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Chapter 8 Gene Expression. The Flow of Genetic Information from DNA via RNA to Protein. Outline of Chapter 8. The genetic code

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Chapter 8Gene Expression

The Flow of Genetic Information from DNA via RNA to Protein


Outline of chapter 8
Outline of Chapter 8

  • The genetic code

    • How triplets of the four nucleotides unambiguously specify 20 amino acids, making it possible to translate information from a nucleotide chain to a sequence of amino acids

  • Transcription

    • How RNA polymerase, guided by base pairing, synthesizes a single-stranded mRNA copy of a gene’s DNA template

  • Translation

    • How base pairing between mRNA and tRNAs directs the assembly of a polypeptide on the ribosome

  • Significant differences in gene expression between prokaryotes and eukaryotes

  • How mutations affect gene information and expression


The triplet codon represents each amino acid
The triplet codon represents each amino acid

  • 20 amino acids encoded for by 4 nucleotides

    • By deduction:

      • 1 nucleotide/amino acid = 41 = 4 triplet combinations

      • 2 nucleotides/amino acid = 42 = 16 triplet combinations

      • 3 nucleotides/amino acid = 43 = 64 triplet combinations

    • Must be at least triplet combinations that code for amino acids


The genetic code 61 triplet codons represent 20 amino acids 3 triplet codons signify stop
The Genetic Code: 61 triplet codons represent 20 amino acids; 3 triplet codons signify stop

Fig. 8.3


A gene s nucleotide sequence is colinear the amino acid sequence of the encoded polypeptide
A gene’s nucleotide sequence is colinear the amino acid sequence of the encoded polypeptide

  • Charles Yanofsky – E. coli genes for a subunit of tyrptophan synthetase compared mutations within a gene to particular amino acid substitutions

  • Trp- mutants in trpA

  • Fine structure recombination map

  • Determined amino acid sequences of mutants


Fig. 8.4 sequence of the encoded polypeptide


  • A codon is composed of more than one nucleotide sequence of the encoded polypeptide

    • Different point mutations may affect same amino acid

    • Codon contains more than one nucleotide

  • Each nucleotide is part of only a single codon

    • Each point mutation altered only one amino acid


A codon is composed of three nucleotides and the starting point of each gene establishes a reading framestudies of frameshift mutations in bacteriophage T4 rIIB gene

Fig. 8.5


Fig. 8.6


Cracking the code biochemical manipulations revealed which codons represent which amino acids
Cracking the code: biochemical manipulations revealed which codons represent which amino acids

  • The discovery of messenger RNAs, molecules for transporting genetic information

    • Protein synthesis takes place in cytoplasm deduced from radioactive tagging of amino acids

  • RNA, an intermediate molecule made in nucleus and transports DNA information to cytoplasm


Synthetic mrnas and in vitro translation determines which codons designate which amino acids
Synthetic mRNAs and in vitro translation determines which codons designate which amino acids

  • 1961 – Marshall Nirenberg and Heinrich Mathaei created mRNAs and translated to polypeptides in vitro

  • Polymononucleotides

  • Polydinucleotides

  • Polytrinucleotides

  • Polytetranucleotides

  • Read amino acid sequence and deduced codons

Fig. 8.7


Fig. 8.8


  • 5’ to 3’ direction of mRNA corresponds to N-terminal-to-C-terminal direction of polypeptide

    • One strand of DNA is a template

    • The other is an RNA-like strand

  • Nonsense codons cause termination of a polypeptide chain – UAA (ocher), UAG (amber), and UGA (opal)

Fig. 8.9


Summary
Summary N-terminal-to-C-terminal direction of polypeptide

  • Codon consist of a triplet codon each of which specifies an amino acid

    • Code shows a 5’ to 3’ direction

  • Codons are nonoverlapping

  • Code includes three stop codons, UAA, UAG, and UGA that terminate translation

  • Code is degenerate

  • Fixed starting point establishes a reading frame

    • UAG in an initiation codon which specifies reading frame

  • 5’- 3’ direction of mRNA corresponds with N-terminus to C-terminus of polypeptide

  • Mutation modify message encoded in sequence

    • Frameshift mutaitons change reading frame

    • Missense mutations change codon of amino acid to another amino acid

    • Nonsense mutations change a codon for an amino acid to a stop codon


Do living cells construct polypeptides according to same rules as in vitro experiments
Do living cells construct polypeptides according to same rules as in vitro experiments?

