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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 l.jpg

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/Learning_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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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 (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 complement’s

      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

H2N

Ca

COOH

R

  • R = CH3 : alanine

  • R = H : glycine



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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


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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)

R1

H

O

R3

H

N

Ca

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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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


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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)


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