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MolCell Mega Class > VEST 2 > Flashcards

VEST 2 Flashcards

1
Q

The pre-mRNA primary transcript consists of exon 5’ UTR protein coding region 3’ UTR and ______ sequences.

A

intron

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2
Q

Internal methylation in RNA can influence stability splicing and ________.

A

translation

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3
Q

Polymerase II transcripts need ________ (snRNA + specific protein complexes) to splice out introns.

A

snRNPs

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4
Q

snRNP 1 binds to the ________ splice site.

A

5’

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5
Q

snRNP 2 binds to the ______________.

A

branchpoint

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6
Q

U2AF binds to the polypyrimidine _________.

A

tract

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7
Q

Alternative splicing generates multiple mRNAs and ________ from a single primary transcript.

A

proteins

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8
Q

The polyA tail consists of approximately 200 __ residues and has multiple functions including protecting the mRNA from 3’ degradation and enhancing translation.

A

A

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9
Q

circRNAs are circular RNAs that regulate ________ in multiple ways.

A

expression

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10
Q

Histone RNAs are stabilized by a 3’ _______ structure.

A

stemloop

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11
Q

Stemloop recruits the stemloop binding protein (______).

A

SLBP

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12
Q

Downstream AAGAAG recruits snRNP ____.

A

U7

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13
Q

SLBP and U7 recruit the FLASHLsm complex and the histone ______ complex HCC which uses components of the CPSF complex including CPSF73 aka CPSF2 to cleave the 3’ end.

A

cleavage

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14
Q

SLBP mediates nuclear export by recruiting nuclear export protein ALYREF and TAPNXF1 nuclear export __________.

A

receptor

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15
Q

lncRNAs like MALAT1 have 3’ triple _________.

A

helices

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16
Q

These serve to protect the lncRNA from the nuclear ___________ and other RNA decay components.

A

exosome

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17
Q

MALAT1 is not known to be _____ from the nucleus.

A

exported

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18
Q

But Addition of the MALAT1 triple helix to a GFP reporter results in efficient nuclear export and _________, so MALAT1 nuclear retention likely requires other sequence in the lncRNA.

A

translation

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19
Q

Different R radical groups have different chemical structures that confer various chemical __________ to the specific amino acid.

A

properties

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20
Q

Nonpolar aliphatic R groups: Mainly hydrocarbons uncharged and _______.

A

hydrophobic

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21
Q

Aromatic R groups: Relatively nonpolar absorb ____ light.

A

UV

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22
Q

Proteins are _________ consisting of amino acids linked by peptide bonds.

A

polymers

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23
Q

Amino acid sequence is its structure

A

primary

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24
Q

This structure folds to create and tertiary structures

A

secondary

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25
Q

Two or more polypeptide chains associate to form structure

A

quaternary

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26
Q

A is a set of nucleotides 3 in number that encodes a single amino acid

A

codon

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27
Q

The genetic code consists of codons

A

64

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28
Q

AUG is the _________ codon.

A

initiation

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29
Q

UAA UAG and UGA are _____________ stop codons.

A

termination

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30
Q

There are 64 possible codons 61 are sense codons and 3 are _____ codons.

A

stop

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31
Q

Degenerate code: A specific amino acid may be specified by more than one _____.

A

codon

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32
Q

Synonymous codons: codons that specify the same ___________.

A

amino acid

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33
Q

Isoaccepting tRNAs different tRNAs can accept the same amino acid but have different __________.

A

anticodons

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34
Q

Reading frame: three ways in which the sequence can be read; in groups of ________. Each different way of reading encodes a different amino acid sequence.

A

three

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35
Q

Nonoverlapping: A single nucleotide may not be included in more than one _________.

A

codon

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36
Q

In Human mitochondria UGA Stop is altered to code for ______.

A

Trp

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37
Q

In Human mitochondria AUA Ile is altered to code for ______.

