Genes and How They Work

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Genes and How They Work

• Chapter 15

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The Nature of Genes

• Early ideas to explain how genes work came from
  studying human diseases.
• Archibald Garrod studied alkaptonuria, 1902
• Garrod recognized that the disease is inherited
  via a recessive allele
• Garrod proposed that patients with the disease
  lacked a particular enzyme
• These ideas connected genes to enzymes.

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The Nature of Genes

• Evidence for the function of genes came from
  studying fungus.
• George Beadle and Edward Tatum, 1941
• studied Neurospora crassa
• used X-rays to damage the DNA in cells of
  Neurospora
• looked for cells with a new (mutant) phenotype
  caused by the damaged DNA

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The Nature of Genes

• Beadle and Tatum looked for fungal cells lacking
  specific enzymes.
• The enzymes were required for the biochemical
  pathway producing the amino acid arginine.
• They identified mutants deficient in each enzyme
  of the pathway.

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The Nature of Genes

• Beadle and Tatum proposed that each enzyme of the
  arginine pathway was encoded by a separate gene.
• They proposed the one gene one enzyme
  hypothesis.
• Today we know this as the one gene one
  polypeptide hypothesis.

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The Nature of Genes

• The central dogma of molecular biology states
  that information flows in one direction
• DNA RNA protein
• Transcription is the flow of information from DNA
  to RNA.
• Translation is the flow of information from RNA
  to protein.

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The Genetic Code

• Deciphering the genetic code required determining
  how 4 nucleotides (A, T, G, C) could encode more
  than 20 amino acids.
• Francis Crick and Sydney Brenner determined that
  the DNA is read in sets of 3 nucleotides for each
  amino acid.

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The Genetic Code

• codon set of 3 nucleotides that specifies a
  particular amino acid
• reading frame the series of nucleotides read in
  sets of 3 (codon)
• only 1 reading frame is correct for encoding the
  correct sequence of amino acids

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The Genetic Code

• Marshall Nirenberg identified the codons that
  specify each amino acid.
• RNA molecules of only 1 nucleotide and of
  specific 3-base sequences were used to determine
  the amino acid encoded by each codon.
• The amino acids encoded by all 64 possible codons
  were determined.

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The Genetic Code

• stop codons 3 codons (UUA, UGA, UAG) in the
  genetic code used to terminate translation
• start codon the codon (AUG) used to signify the
  start of translation
• The remainder of the code is degenerate meaning
  that some amino acids are specified by more than
  one codon.

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Gene Expression Overview

• template strand strand of the DNA double helix
  used to make RNA
• coding strand strand of DNA that is
  complementary to the template strand
• RNA polymerase the enzyme that synthesizes RNA
  from the DNA template

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Gene Expression Overview

• Transcription proceeds through
• initiation RNA polymerase identifies where to
  begin transcription
• elongation RNA nucleotides are added to the 3
  end of the new RNA
• termination RNA polymerase stops transcription
  when it encounters terminators in the DNA sequence

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Gene Expression Overview

• Translation proceeds through
• initiation mRNA, tRNA, and ribosome come
  together
• elongation tRNAs bring amino acids to the
  ribosome for incorporation into the polypeptide
• termination ribosome encounters a stop codon
  and releases polypeptide

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Gene Expression Overview

• Gene expression requires the participation of
  multiple types of RNA
• messenger RNA (mRNA) carries the information from
  DNA that encodes proteins
• ribosomal RNA (rRNA) is a structural component of
  the ribosome
• transfer RNA (tRNA) carries amino acids to the
  ribosome for translation

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Gene Expression Overview

• Gene expression requires the participation of
  multiple types of RNA
• small nuclear RNA (snRNA) are involved in
  processing pre-mRNA
• signal recognition particle (SRP) is composed of
  protein and RNA and involved in directing mRNA to
  the RER
• micro-RNA (miRNA) are very small and their role
  is not clear yet

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Prokaryotic Transcription

• Prokaryotic cells contain a single type of RNA
  polymerase found in 2 forms
• core polymerase is capable of RNA elongation but
  not initiation
• holoenzyme is composed of the core enzyme and the
  sigma factor which is required for transcription
  initiation

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Prokaryotic Transcription

• A transcriptional unit extends from the promoter
  to the terminator.
• The promoter is composed of
• a DNA sequence for the binding of RNA polymerase
• the start site (1) the first base to be
  transcribed

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Prokaryotic Transcription

• During elongation, the transcription bubble moves
  down the DNA template at a rate of 50
  nucleotides/sec.
• The transcription bubble consists of
• RNA polymerase
• DNA template
• growing RNA transcript

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Prokaryotic Transcription

• Transcription stops when the transcription bubble
  encounters terminator sequences
• this often includes a series of A-T base pairs
• In prokaryotes, transcription and translation are
  often coupled occurring at the same time

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Eukaryotic Transcription

• RNA polymerase I transcribes rRNA.
• RNA polymerase II transcribes mRNA and some
  snRNA.
• RNA polymerase III transcribes tRNA and some
  other small RNAs.
• Each RNA polymerase recognizes its own promoter.

