Genetic code 3

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ContentChapter 1 Introduction

Chapter 2 The Structures of DNA and RNA

Chapter 10 Regulation in Eukaryotes

Chapter 4 DNA Mutation and Repair

Chapter 5 RNA Transcription

Chapter 6 RNA Splicing

Chapter 7 Translation

Chapter 8 The Genetic code

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Chapter 9 Regulation in prokaryotes

Chapter 3 DNA Replication

HOW TO LEARN THIS COURSE WELL？

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To learn effectively To preview and review Problem-base learning Making use of class time effectively

Active participation Bi-directional question in class Group discussion Concept map

Tutorship To call for reading, thingking and discussing of investigative

learning

Evaluation (grading) system

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Question in-class and attendance : 10 points Group study and attendance: 20 points Final exam: 70 points Bonus

Molecular Biology of the Gene, 5/E --- Watson et al. (2004)

Part I: Chemistry and Genetics

Part II: Maintenance of the Genome

Part III: Expression of the Genome

Part IV: Regulation

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EXPRESSION OF THE GENOME

Ch 5 : TranscriptionCh 6 : RNA SplicingCh 7 : TranslationCh 8 : The Genetic code

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DNA RNA Protein

Replication

Transcription

TranslationTranslation

The Central DogmaThe Central Dogma

1. Genetic information transfer from polynucleotide chain into polypeptide chain.

2. Take place in ribosomes.3. tRNAs recognize codons.

Topic 1: THE CODE IS Topic 1: THE CODE IS DEGENERATEDEGENERATE

Topic 1: THE CODE IS Topic 1: THE CODE IS DEGENERATEDEGENERATE

CHAPTER 8 The Genetic Code

Codon: degenerateAnticodon: wobbleCodon: degenerateAnticodon: wobble

Many amino acids are specified by more than one codon-degeneracy ( 简并性 ).Codons specifying the same amino acid are called synonyms ( 同义密码子 ).

Many amino acids are specified by more than one codon-degeneracy ( 简并性 ).Codons specifying the same amino acid are called synonyms ( 同义密码子 ).

TABLE 8-1 The Genetic Code

TABLE 8-1 The Genetic Code

CODING ROLE #1

1.Often, when the first two nucleotides are identical, the third nucleotide can be either C or U without changing the code. A and G at the third position are interchangeable as well.

2.Transition in the third position of a codon specifies a same amino acid. Transversion in this position changes the amino acid about half the time.

1.Often, when the first two nucleotides are identical, the third nucleotide can be either C or U without changing the code. A and G at the third position are interchangeable as well.

2.Transition in the third position of a codon specifies a same amino acid. Transversion in this position changes the amino acid about half the time.

Figure 8-1 Codon-anticodon pairing of two tRNA Leu moleculars

Figure 8-1 Codon-anticodon pairing of two tRNA Leu moleculars

CUG CUC

Code degeneracy explains how there can be great variation in the AT/GC ratiosAT/GC ratios in the DNA of various organisms without large changes in the proportion of proportion of amino acidsamino acids in their proteins.

Perceiving Order in the Makeup of the Code

1. The genetic code evolved in such a way as to minimize the deleterious effects of mutations.

2. Code degeneracy may serve as a safety mechanism to minimize errors in the reading of codons.

The C

ode Is Degenerate

CODING ROLE #2

1.The second position of a codon: Pyrimidines-hydrophobic amino acids Purines-polar amino acids2.If the first two positions are both occupied by G

or C, each of the four nucleotides in the third position specifies the same amino acid.

Wobble in the Anticodon( 反密码子具有摇摆性 )

Question: Is there a specif ic tRNA for every codon? (If i t was true, at least 61 different tRNAs would exist.)

The answer is NO

Some tRNA could recognize several different codons

Inosine is present in the anticodon loop as a f ifth base

The C

ode Is Degenerate

Inosine

inosine adenine

Inosine arises through enzymatic modification of adenine

WOBBLE CONCEPT

In 1966, Francis Crick devised the wobble concept. It states that the base at the 5’ end of the anticodon is not as spatially confined as the other two, allowing it to form hydrogen bonds with more than one bases located at the 3’ end of a codon.

Table 8-2 Pairing Combinations with the Wobble Concept

Base in 5’ Anticodon Base in 3’ CodonBase in 5’ Anticodon Base in 3’ Codon

G U or CC GA UU A or GI A, U, or C

G U or CC GA UU A or GI A, U, or C

THE WOBBLE RULES

The pairings permitted are those give ribose-ribose distances close to that of the standard A:U or G:C base pairs.

