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BIOL 415 > Final Exam: Translation > Flashcards

Final Exam: Translation Flashcards

1
Q

What is included in the translation apparatus?

A

mRNA, ribosome, and tRNA

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2
Q

Where is eukaryotic rRNA processed?

A

Transcribed and processed in the nucleolus

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3
Q

What is snoRNA

A

Small nucleolar RNA that assist ribosomal RNA in catalytic modification through cleavage, methylation, and base modification.

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4
Q

What are the three sites of the ribosome?

A

The A site, the P site, and the E site

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5
Q

Define anticodon

A

a sequence of three nucleotides in a tRNA molecule that corresponding to a complementary codon in sequence of mRNA (base-pairs with the codon in mRNA).

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6
Q

Where does the amino acid sequence bind on the tRNA?

A

At the CCA sequence at the 3’ end of the tRNA

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7
Q

What is a aminoacyl tRNA? What is its role?

A

tRNA that is charged due to being bonded with an amino acid. The aminoacyl tRNA brings the amino acid to the ribosome.

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8
Q

Aminoacyl tRNA synthetase

A

enzyme that attaches the appropriate amino acid onto its corresponding tRNA. Responsible for charging tRNA

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9
Q

What occurs at the A site of the ribosome?

A

The A site is the site of the ribosome where the aminoacyl-tRNA enters to base pair with the codon

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10
Q

What occurs at the P site of the ribosome?

A

The site in the ribosome that is occupied by peptidyl-tRNA (the tRNA carrying the newly synthesized polypeptide chain)

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11
Q

Define peptidyl tRNA

A

the tRNA to which the newly synthesized polypeptide chain that has been transferred following peptide bond synthesis during translation

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12
Q

Define deacylated tRNA

A

tRNA that has no amino acid or polypeptide chain attached because it has completed its role in translation and is ready to be released from the ribosome

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13
Q

What are the three stages of translation?

A

Initiation, elongation, and termination

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14
Q

What occurs at the E site of the ribosome?

A

The site of the ribosome that briefly holds deacylated tRNAs before their release

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15
Q

What s translocation?

A

The movement of the ribosome one codon along the mRNA after the addition of each amino acid to the polypeptide chain

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16
Q

Describe the process of initiation

A
  • Reactions that precede the formation of the peptide bond between the first two amino acids of the polypeptide.
  • mRNA binds to the ribosome to form the initiation complex containing aminoacyl-tRNA and the AUG start codon is found
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17
Q

Describe elongation

A
  • Ribosome moves along the mRNA extending the protein by transfer from peptidyl-tRNA to aminoacyl-tRNA
  • Stage where the nucleotide or polypeptide chain is extended by the addition of one amino acid at a time
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18
Q

Describe the process of termination

A

Termination codon is recognizes, polypeptide chain is released from the tRNA, and the ribosome is dissociated from the mRNA.

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19
Q

True or false: initiation requires 50S ribosomal subunits.

A

False: Initiation requires free 30S small subunits for mRNA

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20
Q

What happens to ribosomes released from translation after termination?

A

The ribosomes are released into a pool of free ribosomes where they then dissociate into separate subunits. The 30S subunits then bind with initiation factors to again begin the process of initiation

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21
Q

Define IFs

A

Initiation factor: proteins that stabilize the small 30S subunit of the ribosome at initiation

22
Q

What is meant by the phrase “prokaryotic transcripts are often polycistronic”

A

Most of the prokaryotic mRNAs are polycistronic which means that multiple genes are present on a single transcript and the single promoter initiates transcription of all those genes and regulates their expression.

22
Q

What is meant by the phrase “prokaryotic transcripts are often polycistronic”

A

Most of the prokaryotic mRNAs are polycistronic which means that multiple genes are present on a single transcript and the single promoter initiates transcription of all those genes and regulates their expression.

23
Q

What are polysomes?

A

Polysomes are ensembles of two or more consecutive ribosomes that translate mRNA into proteins

24
Q

True or false: prokaryotic transcription and translation are coupled

A

True

25
Q

What initiation factors are involved in prokaryotic initiation?

A

IF-3: stabilizes free 30S, enables 30S binding to mRNA, checks accuracy of first aminoacyl-tRNA

IF-1: blocks A site (prevents aminoacyl-tRNA from entering)

IF-2: Recruits initiator tRNA to P site

26
Q

What is the function of IF-3 in prokaryotic translation?

A

In initiation, IF-3 binds to the 30S free floating ribosomal subunit. When the 30S is bound to IF-3, it is allowed to bind to mRNA. IF-3 must be released after mRNA is bound to allow large 50S subunit to join. Upon release, IF-3 finds a new 30S subunit to bind to.

27
Q

What is fMet-tRNAf?

A

The special tRNA used to initiate translation in bacteria, chloroplasts, and mitochondria.

28
Q

What initiation factor recognizes fMet-tRNAf?

A

IF-2

29
Q

What is Met-tRNAm?

A

The bacterial tRNA that inserts methionine at internal AUG codons.

30
Q

What are the main differences between fMet-tRNAf and Met-tRNAm?

