Molecular%20Biology%20of%20the%20Gene

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Chapter 10

• Molecular Biology of the Gene

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• http//www.pbs.org/wgbh/nova/body/cellular-factory
  .html
• Video 96 (Genes, DNA, Chrom)

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Information transfer is from DNA ? RNA ? protein

• Replication
• What is it?
• Where does it occur?

Copying DNA for division
In the nucleus
REPLICATION
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Information transfer is from DNA ? RNA ? protein

• Transcription
• What is it?
• Where does it occur?

Making mRNA from DNA
In the nucleus
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Information transfer is from DNA ? RNA ? protein

• Translation
• What is it?
• Where does it occur?

Converting mRNA into a protein
In the cytoplasm, at a ribosome
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2. DNA as source of genetic information

• a. Hershey-Chase experiment showed DNA rather
  than protein to be the genetic material passed on
  from one generation to the next

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DNA
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DNA
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DNA
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DNA
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2. DNA as source of genetic information

• b. additional evidence cell doubles DNA prior
  to mitosis, and then splits the DNA evenly among
  daughter cells

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Watson and Crick
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3. Molecular structure of DNA

• a. Watson and Crick described the three
  dimensional structure of DNA one year after
  Hershey and Chase identified DNA as the genetic
  material

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3. Molecular structure of DNA

• b. DNA, along with RNA, are nucleic acids which
  are composed of nucleotides
• c. Nucleotides consist of a sugar (ribose or
  deoxyribose), a nitrogenous base (A, G, C, T, or
  U), and a phosphate group

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3. Molecular structure of DNA

• d. Structure of single DNA strand
• 1. sugar-phosphate backbone
• 2. bases covalently attached to sugar and hang
  off the side

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3. Molecular structure of DNA

• e. double helical structure
• 1. double stranded
• 2. arranged in helix

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3. Molecular structure of DNA

• 3. hydrogen bonds between nitrogenous bases hold
  strands together (remember, hydrogen bonds are
  weak chemical bonds)

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3. Molecular structure of DNA

• 4. the two strands of DNA run anti-parallel
  i.e., one strand runs in 5-3 direction while
  the other runs in the 3-5 direction The primed
  numbers refer to the C of the sugar. The bases
  are attached to the 1 carbon and the phosphate
  groups are attached at the 5 sugars. Nucleotides
  form covalent bonds between the 3 carbon of one
  and the 5 carbon of the other nucleotide.

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• VIDEO 47 (DNA structure and Replication CC)

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4. DNA replication

• a. complementary base pairing governs how new DNA
  molecules are synthesized using existing DNA as
  templates (fig 10.4)
• 1. A with T
• 2. G with C

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4. DNA replication

• b. DNA synthesis is semiconservative i.e., the
  two strands are separated and each strand is used
  as a separate template.

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4. DNA replication

• c. DNA synthesis occurs along each of the
  separated strands thus resulting in two new
  double-stranded molecules of DNA

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4. DNA replication

• d. New nucleotides are added to a growing strand
  of DNA one at a time, and this energy-requiring
  reaction is catalyzed by an enzyme, DNA polymerase

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4. DNA replication

• e. The new strands are synthesized 5-3 and
  anti-parallel with the template strands (10.5)

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4. DNA replication

• f. The two new strands of DNA are synthesized as
  the leading and lagging strand

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4. DNA replication

• g. process of replication
• 1. the enzyme helicase unwinds the double
  stranded DNA, while single stranded binding
  proteins stabilize the templates

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4. DNA replication

• 2. primase adds RNA primers to the exposed
  templates because DNA polymerase must add new
  nucleotides to a 3 end of an existing nucleotide
  in an already started strand

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5 3
GATACAGCTGTACGTCG
CTATGTCGACATGCAGC
3 5
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4. DNA replication

• 3. DNA polymerase adds one nucleotide at a time
  in the 5 3 direction along the leading strand
  and lagging strand (leading strand is synthesized
  continuously while the lagging strand is
  synthesized in Okazaki fragments)

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4. DNA replication

• 4. Another DNA polymerase replaces the RNA primer
  
• 5. Ligase seals the Okazaki fragments

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Video 48 (DNA, Hot Pockets)
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1. Overview of protein synthesis

• Process DNA to RNA to protein

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1. Overview of protein synthesis

• Specific sequences of DNA in genes code for
  specific sequences of RNA which in turn code for
  specific sequences of amino acids in proteins

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1. Overview of protein synthesis

• compartmentalization
• transcription in nucleus
• translation (protein synthesis) in cytoplasm

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2. Genetic Code

• mRNA is read 3 nucleotides at a time i.e., one
  amino acid coded for by three nucleotides

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2. Genetic Code

• b. each set of three nucleotides is referred to
  as a codon
• c. use genetic code of RNA codons to predict
  amino acid sequence in synthesized peptide

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2. Genetic Code

• c. use genetic code of RNA codons to predict
  amino acid sequence in synthesized peptide

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Using the Chart

• CAU

• The codon CAU codes for His

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3. Transcription

1. Initiation- RNA polymerase binds to promoter
   sequence of DNA, unwinds DNA and starts
   transcription at start site