The ribose-ribose distances: Purine-purine: too long Pyrimidine-pyrimidine: too short

Figure 8-2Wobble base pairing

Figure 8-2Wobble base pairing

The ribose-ribose distances for the wobble pairs are close to those of A:U or G:C base pairs

CRITICAL THINKING

The wobble concept predicted that at least three tRNAs exist for the six serine codons (UCU, UCC, UCA, UCG, AGU, and AGC). Why?

WHY WOBBLE IS ALLOWED AT THE 5’ ANTICODON

The 3-D structure of tRNA shows that the stacking interactions between the flat surfaces of the 3 anticodon bases + 2 followed bases position the first (5’) anticodon base at the end of the stack, thus less restricted in its movements.

The 3’ base appears in the middle of the stack, resulting in the restriction of its movements.

Figure 8-3 Structure of yeast tRNA(Phe)Figure 8-3 Structure of yeast tRNA(Phe)

The adjacent

base

The adjacent base is always a bulky modified purine

residue.

Three Codons Direct Chain Termination

Three codons, UAA, UAG, and UGA signify chain termination.

They are not read by tRNAs but by proteins called release factors (RF1 and RF2 in bacteria and eRF1 in eukaryotes).

The C

ode Is Degenerate

How the Code Was Cracked ( 解开 )

See Chapter 2, Page 35: Establishing the Genetic Code The use of art if icial mRNAs and

the availabil i ty of cell-free systems for carrying out protein synthesis began to make it possible to crack the code

The C

ode Is Degenerate

Stimulation of Amino Acid Incorporation by Synthetic mRNAs

Extracts from E. coli cells can incorporate amino acids into proteins.

After several minutes the synthesis came to a stop because the degradation of mRNA. The addition of fresh mRNA to extracts caused an immediate resumption of synthesis.

This led the scientist an opportunity to elucidate the nature of the code using synthetic RNA

The C

ode Is Degenerate

Figure 8-4 Polynucleotide phosphorylase reactionFigure 8-4 Polynucleotide phosphorylase reaction

How the RNA is synthesized?[XMP]n + XDP = [XMP]n+1 + PHow the RNA is synthesized?[XMP]n + XDP = [XMP]n+1 + P

Experimental Results:

UUU codes for phenylalanine.

CCC codes for proline.

AAA codes for lysine. The guanine residues in poly-G

firmly hydrogen bond to each other and form multistranded triple helices that do not bind to ribosomes.

Mixed Copolymers Allowed Additional Codon Assignments

Poly-AC contain 8 codons: CCC, CCA, CAC, ACC, CAA, ACA, AAC, and AAA.

They code for Asp, Glu, His, Thr & Pro (CCC), Lys (AAA).

The proportions of the 8 codons incorporated into polypeptide products depend on the A/C ratio

The C

ode Is Degenerate

Such experiment can determine the composition of the codons, but not the order of the three nucleotides.

Such experiment can determine the composition of the codons, but not the order of the three nucleotides.

See Table 8-3 on Page 467See Table 8-3 on Page 467

Transfer RNA Binding to Defined Trinucleotide Codons (1964)T

he Code Is D

egenerate

A method to order the nucleotides within some of the codons.Specif ic amino-acyl-tRNA can bind to ribosome-mRNA complexes.The addition of tr inucleotide results in corresponding amino-acyl-tRNA attachment.

A method to order the nucleotides within some of the codons.Specif ic amino-acyl-tRNA can bind to ribosome-mRNA complexes.The addition of tr inucleotide results in corresponding amino-acyl-tRNA attachment.

Codon Assignments from Repeating CopolymersT

he Code Is D

egenerate

Organic chemical and enzymatic techniques were used to prepare synthetic polyribonucleotides with known repeating sequences.

Organic chemical and enzymatic techniques were used to prepare synthetic polyribonucleotides with known repeating sequences.

Figure 8-5 Preparing oligo-ribonucleotidesFigure 8-5 Preparing oligo-ribonucleotides

Table 8-5copolymer Codons

Recognized

Amino Acids Incorporated or

Polypeptide Made

Codon Assignment

(CU)” CUC|UCU|CUC… Leucine 5’-CUC-3’

Serine UCU

(UG)” UGU|GUG|UGU… Cystine UGU

Valine GUG

(AC)” ACA|CAC|ACA… Threonine ACA

Hist idine CAC

(AG)” AGA|GAG|AGA… Arginine AGA

Glutamine GAG

(AUC)” AUC|AUC|AUC… Polyisoleucine 5’-AUC-3’

Topic 2: THREE Topic 2: THREE RULES GOVERN THE RULES GOVERN THE

GENETIC CODEGENETIC CODE

Topic 2: THREE Topic 2: THREE RULES GOVERN THE RULES GOVERN THE

GENETIC CODEGENETIC CODE


THREE RULES

Codons are read in a 5’ to 3’ direction.

