Lab Next Week Announcements Help Session: Monday 6pm LSS 277 Office Hours Chapter 15 and Translation Proteins: Function Proteins: Function Enzymes Transport Structural Components Regulation Communication Defense Enzymes Transport Structural Components Regulation Communication Defense Luciferase Ricin Fibroin Proteins: Structure Composed of amino acids 20 amino acids, similar in basic structure Peptide Bonds Figure 15.6 Joined by peptide bonds, forming polypeptide chains. 1
Figure 15.7 20 amino acids Protein Structure 20 amino acids One? 4 bases (AGCU) = 4 possible codons 20 amino acids One? Two? 4 bases at two positions = 4 2 = 16 codons 20 amino acids One? Two? Three? 4 bases at three positions = 4 3 = 64 codons A triplet code is the most efficient way to code for all 20 amino acids Shown by Crick et al in 1961 2
Cracking the Genetic Code? Cracking the Genetic Code Homopolymers: Poly (A), Poly (U), Poly (G), Poly (C) Determine amino acids for UUU, AAA, GGG, CCC Nirenberg and Matthaei (1961) Cracking the Genetic Code Phe The Poly (G) results were uninterpretable! Pro Figure 15.9 Lys? Cracking the Genetic Code Homopolymers: Poly (A), Poly (U), Poly (G), Poly (C) Determine amino acids for UUU, AAA, GGG, CCC By using other clever methods, the genetic code was fully understood by 1968. First started investigating in 1961.? Figure 15.12 3
Stop Codons Also called termination codons or nonsense codons : Redundancy Isoaccepting trnas carry the same amino acid but have different anticodons. Codons that specify the same amino acid are synonymous. Sense codons specify an amino acid 61 sense codons Only 20 amino acids. The genetic code is a degenerate code Figure 15.12 Degenerate Code: Amino acids may be specified by more than one codon. Degenerate? Wobble: Flexibility in the pairing of the 5 base of the anticodon with the 3 base of the codon Figure 15.13 Initiation Codons and Reading Frame Initiation codon: AUG Bacteria: specifies N-formylmethionine Eukaryotes: specifies methionine Genetic Code is non-overlapping overlapping Except in some viruses 3 possible reading frames 4
Figure 15.14 is Universal**! 3 different reading frames **The (Almost) Universal Genetic Code The problem set frustrates and and infuriates me! The Process of Translation 4 Stages of Translation 1) trna charging: Amino Acids bind to trna 2) Initiation: Necessary components bind to ribosome 3) Elongation: Amino acids joined to growing polypeptide 4) Termination: Protein synthesis stops at stop codon, translation components released from ribosome 5
Stage 1: 1 Binding of AA to trna Aminoacyl-tRNA synthetases: 20 different synthetases Each recognizes a particular amino acid Based on size, charge, R group Each recognizes all the trnas associated with its amino acid (isoaccepting trnas) Sequences in DHU arm, anticodon loop, acceptor stem critical to trna recognition Figure 15.15 Invariant Positions Single Synthetase Recognition Multiple Synthetase Recognition trna Charging: 2 Step Process that Requires energy in the form of ATP Stage 2: 2 Initiation All ingredients required for translation are assembled: Stage 2: 2 Initiation (Bacteria) All components required for translation are assembled: mrna Ribosome (small and large subunits) Initiation factors (3 proteins) Initiator trna with N-formylMethionine attached (fmet-trna fmet ) Guanosine triphosphate (GTP) 6
Initiation: Step 1 mrna binds to small subunit of ribosome Initiation factor 3 (IF-3) keeps large and small subunits separated during initiation Key consensus sequence in Bacteria for ribosome binding: Shine-Delgarno sequence Complementary to a sequence near 3 end of 16S rrna Initiation: Step 1 mrna binds to small subunit of ribosome Initiation factor 3 (IF-3) keeps large and small subunits separated during initiation Key consensus sequence in Bacteria for ribosome binding: Shine-Delgarno sequence Complementary to a sequence near 3 end of 16S rrna Cool! An example of an RNA-RNA interaction! Figure 15.16 Initiation: Step 1 IF-3 prevents large subunit from binding Initiation: Step 2 fmet-trna trna fmet attaches to initiation codon Facilitated by Initiation Factor 2 and GTP Initiation Factor 1 helps keep large and small subunits apart 30S Initiation Complex Small ribosomal subunit, mrna, fmettrna fmet, GTP, Initiation Factors Figure 15.16 Initiation: Step 2 Formation of the 30S Initiation Complex 7
Initiation: Step 3 Figure 15.16 70 S Initiation Complex Large subunit of ribosome joins Initiation Complex IF-1 and IF-2 depart Initiation: Step 3 Formation of the 70S Initiation Complex Eukaryotic Initiation Figure 15.21 No Shine Delgarno sequence 5 Cap important in ribosome-mrna binding More initiation factors required Poly(A) ) tail bound proteins Interact with 5 Cap bound proteins 8