1. Chapters 26 Lehninger 5th Edition
9. Transcription
Chapters 26 Lehninger 5th Edition

2. Transcription DNA -> RNA Translation RNA -> Protein
FIGURE 1–31 DNA to RNA to protein to enzyme (hexokinase). The linear sequence of deoxyribonucleotides in the DNA (the gene) that encodes the protein hexokinase is first transcribed into a ribonucleic acid (RNA) molecule with the complementary ribonucleotide sequence. The RNA sequence (messenger RNA) is then translated into the linear protein chain of hexokinase, which folds into its native three-dimensional shape, most likely aided by molecular chaperones. Once in its native form, hexokinase acquires its catalytic activity: it can catalyze the phosphorylation of glucose, using ATP as the phosphoryl group donor.

3. Genes 1 gene -> 1 protein? Transcription DNA -> RNA Translation
Read a gene from the DNA
DNA -> RNA
Translation
Translate the DNA code to protein code
RNA -> Protein

4. Transcription RNA Polymerase Reads DNA Makes RNA copy of One strand
One gene

5. Transcription Open DNA at promoter Make RNA 5’-> 3’
transcription bubble
Moves along gene
Prevent DNA knotting
DNA topo-isomerases

6. Transcription Initiation Termination
At promoters
Control by Transcription Factors
“Gene expression”
Termination
Processing of the transcript (Eukaryotes)
e.g. remove introns, add stuff to ends, modify bases
Final product
e.g. mature mRNA or mature miRNA

7. Bacterial Promoters Simple Fixed spacing of binding sites
Transcription factors

8. Transcription Factors Bind DNA

9. Bacterial Gene Structure
Simple promoter close to start of transcript
Gene transcribed as one piece of mRNA
Transcription terminates
Terminator signal
Ready to translate m

10. Bacterial Operons Genes may be grouped in Operons Co-regulation
Single transcript

11. Eukaryotic Gene Structure
V. complicated promoters
e.g. Human:
2000 TFs
Spread over 10s of kb
Several kb from coding region
Pieces of mRNA removed before translation
Introns
Rich Roberts, Phil Sharp

12. Eukaryotic gene processing
Remove introns
Splicing
Add 5’ cap
Cleavage of 3’ end of mRNA at polyA site
Add 3’ polyA tail

13. FIGURE Formation of the primary transcript and its processing during maturation of mRNA in a eukaryotic cell. The 5′ cap (red) is added before synthesis of the primary transcript is complete. A noncoding sequence (intron) following the last exon is shown in orange. Splicing can occur either before or after the cleavage and polyadenylation steps. All the processes shown here take place in the nucleus.

14. FIGURE 26-19 Overview of the processing of a eukaryotic mRNA
FIGURE Overview of the processing of a eukaryotic mRNA. The ovalbumin gene, shown here, has introns A to G and exons 1 to 7 and L (L encodes a signal peptide sequence that targets the protein for export from the cell; see Figure 27-38). About three-quarters of the RNA is removed during processing. Pol II extends the primary transcript well beyond the cleavage and polyadenylation site ("extra RNA") before terminating transcription. Termination signals for Pol II have not yet been defined.

15. Alternative transcripts
Alternative polyA sites
Alternative splicing
Alternative exons
Alternative promoters

16. Alternative polyA
FIGURE 26-20a Two mechanisms for the alternative processing of complex transcripts in eukaryotes. (a) Alternative cleavage and polyadenylation patterns. Two poly(A) sites, A1 and A2, are shown.

17. Alternative splicing
FIGURE 26-20b Two mechanisms for the alternative processing of complex transcripts in eukaryotes. (b) Alternative splicing patterns. Two different 3′ splice sites are shown. In both mechanisms, different mature mRNAs are produced from the same primary transcript.

18. FIGURE Alternative processing of the calcitonin gene transcript in rats. The primary transcript has two poly(A) sites; one predominates in the brain, the other in the thyroid. In the brain, splicing eliminates the calcitonin exon (exon 4); in the thyroid, this exon is retained. The resulting peptides are processed further to yield the final hormone products: calcitonin-gene-related peptide (CGRP) in the brain and calcitonin in the thyroid.

19. FIGURE 26-22 Summary of splicing patterns
FIGURE Summary of splicing patterns. Exons are shown in shades of green, and introns/untranslated regions as yellow lines. Positions where polyadenosine is to be added are marked with asterisks. Exons joined in a particular splicing scheme are linked with black lines. The alternative linkage patterns above and below the transcript lead to the top and bottom spliced mRNA products, respectively. In the products, red and orange boxes represent the 5′ cap and 3′ untranslated regions, respectively.

20. RNA Genome? Central dogma: RNA Virus DNA -> RNA -> protein
e.g. HIV:
RNA -> DNA
Reverse transcriptase

21. FIGURE 26-32 Extension of the central dogma to include RNA-dependent synthesis of RNA and DNA.

22. FIGURE Retroviral infection of a mammalian cell and integration of the retrovirus into the host chromosome. Viral particles entering the host cell carry viral reverse transcriptase and a cellular tRNA (picked up from a former host cell) already base-paired to the viral RNA. The tRNA facilitates immediate conversion of viral RNA to double-stranded DNA by the action of reverse transcriptase, as described in the text. Once converted to double-stranded DNA, the DNA enters the nucleus and is integrated into the host genome. The integration is catalyzed by a virally encoded integrase. Integration of viral DNA into host DNA is mechanistically similar to the insertion of transposons in bacterial chromosomes (see Figure 25-45). For example, a few base pairs of host DNA become duplicated at the site of integration, forming short repeats of 4 to 6 bp at each end of the inserted retroviral DNA (not shown).

23. What Controls Gene Expression?
Transcription factors
Regulatory RNAs
miRNA
smRNA
siRNA
Methylation
Chromatin

24. Transcription Factors
Proteins which bind DNA
Enhance or repress gene expression
Families e.g.:
Homeodomain (Hox)
POU domain (Oct-1)
Helix-loop-Helix (c-Myc)
Zinc Fingers (TFIIIA)
Leucine Zipper (c/EBP)
Winged Helix (Fox family)
Helix Turn Helix
At least 10% of genes in Human genome are TFs