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CELL1001 > Cell biology 2: transcription and translation (Dr. Whitmore) > Flashcards

Cell biology 2: transcription and translation (Dr. Whitmore) Flashcards

1
Q

What is the difference between pre-mRNA and mRNA ?

A 
pre-mRNA = introns + exons
mRN = exons
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2
Q

What are the 3 main steps of pre-mRNA processing in the nucleus ?

A
  1. 5’ capping
  2. Splicing
  3. 3’ polyadenylation
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3
Q

What is the difference between T and U ?

A

T has a methyl group on its 5’ C.

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4
Q

What is the consequence of RNA existing as a single strand ?

A

RNA can form intramolecular base-pairs and fold into specific structures. This can lead to non-conventional base-pair interactions (e.g. A-G).

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5
Q

What does transcription do ?

A

Transcription of a gene produces an RNA complementary to one strand of DNA.

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6
Q

Which is the coding strand ?

Which is the template strand ?

A

The coding strand is the DNA equivalent of the RNA strand (w/ T instead of U).
The template strand is the strand complementary to the RNA transcribed.

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7
Q

What is a sigma factor ?

A

A protein needed only for initiation of RNA synthesis. It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase to gene promoters.

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8
Q

What is a promoter ?

A

A region of DNA that initiates transcription of a particular gene (e.g. TATA box). Promoters are located near the transcription start sites of genes, on the same strand and upstream on the DNA (towards the 5’ region of the sense strand).

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9
Q

What is a terminator ?

A

A section of nucleic acid sequence that marks the end of a gene or operon in genomic DNA during transcription.

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10
Q

What is an operon ?

A

A functioning unit of genomic DNA containing a cluster of genes under the control of a single promoter.

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11
Q

What is the rate of RNA synthesis by RNA polymerase ?

A

~100bp/s

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12
Q

In prokaryotes, what is the sequences of events followed by transcription ?

A
  • sigma factor binds to promoter
  • RNAp binds to sigma factor-promoter complex
  • sigma factor dissociates and RNAp shoots down DNA strand
  • RNAp recognises terminator region, it is released along w/ the RNA transcript
  • sigma factor rebinds to RNAp
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13
Q

What is the fct of mRNAs ?

A

Code for protein.

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14
Q

What is the fct of rRNAs ?

A

Form the core of ribosome’s structure + catalyse protein synthesis.

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15
Q

What is the fct of miRNAs (microRNAs) ?

A

Regulate gene expression.

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16
Q

What is the fct of tRNAs ?

A

Serve as adaptors between mRNA and AAs during protein synthesis.

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17
Q

What is the fct of non coding RNAs ?

A

Used in mRNA splicing, gene regulation, telomere maintenance, and many other processes.

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18
Q

What does RNAp I transcribe ?

A

Most rRNA genes.

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19
Q

What does RNAp II transcribe ?

A
  • all protein coding genes
  • miRNA genes
  • other noncoding RNAs (e.g. those in spliceosomes).
20
Q

What does RNAp III transcribe ?

A
  • tRNA genes
  • 5S RNA genes
  • genes for many other small RNAs
21
Q

What are transcription factors ?

A

Proteins that control the rate of the rate of transcription. These include a wide number of proteins, excluding RNAp, that initiate and regulate the transcription of genes.

22
Q

What are some of the transcription factors required by eukaryotic RNAp II ?

A
  • TBP (TATA binding protein)
  • TFIID
  • TFIIB
  • TFIIE
  • TFIIH
  • TFIIF
23
Q

What is the role of TFIIH ?

A
  • unwinds DNA at the transcription start point

- phosphorylates RNAp II, releasing it from most of the general transcription factors

24
Q

What are eukaryotic pre-mRNA molecules caped w/ at the 5’ end ?

A

A 7-methylguanylate cap.

25
Q

Why do eukaryotic pre-mRNA molecules undergo capping and polyadenylation ?

A
  • Stabilize mRNA
  • Aid nuclear export
  • Define mRNA (e.g. tRNA and sRNA are not modified)
  • Checkpoints for protein synthesis machinery
26
Q

How long is the poly-A tail ?

How is it added ?

A

150-250 As long.

Added by enzyme non coded in DNA.

27
Q

What is the bacterial lac operon ?

