisms

A

the same; nearly universal

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31
Q

AUG usually codes for ()

A

methionine

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32
Q

there are usually 3 stop codons

A

UAA, UAG, UGA

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33
Q

evolution has conserved codons so that mutations that change the encoded amino acid usually result in ()

A

a chemically similar amino acid

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34
Q

() is a process that attaches amino acids to tRNAs

A

aminoacylation

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35
Q

in the first step of aminoacylation, the amino acid is activated by the attachment of (1) to form an (2)

A
  1. AMP
  2. aminoacyl adenylate
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36
Q

in the second step of aminoacylation, the enzyme (aaRS) then transfers the amino acid to the () of the terminal adenosine on the tRNA 3’ CCA tail

A

2’ or 3’ OH of the ribose

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37
Q

resulting product of aminoacylation is ()

A

aminoacyl-tRNA

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38
Q

Resulting aminoacyl-tRNA is protected from spontaneous hydrolysis by immediate binding of (1) in bacteria or (2) in eukaryotes

A
  1. EF-Tu
  2. eEF1A
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39
Q

Each amino acid has its own aminoacyl-tRNA synthetase -> The enzyme for a certain amino acid is denoted ()

A

aaRS, e.g. GlyRS

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40
Q

correct amino acid for a tRNA is referred to as ()

A

cognate

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41
Q

Aminoacyl-tRNA synthetases recognize tRNAs by sequence and structural features called (1) found primarily in the (2) and (3).

A
  1. identity elements
  2. anticodon loop
  3. acceptor stems
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42
Q

Aminoacyl-tRNA synthetases use various chemical features to discriminate btw different amino acids.

A

charge, hydrophobicity, size, shape

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43
Q

the correct amino acids are chosen in a ()-step process

A

two

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44
Q

Most aminoacyl-tRNA synthetases have an (1) site and an (2) site (where hydrolytic reaction takes place), which combine to recognize the correct amino acid

A
  1. aminoacylation
  2. editing
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45
Q

() keeps non-cognate amino acids that are too big out of the aminoacylation site

A

Size exclusion

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46
Q

The editing site can accommodate the activated amino acid prior to the transfer of the activated a.a. to the tRNA ()

A

editing pre-transfer

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47
Q

if an amino acid is rejected pre-transfer, the aminoacyl adenylate (activated amino acid) itself is ()

A

hydrolyzed

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48
Q

The editing site can accommodate the amino acid after attachment to the tRNA ()

A

editing post-transfer

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49
Q

If rejection occurs post-transfer, the amino acid is ()

A

cleaved from the tRNA

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50
Q

Cognate aminoacyl-adenylates or aminoacyl-tRNAs (can/cannot) enter the editing site and therefore (are, are not) edited.

A

cannot, are not

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51
Q

There are two classes of aminoacyl-tRNA synthetases, (), each with ~ 10 members

A

class I and II

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52
Q

Class I aminoacyl-tRNA synthetases usually recognize the (1) of the acceptor stem, class II the (2)

A
  1. minor groove
  2. major groove
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53
Q

Class I attaches amino acids to the (1) of the terminal ribose, class II to the (2).

A
  1. 2′ OH
  2. 3’ OH
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54
Q

Some bacteria and archaea have fewer than 20 synthetases–usually those for attaching () are the ones missing

A

glutamine and asparagine

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55
Q

A () changes the side chain of the attached amino acid from an acid to an amide, producing asparagine and glutamine-bound tRNAs

A

transamidase reaction

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56
Q

the large ribosomal subunit has an (1) through which the growing polypeptide emerges -> often a target for (2)

A
  1. exit tunnel
  2. antibiotics
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57
Q

eukaryotic and bacterial ribosomes are generally conserved but differ in their ()

A

composition

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58
Q

the () between the ribosomal subunits (where tRNA substrates bind and function) is rich in rRNA and poor in proteins