Codons are nonoverlapping and the message contains no gaps.

The message is translated in a f ixed reading frame which is set by the init iation codon.

Three Kinds of Point Mutations Alter the Genetic Code

Three Rules G

overn the Genetic C

ode

1. Missense mutation: An alternation that changes a codon specific for one amino acid to a codon specif ic for another amino acid.

2. Nonsense or stop mutation: An alternation causing a change to a chain-termination codon.

1. Missense mutation: An alternation that changes a codon specif ic for one amino acid to a codon specif ic for another amino acid.

2. Nonsense or stop mutation: An alternation causing a change to a chain-termination codon.

3. Frameshift mutation: Insertions or deletions of one or a small number of base pairs that alter the reading frame.

Genetic Proof that the Code Is Read in Units of Three

Three Rules G

overn the Genetic C

ode

A classic experiment involving bacteriophage T4

Because the gene could tolerate three insertions but not one or two, the genetic code must be read in units of three.

A classic experiment involving bacteriophage T4

Because the gene could tolerate three insertions but not one or two, the genetic code must be read in units of three.

Topic 3: SUPPRESSOR Topic 3: SUPPRESSOR MUTATIONS CAN MUTATIONS CAN

RESIDE IN THE SAME RESIDE IN THE SAME OR A DIFFERENT OR A DIFFERENT

GENEGENE

Topic 3: SUPPRESSOR Topic 3: SUPPRESSOR MUTATIONS CAN MUTATIONS CAN

RESIDE IN THE SAME RESIDE IN THE SAME OR A DIFFERENT OR A DIFFERENT

GENEGENE


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Reverse (back) mutations: change an altered nucleotide sequence back to its original arrangement.

Suppressor mutations: suppress the change due to mutation at site A by producing an additional genetic change at site B.

(1) Intragenic suppression (2) Intergenic suppression

Reverse the harmful mutations by a second genetic change

Suppressor genes: genes that cause suppression of mutations in other genes.

Suppressor mutations work by producing good (or partially good) copies of the protein that are made inactive by the original harmful mutation.

Figure 8-6 Suppression of frameshift mutationsFigure 8-6 Suppression of frameshift mutations

Intergenic Suppression Involves Mutant tRNAs

Su

pp

resso

r mu

tatio

ns

Mutant tRNA genes suppress the effects of nonsense mutations in protein-coding genes.

They act by reading a stop codon as if i t were a signal for a specif ic amino acid.

Figure 15-7 aFigure 15-7 a

Figure 8-7 aFigure 8-7 a

Figure 8-7 bFigure 8-7 b

Nonsense Suppressors also Read Normal Termination Signals (OOPs)

Su

pp

resso

r mu

tatio

ns

The act of nonsense suppression is a competit ion between the suppressor tRNA and the release factor.In E. coli, Suppression of UAG codons is efficient, and suppression of UAA codon average is inefficient. Why??.

The act of nonsense suppression is a competit ion between the suppressor tRNA and the release factor.In E. coli, Suppression of UAG codons is efficient, and suppression of UAA codon average is inefficient. Why??.

Topic 4: Topic 4: THE CODE IS NEARLY THE CODE IS NEARLY

UNIVERSALUNIVERSAL

Topic 4: Topic 4: THE CODE IS NEARLY THE CODE IS NEARLY

UNIVERSALUNIVERSAL


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The results of large-scale sequencing of genomes have confirmed the universality of the genetic code.

Benefits of the universal codes(1)Allow us to directly compare the

protein coding sequences among all organisms.

(2) Make it possible to express cloned copies of genes encoding useful protein in different host organism. Example: Human insulin ecpression in bacteria)

However, in certain subcellular organelles, the genetic code is slightly different from the standard code.

Mitochondrial tRNAs are unusual in the way that they decode mitochondrial messages.

Only 22 tRNAs are present in mammalian mitochondria. The U in the 5’ wobble position of a tRNA is capable of recognizing all four bases in the 3’ of the codon.

Table 8-6 Genetic Code of Mammalian MitochondriaTable 8-6 Genetic Code of Mammalian Mitochondria

1. “The genetic code is degenerate” What does it mean? What are the benefits?

2. What is the wobble concept? Is there structural evidence? How the wobble in the anticodon affect the number of tRNAs to recognize the 61 codons?

3. What are the three roles governing the genetic code? What are the mutations altering genetic code?

4. What are suppressor mutations? ( 种类 )5. What are the benefits of the code

universality?

Key points of the chapter

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Genetic code 3