chapter 6 translation. the genetic code translational reading frames
TRANSCRIPT
Chapter 6
• Translation
The genetic code
Translational reading frames
Translational reading frames
tRNAs are adapter molecules
The genetic code
Wobble base pairing
tRNA splicing
tRNA base modification
Amino acid activation
Aminoacyl tRNA linkage
Two adapters are required for translation
Editing by tRNA synthetases
Recognition of tRNA by
synthetases
Polypeptide chain growth:N-terminal to C-terminal
Ribosomes
Ribosomes
tRNA binding sites in the ribosome
tRNA binding sites in the ribosome
tRNA binding sites in the ribosome
IsotypeCodon tRNA tDNA tRNA Genomic Codon Pref by Highly
Anticodon Anticodon Copies Frequency Expr. Genes
AlaGCU Ala-1 AGC IGC 22 22.4 *
GCC 11.9 * GCA Ala-2 TGC UGC 8 20.1 GCG Ala-3 CGC CGC 4 7.8
GlyGGA Gly-1 TCC UCC 31 + 1p 31.4 *
GGC Gly-2 GCC GCC 13 6.4 GGU 11 GGG Gly-3 CCC CCC 3 4.4
ProCCA Pro-1 TGA UGA 32 + 3p 25.9 *
CCU Pro-2 AGG IGG 6 9.1 CCC 4.4 CCG Pro-3 CGG CGG 4 9
ThrACU Thr-1 AGT IGU 17 19.5
ACC 10.3 * ACA Thr-2 TGT UGU 12 20.3 ACG Thr-3 CGT CGU 7 + 1p 8.5
ValGUU Val-1 AAC IAC 18 24.8
GUC 13.2 * GUA Val-2 TAC UAC 5 10.3 GUG Val-3 CAC CAC 5 14.1
Detailed view of translation
The structure of rRNA in the bacterial ribosome
The secondary structure of rRNA in the bacterial ribosome
The position of protein in the bacterial large subunit
The structure of L15 protein in the large subunit
Possible mechanism for peptidyl transferase
Initiation of translation in eukaryotic cells
Initiation of translation in prokaryotic cells
Translation termination
The structure of eRF1 and tRNA
EF-Tu-tRNA EF-G
Peptide tunnel
Peptide tunnel
Polyribosomes (polysomes)
The rescue of a stalled ribosome on an incomplete mRNA
Incorporation of selenocysteine into a polypeptide
Translational frameshifting
INHIBITOR SPECIFIC EFFECTActing only on bacteria
Tetracycline blocks binding of aminoacyl-tRNA to A-site of ribosomeStreptomycin prevents the transition from initiation complex to chain-elongating
ribosome and also causes miscoding
Chloramphenicol blocks the peptidyl transferase reaction on ribosomes
Erythromycin blocks the translocation reaction on ribosomes
Rifamycin blocks initiation of RNA chains by binding to RNA polymerase
Acting on bacteria and eucaryotesPuromycin causes the premature release of nascent polypeptide chains by its
addition to growing chain end
Actinomycin D binds to DNA and blocks the movement of RNA polymerase
Acting on eucaryotes but not bacteria
Cycloheximide blocks the translocation reaction on ribosomes
Anisomycin blocks the peptidyl transferase reaction on ribosomes
α-Amanitin blocks mRNA synthesis by binding preferentially to RNA pol II
Table 6-3. Inhibitors of Protein or RNA Synthesis
Making a functional protein
Molten globule
Cotranslational folding
Steps of protein folding
Hsp70 family of chaperones
Hsp60 family of chaperones
Hsp60 family of chaperones
Protein monitoring
The proteosome degrades cellular proteins
Formation of protein aggregates can cause human disease
Formation of protein aggregates can cause human disease
The RNA World
1) The RNA World and the Origins of Life2) Life Requires Autocatalysis
3) Polynucleotides Can Both Store Information and Catalyze Chemical Reactions**
4) A Pre-RNA World Probably Predates the RNA World**
5) Single-stranded RNA Molecules Can Fold into Highly Elaborate Structures**
6) Self-Replicating Molecules Undergo Natural Selection**
7) How Did Protein Synthesis Evolve?**
8) All Present-day Cells Use DNA as Their Hereditary Material
The structure of potential preRNA molecules
RNAs can fold into complex structures
RNAs can fold into complex structures
An RNA ribozyme
SELEX: Systematic Evolution of Ligands by EXponential enrichment
Table 6-4 Biochemical reactions catalyzed by ribozymes.
ACTIVITY RIBOZYME
Peptide bond formation rRNARNA cleavage, ligation self-splicing intronsDNA cleavage self-splicing intronsRNA splicing self splicing introns, snRNAs?RNA polymerization in vitro selected RNARNA and DNA phosphorylation in vitro selected RNA RNA aminoacylaton in vitro selected RNARNA alkylation in vitro selected RNAAmide bond formation in vitro selected RNAAmide bond cleavage in vitro selected RNAGycosidic bond formation in vitro selected RNAPorphyrin metalation in vitro selected RNA
RNAs can undergo allosteric changes
Hypothesis of the development of modern cells
Describe the structure of a tRNA molecule.
Explain how a tRNA is made.
What is meant by amino acid activation.
What are the two catalytic sites of an tRNA synthetase.
What are the components of a bacterial ribosome?
What is the rate of amino acid addition during translation?
What are the two functions of EF-Tu? What is the function of EF-G?
Explain the steps of peptide chain elongation catalyzed by a ribosome?
Where is energy used in the process of translation?
Describe the structure of a bacterial ribosome.
Describe translational initiation in eukaryotes.
What is different between prokaryotic and eukaryotic translational initiation?
How is translation terminated?
What is a polysome? A uORF? An IRES? A tmRNA?
Briefly explain nonsense mediate mRNA decay. (Nostop mediated mRNA decay?)
What are the differences between hardwired changes to the genetic code and translational recoding?
Name three antibiotic inhibitors of proteins synthesis.
What are the differences between hsp60 and hsp70 mediated protein folding?Explain the process of ubiquitin mediated protein degradation.
True or False. According to the RNA World hypothesis, RNA was the first molecule of heredity and catalysis?
Explain how you would use selex to identify RNAs that bind to a specific DNA sequence.
Chapter 7:
Gene ControlDNA Binding Motifs
Genetics Switches