A

interface

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59
Q

on the () of the ribosome, ribosomal proteins are more evenly distributed

A

exterior

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60
Q

unusual structures of ribosomal proteins

A
  1. globular domains (in exterior)
  2. long extended arms (into core rRNA regions)
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61
Q

long extended arms of ribosomal proteins are usually () amino acids

A

highly basic

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62
Q

ribosome composition differs with ()

A

phylogeny

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63
Q

additional protein and RNA layers called () are found with increasing organism complexity

A

expansion segments

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64
Q

rRNAs in the ribosomal subunits are divided into () based on secondary structure

A

distinct domains

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65
Q

the ()S rRNA has 3 major and 1 minor domains

A

16S (18S in euks)

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66
Q

the ()S rRNA has 6 domains

A

23S (28S in euks)

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67
Q

organization of rRNA domains in the 2 subunits are different:

  • in the small subunit, the domains are (1)
  • in the large subunit, the domains are (2)
A
  1. discrete
  2. interwoven
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68
Q

the large subunit in bacterial ribosomes has a second RNA called the (1); eukaryotes have an additional (2) RNA

A
  1. 5S RNA
  2. 5.8S
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69
Q

ribosomal RNAs and proteins are () across species

A

extremely highly conserved

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70
Q

() are the crucial parts of ribosomes -> were present before other components, which were added later in evolution

A

RNAs

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71
Q

tRNAs bind successively at 3 sites within the ribosome

A
  1. aminoacyl (A) site
  2. peptidyl (P) site
  3. exit (E) site
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72
Q

in translation initiation, the first step is the identification of the (1)

A

AUG initiation codon

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73
Q

the AUG initiation codon is recognized by (1), the ribosome, and (2)

A
  1. initiation factors (IFs)
  2. special initiator methionine tRNA
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74
Q

Early initiation involves the (1) ribosomal subunit, and then the (2) subunit joins the complex

A
  1. small
  2. large
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75
Q

early initiation results in a ribosome with () bound in the P site

A

methionine-loaded tRNA

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76
Q

3 major steps of elongation (translation cycle)

A
  1. decoding at the A site
  2. catalysis of peptide bond formation
  3. translocation
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77
Q

during decoding at the A site, () loads the next charged tRNA into the A site, according to the codon on the mRNA

A

elongation factor Tu (in bacteria)
eEF1A in eukaryotes

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78
Q

EF-Tu/eEF1A loads aminoacyl-tRNAs into the ribosome through ()

A

GTP hydrolysis

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79
Q

() in cells are always complexed with EF-Tu for protection of the linkage between the amino acid and the tRNA from hydrolysis

A

free aminoacyl-tRNAs

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80
Q

peptide bond formation is catalyzed between ()

A

amino acids at the P and A sites

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81
Q

catalysis of peptide bond formation results in the transfer of the growing polypeptide to the tRNA–called ()– in the A site

A

peptidyl-tRNA

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82
Q

during translocation, () promotes the movement of the mRNA-tRNA through the ribosome

A

EFG (in bacteria)
EF2 (in eukaryotes)

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83
Q

action of EFG/EF2 moves the peptidyl-tRNA that was in the A site into the P site and brings a ()

A

new codon into the A site

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84
Q

after a new codon is brought to the A site, the tRNA in the () leaves the codon

A

E site

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85
Q

termination of translation occurs when the ribosome reaches a ()

A

stop codon

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86
Q

stop codons are recognized by (), not tRNAs

A

class I release factors

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87
Q

bacterial RF1 recognizes ()

A

UAA and UAG

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88
Q

bacterial RF2 recognizes ()

A

UAA and UGA

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89
Q

eukaryotic release factor () recognizes all 3 stop codons

A

eRF1

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90
Q

interaction between class I release factors and stop codons promotes ()

A

release of polypeptide from the ribosome

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91
Q

in addition to class I release factors, () are also involved in termination of the translation cycle

A

class 2 release factors

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92
Q

class 2 release factors are also ()

A

GTPases

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93
Q

examples of class 2 release factors

A

RF3 in bacteria
eRF3 in eukaryotes

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94
Q

large and small subunits of the ribosome dissociate and release the remaining tRNA nd mRNA

