One Gene, One Polypeptide

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One Gene, One Polypeptide

• A gene is defined as a DNA sequence.
• There are many steps between genotype and
  phenotype genes cannot by themselves produce a
  phenotype.

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DNA, RNA, and the Flow of Information

• RNA (ribonucleic acid) differs from DNA in three
  ways
• RNA is single-stranded
• The sugar in RNA is ribose, not deoxyribose.
• RNA has uracil instead of thymine.
• RNA can base-pair with single-stranded DNA
• A pairs with U instead of T
• RNA can also fold over and base-pair with itself.

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DNA, RNA, and the Flow of Information

• Francis Cricks central dogma stated that DNA
  codes for RNA, and RNA codes for protein.
• How does information get from the nucleus to the
  cytoplasm?
• What is the relationship between a specific
  nucleotide sequence in DNA and a specific amino
  acid sequence in protein?

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Figure 12.2 The Central Dogma
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DNA, RNA, and the Flow of Information

• Messenger RNA
• mRNA moves from the nucleus of eukaryotic cells
  into the cytoplasm, where it serves as a template
  for protein synthesis.
• Transfer RNA
• tRNA, is the link between the code of the mRNA
  and the amino acids of the polypeptide,
  specifying the correct amino acid sequence in a
  protein.

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Figure 12.3 From Gene to Protein
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Transcription DNA-Directed RNA Synthesis

• Transcription requires the following
• A DNA template for complementary base pairing
• The appropriate ribonucleoside triphosphates
  (ATP, GTP, CTP, and UTP) to act as substrates
• The enzyme RNA polymerase

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Transcription DNA-Directed RNA Synthesis

• Just one DNA strand (the template strand) is used
  to make the RNA.
• The DNA double helix partly unwinds to serve as
  template.
• As the RNA transcript forms, it peels away,
  allowing the already transcribed DNA to be
  rewound into the double helix.

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• Steps of transcription
• Initiation
• Elongation
• Termination

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Transcription DNA-Directed RNA Synthesis

• INITIATION
• The first step of transcription, initiation,
  begins at a promoter, a special sequence of DNA.
• There is at least one promoter for each gene to
  be transcribed.
• The RNA polymerase binds to the promoter region
  when conditions allow.

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Figure 12.4 (Part 1) DNA is Transcribed in RNA
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Transcription DNA-Directed RNA Synthesis

• ELONGATION
• After binding, RNA polymerase unwinds the DNA
  about 20 base pairs at a time and reads the
  template in the 3-to-5 direction (elongation).
• The new RNA elongates from its 5 end to its 3
  end thus the RNA transcript is antiparallel to
  the DNA template strand.
• Transcription errors for RNA polymerases are high
  relative to DNA polymerases.

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Figure 12.4 (Part 2) DNA is Transcribed in RNA
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Transcription DNA-Directed RNA Synthesis

• TERMINATION
• Particular base sequences in the DNA specify
  termination.
• Gene mechanisms for termination vary
• For some, the newly formed transcript simply
  falls away from the DNA template.
• For other genes, a helper protein pulls the
  transcript away.
• In prokaryotes, translation of the mRNA often
  begins before transcription is complete.

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Figure 12.4 (Part 3) DNA is Transcribed in RNA
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The Genetic Code

• A genetic code relates genes (DNA) to mRNA and
  mRNA to the amino acids of proteins.
• mRNA is read in three-base segments called
  codons.
• The number of different codons possible is 64
  (43), because each position in the codon can be
  occupied by one of four different bases.
• The 64 possible codons code for only 20 amino
  acids and the start and stop signals.

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Figure 12.5 The Universal Genetic Code
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The Genetic Code

• AUG, which codes for methionine, is called the
  start codon, the initiation signal for
  translation.
• Three codons (UAA, UAG, and UGA) are stop codons,
  which direct the ribosomes to end translation.

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The Genetic Code

• The genetic code is redundant but not ambiguous.
• Redundancy
• After subtracting start and stop codons, the
  remaining 60 codons code for 19 different amino
  acids.
• This means that many amino acids have more than
  one codon. Thus the code is redundant.
• Lack of ambiguity
• However, the code is not ambiguous. Each codon is
  assigned only one amino acid.

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Preparation for Translation Linking RNAs, Amino
Acids, and Ribosomes

• Transfer RNA
• The molecule tRNA is required to assure
  specificity in the translation of mRNA into
  proteins.
• The tRNAs must read mRNA correctly.
• The tRNAs must carry the correct amino acids.

