Biology Overview

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Biology Overview

• Microarray Database Systems
• 9/18/2002

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Additional Information

• Review papers on microarray
• Genomics, gene expression and DNA arrays (Nature,
  June 2000)
• Microarray - technology review (Natural Cell
  Biology, Aug. 2001)
• Magic of Microarrays (Scientific American, Feb.
  2002)
• Molecular biology tutorial
• http//www.lsic.ucla.edu/ls3/tutorials/

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References

• Class materials are based on
• Introduction to Computational Molecular Biology,
  Setubal and J. Meidanis, PWS Pub. Company, 1997
• Illustrations (http//www.nhgri.nih.gov/DIR/VIP/Le
  arning_Tools/genetic_illustrations.html)
• (http//www.accessexcellence.org/AB/GG/

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Central Dogma of Molecular Biology
replication
transcription
translation
DNA
RNA
Protein
reverse transcription

• understanding the structure and function of
  proteins and nucleic acids

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(No Transcript)
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DNA
replication
transcription
translation
DNA
RNA
Protein
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DNA

• The double helix
• stable
• Nucleotide
• A, T, G, C
• Base pair
• A T
• G C
• Oligonucleotide
• short DNA (tens of nucleotides, or bps)

(http//www.nhgri.nih.gov/)
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DNA (Nucleotide)
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DNA (Detailed)
Nucleotide
5
3
5
Base
3
(http//www.nhgri.nih.gov/)
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DNA Strand

• DNA has canonical orientation
• read from 5 to 3
• antiparallel one strand has direction opposite
  to its complements
• 5 TACTGAA 3
• 3 ATGACTT 5

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RNA
replication
transcription
translation
DNA
RNA
Protein
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RNA

• Types
• messenger RNA
• ribosomal RNA (rRNA)
• transfer RNA (tRNA)

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RNA

• Differences from DNA
• ribose instead of 2-deoxyribose
• U (Uracil) instead of T (Thymine)
• single strand
• may bind to other DNA
• may bind to itself
• various forms
• relatively unstable

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RNA (Detailed)
(http//www.nhgri.nih.gov/)
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Protein
replication
transcription
translation
DNA
RNA
Protein
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Proteins

• Types
• Structural proteins
• tissue building
• Enzymes
• catalysts, enabling otherwise slow biochemical
  reactions
• Others
• specific functions such as oxygen transport,
  antibody defense
• chain of amino acids

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Amino Acids

• Amino acid
• Ca
• hydrogen
• amino group
• carboxy group
• side chain
• what distinguishes amino acids
• 20 common amino acids found in nature

H
Ca
H2N
COOH
R
R CH3 alanine R H glycine
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Common Amino Acids
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Peptide bond
R1
H
Ca
H2N
COOH
Ca
H2N
COOH
H
R2
H
H
R1
H2O
Ca
N
COOH
Ca
C
H2N
O
H
R2
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Proteins as Chains of Amino Acids

• The backbone polypeptide chain
• unidirectional N Ca (CO)
• f and y determine the folding (3-D structure)

H
R1
O
R3
H
Ca
N
C
C
Ca
Ca
N
f
y
O
R2
H
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Primary Structure
(http//www.nhgri.nih.gov/)
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Folding Higher-Order Structure
(http//www.nhgri.nih.gov/)
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DNA Replication
replication
transcription
translation
DNA
RNA
Protein
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DNA Replication

• DNA Helicase
• The enzyme that unwinds the DNA strand.
• DNA Polymerase
• The enzyme that bonds nucleotides to the DNA
  strand during replication.

(http//www.nhgri.nih.gov/)
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Transcription
replication
transcription
translation
DNA
mRNA
Protein
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Gene Structure

• Gene
• A region in a DNA molecule that contains
  information necessary for building a protein or
  an RNA molecule
• Promoter
• a region before a gene that serves as an
  indication to the cellular mechanism that a gene
  is ahead
• Transcription Unit
• the region that is copied into RNA

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Gene Structure
Upstream regulatory region
Downstream regulatory region
Coding sequence
Tc
TL
tL
tc
3
5
Promoter
Transcription unit
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Transcription

• Exon
• the coding region
• Intron
• the skipped region
• Genomic DNA
• the full gene
• Complementary DNA (cDNA)
• exon only
• RNA Polymerase
• the enzyme that unzips DNA and make a
  complimentary RNA strand.

(http//www.nhgri.nih.gov/)
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Message RNA (mRNA)

• the product of transcription
• complement to the template strand
• template strand is read from 3
• similar to the coding strand (T becomes U)

coding strand 5 TGCGCTATC 3 template strand
3 ACGCGATAG 5 mRNA 5 UGCGCUAUC
3
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Altrnative Splicing

• the same genomic DNA can give rise to two or more
  different mRNA molecules by choosing the introns
  and extrons in different ways

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Translation
replication
transcription
translation
DNA
RNA
Protein
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Codon

• a group of three bases (nucleotide triplets) in
  an RNA strand
• each codon stands for a certain amino acid
• except for some codons which code for STOP and do
  not correspond to amino acids

(http//www.nhgri.nih.gov/)
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Translation Protein Synthesis

• mRNA
• leaves the nucleus
• Ribosome
• assembly line for protein synthesis
• contains rRNA
• Transfer RNA (tRNA)
• builds protein chain from mRNA codons
• anti-codon

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Genetic Code
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Genome

• The complete set of DNA contained in an
  organisms cell
• Complexity (in million bps)
• Escherichia coli (backterium) 4.6
• Saccharomyces cerevisiae (yeast) 12.1
• Drosophila melanogaster (fruit fly) 150
• Homo sapiens (man) 3000
• Mus musculus (mouse) 3300

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Gene Expression

• All the processes involved in converting genetic
  information from DNA sequence into proteins.
• all cells contains the same genome, but the set
  of genes expressed are different
• in prokaryotes, no splicing (intron skipping) is
  needed

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Housekeeping Genes

• Genes which encode proteins or RNAs whose
  function is required by all cell types in a
  multicellular organism
• e.g. RNA polymerase, ribosomal protein
• constitutively expressed

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More Terms

• Eukaryotic
• Cell with a nucleus
• Prokaryotic
• Cell without a nucleus
• Open reading frame (ORF)
• A contiguous stretch of a given DNA sequence
  that is
• beginning at the start codon,
• multiple of three
• contains no STOP

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Laboratory Methods Next

• Genome Sequencing
• Human Genome Project
• DNA Cutting
• DNA Cloning
• Polymerase Chain Reaction (PCR)