A

ribosome recycling

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95
Q

in bacteria, () help in dissociation of ribosome during recycling

A

recycling factor RRF and EF-G

96
Q

in eukaryotes, ATPases () help in dissociation of ribosome during recycling

A

Rli1 (in yeast)
ABCE1 (in humans)

97
Q

The () is one model of how tRNAs move through the ribosome -> tRNAs ratchet through the interface region, maintaining contact with one subunit while moving with respect to the other

A

hybrid states model

98
Q

the hybrid states model suggests that (2)

A
  1. tRNAs move first with respect to the large subunit directly following peptide bond formation
  2. anticodon end of tRNA moves with respect to the small subunit
99
Q

in the translation cycle, translation factors generally work in 2 ways

A
  1. as GTPases
  2. simply bind to ribosome
100
Q

many translation factors are (1) that catalyze (2), providing energy and undergoing conformational changes

A
  1. GTPases
  2. GTP hydrolysis
101
Q

other translation factors simply bind to the ribosome and ()

A

stop inappropriate interactions with tRNA or other components of translational machinery

102
Q

() in bacteria prevent initiator tRNA from binding to the A site (thus favoring binding to the P site) and stop the large and small subunits from associating too early

A

IF1 and IF3

103
Q

GTPases are related and have a () that interacts with the phosphates on GTP

A

P-loop motif (Gly-X-X-X-X-Gly-Lys)

104
Q

GTP hydrolysis and the exchange of GDP for GTP can be promoted with the help of proteins:

A
  1. GTPase-activating proteins (GAPs)
  2. guanine-nucleotide exchange factors (GEFs)
105
Q

The ribosome itself can act as a ()

A

GAP

106
Q

Once a cognate aminoacyl-tRNA is in the A site, the ribosome promotes hydrolysis of GTP by (1), thus promoting full acceptance of the aminoacyl-tRNA into A site and release of (2)

A
  1. EFTu
  2. EFTu-GDP
107
Q

Translation can proceed without translation factors, but it is (1)–factors contribute to (2) of the reaction

A
  1. extremely slow
  2. speed and accuracy
108
Q

Many translation factors mimic ()

A

tRNA structures

109
Q

mimicking tRNA structure may be the most efficient way for translation factors to ()

A

access important ribosome interface

110
Q

aside from translation factors, () also mimic tRNA

A

class 1 release factors

111
Q

EFG binds in the A site and promotes translocation of the mRNA-tRNA complex -> very similar in structure to ()

A

EFTu-tRNA

112
Q

freeing of initiation codon allows further rounds of initiation to occur -> many ribosomes pile up on mRNA, resulting in structures called ()

A

polysomes

113
Q

initiator codon is usually AUG, decoded by ()

A

initator tRNA

114
Q

main difference between initiator tRNA in euks vs bacteria

A

bacterial tRNA has a formyl group on Met

115
Q

identity element of bacterial initiator tRNA

A

C-A wobble in acceptor stem

116
Q

identity element of eukaryotic initiator tRNA

A

A-U pair in acceptor stem

117
Q

Both bacterial and eukaryotic initiator tRNA have () in the anticodon stem

A

three G-C pairs

118
Q

identity elements of initiator tRNAs are important () so that initiator tRNAs are not loaded into A

A

anti-determinants for binding of initiator tRNA to EF-Tu

119
Q

Different GTPases are involved in binding of methionyl-tRNA to the P site in eukaryotes and bacteria:

  • Eukaryotes: (1)
  • Bacteria: (2)
A
  1. eIF2
  2. IF2
120
Q

Bacterial mRNAs are often () –having several open reading frame; each open reading frame has its own start and stop codon

A

polycistronic

121
Q

Bacterial Initiation codons usually have a () –this is a polypurine tract 6-8 bases upstream of the initiator AUG

A

Shine-Dalgarno sequence (or ribosome-binding site)

122
Q

Shine-Dalgarno pairs with a polypyrimidine region in the 3′ end of the bacterial 16S rRNA called the (); this pairing guides initiator AUG into the ribosomal P site

A

anti-Shine-Dalgarno sequence

123
Q

The Shine-Dalgarno sequence has the consensus ().