A

Met

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38
Q

In Human mitochondria AGA and AGG Arg are altered to code for _____.

A

Stop

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39
Q

In human nuclear DNA (in a context-dependent manner) UGA Stop is altered to code for ____.

A

Sec

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40
Q

The reading frame of a mRNA sequence is determined by the start codon AUG and sets the _________ start site.

A

translational

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41
Q

The concept of _________ explains why in the 3rd position of the codon 1st position of the anticodon, there is some flexibility in the bonding between the base pairs.

A

wobble

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42
Q

This flexibility allows some tRNAs to pair with more than one _________ on an mRNA.

A

codon

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43
Q

Codon _____________ refers to the relative abundance of the corresponding tRNAs.

A

optimization

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44
Q

Codon optimization is conserved in ___________.

A

mammals

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45
Q

Codon optimization contributes to _________ of translation.

A

speed

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46
Q

The genetic code is degenerate: 64 possible codons encode 20 amino acids, 3 codons are ______________ codons.

A

termination

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47
Q

Some codons are _________.

A

synonymous

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48
Q

Isoaccepting tRNAs are tRNAs with different __________ that accept the same amino acid.

A

anticodons

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49
Q

The wobble position 3 in the codon 1 in the anticodon allows one type of tRNA to pair with more than one mRNA ________.

A

codon

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50
Q

The genetic code is generally nonoverlapping; there are three separate reading frames each set by a _________ codon (usually AUG encoding Met).

A

start

51
Q

Any of the three termination codons (UAA UAG ________) signal the end of translation.

A

UGA

52
Q

The genetic code is almost ________.

A

universal

53
Q

The translation of an mRNA molecule takes place on a __________.

A

ribosome

54
Q

The specificity between an amino acid and its tRNA is determined by each individual aminoacyl-tRNA __________.

A

synthetases

55
Q

There are exactly ___ different aminoacyl-tRNA synthetases in a cell.

A

20

56
Q

An amino acid attaches to the 3’ end of a ______ in translation.

A

tRNA

57
Q

tRNA charging: the attachment of a tRNA to its appropriate _________.

A

amino acid

58
Q

The Shine–Dalgarno consensus sequence in bacterial cells is recognized by the _______ unit of ribosome.

A

small

59
Q

The Kozak sequence in eukaryotic cells facilitates the identification of the ______ codon.

A

start

60
Q

The initiation or start codon in bacterial cells is usually _________, which codes for formyl-methionine amino acid.

A

AUG

61
Q

When AUG encodes an internal methionine, the amino acid is not formylated and utilizes a different tRNA molecule.

A

formylated

62
Q

The initiation codon in eukaryotic cells is usually AUG and encodes an _________ methionine both at the initiation and internal positions.

A

unformylated

63
Q

However, like in bacterial systems, the tRNA which codes for this initiator methionine is ________ than the internal methionine tRNAs.

A

different

64
Q

During initiation in bacterial cells, the nucleotides in the Shine-Dalgarno sequence base pair with their complementary nucleotides in the 16s small ribosomal RNA, allowing the small ribosomal subunit to attach to the mRNA in position for the initiation of ____________.

A

translation

65
Q

The Kozak sequence is a _______ sequence in eukaryotic cells that surrounds the start codon.

A

consensus

66
Q

Translation initiation requires initiation factors and _______.

A

GTP

67
Q

Note that mRNA secondary structures are unwound by _________ activity located in the small ribosomal subunit.

A

helicase

68
Q

In eukaryotes, translation initiation is facilitated by interactions between the proteins binding the polyA tail and the _______ proteins.

A

cap-binding

69
Q

Initiation factor eIF4G and eIF4E interact with both the polyA binding proteins and ________ proteins.

A

capbinding

70
Q

A-site aminoacyl – tRNA site – holds the tRNA carrying the next amino acids to be added to a polypeptide ______.

A

chain

71
Q

P-site peptidyl – tRNA site – holds the tRNA attached to the growing ________ chain.

