1. Lecture 4: DNA transcription
1) What is the central dogma of molecular biology
2) What are the steps involved in transcribing a primary RNA transcript?
3) How does eukaryotic post-transcriptional processing convert a primary transcript into messenger RNA?
4) Write notes on promoters, enhancers and transcription factors

2. Central dogma of molecular biology

3. Transcription DNA directed RNA synthesis
What is the biological significance?
Allows selective expression of genes
Regulation of transcription controls time, place and level of protein expression

4. Basic structure of a gene
Regulatory region
coding region

5. E:\Lessons\5-4_Transc-Transl-b3\Transc-Transl.swf
Transc-Transl.htm

6. Transcription
Transcription is the mechanism by which a template strand of DNA is utilized by specific RNA polymerases to generate one of the three different types of RNA.

7. Types of RNA 1) Messenger RNA (mRNA)
This class of RNAs are the genetic coding templates used by the translational machinery to determine the order of amino acids incorporated into an elongating polypeptide in the process of translation.

8. Types of RNA….. 2) Transfer RNA (tRNA)
This class of small RNAs form covalent attachments to individual amino acids and recognize the encoded sequences of the mRNAs to allow correct insertion of amino acids into the elongating polypeptide chain.

9. Types of RNA….. 3) Ribosomal RNA (rRNA)
This class of RNAs are assembled, together with numerous ribosomal proteins, to form the ribosomes. Ribosomes engage the mRNAs and form a catalytic domain into which the tRNAs enter with their attached amino acids. The proteins of the ribosomes catalyze all of the functions of polypeptide synthesis

10. Where does transcription take place?

11. Transcription in eukaryotes
Step 1: transcribing a primary RNA transcript
Step 2: modification of this transcript into mRNA

12. Step 1 - overview Initiation Polymerisation C. Termination
A) RNA polymerase binds to promoter & opens helix
B) De novo synthesis using rNTPs as substrate
Chain elongation in 5’-3’ direction
C) stops at termination signal

13. A) Initiation: ENZYME RNA polymerase holoenzyme
an agglomeration of many different factors that together direct the synthesis of mRNA on a DNA template
Has a natural affinity for DNA

14. Initiation: SIGNAL specific DNA sequences called promoters
1) Region where RNA polymerase binds to initiate transcription
2) Sequence of promoter determines direction of RNA polymerase action
3) Rate of gene transcription depends on rate of formation of stable initiation complexes

15. PROMOTERS Prokaryotes Fig 29-10: Voet and Voet Near 5’ end of operons
Pribnow box – consensus sequence TATAAT
Fig 29-10: Voet and Voet

16. PROMOTERS Eukaryotes Near 5’ end of genes Recognised by RNA pol II
Consensus promoter sequence for
constitutive structural genes – GGGCGG
Selective structural genes – TATA

17. ENHANCERS Sequences that are associated with a promoter
Enhance the activity of a promoter due to its association with proteins called transcription factors
Enhancers mediate most selective gene expression in eukaryotes

18. Polymerisation RNA polymerase binds to promoter & opens helix
RNA polymerase catalyses addition of rNTPs in the 5’-3’ direction
RNA polymerase generates hnRNAs (~ nt long) & all other RNAs
Stops at termination signal

19. Termination specific termination sequence
e.g E.coli needs 4-10A followed by a palindromic GC rich region
Additional termination proteins
e.g. Rho factor in E.coli

20. Step 2: Modification Post transcriptional processing 3 main steps
RNA capping,
polyadenylation
splicing

21. Post transcriptional processing
Control of gene expression following transcription but before translation
Conversion of primary transcript into mature mRNA
Occurs primarily in eukaryotes
Localised in nucleus

22. Post transcriptional processing

23. 1) Capping Addition of 7 methylguanosine at 5’ end
Mediated by guanylyltransferase
Probably protects against degradation
Serves as recognition site for ribosomes
Transports hnRNA from nucleus to cytoplasm

24. 2) Tailing Addition of poly(A) residues at 3’ end
Transcript cleaved 15-20nt past AAUAAA
Poly(A)polymerase and cleavage & polyadenylation specificity factor (CPSF) attach poly(A) generated from ATP

25. 3) Splicing Highly precise removal of intron sequences
Performed by spliceosomes (large RNA-protein complex made of small nuclear ribonucleoproteins)
Recognise exon-intron boundaries and splice exons together by transesterification reactions

26. Cell type-specific splicing
Differential splicing in specific tissues

27. Regulation of gene expression
Prokaryotes
Mainly at transcriptional level
Sets of genes transcribed together (polycistronic)
E.g. lac operon and trp operon in bacteria
Eukaryotes
Other levels of regulation inlcude posttranscriptional and posttranslational regulation
Each gene transcribed independently (monocistronic)

28. RNA polymerase
Prokaryotes
single multisubunit RNA polymerase complex

29. RNA polymerase Eukaryotes - 3 types exist RNA pol I RNA pol II
RNA pol III
Located in nucleoli
Located in nucleoplasm
Synthesises most rRNA precursors
Synthesises mRNA precursors
Synthesises 5S rRNA, tRNA, snRNAs

30. (RNA)n + rNTP = (RNA)n+1 + Ppi
RNA polymerase
Enzymes that catalyse the formation of RNA using DNA as a template
De novo synthesis using rNTP as substrates
1960 – J Hurwitz & S Weiss
(RNA)n + rNTP = (RNA)n+1 + Ppi
Antibiotics such as Rifampicin / rifamycin B inhibit RNA polymerase activity

31. Gene expression efficiency
When to transcribe gene?
How many copies to be transcribed?

32. DNA binding proteins Examples include Transcription factors
Proteins that recognise & bind to specific DNA sequences
Recognition determined by specific structural motifs
e.g. helix – loop –helix, zinc finger, leucine zipper
Examples include
Transcription factors
general transcription factors
Upstream transcription factors
Inducible transcription factors
Activators
Repressors (silencers)

33. How does transcriptional control differ in pro and eukaryotes?
Prokaryotes
Genes are usually switched ‘on’ by default
Repressor proteins needed to ‘stop’ transcription
Eukaryotes
Genes are usually switched ‘off’ by default
Transcriptional activators needed to induce transcription
Regulated by chromatin structure, DNA methylation etc

34. Lac operon
Fig 29-3/5
: Voet and Voet

35. Fig 8-20: Essential Cell Biology by Alberts et al