Population Genetics

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Review Proteins and their function in the early
stages of replication
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3
2
1
1 initiator proteins 2 single strand binding
proteins 3 helicase 4 topoisomerase (gyrase)
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Replication

• Two DNA polymerase enzymes are necessary for
  replication in E. coli
• DNA polymerase I
• DNA polymerase III

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• - Along each template DNA strand, leading and
  lagging strands can be observed.
• - The names were suggested based on synthesis at
  any given region.
• At any particular point in the DNA strand, if
  there is a leading
• strand, the complementary strand will have
  lagging strand.

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Replication

• Two DNA polymerase enzymes are necessary for
  replication in E. coli
• DNA polymerase I
• DNA polymerase III
• Both have polymerase and exonuclease activities
  (functions)
• First let us take a look at the polymerase
  activity aspect of DNA polymerases and then
  discuss exonuclease activities

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Replication

• DNA Polymerase III
• Synthesize new DNA in the 5 ? 3 direction
• Synthesizes long sequences of new DNA
• Is highly processive synthesizes DNA for a long
  period of time without releasing the template
• For example, synthesizes leading strand
• DNA Polymerase I
• Synthesize new DNA in the 5 ? 3 direction
• Only synthesizes short sequences of new DNA
• But before it could do this, it needs to remove
  RNA primers
• This is achieved by its 5 ? 3 exonuclease
  activity

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5? 3 exonuclease activity of DNA polymerase I
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Replication

• The phosphodiester backbone of adjacent DNA
  fragments must be joined after DNA synthesis by
  DNA polymerases I and III
• This is done by the enzyme DNA ligase

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Both DNA polymerases have proof
reading activity This is a 3 ? 5 exonuclease
activity
DNA Polymerase activity
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Replication

• DNA Polymerase I
• Synthesize new DNA in the 5 ? 3 direction
• Only synthesizes short sequences of new DNA
• 3 ? 5 exonuclease activity (proofreading)
• 5 ? 3 exonuclease activity (remove primers)
• DNA Polymerase III
• Synthesize new DNA in the 5 ? 3 direction
• Synthesizes long sequences of new DNA
• 3 ? 5 exonuclease activity (proofreading)

NOTE DNA polymerase III does not have the 5 ?
3 exonuclease activity
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• This week we will complete
• Chapter 13 (transcription)
• Pages 348 361
• Chapter 15 (translation)
• Pages 409 - 421

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The Central Dogma(Francis Crick, 1958)
(Transcription)
(Translation) DNA ? RNA ?
Protein (Gene/Genotype)
(Phenotype) An informational process between the
genetic material (genotype) and the protein
(phenotype)
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Properties of RNA
RNA has the sugar ribose rather than deoxyribose
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Properties of RNA Nucleotides carry the bases
adenine, guanine and cytosine (like DNA)
But uracil is found in place of thymine
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Structure of RNA

• Designate the Nucleotides
• Purines
• Guanine G
• Adenine A
• Pyrimidines
• Uracil U
• Cytosine C

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• Structure of RNA
• Nucleotides join together, forming a
  polynucleotide chain, by phosphodiester bonds

A phosphodiester bond
A phosphodiester bond
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Usually single-stranded
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Can have a much greater variety of complex three
dimensional shapes than double-stranded DNA
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Classes of RNA for Transcription and Translation

• Informational RNA (intermediate in the process of
  decoding genes into polypeptides)
• Messenger RNA (mRNA)
• Functional RNAs (never translated into proteins,
  serve other roles)
• Transfer RNAs (tRNA)
• Transport amino acids to mRNA and new protein
• Ribosomal RNAs (rRNA)
• Combine with an array of proteins to form
  ribosomes platform for protein synthesis
• Small nuclear RNAs (snRNA)
• Take part in the splicing of primary transcripts
  in eukaryotes
• Small cytoplasmic RNAs (scRNA)
• Direct protein traffic in eukaryotic cells
• Micro RNAs (miRNA)
• Inhibits translation and induces degradation of
  complementary mRNA

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RNA nucleotide sequences are complementary to DNA
molecules
New RNA is synthesized 5 to 3 and antiparallel
to the template
DNA template
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DNA template Complementary
RNA Adenine Uracil Guanine
Cytosine Cytosine Guanine Thymine
Adenine
Synthesized 5 to 3 and antiparallel to the
template
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Only one strand of the DNA acts as a template for
transcription
The template strand can be different for
different genes But. For each gene only one
strand of DNA serve as a template
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Transcription Catalyzed by the enzyme RNA
polymerase
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Single RNA polymerase (Prokaryotes) Core enzyme
Holoenzyme 2 ?,1 ? and 1 ? subunits 2 ?, 1
?, 1 ? subunits plus s subunit Polymerizes
RNA Finds initiation sites
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Initiation The region that signals the
initiation of transcription is a promoter
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- 35 bases from initiation of transcription Recogn
ized by RNA polymerase
- 10 bases from initiation of transcription Unwind
ing of DNA double helix begins here
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Elongation RNA is polymerized in 5 ? 3
direction
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Elongation NTPS (ATP, GTP, CTP, UTP) are added
The energy is derived by splitting the
high-energy triphosphate bond
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Termination RNA polymerase recognizes signals
(sequence) for chain termination
Releases the RNA and enzyme from the template
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Animation on Transcription
http//highered.mcgraw-hill.com/sites/0072556781/s
tudent_view0/chapter12/animation_quiz_1.html