A

Lactose operon = operon required for the transport and metabolism of lactose in E. Coli and many other enteric bacteria. Although glucose is the preferred carbon source for most bacteria, the lac operon allows for the effective digestion of lactose when glucose is not available.

28
Q

How many genes can a bacterial mRNA code for ?

A

Often several.

29
Q

What signals the beggining/end of an intron ?

A

Special nt sequences in a pre-mRNA transcript.

30
Q

Which molecules perfom mRNA splicing ?

A

Small nuclear RNAs and proteins called ‘snurps’ or snRNPs.

31
Q

What is the advantage of having an intron-exon structure ?

A
  • some pre-mRNAs undergo alternative RNA splicing to produce various mRNAs and proteins
    from the same gene
  • many exons encode specific protein domains, and ‘exon-shuffling’ may have contributed to
    the evolution of new genes and proteins
  • protection against genetic mutations ?
32
Q

How many codons are there ?
How many AAs ?
Why ?

A

4^3 = 64 codons
20 AAs
Degeneracy of the genetic code

33
Q

What is the structure of tRNA ?

A

That of a cloverleaf w/ the AAs attached to the 3’ end and an anti-codon loop capable of binding the appropriate codon.

34
Q

What is an aminoacyl tRNA synthetase (aaRS) ?

A
  • an enzyme that attaches the appropriate AA onto its tRNA (the one w/ the anti codon of that AA)
  • there are 20aaRSs –> 1 for each AA
  • linkage of AA to tRNA: ATP –> AMP
35
Q

What are ribosomes ?

A
  • the protein builders the cell –> covalently link one AA to another and build long chains
  • found in both prokaryotes and eukaryotes
  • 2 subunits: 1 large (~49 proteins + 3 rRNAs, covalently links AAs together), 1 small (~33 proteins + 1 rRNA, matches tRNA to mRNA codon)
36
Q

What are the 4 steps in which translation takes place ?

A
  1. Charged tRNA binds to mRNA by forming base pairs with the correct nucleotide triplet
  2. AA in P-site is uncoupled from tRNA and a covalent peptide bound is formed with the amino-acid linked to the tRNA in the A site
  3. Large subunit shifts relative to the small subunit -> tRNAs move to E and P sites
  4. Small subunit moves 3 nucleotides along the mRNA. Empty tRNA is ejected, empty A site is ready to receive next charged tRNA.
37
Q

What are the tRNA sites of the ribosome ?

A

A (acceptor) site = binds to the aminoacyl tRNA, which holds the new amino acid to be added to the polypeptide chain
P (peptidyl) site = binds to the tRNA holding the growing polypeptide chain of amino acids
E (exit) site = serves as a threshold, the final transitory step before a tRNA now bereft of its AA is let go by the ribosome.

38
Q

How many binding sites does the ribosome have ?

A

4: 1 for mRNA, 3 for tRNAs

39
Q

When does translation stop ? In what direction is the mRNA read ?
In what direction is the protein synthesised ?

A

Process is repeated until STOP codon (UAA, UAG, UGA) is encountered. mRNA is translated in 5’ to 3’ direction, protein from N-terminus to C-.

40
Q

How does translation start and stop ?

A
  1. The small ribosomal subunit, w/ bound initiator tRNA (bound to Met) and translation initiation factor, moves along mRNA searching for first AUG
  2. Small subunit finds AUG, translation initiation factors dissociate, large subunit binds
  3. Charged tRNA binds to A site (step 1)
  4. First peptide bond forms (step 2)
  5. Ribosome meets STOP codon
  6. Binding of release factor to the A site
  7. Termination –> peptidyl transferase adds H20 instead of AA (COOH)
  8. Ribosome dissociates
41
Q

How can antibiotics act at gene or protein level ?

A

By inhibiting bacterial protein or RNA synthesis.

42
Q

What does tetracycline do ?

A

Blocks binding of aa-tRNA to A site of ribosome.

43
Q

What does streptomycin do ?

A
  • Prevents the transition from initiation complex to chain elongation
  • Causes miscoding
44
Q

What does chloramphemicol do ?

A

Blocks the peptidyl transeferase reaction on ribosome.

45
Q

What does cycloheximide do ?

A

Blocks the translocation reaction of ribosome.

46
Q

What does rifamycin do ?

A

Blocks initiation of transcription by binding to RNAp.

CELL1001 (16 decks)

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