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3. Transcription
ATG CAT GTC GAT CAC TAA AGT TTA
AUG CAU GUC GAU CAC UAA AGU UUA
ATG CAT GTC GAT CAC TAA AGT TTA
TAC GTA CAG CTA GTG ATT TCA AAT

• b. Elongation RNA polymerase makes new strand
  of RNA in 5 to 3 direction i.e., it adds new
  nucleotides to the 3 end of the growing RNA
  strand, DNA reforms double strand behind
  polymerase

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3. Transcription

• c. Termination RNA polymerase reaches a
  terminator sequence of DNA and polymerase along
  with the newly synthesized mRNA are released

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3. Transcription

• d. Eukaryotic RNA is processed in the nucleus
  before final mRNA is sent to cytoplasm

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3. Transcription

• e. One gene (DNA) is read at a time by RNA
  polymerase in eukaryotes (monocystronic)

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3. Transcription

• f. Multiple genes can be read at a time by RNA
  polymerase in prokaryotes (polycystronic)

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4. Translation

• synthesis of proteins using RNA as a template
• catalyzed by ribosomes in the cytoplasm

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What Translation Looks Like
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4. Translation

• c. involves a variety of other players
• 1. t RNA transfer
• 2. m RNA messenger
• 3. r RNA ribosomal

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5. tRNA

• interpreters between nucleic acid language and
  protein language i.e., translation
• single stranded nucleic acid made via
  transcription just like mRNA

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5. tRNA

• c. 3 end of tRNA binds amino acid
• d. anticodon sequence of tRNA base pairs with
  corresponding codon on mRNA therefore, anitcodon
  codon binding determines which amino acid is
  added to the growing peptide

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6. Ribosome (fig 10.12)

• Catalyze protein synthesis
• two ribosomal subunits large and small

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6. Ribosome

• c. mRNA binding site on small ribosomal subunit
• d. two tRNA binding sites known as P and A on
  large ribosomal subunit

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6. Ribosome (fig 10.12)

• e. an anticodon of a tRNA binds to the ribosome
  when its anticodon base pairs with a mRNA codon
  present in that same binding site

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6. Ribosome (fig 10.12)

• f. P site holds the tRNA attached to growing
  peptide
• g. A sites holds the tRNA attached to the new
  (incoming) amino acid

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What Translation Looks Like
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7. Initiation of translation

• small ribosomal subunit binds mRNA
• a special initiator tRNA with anticodon UAC binds
  to start codon AUG (this tRNA carries amino acid
  methionine)

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7. Initiation of translation

• c. large ribosomal subunit binds with small
  ribosomal subunit placing initiator tRNA in P
  site and leaving A site empty for the next tRNA
  to bind

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8. Elongation of translation (fig 10.14)

• an incoming tRNA/amino acid binds to unoccupied A
  site
• ribosome catalyzes formation of peptide bond
  between new amino acid and growing peptide, and
  the growing peptide is released from the tRNA in
  the P site
• tRNA in A site is translocated to P site, moving
  the mRNA along with it a distance of 3
  nucleotides i.e., one codon
• the mRNA moves along the ribosome one codon at a
  time

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9. Termination of translation

• The A site of the ribosome reaches a stop codon
  (UAA, UAG, or UGA) in the mRNA molecule
• a releasing factor binds to the stop codon
  instead of another tRNA molecule
• Releasing factor catalyzes release of peptide
  from ribosome
• Translation assembly falls apart and can be used
  again

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10. Overview of translation (fir 10.15)

• amino acids ? polypeptide (protein)
• mRNA carries the message of the genetic code
  from the nucleus to the cytoplasm
• tRNA/amino acid complex in cytoplasm
• ribosome brings tRNA/amino acid to mRNA in a
  particular order as dictated by mRNA nucleotide
  sequence
• ribosomes catalyze binding of amino acids into
  polypeptide i.e., formation of peptide bonds

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Mutations

• Mutations are random changes in the DNA sequence.
• Gene mutations are relatively small affecting
  only one or two genes.
• Point mutations are caused by substitutions and
  usually result in the change of one amino acid,
  and causing no change about 30 of the time.
• Frameshift mutations are usually caused by a
  deletion. The affect all of the codons that
  follow the deletion. This will change many of the
  amino acids in the protein molecule.

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Substitution / Point Mutation
AUG CAU GUC GAU CAC UAA AGU UUA
AUG CAU GUC GGU CAC UAA AGU UUA
AUG CAU GUC GAU CAU UAA AGU UUA
AUG CAU GUC GAU CAC GAA AGU UUA
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Deletion / Frameshift
AUG CAU GUC GAU CAC UAA AGU UUA
AUG CAU GUC GAU CAC UAA AGU UUA
AUG CAU GUC GUC ACU AAA GUU UAG
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Protein Synthesis (Copy)
1st Step 2nd step
Name of process Transcription Translation
Location Nucleus Cytoplasm
Enzymes or other substances required DNA, Helicase, RNA Polymerase tRNA, amino acids, Ribosome
What is read (goes in) DNA mRNA
Is Produced mRNA, Replicated DNA Protein, (polypeptides)