1. Chapter 3. Cytoplasm, ribosome and RNAs
2nd Edition

2. 3.1 Structure and function of cytoplasm
3.2 Ribosome
3.3 Ribozyme
3.4 Non-coding RNA

3. 3.1.1 Structure of Cytoplasm
Cytosol
Organelles
Cytoplasmic inclusions
2nd Edition

4. Cytosol Dissolved nutrients and waste products
Dissolved macromolecules, such as RNAs and proteins
Many salts
2nd Edition

5. Organelles
(1) nucleolus; (2) nucleus; (3)ribosomes; (4) vesicle; (5) rough endoplasmic reticulum (ER); (6) Golgi apparatus;(7)cytoskeleton; (8)smoothER;(9)mitochondria; (10) vacuole; (11) cytosol; (12) lysosome; (13) centrioles within centrosome
2nd Edition

6. Cytoplasmic inclusions
crystals of calcium oxalate or silicon dioxide in plants,
granules of starch, glycogen, or polyhydroxybutyrate, which can store energy.
Lipid droplets, storing fatty acids and sterols
2nd Edition

7. 3.1.2 Functions of Cytoplasm
Metabolic pathways and biochemical reactions
Ubiquitin-proteasome system
The functions of organelles
Maintenance and movement
Storage
2nd Edition

8. 3.2 RIBOSOME
The ribosome is a ribonucleoprotein particle composed of RNA and protein，and serves as the site of protein synthesis.
2nd Edition

10. Transcription

11. mRNA structure in Eukaryotes and prokaryotes

12. Comparison of Ribosome Structure in Bacteria, Eukaryotes, and Mitochondria

13. polyribosome or polysome
Prokaryotes
Eukaryotes
sediments
70S
80S
MW(kDa）
2.5×103
3.9～4.5×103
Subunit
50S\30S
60S\40S
Abundance
15×102-18×103个/cell
个/cell
The other
  polyribosome or polysome
free ribosome
membrane-bound
polyribosome or polysome

14. Secondary structure of tRNA
Figure 6-52a Molecular Biology of the Cell (© Garland Science 2008)

15. How is an amino acid added to tRNA?
Reaction 1: The aminoacyl-tRNA synthetase couples an amino acid to AMP, derived from ATP, to form an aminoacyl-AMP, with pyrophosphate (P-P) as a by-product. Reaction 2: The synthetase replaces the AMP in the aminoacyl-AMP with tRNA, to form an aminoacyl-tRNA, with AMP as a by-product. The amino acid is joined to the 3'-hydroxyl group of the terminal adenosine of the tRNA.

16. tRNA structure

17. Initiation in Prokaryote
1.Dissociation of the 70S ribosome into 50S and 30S subunits, under the influence of RRF and EF-G.
2. Binding of IF3 to the 30S subunit, which prevents reassociation between the ribosomal subunits.
3. Binding of IF1 and IF2–GTP alongside IF3. This step probably occurs simultaneously with step 2.
4. Binding of mRNA and fMet-tRNAfMet to form the 30S initiation complex. These two components can apparently bind in either order, but IF2 sponsors fMet-tRNAfMet binding, and IF3 sponsors mRNA binding. In each case, the other initiation factors also help.

18. 5. Binding of the 50S subunit, with loss of IF1 and IF3.
6. Dissociation of IF2 from the complex, with simultaneous hydrolysis of GTP. The product is the 70S initiation complex, ready to begin elongation.

19. SD sequence
Initiation codon

20. Initiation in Eukaryotes
(a) The eIF3 factor converts the 40S ribosomal subunit to 40SN,which resists association with the 60S ribosomal particle and is ready to accept the initiator aminoacyl-tRNA.
(b) With the help of eIF2, Met-tRNAiMet binds to the 40SN particle, forming the 43S complex.
(c) Aided by eIF4F the mRNA binds to the 43S complex, forming the48S complex.
(d) The eIF1 and 1A factors promote scanning to the initiation codon.
(e) The eIF5 factor promotes hydrolysis of eIF2-bound GTP, which is a precondition for ribosomal subunit joining. eIF5B has a ribosome-dependent GTPase activity that helps the 60S ribosomal particle bind to the 48S complex, yielding the 80S complex that is ready to begin translating the mRNA.

22. Elongation
Transfer of proper aminoacyl-tRNA from cytoplasm to A-site of ribosome.
Covalent linkage of new amino acid to growing polypeptide chain - peptidyl transfer.
Movement of tRNA from A-site to P-site and simultaneous movement of mRNA by 3 nucleotides - translocation.

23. Figure 6-64 Molecular Biology of the Cell (© Garland Science 2008)

25. Figure 6-66 (part 1 of 4) Molecular Biology of the Cell (© Garland Science 2008)

26. Figure 6-66 (part 2 of 4) Molecular Biology of the Cell (© Garland Science 2008)

27. Figure 6-66 (part 3 of 4) Molecular Biology of the Cell (© Garland Science 2008)

28. Figure 6-67 Molecular Biology of the Cell (© Garland Science 2008)

29. TERMINATION OF PROTEIN SYNTHESIS
1. The mRNA Signal
STOP Codons: UAA, UAG, or UGA
There are no tRNAs that recognize the STOP codons UAA, UAG, or UGA.
2. Soluble Protein Release Factors
RF1 responds to UAA or UAG RF2 responds to UAA or UGA RF3, a GTPase (like EF-Tu and binds in a similar A-site location)

30. Termination

31. Figure 6-76a Molecular Biology of the Cell (© Garland Science 2008)

32. Figure 6-9 Molecular Biology of the Cell (© Garland Science 2008)

33. Figure 6-79 Molecular Biology of the Cell (© Garland Science 2008)

34. Table 6-4 Molecular Biology of the Cell (© Garland Science 2008)

35. Figure 6-84 Molecular Biology of the Cell (© Garland Science 2008)

36. Figure 6-85 Molecular Biology of the Cell (© Garland Science 2008)

37. Figure 6-86 Molecular Biology of the Cell (© Garland Science 2008)

38. Figure 6-88 Molecular Biology of the Cell (© Garland Science 2008)

39. 3.3 RIBOZYME
Ribozymes
A ribozyme is defined as an RNA molecule capable of catalyzing a chemical reaction in the absence of proteins.
Deoxyribozymes
Deoxyribozymes or DNA enzymes or catalytic DNA, rDNAzymes are artificially DNA molecules that have the ability to perform a chemical reaction, such as catalytic action.

40. (1) Peptidyl transferase 23S rRNA
(2) RNase P
(3) Spliceosomes
(4) Leadzyme
(5) Hammerhead ribozyme

41. self-cleaving RNAs
RNase P
Spliceosomes

42. NON-CODING RNA

43. Table 6-1 Molecular Biology of the Cell (© Garland Science 2008)

46. miRNA and siRNA cause degradation of cognate mRNAs

47. RISC (RNA induced silencing complex)

48. Questions: Give short definitions of the following terms: Cytoplasm
Proteasome
Ribosome
Ribozyme
Deoxyribozyme
Small RNA
microRNA
Please compare the the components and the structure of ribosome between prokaryotes and eukaryotes.
Please expatiate the tanslation procedure.
Give 5 examples of naturally occurring ribozymes.
What’s the function of non-coding RNAs?
Explain the structures and functions of Cytoplasm.

49. THANKS!