  • Studies of how mutations affect amino-acid composition of polypeptides encoded by a gene

  • Missense mutations induced by mutagens should be single nucleotide substitutions and conform to the code

Fig. 8.10 a


  • Proflavin treatment generates Trp rules as - mutants

  • Further treatment generates Trp+ revertants

    • Single base insertion (Trp-) and a deletion causes reversion (Trp+)

Fig. 8.10 b


Genetic code is almost universal but not quite
Genetic code is almost universal but not quite rules as

  • All living organisms use same basic genetic code

    • Translational systems can use mRNA from another organism to generate protein

    • Comparisons of DNA and protein sequence reveal perfect correspondence between codons and amino acids among all organisms


Transcription
Transcription rules as

  • RNA polymerase catalyzes transcription

  • Promoters signal RNA polymerase where to begin transcription

  • RNA polymerase adds nucleotides in 5’ to 3’ direction

  • Terminator sequences tell RNA when to stop transcription


Initiation of transcription
Initiation of transcription rules as

Fig. 8.11 a


Elongation
Elongation rules as

Fig. 8.11 b


Termination
Termination rules as

Fig. 8.11 c


Information flow
Information flow rules as

Fig. 8.11 d



In eukaryotes rna is processed after transcription
In eukaryotes, RNA is processed after transcription rules as

  • A 5’ methylated cap and a 3’ Poly-A tail are added

  • Structure of the methylated cap



Rna splicing removes introns
RNA splicing removes introns rules as

  • Exons – sequences found in a gene’s DNA and mature mRNA (expressed regions)

  • Introns – sequences found in DNA but not in mRNA (intervening regions)

  • Some eukaryotic genes have many introns


Dystrophin gene underlying duchenne muscular dystrophy dmd is an extreme example of introns
Dystrophin gene underlying Duchenne muscular dystrophy (DMD) is an extreme example of introns

Fig. 8.15



Fig. 8.17


  • Alternative splicing exons

    • Different mRNAs can be produced by same transcript

    • Rare transplicing events combine exons from different genes

Fig. 8.18


Translation
Translation exons

  • Transfer RNAs (tRNAs) mediate translation of mRNA codons to amino acids

    • tRNAs carry anticodon on one end

      • Three nucleotides complementary to an mRNA codon

    • Structure of tRNA

      • Primary – nucleotide sequence

      • Secondary – short complementary sequences pair and make clover leaf shape

      • Tertiary – folding into three dimensional space shape like an L

    • Base pairing between an mRNA codon and a tRNA anticodon directs amino acid incorporation into a growing polypeptide

    • Charged tRNA is covalently coupled to its amino acid




Base pairing between mRNA codon and tRNA anticodon determines where incorporation of amino acid occurs

Fig. 8.21



Rhibosomes are site of polypeptide synthesis
Rhibosomes are site of polypeptide synthesis acids they carry

  • Ribosomes are complex structures composed of RNA and protein

Fig. 8.23


Mechanism of translation
Mechanism of translation acids they carry

  • Initiation sets stage for polypeptide synthesis

    • AUG start codon at 5’ end of mRNA

    • Formalmethionine (fMet) on initiation tRNA

      • First amino acid incorporated in bacteria

  • Elongation during which amino acids are added to growing polypeptide

    • Ribosomes move in 5’-3’ direction revealing codons

    • Addition of amino acids to C terminus

    • 2-15 amino acids per second

  • Termination which halts polypeptide synthesis

    • Nonsense codon recognized at 3’ end of reading frame

    • Release factor proteins bind at nonsense codons and halt polypeptide synthesis


Initiation of translation
Initiation of translation acids they carry

Fig. 8.24 a


Elongation1
Elongation acids they carry

Fig. 8.24 b


Termination of translation
Termination of translation acids they carry

Fig. 8.24 c



Significant differences in gene expression between prokaryotes and eukaryotes
Significant differences in gene expression between prokaryotes and eukaryotes

  • Eukaryotes, nuclear membrane prevents coupling of transcription and translation

  • Prokaryotic messages are polycistronic

    • Contain information for multiple genes

  • Eukaryotes, small ribosomal subunit binds to 5’ methylated cap and migrates to AUG start codon

    • 5’ untranslated leader sequence – between 5’ cap and AUG start

    • Only a single polypeptide produced from each gene

  • Initiating tRNA in prokaryotes is fMet

  • Initiating tRNA in eukaryotes is by unmodified Met.


  • Nonsense suppression prokaryotes and eukaryotes

    • (a) Nonsense mutation that causes incomplete nonfunctional polypeptide

    • (b) Nonsense-suppressing mutation causes addition of amino acid at stop codon allowing production of full length polypeptide

Fig. 8.28


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