15 | Transcription

Question 0

Transcription

Answer 0

The enzymatic production of an exact complementary strand of RNA upon a DNA template

Question 1

Discrete Steps of Transcription

Answer 1

(1) Binding
(2) Formation
(3) Initiation
(4) Elongation
(5) Termination (& Recycling)

Question 2

mRNA

Answer 2

(Messenger RNA)

Encode the amino acid sequence of one or more polypeptides specified by a gene or a set of genes

Question 3

tRNA

Answer 3

(Transfer RNA)

Read information encoded in mRNA and provide the appropriate amino acid to a growing polypeptide chain during protein synthesis

Question 4

rRNA

Answer 4

(Ribosomal RNA)

Constituents of ribosomes, the intricate cellular machines of protein synthesis

Question 5

RNA Polymerase

Answer 5

Specialized enzymes that catalyze transcription in cells and viruses

Question 6

How does RNA transcription differ from DNA replication?

Answer 6

(1) No primer required to begin
(2) Involves sections not entirety of DNA
(3) Only one strand serves as template

Question 7

Transcriptome

Answer 7

Entire set of transcripts within a cell

Question 8

RNA polymerase core

Answer 8

Subunits of the enzyme necessary to catalyze a reaction carried out by a polymerase

Question 9

sigma (σ) factor

Answer 9

Transient subunit of RNA polymerase that direct enzyme to specific site upon DNA

Question 10

E.coli RNA Polymerase Structure

Answer 10

Five polypeptide subunits:

β’ / β / α (2-copies) / ω

Question 11

RNA polymerase holoenzyme

Answer 11

The six subunits of the polymerase core plus the sigma factor

Question 12

RNA Polymerase I

Answer 12

Transcribes genes encoding large rRNA precursors

Question 13

RNA Polymerase II

Answer 13

Encodes nearly all protein-coding genes to make mRNA

Question 14

RNA Polymerase III

Answer 14

Transcribes genes encoding smaller functional RNAs (tRNA, snRNA, 5S rRNA)

Question 15

How were the structure of bacterial and yeast RNA polymerases determined?

Answer 15

Via x-ray crystallography

Question 16

Initiation

Answer 16

When RNA polymerase binds to specific sequence on DNA

Question 17

Promoter

Answer 17

Specific sequence on DNA at which initiation occurs

Question 18

Elongation

Answer 18

Addition of nucleotides to growing RNA strand

Question 19

Termination

Answer 19

Release of product RNA when polymerase reaches end of gene

Question 20

Template strand

Answer 20

Complement of the coding strand

Question 21

Coding strand

Answer 21

Identical in nucleotide sequence to the RNA transcribed on the gene

Question 22

Closed complex

Answer 22

Formed during first step of transcription when polymerase binds the promoter and DNA remains intact

Question 23

Open complex

Answer 23

Formed during the second step of transcription when the bound DNA is partially unwound ~10bp upstream from the transcription start site

Question 24

Initiation

Answer 24

Conformational change in transcriptional complex occurs that is required for elongation to take place

Question 25

Promoter clearance

Answer 25

Movement of transcription complex away from promoter

Question 26

Elongation complex

Answer 26

End result of promoter clearance. Tightly bound, highly efficient transcript synthesis complex

Question 27

Why is RNA synthesis processive?

Answer 27

Once elongation begins the kinetics of the polymerization reaction favor the addition of a nucleotide over the premature release of the transcript

Question 28

Actinomycines

Answer 28

A class of polypeptide antibiotics isolated from soil bacteria of the genus Streptomyces. (e.g. Actinomycin D, Acridine, Rifampicin)

Question 29

Actinomycin D Mechanism of Action

Answer 29

Inhibits transcription elongation by RNA polymerase

Question 30

α-amanitin

Answer 30

Naturally bio-defense antibiotic of a mushroom

Question 31

RNA polymerase binds to the DNA of E. coli within what range?

Answer 31

A 100bp range between ~70bp before start site to ~30bp after

Question 32

σ70

Answer 32

The most common sigma factor in E.coli

Question 33

Consensus sequence

Answer 33

Sequence of nucleotides statistically determined to be most commonly found at a particular position on DNA. Critical in the identification of promoter regions.

Question 34

Upstream promoter (UP) element

Answer 34

AT-rich recognition element found between -40 and -60 of the promoters in certain highly expressed genes

Question 35

Abortive initiation

Answer 35

When, within the first 8-10 phosphodiester bonds, a transcript is released prior to completion and the assembled polymerase holoenzyme begins RNA synthesis upon the same template again.

Question 36

Pyrophosporolysis

Answer 36

Reverse polymerization reaction

Question 37

Kinetic proofreading

Answer 37

Catalytic, accuracy ensuring result of stalling by polymerase during transcription

Question 38

Nucleolytic proofreading

Answer 38

Hydrolytic, accuracy ensuring nuclease activity inherent to RNA polymerase

Question 39

Termination sequence

Answer 39

Occurs when transcription stops at a certain sequence and the haloenzyme disassociates from the DNA template.

Question 40

ρ-dependent

Answer 40

Termination of transcription at the "rut": a CA-rich sequence

Question 41

ρ-independent

Answer 41

Termination involving a hair-pin loop followed a sequence of A-U interactions

Question 42

TBP

Answer 42

(TATA-binding protein) A transcription factor shared by all eukaryotic RNA polymerases that binds to the "TATA" box at initiation

Question 43

Preinitiation complex

Answer 43

Association of transcription factors, promoter DNA and Poly I

Question 44

Steps of Transcription at Poly II promoters

Answer 44

(1) Recruitment (2) Formation (3) Phosphorylation (4) Elongation (5) Dephosphorylation [termination]

Question 45

Mediator complex

Answer 45

Multi-protein that acts as intermediary between specific transcription factors as a coactivator. aka: Transcriptional Coactivator

Question 46

Keys of Eukaryotic Transcription

Answer 46

(1) Takes place in nucleus (2) Three RNA-polymerases recognize three sets of promoters (3) Additional proteins required for promoter recognition (4) Transcripts require processing (removal of RNA seq.) to make a mature product (final product)