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