Lecture 3

Question 1

What is transcription?

Answer 1

Transcription: copying DNA sequences into an RNA molecule

Question 2

Transcription is the first step of gene expression.

Explain how/why..

Answer 2

1 * Before protein can be made, RNA must be transcribed.

2 * RNA is synthesised using the DNA as a template in a process similar to DNA synthesis - but the mRNA remains as a single strand

Question 3

What is RNA?

participates?

Answer 3

Ribonucleic acid (RNA) Consists of a Single Strand of
Ribonucleotides

participates in a Variety of
Cellular Functions

Question 4

How does it differ from DNA? sugar, bases, strands?

Answer 4

Differs from DNA:
1. Sugar: Ribose

2. Bases: A, G , C, U
3. SINGLE-STRANDED (easily degraded, forms secondary structures)

Question 5

What are the 3 main types of RNA?

Answer 5

Three main types of RNA:

CODING:

1. mRNA (messenger) “code” (5%)

FUNCTIONAL:

2. tRNA (transfer) one for each AA (15%)
3. rRNA (ribosomal) part of ribosomes (80%)

Question 6

All cellular types of RNA are transcribed from DNA.

EXPLAIN THE STEP =4

Answer 6

1. Some RNAs are transcribed in both prokaryotic and eukaryotic cells
   - mRNA
   -rRNA
   - tRNA
2. …Some are only produced in EUKARYOTES,..
   - Pre-mRNA
   - small nuclear RNA (snRNA)
   - Small nucleolar RNA (snoRNA)
   - small interfering RNA (siRNA)
   - Piwi-interacting RNA (piRNA)
3. and others are only Produced in PROKARYOTES.
   - CRISPR RNA (crRNA)
4. some viruses copy RNA directly from RNA

Question 7

An RNA molecule is synthesised from one strand of DNA, the template strand.

Answer 7

1. RNA synthesis is complementary and antiparallel to the template strand.
2. New Nucleotides are added to the 3’-OH group of the growing RNA, so transcription proceeds in a 5’ TO 3’ Direction.
3. The non- template strand is not usually transcribed.

Question 8

The template DNA strand is transcribed; the resulting
mRNA has the SAME SEQUENCE and POLARITY as the NON-TEMPLATE (UNTRANSCRIBED) DNA strand

Answer 8

The template DNA strand is transcribed; the resulting
mRNA has the SAME SEQUENCE and POLARITY as the NON-TEMPLATE (UNTRANSCRIBED) DNA strand

Question 9

A transcription unit is a stretch of DNA that encodes
an RNA molecule and the sequences necessary for
its transcription

Answer 9

A TRANSCRIPTION UNIT= is a STRETCH of DNA that ENCODES
an RNA molecule and the SEQUENCES NECESSARY for
its TRANSCRIPTION.

Question 10

Like replication, transcription requires three major components:

Answer 10

1. A DNA template
2. The raw materials needed to build a new RNA molecule
3. The transcription apparatus - the proteins necessary for catalyzing synthesis of RNA

Question 11

MAIN TRANSCRIPTION ENZYME?

Answer 11

RNA POLYMERASE

Question 12

Transcription summary/overview = 3

Answer 12

1 * Transcription begins when RNA POLYMERASE binds to a PROMOTER SEQUENCE
NEAR BEGINNING OF A GENE

2 * RNA polymerase uses one of the DNA strands (the TEMPLATE strand) as a
template to make a NEW, COMPLEMENTARY RNA MOLECULE.

3 * Transcription ends in a process called TERMINATION, which occurs when SEQUENCES OF THE RNA SIGNAL THAT TRANSCRIPTION IS FINISHED.

Question 13

Bacterial cells have one type of RNA polymerase

Answer 13

In bacterial RNA polymerase, the core enzyme consists of five subunits:
two, 2 copies of alpha (α),
a single, 1 copy of beta (β),
a single copy of beta prime
(β′),
and a single copy of omega (ω).

The core enzyme catalyzes the elongation of the RNA molecule by the addition of RNA nucleotides.
(a) The sigma factor
(σ) joins the core to form the holoenzyme, which is capable of binding to a
promoter and initiating transcription.

Question 14

Eukaryotic cells possess several distinct types of RNA
polymerase that transcribe different kinds of RNA molecules.

TYPE, PRESENT IN, TRANSCRIBES

Answer 14

1. RNA polymerase I - All eukaryotes - Larger rRNAs
2. RNA polymerase II - All eukaryotes - Pre-mRNAs, snoRNAs, some miRNAs, some snRNAs
3. RNA polymerase III - All eukaryotes - tRNAs, small rRNAs, some miRNAs, some snRNAs
4. RNA Polymerase IV - plants - siRNAs that silence transposons
5. RNA polymerase V - plants - siRNAs that affect chromatin

Question 15

Transcription consists of three stages: WHAT ARE THEY?

