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Biology Overview. Microarray Database Systems 9/18/2002. 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)

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biology overview

Biology Overview

Microarray Database Systems

9/18/2002

additional information
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/
references
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/Learning_Tools/genetic_illustrations.html)

(http://www.accessexcellence.org/AB/GG/

central dogma of molecular biology
Central Dogma of Molecular Biology

replication

transcription

translation

DNA

RNA

Protein

reverse

transcription

  • understanding the structure and function of proteins and nucleic acids
slide6
DNA

replication

transcription

translation

DNA

RNA

Protein

slide7
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/)

dna detailed
DNA (Detailed)

Nucleotide

5’

3’

5’

Base

3’

(http://www.nhgri.nih.gov/)

dna strand
DNA Strand
  • DNA has canonical orientation
    • read from 5’ to 3’
    • antiparallel: one strand has direction opposite to its complement’s

5’ … TACTGAA … 3’

3’ … ATGACTT … 5’

slide11
RNA

replication

transcription

translation

DNA

RNA

Protein

slide12
RNA
  • Types
    • messenger RNA
    • ribosomal RNA (rRNA)
    • transfer RNA (tRNA)
slide13
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
rna detailed
RNA (Detailed)

(http://www.nhgri.nih.gov/)

protein
Protein

replication

transcription

translation

DNA

RNA

Protein

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

H

H2N

Ca

COOH

R

  • R = CH3 : alanine
  • R = H : glycine
peptide bond
Peptide bond

R1

H

H2N

Ca

COOH

H2N

Ca

COOH

H

R2

H

H

R1

H2O

N

Ca

COOH

H2N

Ca

C

H

O

R2

proteins as chains of amino acids
Proteins as Chains of Amino Acids
  • The backbone: polypeptide chain
    • unidirectional: – N – Ca – (CO) –
    • f and y determine the folding (3-D structure)

R1

H

O

R3

H

N

Ca

C

C

Ca

Ca

N

f

y

O

R2

H

primary structure
Primary Structure

(http://www.nhgri.nih.gov/)

folding higher order structure
Folding: Higher-Order Structure

(http://www.nhgri.nih.gov/)

dna replication
DNA Replication

replication

transcription

translation

DNA

RNA

Protein

dna replication24
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/)

transcription
Transcription

replication

transcription

translation

DNA

mRNA

Protein

gene structure
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

gene structure27
Gene Structure

Upstream regulatory region

Downstream regulatory region

Coding sequence

Tc

TL

tL

tc

3’

5’

Promoter

Transcription unit

transcription28
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/)

message rna mrna
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’

altrnative splicing
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
translation
Translation

replication

transcription

translation

DNA

RNA

Protein

codon
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/)

translation protein synthesis
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
genome
Genome
  • The complete set of DNA contained in an organism’s 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
gene expression
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
housekeeping genes
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
more terms
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
laboratory methods next
Laboratory Methods: Next
  • Genome Sequencing
    • Human Genome Project
  • DNA Cutting
  • DNA Cloning
  • Polymerase Chain Reaction (PCR)
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