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

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RNA Polymerase 5

Binds to initiation site through sequences called promoter elements that are recognized by  factor 6

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Once initiation occurs  factor dissociates 9

Recognized by  70 Recognized by  32 10

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. 12

Transcription is tightly regulated Not all genes are transcribed equally 13

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 14

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The lac operon 20

Eukaryotic transcription Heterochromatin: transcriptionally inactive Euchromatin: may be transcriptionally active Eukaryotic RNAP have almost no affinity for promoters on their own 21

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 22

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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 24

Functionally equivalent to  factor 25

Gaining access to the DNA template Histones must be modified to access DNA Histone acetyltransferases: decrease + charge Histone deacetylases: increase + charge 26

Lysine Acetyllysine 27

5% of cytidine residues are methylated at the 5 position These are most often found at CG sequences Hypermethylation is associated with heterochromatin Gene Silencing 28

Recruiting RNA polymerase 29

Regulated Transcription 30

Regulated Transcription 31

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 32

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Post-transcriptional control 37

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RNA Editing Changes the Meaning 40

RNA Editing Changes the Meaning C to U A to I 41

There are many ways to regulate the meaning of genes after transcription Prevent translation 42

There are many ways to regulate the meaning of genes after transcription Degrade the message 43

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Target the mRNA 46

What about mistakes? Nonsense Mediated Decay 47