A

AGGAGGU

124
Q

sequence deviation from Shine-Dalgarno consensus controls () of translation

A

strength (how strongly ribosomes bind to mRNA)

125
Q

In the absence of mRNA or f-Met-tRNAMet, () bind in the A and E sites in the small ribosomal subunit

A

IF1 and IF3

126
Q

3 initiation factors that help guide f-Met-tRNAMet to the P site

A

IF1, IF2, IF3

127
Q

initiation factor that is a GTPase and is involved in hydrolyzing GTP to provide energy for joining the large and small ribosomal subunits

A

IF2

128
Q

All three initiation factors are () when the subunits combine– initiation is complete

A

displaced

129
Q

eukaryotic initiation uses () mechanism for identifying AUG start site

A

scanning

130
Q

Eukaryotic mRNAs only usually encode one protein–they are ()

A

monocistronic

131
Q

in eukaryotes, recognition of the AUG is sensitive to the sequence context–the () (consensus: (A/G)XXAUGG)

A

Kozak sequence

132
Q

in eukaryotic mRNA, the 5’ cap is bound by (1) and the 3’ tail by (2). These interact with each other via a complex of other factors

A
  1. eIF4E
  2. PABP
133
Q

interactions of initiation factors bound to 5’ cap and 3’ tail and other factors form a (), and may function as a quality control to weed out unfinished or damaged mRNAs.

A

closed loop complex

134
Q

The (1) ribosomal subunit, bound to a number of initiation factors, is primed to scan the mRNA -> this is called the (2)

A
  1. 40S
  2. “43S” complex, or pre-initiation complex (PIC)
135
Q

() are orthologs of bacterial IF1 and IF3 and bind in the A and E sites

A

eIF1A and eIF1

136
Q

(): initiator tRNA + eIF2 + GTP; important for loading of P site

A

eIF2 ternary complex

137
Q

eIF2 ternary complex is brought to () via interactions with eIF3 and eIF4G

A

closed mRNA loop

138
Q

() in eukaryotes are thought to unwind mRNA secondary structure and let the initiator tRNA check codons for a suitable AUG

A

eIF4A and eIF4B

139
Q

The eukaryotic IF2 (eIF5B) catalyzes () and triggers the dissociation of remaining bound initiation factors.

A

large subunit joining

140
Q

summary of decoding step in elongation (for both euks and bacteria)

A

ribosome selects an aminoacyl-tRNA with an anti-codon that is complementary to the mRNA codon in the A site.

141
Q

The codon/anti-codon interaction can be cognate: (1), near-cognate: (2) and non-cognate: (3)

A
  1. fully accurate
  2. single mismatch
  3. more than one mismatch
142
Q

The fidelity of decoding can be increased (regulated) by two different mechanisms:

A
  1. thermodynamic contributions to fidelity
  2. kinetic contributions to fidelity
143
Q

Cognate aminoacyl-tRNAs bind more strongly with the ribosome than non-cognate and near-cognate ones

A

thermodynamic contributions to fidelity

144
Q

Binding differences between cognate, near-cognate, and non-cognate codons can be utilized both () -> provides the ribosome with two opportunities to discriminate btw cognate and others, thereby increasing fidelity of selection.

A

before and after GTP hydrolysis on EFTu

145
Q

in the context of kinetic contributions to decoding fidelity, geometry of the small helix of RNA formed by codon+anticodon is evaluated in its minor groove by () of the ribosome

A

‘decoding center’

146
Q

(): conformational changes in the ribosomes triggered by cognate helix recognition leads ribosome to act as GAP on EFTu to increase rate of GTPase activation

A

kinetic contributions to the fidelity of decoding

147
Q

increased rate of GTPase activation promotes more rapid () of the aminoacyl-tRNA fully in the A site

A

accommodation

148
Q

() starts with the transfer of the polypeptide chain to the aminoacyl-tRNA in the A site

A

peptide bond formation

149
Q

the () site has highly conserved rRNA elements that surround 2 tRNA substrates and position them for catalysis

A

peptidyl transferase active site

150
Q

nearly no () exist around the peptidyl transferase active site

A

ribosomal proteins

151
Q

how is catalysis promoted in the peptidyl transferase active site?