A

polypeptide

72
Q

E-site – the exit site from which tRNA molecules leave the _________.

A

ribosome

73
Q

Each amino acid added to the growing end of the polypeptide chain is selected by complementary base-pairing between the _________ on its attached tRNA molecule and the next codon on the mRNA chain.

A

anticodon

74
Q

____________ formation between the 2 amino acids occurs in the large ribosomal subunit; the catalytic activity for this reaction is a property of a large rRNA component.

A

peptide bond

75
Q

Numerous studies link m6A to _________ translation via 3 distinct mechanisms.

A

increased

76
Q

The m6A reader DF1 binds the eukaryotic translation initiation factor eIF3, the multiprotein complex that recruits the ________ ribosome subunit to mRNAs which enhances their translation.

A

small

77
Q

Since DF1-binding sites are mostly around stop codons in the 3’ UTRs, this model implies DF1 recruits ______ to these regions.

A

eIF3

78
Q

Presumably when the 3’ UTR region loops to interact with the 5’ _______ complex, translation is enhanced.

A

cap

79
Q

5’ UTR m6A residues bind to ______.

A

eIF3

80
Q

The ______ bypasses the normal requirement for eIF4E normally recruited by the 5’ cap complex.

A

m6A

81
Q

Because only a few 5’ UTRs have m6A residues, this mechanism is limited to a small number of ___________.

A

mRNAs

82
Q

Direct translation activation is done by ________, the m6A methylating complex.

A

METTL3

83
Q

The _______ protein complex is thought to bind eIF3 to create the loop between the 3’ and 5’ UTRs, which might facilitate ribosomal assembly and function.

A

METTL3

84
Q

The termination codons are UAA, UAG, and _____.

A

UGA

85
Q

Translation ends when a ________ codon is encountered.

A

stop

86
Q

Translation consists of tRNA charging, initiation, elongation, and _________. In this process, amino acids are linked together in the order specified by mRNA to create a polypeptide chain. A number of initiation elongation and release factors take part in the process and energy is supplied by ATP and GTP.

A

termination

87
Q

RQC – __________ Quality Control Complex exists to monitor harmful peptides and mRNA lacking a stop codon.

A

Ribosome

88
Q

Ribosomal _________ occurs due to the ribosome translating through a stop codon, lack of a stop codon, or defective tRNAs.

A

stalling

89
Q

Inhibition of translation _______ through ribosomal defects occurs.

A

elongation

90
Q

The RQC complex facilitates _________ of the peptide which targets it for lysosomal or proteasomal degradation.

A

ubiquitination

91
Q

Selenocysteine is encoded by ____ stop codons.

A

UGA

92
Q

Approximately 25 _______ exist in the human genome.

A

selenoproteins

93
Q

Selenoproteins are involved in cell signaling and redox _________.

A

homeostasis

94
Q

Examples of __________ include: Glutathione peroxidases (GPX18), Thioredoxins reductases (THX 13), Iodothyronine deiodinases (DIO13), and Selenoprotein P (SELENOP) and related.

A

selenoproteins

95
Q

Serine is converted to selenocysteine on the charged ______.

A

tRNA

96
Q

SECIS recruits the SECIS binding protein (SBPB2), which scaffolds the elongation factor Sec (________).

A

EFSec

97
Q

EFSec facilitates Sec-charged tRNA binding to the _____ codon.

A

UGA

98
Q

Messenger RNA surveillance: Detect and deal with errors in _____.

A

mRNA

99
Q

Nonsense-mediated mRNA decay: eliminating mRNA containing premature _________ codons; recruited by exon _______ complexes.

A

termination

100
Q

Ribosomal _______, also known as translational frameshifting or translational recoding, is a process that occurs during translation that results in the production of multiple unique proteins from a single mRNA.

A

frameshifting

101
Q

Ribosomal frameshifting can be programmed by the nucleotide sequence of the mRNA and is sometimes affected by the secondary mRNA _________.