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Preparation for Translation Linking RNAs, Amino
Acids, and Ribosomes

• The codon in mRNA and the amino acid in a protein
  are related by way of an adaptera specific tRNA
  molecule.
• tRNA has three functions
• It carries an amino acid.
• It associates with mRNA molecules.
• It interacts with ribosomes.

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Preparation for Translation Linking RNAs, Amino
Acids, and Ribosomes

• A tRNA molecule has 75 to 80 nucleotides and a
  three-dimensional shape (conformation).
• The shape is maintained by complementary base
  pairing and hydrogen bonding.
• The three-dimensional shape of the tRNAs allows
  them to combine with the binding sites of the
  ribosome.

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Figure 12.7 Transfer RNA
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Preparation for Translation Linking RNAs, Amino
Acids, and Ribosomes

• At the 3 end of every tRNA molecule is a site to
  which its specific amino acid binds covalently.
• Midpoint in the sequence are three bases called
  the anticodon.
• The anticodon is the contact point between the
  tRNA and the mRNA.
• The anticodon is complementary (and antiparallel)
  to the mRNA codon.
• The codon and anticodon unite by complementary
  base pairing.

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Preparation for Translation Linking RNAs, Amino
Acids, and Ribosomes

• Amino acids are attached to the correct tRNAs by
  activating enzymes called aminoacyl-tRNA
  synthetases.

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Preparation for Translation Linking RNAs, Amino
Acids, and Ribosomes

• Each ribosome has two subunits a large one and a
  small one.
• When they are not translating, the two subunits
  are separate.

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Figure 12.9 Ribosome Structure
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Preparation for Translation Linking RNAs, Amino
Acids, and Ribosomes

• The large subunit has four binding sites
• The T site where the tRNA first lands
• The A site where the tRNA anticodon binds to the
  mRNA codon
• The P site where the tRNA adds its amino acid to
  the polypeptide chain
• The E site where the tRNA goes before leaving the
  ribosome

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Preparation for Translation Linking RNAs, Amino
Acids, and Ribosomes

• The small ribosomal subunit plays a role in
  validating the three-base-pair match between the
  mRNA and the tRNA.
• If hydrogen bonds have not formed between all
  three base pairs, the tRNA is ejected from the
  ribosome.

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• Translation
• Initiation
• Elongation
• Termination

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Figure 12.3 From Gene to Protein
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Translation RNA-Directed Polypeptide Synthesis

• INITIATION
• Translation begins with an initiation complex a
  charged tRNA with its amino acid and a small
  subunit, both bound to the mRNA.
• This complex is bound to a region upstream of
  where the actual reading of the mRNA begins.
• The start codon (AUG) designates the first amino
  acid in all proteins.
• The large subunit then joins the complex.
• The process is directed by proteins called
  initiation factors.

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Figure 12.10 The Initiation of Translation
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Translation RNA-Directed Polypeptide Synthesis

• ELONGATION
• Ribosomes move in the 5-to-3 direction on the
  mRNA.
• The large subunit catalyzes two reactions
• Breaking the bond between the tRNA in the P site
  and its amino acid
• Peptide bond formation between this amino acid
  and the one attached to the tRNA in the A site
• This is called peptidyl transferase activity.

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Figure 12.11 Translation The Elongation Stage
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Translation RNA-Directed Polypeptide Synthesis

• After the first tRNA releases methionine, it
  dissociates from the ribosome and returns to the
  cytosol.
• The second tRNA, now bearing a dipeptide, moves
  to the P site.
• The next charged tRNA enters the open A site.
• The peptide chain is then transferred to the P
  site.
• These steps are assisted by proteins called
  elongation factors.

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Translation RNA-Directed Polypeptide Synthesis

• TERMINATION
• When a stop codonUAA, UAG, or UGAenters the A
  site, a release factor and a water molecule enter
  the A site, instead of an amino acid.
• The newly completed protein then separates from
  the ribosome.

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Figure 12.12 The Termination of Translation
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Regulation of Translation

• Polysomes are mRNA molecules with more than one
  ribosome attached.
• These make protein more rapidly, producing
  multiple copies of protein simultaneously.

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Figure 12.13 A Polysome (Part 1)
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Figure 12.3 From Gene to Protein
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Posttranslational Events

• Two posttranslational events can occur after the
  polypeptide has been synthesized
• The polypeptide may be moved to another location
  in the cell, or secreted.
• The polypeptide may be modified by the addition
  of chemical groups, folding, or trimming.

