Jeff Young, Botanist [e-mail] x3638 Office: BI412

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DNA ...the genetic material.

• Deoxyribonucleic Acid
• a double stranded, helical nucleic acid molecule
  capable of replicating and determining the
  inherited structure of a cells proteins.

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Central Dogma(s)
DNA
Genome
RNA
Protein
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Expanded Central Dogma

• Genome... the dynamic complement of heritable
  genetic material,
• Transcriptome... mRNA component in an
  individual,
• complexity increases resulting from transcription
  control and transcription and post-transcription
  modifications,
• Proteome... the protein component of an
  individual,
• complexity increases due to translational
  efficiancy, post-translational modification,
  protein-protein interactions, etc.

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Complexity

• 1021 stars (estimated) in the Universe,
• astronomical,
• If the human genome codes for 100,000 proteins,
  all possible combinations of genes being off or
  on yields 1030,000 discrete states,
• per cell,
• at any one moment over the span of a lifetime.

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Central Dogma genetics focus
DNA
transcription
Replication
RNA
translation
Protein
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Nucleic AcidsDNA/RNA

• polymers consisting of monomers termed
  nucleotides,

A, G, C, T/U

• nucleotides a molecule composed of,
• a pentose sugar,
• a phosphate group,
• and an organic molecule called a nitrogenous
  base.

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Phosphodiester BondsNote 5- 3Orientation
Polynucleotides
Adenine Thymine Guanine Cytosine
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5
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Anti-Parallel

• ...DNA is a double stranded molecule and orients
  in an anti-parallel fashion,

orientation is in reference to the
phosphodiester bonds.
Complementary strands arent identical,
yet????????
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Please study this slide.
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Complementary StrandsTemplates for Copying

• single-stranded DNA can serve as a template for
  high-fidelity duplication,
• makes DNA for growth, repair and hereditary
  purposes (Replication),
• makes RNA for the synthesis of proteins
  (Transcription).

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DNA Replicationmeiosis I
Homologous Chromosomes
Sister Chromatids
A-
a-
B-
b-
One Chromosome
3-TTTCCGACTAGT-5
5-AAAGGCTGATCA-3 3-TTTCCGACTAGT-5
5-AAAGGCTGATCA-3
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DNA Replication

• Template,
• Enzymes,
• Primer (to prime synthesis),
• dNTPs
• d (deoxy), N (A,T,G,or C),
• Energy.

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Enzyme 1

• Helicases enzymes that unwind the DNA double
  helix for DNA replication
• Dna/A, Dna/B, Dna/C,
• - proteins that bind to specific DNA sequences.

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Enzyme 2
Primase

• Primase provides a short, complementary strand
  of RNA that is required for DNA synthesis from a
  naked DNA template.

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DNA polymerase III the enzyme that adds
complementary nucleotides to the backbone, based
on the sequence of the single stranded template.
5 --gt 3 synthesis.
Enzyme 3
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DNA Synthesis test yourself
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Fidelity So FarMitosis

• the initial synthesis produces errors at a rate
  of 1 in 105-8,
• proof-reading during replication 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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Central Dogma genetics focus
DNA
transcription
RNA
translation
Protein
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RNA Structure
single stranded, can form base pairing with
DNA, or RNA, no simple regular secondary
structure.
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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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Gene Expression refers to cellular control of
transcription,

• 5 DNA sequences and associated molecules
• direct when and where a gene is expressed,
• influence the amount of expression,
• strong promoter (high rate of transcription),
• weak promoter (low rate of transcription).

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Structural Region (peptide sequence)

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

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E. coli Promoter Sequencesconsensus sequence
alignment (from a MSA)
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Promoter Regions
DNA sequence changes alter promoter function.
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Transcription Factor Terms

• cis-acting elements
• DNA sequences that serve as attachments sites for
  the DNA-binding proteins that regulate the
  initiation of transcription.

• trans-acting elements
• the DNA-binding proteins that regulate the
  initiation of transcription.

Modulators of expression can act at great
distances.
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Eukaryotic Initiation
Apply the terms from the previous slide to the
appropriate components on this figure.
Please study this slide.
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Structural Regioncoding region

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

Terminator
5
3
transcription unit
RNA polymerase begins transcription here.
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Complementary StrandsTemplates for Copying

• single-stranded DNA can serve as a template for
  high-fidelity duplication,
• makes DNA for growth, repair and hereditary
  purposes (Replication),
• makes RNA for the synthesis of proteins
  (Transcription).

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RNA Synthesis
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Elongation

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

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

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Question what does the coding strand sequence
tell you about the mRNA sequence?
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hnRNA vs. mRNAheterogeneous nuclear vs. messenger

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

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Post Transcriptional Modification Ieukaryotes

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

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Post Transcriptional Modification II eukaryotes

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

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Eukaryotic Intron Excision(sequence is important)
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Spliceosomesconfer sequence specificity

• ... small nuclear RNAs (snRNAs)
• RNA molecules that act as catalysts in
  spliceosomes,
• work in concert with gt 100 proteins to
  facilitate intron identification and removal,
• snRNPs RNA/Protein structures.

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U1 and U2snRNAs

• U1 binds to the 5 exon/intron junction.
• U2 binds to the adenosine region at the branch
  site.

Think about the required specificity for intron
identification in cells.
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Alternate mRNA Procesing
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Polyadenylationlots of adenines.
AAUAA consensus poly-A recognition site.
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Alternate mRNA Processing
20,000 genes --gt 100,000 proteins
recognition of different poly-A sites.
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Complexity

• Calcitonin gene

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GeneticsIn the News
Devil Anse Hatfield
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http//www.ncbi.nlm.nih.gov/entrez/query.fcgi?dbO
MIM
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Translation

• 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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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 by recognizing the appropriate codon in the
  mRNA,
• rRNA (ribosomal RNA) together with proteins,
  it forms the structure of ribosomes that
  coordinate the sequential coupling of tRNA
  molecules from the series of mRNA codons.

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The Ends to the Means

• Specific anti-codons for specific amino acids.
• anti complementary

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Ribosomes

• a supramolecular complex of rRNA and proteins,
  approximately 18 - 22 nm in diameter,
• the site of protein synthesis,

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Central Dogma genetics focus
DNA
transcription
RNA
translation
Protein
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Elongation (3 steps)
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Peptide Linkage
How does N-terminus and C-terminus relate to DNA
5, 3 orientation?
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Peptide Sequence 1o, 2o, 3o, 4o
Structure/Function
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Whats 5, 3, N-terminus, C-terminus?
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How does a base change, change things?if you
understand this, youve got it.
in the promoter region, in an exon, in an
intron, at a splice site, at an AAUAAA site,
etc.
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For Monday

• Reading assignment
• Chapter 2
• Review Chapter 6, and/or your General Biology
  Text for Central Dogma