A
  1. nucleophilic attack (chemical rxn)
  2. conformational change due to binding of aminoacyl-tRNA in A site
152
Q

(1) are universally conserved (2) residues in characteristic loops (3) of 23S rRNA (or 28S rRNA in euk.) form Watson-Crick base pairs with 3’ CCA tails.

A
  1. positioning elements
  2. guanosine
  3. A and P loops
153
Q

The () of the peptidyl-tRNA, critically positioned in the active site, catalyzes the transfer by facilitating proton transfer to promote nucleophilic attack

A

2′ OH

154
Q

() rearrangements are involved in translocation.

A

Large structural

155
Q

EFG can bind in the A site and seems to promote the () -> EFG mimics the tRNA bound to EFTu

A

structural rearrangements

156
Q

example of large structural rearrangements involved in translocation

A

hybrid states (ratchet model)

157
Q

(), not tRNAs, mediate termination

A

Class 1 release factors (RF)

158
Q

main difference between Class 1 RFs and tRNA

A

RF1s are proteins

159
Q

Class I RFs in bacteria and eukaryotes are unrelated (i.e. evolutionarily distinct), but have the same () that is needed for catalysis (a, b)

A

GGQ motif

160
Q

RF3 (bacteria) derives from (1), while eRF3 (euks.) derives from (2)

A
  1. EFG
  2. EFTu
161
Q

in bacteria, GTP-bound RF3 promotes () after peptide release, coupling GTP hydrolysis to this event

A

dissociation of class I RFs (RF1/2)

162
Q

role of class II eRF3 in euks

A
  1. escorts eRF1 to ribosome
  2. uses GTP hydrolysis to promote its own departure from pre-termination complex
163
Q

after departure if eRF3, () binds to where eRF3 was to promote peptide release in the absence of ATP hydrolysis

A

AAA+ ATPase ABCE1

164
Q

Similar to peptide bond formation, () appears to be a key component in the peptide-releasing hydrolytic reaction, working together with conserved GGQ motif on class 1 release factor.

A

2’ OH of the peptidyl-tRNA

165
Q

term for mistakes during translation

A

miscoding

166
Q

mismatch in codon/anti-codon helix at triggers a () in the A site

A

decrease in fidelity

167
Q

The faulty peptide is detected, and then degraded, likely by the (). This acts as a quality control mechanism

A

cellular peptidases and proteases

168
Q

in bacterial ribosome recycling, the recycling substrates are (3)

A
  1. ribosome complex
  2. mRNA
  3. deacetylated tRNA
169
Q

in bacterial ribosome recycling, the () acts with EFG (and GTP hydrolysis) and promotes disassembly.

A

ribosome recycling factor (RRF)

170
Q

in bacterial ribosome recycling, () binds to the small ribosomal subunit to stabilize the dissociated state

A

IF3

171
Q

in eukaryotic ribosomal recycling, eRF1 remains ribosome-bound after the peptide release in the A site in order to ()

A

promote ribosomal subunit dissociation from the A site

172
Q

eRF1-promoted subunit dissociation is further enhanced by () through ATP hydrolysis.

A

AAA+ ATPase ABCE1 in mammals (Rli1in yeast)

173
Q

Similar to bacteria, () in eukaryotes trap dissociated subunits

A

core IFs (eIF1, eIF1A, eIF3)

174
Q

because most bacterial mRNAs are often polycistronic, initiation, elongation, termination, and ribosome take place ()

A

independently

175
Q

in bacteria, he rate of () from mRNA is a crucial factor in determining how much ‘scanning’ for another AUG can occur.

