Chapter 3. Cytoplasm, ribosome and RNAs 2nd Edition

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

3.1.1 Structure of Cytoplasm Cytosol Organelles Cytoplasmic inclusions 2nd Edition

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

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

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

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

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

Transcription

mRNA structure in Eukaryotes and prokaryotes

Comparison of Ribosome Structure in Bacteria, Eukaryotes, and Mitochondria

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 106-107 个/cell The other   polyribosome or polysome free ribosome membrane-bound polyribosome or polysome

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

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.

tRNA structure

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.

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.

SD sequence Initiation codon

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.

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.

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

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

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

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

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

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)

Termination

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

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

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

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

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

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

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

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

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.

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

self-cleaving RNAs RNase P Spliceosomes

3.4 NON-CODING RNA

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

miRNA and siRNA cause degradation of cognate mRNAs

RISC (RNA induced silencing complex)

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.

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