Jeff Young, Plant Geneticist youngbiol.wwu.edu x3638 Office: BI412

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Jeff Young, Plant Geneticistyoung_at_biol.wwu.edux3
638Office BI412
Office Hours MTW 300 - 400 PM by
appointment.
Arabidopsis thaliana Genome-based, molecular
study of plant physiology and environmental
responses.
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Schedule

• Today
• DNA replication, error control,
• DNA transcription, begin translation
• Monday
• finish translation.

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DNA Template

• single-stranded DNA serves as a template for
  high-fidelity duplication,
• makes DNA for growth, repair and hereditary
  purposes,
• makes RNA for the synthesis of proteins.

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Replication

• the synthesis of DNA from a DNA template.

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Fidelity

• the initial synthesis produces errors at a rate
  of 1 in 105-8,
• proof-reading during synthesis improves the
  error rate to 1 in 108-12,
• this occurs at a rate of up to 1000 bp a second.

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DNA Template

• single-stranded DNA serves as a template for
  high-fidelity duplication,
• makes DNA for growth, repair and hereditary
  purposes,
• makes RNA for the synthesis of proteins.

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DNA to Protein
RNA molecules are the intermediaries.
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Molecular Dogma

• Each 3 base pairs of DNA codes for a specific
  amino acid.

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Transcription

• the synthesis of RNA from a DNA template.

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RNA

• Ribonucleic Acid type of nucleic acid
  consisting of monomers with a phosphorylated
  ribose sugar and the nitrogenous bases,
• adenine (A),
• cytosine (C),
• guanine (G),
• Uracil (U) instead of Thymine (T).

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Deoxyribose vs. Ribose

• pentose sugars.

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RNA Instability

• RNA provides short term information storage.

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A-T in DNA, A-U in RNA

• ... Uracil (U) replaces Thymine (T) in RNA
  synthesis.

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RNA

• single stranded,
• can form base pairing with DNA, or RNA,
• no simple regular secondary structure.

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RNA Secondary Structure

• like proteins, the specific sequence of
  nucleotides define different secondary
  structures, some of which contribute to function.

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mRNA, tRNA and rRNA

• mRNA (messenger RNA) a type of RNA synthesized
  from DNA that specifies the primary structure for
  a protein,
• tRNA (transfer RNA) an RNA molecule that acts
  as an interpreter between nucleic language and
  protein language by picking up specific amino
  acids and recognizing the appropriate codons in
  the mRNA,
• rRNA (ribosomal RNA) together with proteins,
  it forms the structure of ribosomes that
  coordinate the sequential coupling of tRNA
  molecules to the series of mRNA codons.

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Central Dogma Exception

• ...RNA viruses use RNA as the genetic material.

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Retrovirus

• RNA virus code for an enzyme (reverse
  transcriptase) that transcribes DNA from an RNA
  template,
• the retrovirus creates (transcribes) a
  complementary DNA strand from its RNA sequence,
• the complimentary DNA strand becomes incorporated
  into the host cells chromosome,
• host mediated replication and subsequent
  transcription complete the viral life cycle.

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Units of Heredity
chromosome
...ata cgt act atc... ...tat
gca tga tag...
codons
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General Gene Structure
Terminator
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Promoter Region
Structural Region
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Promoter

• a non-transcribed region a short distance from
  5end of a gene that acts to regulate
  transcription,
• RNA polymerase is weakly attracted to DNA in
  general, but is strongly attracted to promoter
  sequences and associated molecules.

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Expression

• expression refers to cellular control of
  transcription, promoters have a strong influence
  on expression,
• ...promoters differ in sequence and in function,
• promoters contain temporal and spatial elements
  also, directing when and where a gene is
  expressed,
• genes may be expressed at a high rate by a strong
  promoter, or low rate by a weak promoter.

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Promoters

• promoters contain DNA sequences that influence
  expression directly, or indirectly,
• - directly RNA polymerase binds differentially
  to specific promoter sequences,
• indirectly proteins (transcription factors,
  enhancers, supressors, etc.)

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Initiation Complex

• ...Transcription Factors
• proteins,
• from expressed genes,
• themselves under transcriptional control.

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Transcription

• ...the synthesis of mRNA from a DNA template.

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mRNA Synthesis

• Template (DNA) and Promoter,
• Nucleoside triphosphates (NTPs),
• N A,U,G,or C,
• Enzymes (RNA polymerases),
• Energy (as in replication, from phosphate bonds).

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Structural Region

• the portion of a gene that specifically codes
  for a protein.

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3
transcription unit
RNA polymerase begins transcription here.
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Terminator

• a sequence of nucleotides (AAUAAA in the
  transcribed molecule) that specifies the end of
  the transcription unit.

Terminator
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3
transcription unit
RNA polymerase begins transcription here.
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RNA Synthesis
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Elongation

• Nucleotides are added to the 3 end of the
  elongating RNA.

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Elongation and Error Rate

• proofreading does not accompany RNA synthesis,
  errors occur at about 1 in 104-5 bp,
• why is so much energy spent on DNA proofreading
  and repair and none on transcription fidelity?

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mRNA vs. pre-mRNA

• prokaryotic mRNA synthesis described so far,
  requires little, or no further modification prior
  to translation into proteins,
• eukaryotic mRNA requires extensive modifications.

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Post Transcriptional Modification I

• Occurs in the nucleus.
• Increases stability, may help transport and
  sorting.

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Post Transcriptional Modification II

• Introns affect expression.
• Differential splicing can alter the final
  proteins function.
• Provides functional cassettes, for evolutionary
  mixing and matching.

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small nuclear Riboproteins(snRNPs)

• Introns are spliced out at structure called
  sliceosomes,
• mRNA remains relatively stable, introns are
  digested rapidly.

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Genetic Code

• RNA is an intermediary in the transfer of
  information from DNA to the synthesis of protein,
• how is that information organized?

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Information Capacity

• need code for 20 Amino Acids,
• two base-pair code,
• 16 different combinations of 4 bases (42),
• aa, at, ac, ag, tt, tc, tg, cc, cg, gg, ta, ca,
  ga, ct, gt, gc,
• three base-pair code,
• 64 combinations of 4 bases (43).

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Codons

• a triplet of nucleotide bases that specifies or
  encodes the information for a specific amino
  acid,
• also need codons to indicate the beginning and
  end of the protein to be synthesized.

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Start/Stop Codons

• AUG codes for the start of translation, also a
  methionine,
• most proteins thus begin with the amino acid
  methionine,
• UAA, UAG and UGA are stop codons, indicating the
  C terminus of the protein.

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Code is Degenerate

• 20 amino acid codons
• start and stop codons
• 20-some required
• 64 possible
• All combinations are used.

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Translation

• the synthesis of a polypeptide. This occurs on
  ribosomes using the information encoded on mRNA,
• tRNA molecules mediate the transfer of
  information between mRNA and the growing
  polypeptide.

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tRNA
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