A

small subunit dissociation

176
Q

for the case of monocistronic eukaryotic mRNA, () often regulate gene expression

A

upstream open reading frames (uORFs)

177
Q

upstream open reading frames (uORFs) regulate gene expression via reinitiation of translation from ()

A

a not fully recycled ribosome

178
Q

how are ribosomes rescued from ribosome pausing/stalling/arresting?

A
  1. arrest-causing mRNA targeted for mRNA decay
  2. falsely incomplete polypeptide is targeted for proteolysis
  3. ribosomes are recycled
179
Q

why are truncated mRNAs problematic in bacteria

A

bacterial translation can’t distinguish between truncated mRNAs and intact full length mRNAs

180
Q

measures in eukaryotes that make truncated mRNA less problematic

A
  1. cap/tail-dependent translation initiation
  2. spatially regulated transcription and translation
181
Q

Bacterial ribosomes arrested by truncated mRNA can be rescued by the ()

A

tmRNA-SmpB complex

182
Q

tmRNA first acts as a tRNA: carries () residue to the growing peptide chain

A

alanine

183
Q

tmRNA then acts as an mRNA: encodes a short degradation tag of ()

A

11 a.a. including a stop codon

184
Q

tagged incomplete polypeptide is targeted to (1) and truncated mRNA is decayed by (2).

A
  1. proteases
  2. RNases
185
Q

tRNA-SmpB binding is blocked when () in the A site and mRNA channel

A

mRNA is present

185
Q

() binds like the C-terminal tail of SmpB and recruits RF2 for termination

A

ArfA

185
Q

() binds like termination factors RF1and RF2 and directly releases the polypeptide

A

ArfB

186
Q

ArfA production is tightly regulated by (), and is thought to act as a back-up system

A

tmRNA presence

187
Q

No-go decay (NGD) rescues ribosome stalling caused by (2)

A

1) scarce aa-tRNA
2) specific peptide stalling sequences

188
Q

Non-stop decay (NSD) rescues ribosome arrest caused by (2)

A

1) premature polyadenylation
2) no stop codon at the end of ORF

189
Q

long string of As in an ORF without a stop codon

A

premature polyadenylation

190
Q

when there is no () at the end of ORF, the ribosome reads into polyA tail

A

stop codon

191
Q

In NSD/NGD, () stack up, triggering endonuclease cleavage of mRNA in the A site

A

stalled ribosomes

192
Q

Stalled ribosomes can be dissociated through the activity of ()

A

Pelota and Hbs1

193
Q

Pelota (Dom34 in yeast) and Hbs1 are () that recruit the recycling factor ABCE1.

A

termination factor homologs (eRF1 and
eRF3, respectively)

194
Q

Nonsense-mediated decay (NMD) rescues ribosome arrest caused by ()

A

premature termination codon (PTC)

195
Q

In more complex eukaryotes, stop codons are usually found in the (1), so stop codons found elsewhere are marked as (2)

A
  1. final exon
  2. premature
196
Q

Splicing leaves a protein complex - the EJC - at the ()

A

exon:exon junction

197
Q

Stop codons occurring (upstream/downstream) of an EJC indicate that the mRNA is faulty

A

upstream

198
Q

The () system targets incomplete proteins for degradation

A

ribosome quality control (RQC)

199
Q

in the RQC system, () bind to the 60S subunit with the incomplete protein

A

NEMF and Ltn1

200
Q

NEMF and Ltn1 binding to the 60S subunit with the incomplete protein stimulates addition of ()

A

CAT tails (a string of alanines and threonines)

201
Q

The CAT tails facilitate (), which leads to degradation of the incomplete protein

A

ubiquitination

202
Q

() is where the readout is reprogrammed in an mRNA-specific fashion

A

Recoding

203
Q

in recoding, a codon is interpreted differently in a specific (), and in competition
with the normal reading of the codon.

A

mRNA

204
Q

() is where stop codons are misread and termination fails to occur.

A

Nonsense suppression

205
Q

() is where the mRNA shifts so that peptide synthesis proceeds in a different reading frame.

