3 main types of RNA

• All are made from a DNA Template• mRNA: encode AA sequence of one of

more polypeptides from a gene or set of genes

• tRNA: reads info. In mRNA and transfers appropriate AA to growing peptide chain

• rRNA: part of ribosome, cellular machines synthesize proteins

Transcription

1

Synthesis

• Resembles DNA replication in its chemical mechanism, polarity, use of template

• Has initiation, elongation, termination phase

• Does not need a primer, only involves limited segment of DNA molecule

2

RNA Polymerase

• DNA directed RNA polymerase

• DNA template

• Nucleotides (ATP, CTP, UTP, GTP)

• Builds in the 5’ to 3’ direction

3

4

RNA Polymerase

5

Binds to initiation site through sequences called promoter elements that are

recognized by factor

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7

8

Once initiation occurs factor dissociates

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Recognized by 70

Recognized by 32

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RNA Polymerase has helicase activity

Gyrases/topoisomerases are needed to prevent positive supercoiling ahead of the

transcription bubble 11

An electron micrograph of three contiguous ribosomal genes from oocytes of the

salamander Pleurodeles waltl undergoing transcription.

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Transcription is tightly regulated

Not all genes are transcribed equally

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Transcription Factor

• Upstream of RNAP II initiation site, different combinations of specific DNA sequences each is recognized by corresponding site specific DNA binding protein

• Each combination of DNA sequence and cognate DNA binding protein represent a control module

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15

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17

18

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The lac operon

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Eukaryotic transcription

Heterochromatin: transcriptionally inactiveEuchromatin: may be transcriptionally active

Eukaryotic RNAP have almost no affinity for promoters on their own

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Eukaryotic RNA Polymerases

• RNAP I: synthesis of transcripts called preribosomal RNA – precursor 18s, 5.8s, 28s RNA

• RNAP II: synthesis of mRNA

• RNAP III: synthesize tRNA

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RNA Polymerase II

• Has 12 subunits

• Needs transcription factors that stimulate the enzyme to bind to a nearby promoter

• General TF required at every RNAP II promoter

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Functionally equivalent to

factor

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Gaining access to the DNA template

Histones must be modified to access DNA

Histone acetyltransferases: decrease + chargeHistone deacetylases: increase + charge 26

NH3+

NH

O

CH3

Lysine

Acetyllysine

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5% of cytidine residues are methylated at the 5 position

N

NH

NH2

O

These are most often found at CG sequences

Hypermethylation is associated with heterochromatin

Gene Silencing

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Recruiting RNA polymerase

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Regulated Transcription

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Regulated Transcription

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RNA Processing

• Most RNA is processed after synthesis• Ribozymes: catalyze post-transcriptional

processing• Primary Transcript: newly synthesized RNA

molecule – occurs in mRNA and tRNA –contains sequence encoding one gene but encoded polypeptide not continuous

• Noncoding Regions: introns• Coding Region: exons

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Post-transcriptional control

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RNA Editing Changes the Meaning

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RNA Editing Changes the Meaning

C to U

A to I

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There are many ways to regulate the meaning of genes after transcription

Prevent translation

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There are many ways to regulate the meaning of genes after transcription

Degrade the message

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Target the mRNA

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What about mistakes?Nonsense Mediated Decay

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