Topic 6-L1- Transcription

Question 1

DNA encodes genes, but itself is inert. For DNA sequences to carry
out functions, it must be converted to

Answer 1

RNA via transcription

Question 2

Transcription uses an enzyme called

Answer 2

RNA polymerase

Question 3

RNA polymerase works by

Answer 3

• Binds to DNA template and makes an RNA copy of one of two strands
• Copied strand = coding strand, other strand = template strand
• Only builds RNAs 5’ - 3’ – Because transcription goes in only one
  direction and in opposite directions on each strand

Question 4

During transcription, Coding strand matches RNA sequence…

Answer 4

except T is Template strand replaced with U

Question 5

RNA polymerase core enzyme made up of 4 subunits:

Answer 5

⍺ (2 copies)
β
β’
ω. 
Holoenzyme also includes additional subunit,     (sigma factor)

Question 6

Sigma factor in holoenzyme binds

Answer 6

promoter region, then dissociates from core enzyme

Question 7

Core enzyme unwinds DNA to expose template —>

Answer 7

forms transcription bubble

Question 8

Using NTPs (ATP, CTP, GTP, UTP) as
substrates and the template strand as guide, the

Answer 8

RNA chain is built one nucleotide at a time

Question 9

Ultimately, RNA polymerase will encounter a transcriptional

Answer 9

terminator and will dissociate from the template & release the RNA

Question 10

Transcription will (generally) continue until RNA polymerase (RNAP)
encounters a

Answer 10

transcriptional terminator. RNAP then dissociates from DNA, stops making RNA & releases transcript.

Question 11

Intrinsic (rho-independent) terminators form when

Answer 11

RNA hairpin structures form, followed by a string of “U” residues. U residues act as pause signal for RNAP – formation of hairpin forces RNAP off template.

Question 12

Rho-dependent terminators: A

protein called

Answer 12

Rho binds RNA as it is being transcribed and causes RNA polymerase to dissociate after it encounters certain sequences

Question 13

Transcriptional initiation is guided by DNA sequences called

Answer 13

promoters

Question 14

Whether or not a sequence acts as a promotor

Answer 14

promoter is active dictated by binding of sigma factors & the activity of regulatory proteins

Question 15

The housekeeping (most commonly used/most important) sigma factor
is called

Answer 15

SIGMA70 (or RpoD) – it recognizes two sequences upstream of the
transcriptional start site.

Question 16

Bacterial promoters

Answer 16

• Transcriptional start site: sequence ~35 bp upstream of the +1 site
• Pribnow box : ~10 bp upstream of the +1 site. This sequence (TATAAT)

Question 17

There are 3 major classes of RNAs (and other non-coding RNAs with
a range of functions – often regulatory):

Answer 17

• Messenger RNA (mRNA): converted to protein via translation
• Transfer RNA (tRNA): functional RNAs, used in translation process
• Ribosomal RNA (rRNA): functional RNAs, used in translation process

Question 18

Open reading frames (ORFs) are sequences that are

Answer 18

translated into proteins

Question 19

mRNAs contain both ORFs and untranslated regions (UTRs) - which are?

Answer 19

parts of the mRNA transcript that are not translated into protein

Question 20

mRNAs that encodes multiple ORFs are _________ and are called _______

Answer 20

polycistronic operons

Question 21

Genes in an operon are

Answer 21

cotranscribed

Question 22

5’UTR –

Answer 22

everything from first transcribed residue (+1) through the start codon of gene. Contains ribosome binding site (RBS)

Question 23

ORF

Answer 23

Start codon (e.g. ATG) through stop codon (e.g. TAA)

Question 24

3’ UTR

Answer 24

everything from the stop codon of the gene through the final transcribed residue. Often contains transcriptional terminator sequences

Question 25

transcription is different in eukaryotes since they

Answer 25

• Have 3 RNA polymerases. RNA polymerase II produces mRNA (encode proteins). Others encode RNA transcripts that are not translated (e.g. rRNA, tRNA, and other RNAs)
• Are more complex = 12+ subunits
• Require transcription factors to recognize promoters – they bind specific DNA sequences & recruit RNA polymerase (e.g TATA box)

Question 26

Do eukaryotes use operons?

Answer 26

NO, each gene has its own promoter

Question 27

Eukaryotic primary mRNA transcripts contain

Answer 27

protein-coding exons and non-

coding introns. mRNAs are processed (spliced) to remove introns

Question 28

Eukaryotic mRNAs are

Answer 28

polyadenylated at the end (3’) of transcript and capped at 5’ end using a modified G residues attached using an unusual linkage

Question 29

Where does transcription and translation occur in eukaryotes

Answer 29

transcription in nucleus

translation in cytoplasm

Question 30

The archaeal RNA polymerase resembles

Answer 30

RNA polymerase II from eukaryotes and has 11-13 subunits.

Question 31

Archaea RNA polymerase is recruited to

Answer 31

promoters using transcription factors (related to eukaryotic proteins)

Question 32

Do archaea use TATA boxes and transcriptional factors that bind these elements and recruit RNA polymerase?

Answer 32

Yes

Question 33

Are archaea more complicated then eukaryotes

Answer 33

NO, eukaryotes more complex

Question 34

Archaea do not have :

Answer 34

• 5’ cap,
• poly A tail, mRNAs
• introns & are not spliced
• nucleus – transcription and translation often coupled (like in bacteria)

Question 35

Do archaea not use operons like eukaryotes?

Answer 35

No they do use operons like bacteria

multiple genes encoded by one RNA (single promoter controls expression of several genes)