A

fMet-tRNAf features:

  • three G-C base pairs are required for entry into the P site
  • Recruited by IF-2
  • The bases at the last position of the stem are not base paired in fMet-tRNAf that are base paired in all other tRNA.
31
Q

Define Shine-Dalgarno Sequence

A
  • ribosomal binding site in bacterial messenger RNA that enables initiation of protein synthesis by aligning the ribosome with the start codon (located about 10 bp before AUG).
  • The polypurine sequence AGGAGG centered about 10 bp before AUG initiation codon on bacterial mRNA.
  • Sequence is complementary to the sequence at the 3’ end of the 16S rRNA
  • Specific for bacteria and some chloroplasts and mitochondrial transcripts
  • Distinguishes internal AUG from initiation codons
32
Q

True or false: aminoacyl-tRNAs can freely bind to the ribosome without aid

A

False: aminoacyl-tRNAs controlled by accessory factors. Accessory factors are needed for aminoacyl-tRNAs to associate with the ribosome

33
Q

What is the accessory factor used in initiation of prokaryotic translation? What is the role of this accessory factor?

A

IF-2

IF-2 recruits the initiator tRNA (and only initiator tRNA) to the 30S mRNA complex. When the large 50S subunit joins the 30S subunit, IF-2 is released and GTP is hydrolyzed GDP

34
Q

Define IRES

A

Internal ribosome entry site: a eukaryotic mRNA sequence that allows a ribosome to initiate polypeptide translation without migrating form the 5’ end (avoids “scanning”).

Genomes that contain IRESs can allow multiple ribosomes to bind at the same time and initiate translation

35
Q

What is the Kozak sequence?

A

protein translation initiation site in eukaryotic mRNA

36
Q

What is the “scanning method” in eukaryotes?

A

The 40S subunit initially recognizes the 5’ cap on the mRNA the migrates down the mRNA until it reaches the start (AUG codon). Once at the AUG codon, the initiation complez can form.

37
Q

Define ribozyme

A
  • an RNA that has catalytic activity
  • an RNA molecule with a well-defined tertiary structure that enables it to act like a protein enzyme in catalyzing biochemical and metabolic reactions within a cell.
38
Q

What is EF-Tu? What is its role?

A
  • the elongation factor that binds aminoacyl-tRNA and places it into the A site of the bacterial ribosome
  • EF-Tu-GTP places aminoacyl-tRNA on the ribosome and is then released as EF-Tu-GDP. EF-Ts replaces GDP for GTP.
39
Q

Define peptidyl transferase

A

the activity of the large ribosomal subunit that synthesizes a peptide bond when an amino acid is added to a growing peptide chain

-The process of creating peptide bonds between the amino acids in translation

40
Q

What is meant by the hybrid state model of translocation?

A

Translocation occurs in two stages:

  1. The shift f the 50S subunit relative to the 30S subunit
  2. 30S subunit moves along the mRNA to restore the original configuration.
41
Q

True or false: EF-G is structurally different from aminoacyl-tRNA-EF-Tu

A

False: EF-G is structurally similar to aminoacyl-tTNA-EF-Tu

42
Q

Define RF protein

A

Release factor protein: a protein required to terminate polypeptide translation to cause release of the completed polypeptide chain and the ribosome from the mRNA

43
Q

Draw the anatomy of the 30S ribosomal subunit

A

The 30S subunit has a head separated from the body by the neck with a protruding platform.

44
Q

Draw the anatomy of the 50 S

A

Central protuberance where the 5S rRNA is located separated by a notch from a stalk made of copies of the protein L7

45
Q

How do the small and large sub units of the ribosome fit together

A

The platform of the 30S subunit fits into the notch of the 50S subunit to form the 70S subunit

46
Q

Where are most contacts between ribosomal subunits made?

A

Most of the contacts between the ribosomal subunits are made between the 16S and the 23S rRNAs

47
Q

Why is the orientation of the tRNA important during translation?

A

Orientation of the tRNA allows binding of adjacent codons

-The three tRNAs have different orientations on the ribosome. mRNA turns between the P and A sites to allow aminoacyl-tRNAs to bind adjacent codons

48
Q

True or false: The bacterial ribosome has one active center

A

False: the bacterial ribosome has several active centers

49
Q

What are the two active roles of rRNA in translation?

A
  1. Catalysis:
    - Peptide bod formation requires acid-base catalysis where an H atom is transferred to a basic residue. rRNA facilitates catalysis reaction by bringing substrates closer together.
  2. Substrate recognition:
    - 3’ end of the 16S rRNA binds to mRNA a initiation.
    - 23S rRNA has bases that bind to the CCA sequence at the 3’ end of the tRNAs in both P and A sites.
50
Q

What are the 4 mechanisms of translation level control?

A
  1. Poor mRNA:
    - ribosomes do not translate small amounts of mRNA very well
  2. Alternative codon usage:
    - Multiple codons exist for most amino acids. Not all codons are decoded equally by tRNAs. Codons with less abundant tRNAs will be translated more slowly.
  3. Active binding of repressors
    - A regulator protein may block translation by binding to the mRNA site where the ribosome should bind.
  4. Formation of secondary structure
    - During translation, ribosomes disrupt secondary structure. This exposes the second initiation site initially blocked by the formation of the secondary structure.
    - allows for progressive translation at the newly exposed initiation site.

BIOL 415 (7 decks)

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