1. Why is dna preferred over rna?

2. Function of other type of rna

3. Typesof rna – mrna (5%) most heterogenous , trna (smallest) 76 – 90 nucleotides( physical
link between mrna and amino acid ), r rna – nucleolous (80%) 60% r rna + 40 % ribosomal
proteins form different subunits of ribosome { intiates the protein synthesis by linking t rna
and m rna }
4. Prokaryote gene structure
~ region 5` of the promoter sequence is called upstream sequence region 3` of the
terminator sequence is called downstream sequence
5. Genes are composed of 3 sequence regions
~promoter -located upstream of the sequence that codes of rna , site of interaction of rna
polymerase , region that gives the location and direction to start transcribing
~rna coding sequence – the sequence of dna that will code of rna
~terminator sequence

The nucleotide pair in the dna that corresponds to the site from which 1st mrna is transcribed is
called as the +1 site

The choice of the template strand is for each gene is determined by the location and orientation of
the promoter

Operons – promoter , operator and related gene

Rnap has intrinsic helicase property , intrinsic proof reading replacement capabilities and
termination recognition capability

Rnap guides the nucleotide to the position and facilitates attachment and elongation

Sigma factor bind to the promoter sequence , core enzyme binds to the sigma factor and promoter
region – closed promoter complex / preinitiation complex

Rna polymerase binds to the -10 sequence placed in the position to start transcribing , sigma factor
is released to start transcribing

Transcription bubble

Elongation begins with the release of the sigma factor -40 nucleotides per second

Termination – rho dependent and rho independent ( specific sequence in the dna template strand )

Rho independent ( intrinsic ) – mrna forms a stem loop structure by a sequence which base pairs
with itself , this slows down the polymerase , upstream we have a weak u a region which weekly
interacts with the dna template

The stem loop structure that stops the polymerase along with weak ua interaction site induces
enough instability for the core enzyme to break away and liberate free mrna

Rho dependent termination – at the end of the gene there is a repeated g sequence which slows
down the polymerase this is where the rho protein collides with the polymerase leading to the
release of nascent mrna from the transcription bubble

Rho attaches to the mrna with the energy gained from hydrolysis of atp , whether it will lead to
termination or not depends upon how fast the rho factor moves to catch the polymerase in the
elongation complex
Elongation is highly conserved in both prokaryotes and eukaryotes but intiation and termination
differ greatly

Initiation – consensus sequence located upstream of the coding sequence

Eukaryotic promoter – core, proximal distal ( transcription regulatory sequences )

Core promoter – rna polymerase binding site tata box and transcription start site

Proximal – located 250 base pairs upstream of the tss binds with transcription regulatory factors

Transcription factors – affects the rate of transcription by binding to specific dna sequence

Distal – regulatory sequences

Enhancer: an enhancer is a short (50–1500 bp) region of DNA that can be bound by proteins

(activators) to increase the rate of transcription.

Silencer: is a DNA sequence capable of binding transcription repressor proteins.

The conventional hallmark of TSSs in most eukaryotes is addition of a 7-methyl guanosine cap
structure to the 5'-triphosphate of the first base transcribed by RNA polymerase II.

Introns are integral to gene expression regulation

Rna polymerase 2 is a multi subunit enzyme made up of 12 subunits central to eukaryotic gene
expression

Preinitiation complex - RNA polymerase along with general transcription factors binds to the
promoter region of the gene to form a closed complex called the preinitiation complex.

Binding of tbp to the tata box intiates the formation of pre initiation complex

Abortive intiation – many of the intiated syntesaes are aborted before the transcript reaches a
significant length of 10 nucleotides

It keeps on making and aborting transcripts until it Is able to form a transcript that surpass the
length of 10 nucleotides

After this it proceeds to elongation

Promoter escapes to start elongation

Base selection – rna polymerase specifically selects the correct nucleoside triphosphate ( NTP) that
correctly base pairs with the dna

Pyrophosphorylitic editing – removes the incorrectly inserted ribo nucleotide by reversing the the
polymerization reaction reincorporation of ppi using active site

Hydrolytic editing – rna polymerase back traces and cleave the mis incorporated sequence gre
factor

Termination ( allosteric / anti terminator )

This model, proposes that transcription through the poly(A) site leads to conformational changes of
the elongation complex by dissociation of elongation factors and/or association of termination
factors.
It suggests that termination happens due to structural changes in the rna polymerase after binding
to or losing some proteins that leads to detaching itself from the dna strand

AAUAAA hexamer.

Torpedo model – rapid degradation at the 3’rna after clevage at poly a site

Why rna processing ?

If not processed it will lead to degradation

The processing recruits proteins for its export from the nucleus to the cytoplasm

5’capping . splicing . 3’ end cleavage and polyadenylation

Capping stabilizes the rna protects from attack from exonuclease , promotes splicing ,
polyadenylation and nuclear export

Spliceosomes – proteins and small nuclear rna

GT-AG rule

Introns – regulation of gene expression , alternative splicing , regulation of non sense mediated
decay

Alternative splicing – cellular differentiation and organism development helps one gene to encode
more than one protein – generates comples proteome / protein diversity

3’ rna processing – cleavage and polyadenylation

Poly a tail acts as a stabilizer of mrna

Adenosine – ionosine