1. Transcription

2. RNA Structure Composition of RNA in metabolically active cell
Ribose: both 2’ and 3’ OH
Uracil(U) instead of thymine (T)
Mostly single strand
Secondary structure
Intrastrand base-pairing
Composition of RNA in metabolically active cell
mRNA: 3~5 %
rRNA: 90%
tRNA: 4%

3. RNA Polymerase RNA synthesis using ssDNA as a template Prokaryote
One RNA polymerase
Eukaryote
RNA Pol I rRNA (28S, 5.8S, 18S)
RNA Pol II mRNA
RNA Pol III tRNA, 5S rRNA
5’ to 3’ RNA synthesis

4. Transcription and Translation in Prokaryote
* Promoter region
--- RNA polymerase binding site
* Termination sequence

5. Genes Gene Specific nucleotide sequence that is transcribed into RNA
Structural gene
Gene encoding protein
Polycystronic transcription
Prokaryote only
Transcription of multiple genes in one transcription unit
-35
-10
Operator
ORF1
ORF2
ORF3
Terminator
promoter
mRNA

6. Transcription and Translation in Eukaryote
Exon: 150~ 200 bp
Intron: 40 ~ 10,000 bp (intervening sequence)

7. Splicing of a Eukaryotic Primary RNA Transcript

8. Alternative Splicing
Generation of tissue-specific proteins from the same structural gene
Different pattern of exon splicing from a primary transcript

9. A small number of eukaryotic structural genes lack intron (e. g
A small number of eukaryotic structural genes lack intron (e.g. olfactory genes).
Exon-skipping mechanism generates different gene products in different tissues from the same structural gene.

10. Translation

11. Initiation of Translation in Prokaryotes
(1) mRNA + small ribosomal subunit
↑Ribosome binding site
(Shine-Dalgarno [SD]
sequence)
(2) + fMet-tRNAfMet
(f: formyl)
(3) + large ribosomal unit

12. tRNA
anticodon
(tRNA, 5’-CAU-3’)
 codon
(mRNA, 5’-AUG-3’)

13. Genetic Code Information in DNA  amino acid sequence in protein mRNA
5’ GCA GCA CUA GGA GAG AAG 3’
Codon: triplet of RNA bases
20 amino acids in nature
Codon (nt)
Amino acid 1 4 2 16 3 64

14. Genetic Code

15. Initiation of Translation in Eukaryotes
(1) Met-tRNAMet + small ribosomal subunit
(along with initiation factors)
(2) + 5’ end of mRNA  The complex migrates along the mRNA until an AUG is encountered.
(3) + large ribosomal subunit

16. Translation Initiation Elongation Termination
Elongation and termination phases are very similar in prokaryotes and eukaryotes.

17. Elongation Phase of Translation
5’3’ direction at a rate of about 15 amino acids per sec.
A single mRNA can be translated simultaneously by a number of ribosomes

18. Table 3.2 Genetic code and codon usage

19. Termination stop (termination) codon ~ UAA, UAG, UGA
no tRNAs which bind to stop codons
Protein(s) (termination factor, or release factor) binds to the ribosome.

20. In most proteins, the methionine at the N-terminus is cleaved off, leaving the second encoded amino acid as the N-terminal moiety.

21. Amino Acids and Primary Structure
Amino group
Carboxyl group
R group; 20 Side chains
Peptide bond
Between NH2 and COOH
Polypeptide
A chain of amino acids
N terminus and C terminus

22. Amino Acids

23. Regulation of Transcription in Bacteria

25. Operon Promoter region
Frequently, bacterial structural genes that encode proteins for a single metabolic pathway are contiguous. This arrangement is called an operon.
Promoter region
-10 region (TATAAT, TATA box, Pribnow box)
-35 region (TTGAC sequence)

26. Negative controlled system
Repressor
Induction of the on state
Effector molecule (derepressor)
Induction of the off state
IR: inactive repressor,
aporepressor
C: corepressor

27. Positive controlled system
Activator
Promoting RNA polymerase activity
Repressed by an effector molecule

28. Regulation of Transcription in Eukaryotes

29. Unlike the situation in prokaryotes, operons are almost never found in the genomes of eukaryotes. In addition to DNA-protein interactions, protein-protein associations are important for regulating eukaryotic transcription.
Promoter region
-25 bp (TATA box, or Hogness box)
8 nucleotides including TATA sequence
-75 bp (CCAAT sequence, “cat” box)
-90 bp (GC box --- repeated GC)

30. Promoter region

31. Transcription initiation complex