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Eukaryotic Transcription

• Initiation of transcription of mRNA requires a
  series of transcription factors
• transcription factors proteins that act to bind
  RNA polymerase to the promoter and initiate
  transcription

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Eukaryotic pre-mRNA Splicing

• In eukaryotes, the primary transcript must be
  modified by
• addition of a 5 cap
• addition of a 3 poly-A tail
• removal of non-coding sequences (introns)

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Eukaryotic pre-mRNA Splicing

• The spliceosome is the organelle responsible for
  removing introns and splicing exons together.
• Small ribonucleoprotein particles (snRNPs) within
  the spliceosome recognize the intron-exon
  boundaries
• introns non-coding sequences
• exons sequences that will be translated

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tRNA and Ribosomes

• tRNA molecules carry amino acids to the ribosome
  for incorporation into a polypeptide
• aminoacyl-tRNA synthetases add amino acids to the
  acceptor arm of tRNA
• the anticodon loop contains 3 nucleotides
  complementary to mRNA codons

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tRNA and Ribosomes

• The ribosome has multiple tRNA binding sites
• P site binds the tRNA attached to the growing
  peptide chain
• A site binds the tRNA carrying the next amino
  acid
• E site binds the tRNA that carried the last
  amino acid

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tRNA and Ribosomes

• The ribosome has two primary functions
• decode the mRNA
• form peptide bonds
• peptidyl transferase is the enzymatic component
  of the ribosome which forms peptide bonds between
  amino acids

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Translation

• In prokaryotes, initiation of translation
  requires the formation of the initiation complex
  including
• an initiator tRNA charged with N-formylmethionine
• the small ribosomal subunit
• mRNA strand
• The ribosome binding sequence of mRNA is
  complementary to part of rRNA

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Translation

• Elongation of translation involves the addition
  of amino acids
• a charged tRNA binds to the A site if its
  anticodon is complementary to the codon at the A
  site
• peptidyl transferase forms a peptide bond
• the ribosome moves down the mRNA in a 5 to 3
  direction

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Translation

• There are fewer tRNAs than codons.
• Wobble pairing allows less stringent pairing
  between the 3 base of the codon and the 5 base
  of the anticodon.
• This allows fewer tRNAs to accommodate all codons.

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Translation

• Elongation continues until the ribosome
  encounters a stop codon.
• Stop codons are recognized by release factors
  which release the polypeptide from the ribosome.

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Translation

• In eukaryotes, translation may occur on ribosomes
  in the cytoplasm or on ribosomes of the RER.
• Signal sequences at the beginning of the
  polypeptide sequence bind to the signal
  recognition particle (SRP)
• The signal sequence and SRP are recognized by RER
  receptor proteins.

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Translation

• The signal sequence/SRP holds the ribosome on the
  RER.
• As the polypeptide is synthesized it passes
  through a pore into the interior of the
  endoplasmic reticulum.

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Mutation Altered Genes

• Point mutations alter a single base.
• base substitution mutations substitute one base
  for another
• transitions or transversions
• also called missense mutations
• nonsense mutations create stop codon
• frameshift mutations caused by insertion or
  deletion of a single base

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Mutation Altered Genes

• triplet repeat expansion mutations involve a
  sequence of 3 DNA nucleotides that are repeated
  many times
• triplet repeats are associated with some human
  genetic diseases
• the abnormal allele causing the disease contains
  these repeats whereas the normal allele does not

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Mutation Altered Genes

• Chromosomal mutations change the structure of a
  chromosome.
• deletions part of chromosome is lost
• duplication part of chromosome is copied
• inversion part of chromosome in reverse order
• translocation part of chromosome is moved to a
  new location

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Mutation Altered Genes

• Too much genetic change (mutation) can be harmful
  to the individual.
• However, genetic variation (caused by mutation)
  is necessary for evolutionary change of the
  species.