Lecture 3 Flashcards
What is transcription?
Transcription: copying DNA sequences into an RNA molecule
Transcription is the first step of gene expression.
Explain how/why..
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
What is RNA?
participates?
Ribonucleic acid (RNA) Consists of a Single Strand of
Ribonucleotides
participates in a Variety of
Cellular Functions
How does it differ from DNA? sugar, bases, strands?
Differs from DNA:
1. Sugar: Ribose
- Bases: A, G , C, U
- SINGLE-STRANDED (easily degraded, forms secondary structures)
What are the 3 main types of RNA?
Three main types of RNA:
CODING:
- mRNA (messenger) “code” (5%)
FUNCTIONAL:
- tRNA (transfer) one for each AA (15%)
- rRNA (ribosomal) part of ribosomes (80%)
All cellular types of RNA are transcribed from DNA.
EXPLAIN THE STEP =4
- Some RNAs are transcribed in both prokaryotic and eukaryotic cells
- mRNA
-rRNA
- tRNA - …Some are only produced in EUKARYOTES,..
- Pre-mRNA
- small nuclear RNA (snRNA)
- Small nucleolar RNA (snoRNA)
- small interfering RNA (siRNA)
- Piwi-interacting RNA (piRNA) - and others are only Produced in PROKARYOTES.
- CRISPR RNA (crRNA) - some viruses copy RNA directly from RNA
An RNA molecule is synthesised from one strand of DNA, the template strand.
- RNA synthesis is complementary and antiparallel to the template strand.
- New Nucleotides are added to the 3’-OH group of the growing RNA, so transcription proceeds in a 5’ TO 3’ Direction.
- The non- template strand is not usually transcribed.
The template DNA strand is transcribed; the resulting
mRNA has the SAME SEQUENCE and POLARITY as the NON-TEMPLATE (UNTRANSCRIBED) DNA strand
The template DNA strand is transcribed; the resulting
mRNA has the SAME SEQUENCE and POLARITY as the NON-TEMPLATE (UNTRANSCRIBED) DNA strand
A transcription unit is a stretch of DNA that encodes
an RNA molecule and the sequences necessary for
its transcription
A TRANSCRIPTION UNIT= is a STRETCH of DNA that ENCODES
an RNA molecule and the SEQUENCES NECESSARY for
its TRANSCRIPTION.
Like replication, transcription requires three major components:
- A DNA template
- The raw materials needed to build a new RNA molecule
- The transcription apparatus - the proteins necessary for catalyzing synthesis of RNA
MAIN TRANSCRIPTION ENZYME?
RNA POLYMERASE
Transcription summary/overview = 3
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.
Bacterial cells have one type of RNA polymerase
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.
Eukaryotic cells possess several distinct types of RNA
polymerase that transcribe different kinds of RNA molecules.
TYPE, PRESENT IN, TRANSCRIBES
- RNA polymerase I - All eukaryotes - Larger rRNAs
- RNA polymerase II - All eukaryotes - Pre-mRNAs, snoRNAs, some miRNAs, some snRNAs
- RNA polymerase III - All eukaryotes - tRNAs, small rRNAs, some miRNAs, some snRNAs
- RNA Polymerase IV - plants - siRNAs that silence transposons
- RNA polymerase V - plants - siRNAs that affect chromatin
Transcription consists of three stages: WHAT ARE THEY?
(1) initiation,
(2) elongation and
(3) termination
EXPLAIN WHAT HAPPENS IN INITIATION: 6
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
- A consensus sequence consists of the most commonly encountered nucleotides
6.RNA polymerase must bind to the sigma factor to initiate
transcription
What happens during elongation?
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.
What happens during Termination?
Termination:
* Transcription ends after a terminator has been
transcribed
Genes transcribed by RNA polymerase II have
a core promoter
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.
There are some important differences between
bacterial and eukaryotic transcription.
In eukaryotes: EXPLAIN 3
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.
Initiation of transcription at RNA polymerase II promoters requires transcription factors
- TFIID binds to TATA box in the core promoter.
- Then transcription factors and RNA polymerase II bind to the core promoter.
- Transcription factors bind to sequences in enhancers.
- DNA loops out, allowing the proteins bound to the enhancer to interact with the basal transcription apparatus.
- 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”
Transcription elongation in eukaryotes; RNA polymerase II
grabs the DNA and bends it
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.
Transcription termination
in eukaryotes
1.RNA polymerase adds nucleotides to the 3 ′ end of the growing RNA molecule until it transcribes a terminator.
- three eukaryotic RNA
polymerases use different
mechanisms for termination
What are the three eukaryotic RNA
polymerases use different
mechanisms for termination.
AND EXPLAIN THEM…
- RNA polymerase I - termination factor similar to
rho - RNA polymerase III - ends transcription after
transcribing a terminator sequence - 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
Transcription termination
in eukaryotes STEP = 6
- RNA polymerase 11 transcribes well past the coding sequences of most genes.
- Cleavage takes place at the 3’ coding region of the RNA…
- …while RNA polymerase continues transcribing.
- The Rat 1. exonuclease attaches to the 5’ end of the trailing of RNA…
- …and moves toward the RNA polymerase, degrading the as it goes.
- 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.