A

Frameshifting

206
Q

Nonsense suppression is rare, but more common when associated with ()

A

specific mRNA elements

207
Q

A hexanucleotide motif () found 3′ of the stop codon in some viral mRNAs triggers increased read-through by near-cognate aminoacyl-tRNAs.

A

CARYYA; R for purines, Y for pyrimidines

208
Q

() in Murine Leukemia Virus (MuLV) is made by nonsense suppression.

A

Gag-Pol precursor

209
Q

Sometimes, UAG is misread by Gln-tRNAGln promoted by a 3′ proximal () in the mRNA (though it still needs to compete with termination factors) -> producing Gag-Pol fusion gene.

A

pseudoknot

210
Q

Stop codons can also allow incorporation of ()

A

non-standard amino acids.

211
Q

(1)– the “twenty-first amino acid”-is similar to cysteine, but has a (2) instead of a sulfur.

A
  1. Selenocysteine
    2 selenium
212
Q

Selenocysteine is incorporated into several enzymes in catalytic sites, where it can act as a ().

A

strong reducing agent

213
Q

In E.coli, the () is found immediately 3′ of the UGA that will be recoded

A

SelenoCysteine Insertion Sequence (SECIS)

214
Q

A twenty-second amino acid () is a modified lysine found in methyltransferase genes at catalytic sites

A

pyrrolysine

215
Q

Pyrrolysine is incorporated at the () in a similar way to selenocysteine.

A

UGA stop codon

216
Q

EFTu-a standard pathway-is thought to be involved in loading of the ().

A

special tRNA

217
Q

If the ribosome moves by a different number of nucleotides (a number that is not a multiple of three), the reading frame is ().

A

shifted

218
Q

Frameshifting occurs most often () nucleotides from the original, in very specific mRNA contexts.

A

+1 or -1

219
Q

() frameshifting can be involved in gene regulation

A

Programmed

220
Q

An example of programmed frameshifting is the production of ()

A

bacterial termination factor RF2

221
Q

Frameshifting is also needed in many retroviruses for the production of ()

A

Pol

222
Q

() are small molecules that kill or disrupt organism growth.

A

Antibiotics

223
Q

() mean that some good antibiotics are those that target the ribosome and other translation proteins.

A

Small differences in translation between bacteria and eukaryotes

224
Q

stops bacterial growth by blocking the synthesis of peptidoglycans required for cell wall.

A

penicillin

225
Q

(): selectively inhibits bacterial transcription by targeting distinctive pockets on bacterial RNA Pol.

A

Rifampicin

226
Q

Two important naturally-occurring antibiotic groups are the (1) and the (2)

A
  1. aminoglycosides (including kanamycin)
  2. macrolides (including erythromycin
227
Q

() and similar drugs block the tunnel in the ribosome that the peptide exits from. This stops translation by preventing it from proceeding.

A

Erythromycin

228
Q

Bacteria can develop () to antibiotics that interfere with translation

A

resistance

229
Q

Mutations that confer resistance are often found in parts of the (). The location and activity of the mutations can tell us more about how ribosomes work.

A

ribosome

230
Q

() acts as a miscoding agent–causing ribosomes to misread mRNA so proteins are full of errors.

A

streptomycin

231
Q

Streptomycin works by binding the small ribosomal subunit and induces conformational changes that normally only occur when () – thus allowing incorrect amino acids to be incorporated.

A

the cognate tRNA binds

232
Q

Streptomycin-resistant bacteria have mutations near the streptomycin binding pocket–these mutations cause translation to slow down and increase fidelity. (())

A

restrictive protein synthesis

233
Q

Organisms often produce antibiotics to (1) or as a (2).

A
  1. reduce local competition
  2. defense mechanism
234
Q

A new synthetic class–()–is structurally different from natural antibiotics, so resistance has been slow to develop.

A

oxazolidinones

235
Q

example of oxazolidinones

A

linezolid

BS209: Molecular Biology (8 decks)

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