Answer 15

(1) initiation,
(2) elongation and
(3) termination

Question 16

EXPLAIN WHAT HAPPENS IN INITIATION: 6

Answer 16

Initiation: the transcription apparatus assembles on the
promoter and begins the synthesis of RNA

1 - promoter recognition

2 - formation of a transcription bubble

3 - creation of the first bonds between rNTPs

4 - escape of the transcription apparatus from the promoter

5. A consensus sequence consists of the most commonly encountered nucleotides

6.RNA polymerase must bind to the sigma factor to initiate
transcription

Question 17

What happens during elongation?

Answer 17

1 * At the end of initiation, RNA polymerase undergoes a conformational change - allows it to escape from the
promoter and begin transcribing downstream.

2 * Transcription takes place within the transcription
bubble.

• Topoisomerase enzymes relieve stress.

Question 18

What happens during Termination?

Answer 18

Termination:
* Transcription ends after a terminator has been
transcribed

Question 19

Genes transcribed by RNA polymerase II have
a core promoter

Answer 19

Y: any pYrimidine (CIT)
R: any puRine (AIG)
N: any of the four bases

The promotoers of genes transcribed by RNA polymerase II consist of two primary parts;
A CORE PROMOTER
A REGULATORY PROMOTER

Both parts typically contain consensus sequences, but not all the consensus sequences are found in all promoters.

Question 19

There are some important differences between
bacterial and eukaryotic transcription.

In eukaryotes: EXPLAIN 3

Answer 19

1 * There are three different RNA polymerases, each of which transcribes a different class of RNA and recognizes a different type of promoter

2 * Many accessory proteins take part in the binding of eukaryotic RNA polymerases to DNA templates, and the different types of promoters require different proteins.

3 * The initiation of transcription requires modification of chromatin structure so that DNA is accessible to the transcription machinery.

Question 20

Initiation of transcription at RNA polymerase II promoters requires transcription factors

Answer 20

1. TFIID binds to TATA box in the core promoter.
2. Then transcription factors and RNA polymerase II bind to the core promoter.
3. Transcription factors bind to sequences in enhancers.
4. DNA loops out, allowing the proteins bound to the enhancer to interact with the basal transcription apparatus.
5. Transcription factors bind to sequences in the regulatory promoter and interact with the basal transcription apparatus through the mediator.

Transcription is initiated at RNA polymerase II promoters. Transcription is initiated by the binding of the TFIID transcription factor to the TATA box, followed by the binding of preassembled HOLOENZYME containing general transcription factors, RNA polymerase II, and the mediator.

TBP stands for ‘TATA BINDING PROTEIN”

Question 21

Transcription elongation in eukaryotes; RNA polymerase II
grabs the DNA and bends it

Answer 21

Transcription elongation in eukaryotes; RNA polymerase II
grabs the DNA and bends it

The structure of RNA polymerase II is a source of insight into its function.

The DNA double helix enters RNA polymerase II through a cleft in the enzyme and unwinds.

The DNA-RNA duplex is bent at a right angle, which positions 3’ end of the RNA at the active site of the enzyme.

at the active site, new nucleotides are added to the 3’ end of growing RNA molecule.

Question 22

Transcription termination
in eukaryotes

Answer 22

1.RNA polymerase adds nucleotides to the 3 ′ end of the growing RNA molecule until it transcribes a terminator.

2. three eukaryotic RNA
   polymerases use different
   mechanisms for termination

Question 23

What are the three eukaryotic RNA
polymerases use different
mechanisms for termination.

AND EXPLAIN THEM…

Answer 23

1. RNA polymerase I - termination factor similar to
   rho
2. RNA polymerase III - ends transcription after
   transcribing a terminator sequence
3. RNA Polymerase II - Transcription is terminated
   when an exonuclease enzyme attaches to the
   cleaved 5’ end of the RNA, moves down the RNA,
   and reaches the polymerase enzyme

Question 24

Transcription termination in eukaryotes STEP = 6

Answer 24

1. RNA polymerase 11 transcribes well past the coding sequences of most genes. 2. Cleavage takes place at the 3' coding region of the RNA... 3. ...while RNA polymerase continues transcribing. 4. The Rat 1. exonuclease attaches to the 5' end of the trailing of RNA... 5. ...and moves toward the RNA polymerase, degrading the as it goes. 6. When Rat 1 reaches the polymerase, transcription is terminated. Termination of ranscription by RNA polymerase II requires the Rat1 exonuclease. Cleavage of the pre-mRNA produces a 5' end to which Rat1 attaches. Rat1 degrades the RNA molecule in the direction. When Rat1 reaches the polymerase, transcription is halted.