Announcements. Chapter 15. Proteins: Function. Proteins: Function. Proteins: Structure. Peptide Bonds. Lab Next Week. Help Session: Monday 6pm LSS 277

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Announcements Announcements

• Lab Next Week

• Help Session: Monday 6pm LSS 277

• Office Hours

Chapter 15 Chapter 15

The Genetic CodeGenetic Codeand Translation

Proteins:

Proteins:

Function

• Enzymes

• Transport

• Structural Components

• Regulation

• Communication

• Defense

Proteins:

Proteins:

Function

• Enzymes

• Transport

• Structural Components

• Regulation

• Communication

• Defense

Luciferase

Fibroin Ricin

Proteins:

Proteins:

Structure

• Composed of amino acids

– 20 amino acids, similar in basic structure

• Joined by peptide bonds, forming polypeptide chains.

Peptide Bonds

Figure 15.6

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Protein Structure Protein Structure

Figure 15.7

The Genetic Code The Genetic Code

• How many nucleotides are necessary for amino acid specification?

•• 2020amino acids

The Genetic Code The Genetic Code

• One?

– 4 bases (AGCU) = 4 possible codons

The Genetic Code The Genetic Code

• One?

• Two?

– 4 bases at two positions = 44²²= 16 codons

The Genetic Code The Genetic Code

• One?

• Two?

• Three?

– 4 bases at three positions = 44³³= 64 codons

The Genetic Code The Genetic Code

•

• A triplet code is the most efficient way A triplet code is the most efficient way to code for all 20 amino acids

to code for all 20 amino acids

• Shown by Crick et al in 1961

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Cracking the Genetic Code Cracking the Genetic Code

?

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)

Figure 15.9

Cracking the Genetic Code Cracking the Genetic Code

Phe Phe

Lys Lys Pro Pro

The Poly (G) The Poly (G) results were results were uninterpretable uninterpretable!!

??

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

• By using other clever methods, the genetic code was fully understood by 1968.

– First started investigating in 1961.

The Genetic Code The Genetic Code

? ?

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The Genetic Code The Genetic Code

Figure 15.12 Stop Stop CodonsCodons Also called termination termination codonscodons

or nonsense nonsense codons codons

The Genetic Code

The Genetic Code: RedundancyRedundancy

•• IsoacceptingIsoacceptingtRNAstRNAscarry the same amino acid but have different anticodons.

• Codons that specify the same amino acid aresynonymous.synonymous.

•• SenseSensecodons specify an amino acid – 61 sense codons

• Only 20 amino acids.

– The genetic code is a degenerate codedegenerate code

Degenerate?

Degenerate Code

Degenerate Code: Amino acids may be specified by more than one codon.

Figure 15.13

Wobble

Wobble: “Flexibility” in the pairing of the 5’ base of the anticodon with the 3’ base of the codon

Initiation

Initiation CodonsCodons and Reading and Reading Frame

Frame

•• Initiation Initiation codoncodon: AUG

– Bacteria: specifies N-formylmethionine – Eukaryotes: specifies methionine

• Genetic Code is nonnon--overlappingoverlapping ––Except in some virusesExcept in some viruses

• 3 possible reading framesreading frames

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Figure 15.14

3 different 3 different reading reading frames frames

The Genetic Code is Universal**!

**The (AlmostAlmost) Universal Universal Genetic Code

The problem set The problem set frustrates and frustrates and andand

infuriates me!

The Process of Translation

4 Stages of Translation

• 1) tRNAtRNAchargingcharging:

– Amino Acids bind to tRNA

• 2) Initiation:Initiation:

– Necessary components bind to ribosome

• 3) Elongation:Elongation:

– Amino acids joined to growing polypeptide

• 4) Termination:Termination:

– Protein synthesis stops at stop codon, translation components released from ribosome

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Stage 1

Stage 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

Invariant Positions Invariant Positions Single

Single SynthetaseSynthetaseRecognitionRecognition Multiple

Multiple SynthetaseSynthetaseRecognitionRecognition

tRNA Charging:

2 Step Process that Requires energy in the

form of ATP Figure 15.15

Stage 2

Stage 2: Initiation

• All ingredients required for translation are assembled:

Stage 2

Stage 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)

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Initiation: Step 1

•• mRNA binds to small subunit of mRNA binds to small subunit of ribosome

ribosome

– Initiation factor 3(IF-3) keeps large and small subunits separated during initiation

• Key consensus sequence in Bacteria for ribosome binding: ShineShine--DelgarnoDelgarno sequence

sequence

– Complementary to a sequence near 3’ end of 16S rRNA

Initiation: Step 1

•• mRNA binds to small subunit of mRNA binds to small subunit of ribosome

ribosome

– Initiation factor 3(IF-3) keeps large and small subunits separated during initiation

• Key consensus sequence in Bacteria for ribosome binding: ShineShine--DelgarnoDelgarno sequence

sequence

– Complementary to a sequence near 3’ end of 16S rRNA example of an ^{Cool! An}

RNA-RNA interaction!

Figure 15.16

Initiation: Step 1 Initiation: Step 1 IF-3 prevents large subunit from

binding

Initiation: Step 2

•• fMet-fMet-tRNAtRNA^fMet^fMetattaches to initiation attaches to initiation codon

codon

– Facilitated by Initiation Factor 2and GTP – Initiation Factor 1helps keep large and small

subunits apart

•

• 30S Initiation Complex30S Initiation Complex

– Small ribosomal subunit, mRNA, fMet- tRNA^fMet, GTP, Initiation Factors

Figure 15.16

Initiation: Step 2 Initiation: Step 2 Formation of the 30S Initiation

Complex

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Initiation: Step 3

•• 70 S Initiation Complex70 S Initiation Complex

– Large subunit of ribosome joins Initiation Complex

– IF-1 and IF-2 depart

Figure 15.16

Initiation: Step 3 Initiation: Step 3 Formation of the 70S Initiation

Complex

Eukaryotic Initiation

•• No Shine DelgarnoNo Shine Delgarnosequencesequence

– 5’ Cap important in ribosome-mRNA binding

•

• More initiation factors requiredMore initiation factors required

•• Poly(A) tail bound proteinsPoly(A) tail bound proteins – Interact with 5’Cap bound proteins

Figure 15.21