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Figure 12.14 Destinations for Newly Translated
Polypeptides in a Eukaryotic Cell
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Posttranslational Events

• As the polypeptide chain forms, it folds into its
  3-D shape.
• The amino acid sequence also contains an address
  label indicating where in the cell the
  polypeptide belongs. It gives one of two sets of
  instructions
• Finish translation and be released to the
  cytoplasm.
• Stall translation, go to the ER, and finish
  synthesis at the ER surface.

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Posttranslational Events

• Polypeptides destined for the ER have a
  25-amino-acid-long leader sequence.
• Before translation is finished, the leader
  sequence binds to a signal recognition particle.
• This stalls protein synthesis until the ribosome
  attaches to a specific receptor protein on the
  surface of the ER.
• Translation continues with the protein moving
  through a pore in the ER membrane.

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Posttranslational Events

• Other signals are needed to direct further
  protein sorting
• Sequences of amino acids that allow the protein
  to stay in the ER
• Sugars added in the Golgi apparatus to form
  glycoproteins, which go to lysosomes or the
  plasma membrane
• Proteins with no signals from the ER go through
  the Golgi apparatus and are secreted from the
  cell.

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Posttranslational Events

• Most proteins are modified after translation.
• These modifications are often essential to the
  functioning of the protein.
• Three types of modifications
• Proteolysis (cleaving)
• Glycosylation (adding sugars)
• Phosphorylation (adding phosphate groups)

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Figure 12.16 Posttranslational Modifications to
Proteins
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Mutations Heritable Changes in Genes

• Mutations are heritable changes in DNAchanges
  that are passed on to daughter cells.
• Multicellular organisms have two types of
  mutations
• Somatic mutations are passed on during mitosis,
  but not to subsequent generations.
• Germ-line mutations are mutations that occur in
  cells that give rise to gametes.

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Mutations Heritable Changes in Genes

• All mutations are alterations of the DNA
  nucleotide sequence and are of two types
• Point mutations are mutations of single genes.
• Chromosomal mutations are changes in the
  arrangements of chromosomal DNA segments.

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Mutations Heritable Changes in Genes

• Point mutations result from the addition or
  subtraction of a base or the substitution of one
  base for another.
• Point mutations can occur as a result of mistakes
  during DNA replication or can be caused by
  environmental mutagens.
• Because of redundancy in the genetic code, some
  point mutations, called silent mutations, result
  in no change in the amino acids in the protein.

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Silent Mutation
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Mutations Heritable Changes in Genes

• Some mutations, called missense mutations, cause
  an amino acid substitution.
• An example in humans is sickle-cell anemia, a
  defect in the b-globin subunits of hemoglobin.
• The b-globin in sickle-cell differs from the
  normal by only one amino acid.
• Missense mutations may reduce the functioning of
  a protein or disable it completely.

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Missense mutation
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Mutations Heritable Changes in Genes

• Nonsense mutations are base substitutions that
  substitute a stop codon.
• The shortened proteins are usually not functional.

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Nonsense mutation
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Mutations Heritable Changes in Genes

• A frame-shift mutation consists of the insertion
  or deletion of a single base in a gene.
• This type of mutation shifts the code, changing
  many of the codons to different codons.
• These shifts almost always lead to the production
  of nonfunctional proteins.

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Frame-shift mutation
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Mutations Heritable Changes in Genes

• Spontaneous mutations are permanent changes,
  caused by any of several mechanisms
• DNA polymerase sometimes makes errors in
  replication which can escape being repaired.
• Meiosis is imperfect. Nondisjunction and
  translocations can occur.

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Mutations Heritable Changes in Genes

• Induced mutations are permanent changes caused by
  some outside agent (mutagen).
• Mutagens can alter DNA in several ways
• Altering covalent bonds in nucleotides
• Adding groups to the bases
• Radiation damages DNA
• Ionizing radiation (X rays) produces free
  radicals.
• Ultraviolet radiation is absorbed by thymine and
  causes interbase covalent bonds to form.

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Mutations Heritable Changes in Genes

• Mutations have both benefits and costs.
• Germ line mutations provide genetic diversity for
  evolution, but usually produce an organism that
  does poorly in its environment.
• Somatic mutations do not affect offspring, but
  can cause cancer.

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Mutations Heritable Changes in Genes

• Mutations are rare events and most of them are
  point mutations involving one nucleotide.
• Mutations can be detrimental, neutral, or
  occasionally beneficial.
• Random accumulation of mutations in the extra
  copies of genes can lead to the production of new
  useful proteins.