A

structure

102
Q

In viruses, ribosomal frameshifting allows encoding of multiple types of _______ from the same mRNA.

A

proteins

103
Q

Ribosomal frameshifting is controlled by a _________ sequence and a RNA secondary structure.

A

slippery

104
Q

Slippery sequences can potentially make the reading ribosome slip and skip a number of nucleotides (usually only 1) and read a completely different _______ thereafter.

A

frame

105
Q

The RNA secondary structure (which can be a stemloop) pauses the ribosome on the slippery site during translation, forcing it to relocate and continue replication from the _____ position. It is believed that this occurs because the structure physically blocks movement of the ribosome by becoming stuck in the ribosome mRNA tunnel.

A

-1

106
Q

Both gag and pol proteins are required for reverse _________, which is essential to HIV1 replication.

A

transcriptase

107
Q

Polyribosomes are multiple ________ attached to the same mRNA strand.

A

ribosomes

108
Q

Polyribosomes make multiple copies of the same _______ from a single mRNA strand.

A

protein

109
Q

Polyribosomes allow a cell to quickly make many copies of the _________.

A

protein

110
Q

Protein synthesis consists of 4 steps:
1) binding of amino acids to the appropriate tRNAs
2) _________
3) elongation
4) termination

A

initiation

111
Q

The binding of an amino acid to the appropriate tRNA requires the presence of a specific aminoacyl-tRNA _________ and ATP. The amino acid is attached by its carboxyl end to the 3’ end of the tRNA.

A

synthetase

112
Q

In bacterial translation, initiation the _____ ribosomal subunit attaches to the mRNA over the initiation codon by mRNA and rRNA interactions at the Shine-Delgarno region. The initiator tRNA and its associated formyl-methionine amino acid along with the large ribosomal subunit join the complex.

A

small

113
Q

In eukaryotic translation initiation, the small ribosomal subunit binds to the ___ end of the mRNA after recruitment by proteins on the 5’cap complex and polyA tail. The small subunit then scans downstream until it encounters the first AUG start codon at the Kozak consensus sequence; at this point, the initiator methionine tRNA and the large ribosomal complex are added to form the complete ribosome.

A

5’

114
Q

In elongation, a charged tRNA enters the ____ site of the ribosome, a peptide bond is formed between the amino acids in the A and P sites, and the ribosome moves (translocates) along the mRNA to the next codon. GTP is a required energy source for these processes.

A

A

115
Q

Translation is terminated when the ribosome encounters a ________ codon. Release factors and GTP are required to bring about termination.

A

termination

116
Q

Each mRNA molecule may be simultaneously translated by several ribosomes in what is called a __________ or polysome.

A

polyribosome

117
Q

Cells possess mRNA ________ mechanisms that eliminate mRNAs with errors that may create problems in translation.

A

surveillance

118
Q

Some proteins undergo __________ modifications to support or modify their functions.

A

posttranslational

119
Q

DNA – Triplet code mRNA – _____ tRNA – Anticodon

A

Codon

120
Q

The genetic code determines how nucleotide sequences specify the amino acid sequence of a protein DNA → RNA → _______. Each codon, consisting of 3 mRNA nucleotides, encodes a specific amino acid. The codons are written and read in a 5’→ 3’ direction as they appear in the mRNA.

A

Protein

121
Q

Amino acids are assembled into polypeptides proteins in the _______ through the mechanism known as “translation”. tRNAs bring specific amino acids to be added to the polypeptide chain. The specific amino acid is determined by the codon sequence.

A

ribosome

122
Q

Translation consists of initiation, elongation, and ________ processes

A

termination

123
Q

In some cases the UGA stop codon encodes _________ (Sec)

A

selenocysteine

124
Q

The Sec tRNA is recruited by a stem-loop structure in the 3’ UTR, the stem loop binding protein (SLBP), and the selenocysteine elongation factor ______.

A

EFSec

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