TRANSCRIPTION--- SYNTHESIS OF RNA Dr. Zakira Naureen

Previously we have studied Central dogma of molecular biology DNA Structure and Replication Enzymes and factors involved in Replication Three types of RNA m RNA; t RNA; r RNA

Learning objectives What is gene ? What is Transcription? Structure of RNA polymerases

Genes A gene is a region of DNA that controls a discrete hereditary characteristic, usually corresponding to a single mRNA which will be translated into a protein. In eukaryotes, the genes have their coding sequences (exons) interrupted by non-coding sequences (introns). In humans, genes constitute only about 2-3% of DNA, the rest is “junk” DNA.

protein Eukaryotic Gene Structure transcription translation 5’ - Promoter Exon1 Intron1 Exon2 Terminator – 3’ UTR splice splice UTR transcription Poly A translation protein

Prokaryotic Gene Structure Promoter CDS Terminator UTR UTR Genomic DNA transcription mRNA translation protein

Prokaryote gene versus Eukaryote gene

What is Transcription ? It is the process of copying DNA to RNA. It differs from DNA synthesis in that only one strand of DNA, the template strand, is used to make mRNA. Unlike DNA replication, it does not need a primer to start. It can involve multiple RNA polymerases. Transcription is divided into 3 stages Initiation Promoter recognition and binding Initiation of polymerization of NTPs Elongation Termination

Transcription Tools Template DNA DNA-dependent RNA polymerase ATP, GTP, CTP, and UTP are required, Mg2+ Transcription factors ATP

The coding strand and the template strand of DNA The important thing to realize is that the genetic information is carried on only one of the two strands of the DNA. This is known as the coding strand. The other strand is known as the template strand, and is complementary to the coding strand. If you took the template strand and built a new DNA strand on it (as happens in DNA replication), you would get an exact copy of the original DNA coding strand formed. Almost exactly the same thing happens when you make RNA. If you build an RNA strand on the template strand, you will get a copy of the information on the DNA coding strand - but with one important difference.

The Code is read from 5’ to 3’

The Basics of Transcription

DNA Dependent RNA Polymerase It’s a holoenzyme Structure and function are fundamentally similar in Prokaryotes and Eukaryotes ( few exceptions) Bacterial RNA Polymerases are composed of 4 core subunits (2 small + 2 large ) + Sigma factor (σ)– determines promoter specificity Core + σ = holoenzyme Binds promoter sequence

continued In eukaryotes the DNA dependent RNA Polymerase has several other binding factors i.e. Transcription factors More than one polymerases are required to make all different types of RNA unlike bacterial RNA Polymerase that can catalyze formation of all three RNA molecules. Three polymerases for 3 RNA molecules RNA pol I--------rRNA RNA pol II-------mRNA RNA pol III------tRNA

PROMOTER Sigma factors recognize consensus -10 and -35 sequences

continued Promoter determines: Which strand will serve as a template. Transcription starting point. Strength of polymerase binding. Frequency of polymerase binding.

Prokaryotic Promoter One type of RNA polymerase. Pribnow box located at –10 (6-7bp) –35 sequence located at -35 (6bp) Sigma factor actually recognizes this and binds here

Eukaryote Promoter Goldberg-Hogness or TATA located at –30 Additional regions at –100 and at –200 Possible distant regions acting as enhancers or silencers (even more than 50 kb).

Promoter Sequence

Promoter Strong promoter resemble the consensus sequence. Mutations at promoter sites can influence transcription. Human gene Beta globin

Stages of Transcription Initiation – the RNA polymerase enzyme binds to a promoter site on the DNA and unzips the double helix. Elongation – free nucleotides bind to their complementary pairs on the template strand of the DNA elongating the RNA chain which is identical to the informational strand of DNA, except that the nucleotide thymine in DNA is replaced by uracil in RNA. The polymerase moves along the DNA in the 3’ to 5’ direction, extending the RNA 5’ to 3’. Termination – specific sequences in the DNA signal termination of transcription; when one of these is encountered by the polymerase, the RNA transcript is released from the DNA and the double helix can zip up again.

Transcription video

Chain Initiation First phase of transcription is initiation Initiation begins when RNA polymerase binds to promoter and forms closed complex After this, DNA unwinds at promoter to form open complex, which is required for chain initiation

Initiation

Chain Elongation After strands separated, transcription bubble of ~17 bp moves down the DNA sequence to be transcribed RNA polymerase catalyzes formation of phosphodiester bonds between the incorp. ribonucleotides Topoisomerases relax supercoils in front of and behind transcription bubble

Elongation

Chain Elongation (Cont’d)

Chain Termination Two types of termination mechanisms: • intrinsic termination- controlled by specific sequences, termination sites Termination sites characterized by two inverted repeats

Chain Termination (Cont’d) Other type of termination involves rho () protein Rho-dependent termination sequences cause hairpin loop to form

Transcription in Eukaryotes Three RNA polymerases are known; each transcribes a different set of genes and recognizes a different set of promoters: • RNA Polymerase I- found in the nucleolus and synthesizes precursors of most rRNAs • RNA Polymerase II- found in the nucleoplasm and synthesizes mRNA precursors • RNA Polymerase III- found in the nucleoplasm and synthesizes tRNAs, other RNA molecules involved in mRNA processing and protein transport

RNA Polymerase II Most studied on the polymerases Consists of 12 subunits RPB- RNA Polymerase B

How does Pol II Recognize the Correct DNA? Four elements of the Pol II promoter allow for this phenomenon

Initiation of Transcription Any protein regulator of transcription that is not itself a subunit of Pol II is a transcription factor Initiation begins by forming the preinitiation complex Transcription control is based here

General Transcription Initiation Factors

Transcription Order of Events Less is known about eukaryotes than prokaryotes The phosphorylated Pol II synthesizes RNA and leaves the promoter region behind GTFs are left at the promoter or dissociate from Pol II

Elongation and Termination Elongation is controlled by: pause sites, where RNA Pol will hesitate anti-termination, which proceeds past the normal termination point positive transcription elongation factor (P-TEF) and negative transcription elongation factor (N-TEF) Termination begins by stopping RNA Pol; the eukaryotic consensus sequence for termination is AAUAAA