a modern introduction to molecular biologychazelle/courses/bib/dnalecture.pdf1 a modern introduction...

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A modern introduction toMolecular biology

Lecture 1, COS/MOL 455/551, Fall 2006

Complexity and scales of organization

~1A0 Time: 10-6 sec. to 109 yrs.

~1 m

2

Diversity of forms

Diversity of forms

3

Prokaryotes Eukaryotes

Universal phylogenetic tree

Woese et al.

Universal phylogenetic tree

Woese et al.

4

Prokaryote vs. Eukaryote

Brown, Genomes

Epistemology

5

Understanding:

• Morphology• Constituents• Chemical transformations• Physiology• Growth• Evolution• Information processing

E. coli

Darnell, Molecular Cell Biology

Understanding:

• Morphology• Constituents• Chemical transformations• Physiology• Growth• Evolution• Information processing

Nucleic Acids

Proteins

Lipids

Salts &Small molecules

Lehninger, Principles of Biochemistry

6

Understanding:

• Morphology• Constituents• Chemical transformations• Physiology• Growth• Evolution• Information processing

Metabolism

Darnell, Molecular Cell Biology

Understanding:

• Morphology• Constituents• Chemical transformations• Physiology• Growth• Evolution• Information processing

Mitochondrion

Darnell, Molecular Cell Biology

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Understanding:

• Morphology• Constituents• Chemical transformations• Physiology• Growth• Evolution• Information processing

Development

Darnell, Molecular Cell Biology

Understanding:

• Morphology• Constituents• Chemical transformations• Physiology• Growth• Evolution• Information processing

Woese et al.

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Understanding:

• Morphology• Constituents• Chemical transformations• Physiology• Growth• Evolution• Information processing

DNA RNA Protein

Lehninger, Principles of Biochemistry

Structure & dynamics of networks

Protein-protein interactions

Genetic interactionsRegulatory interactions

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Lehninger, Principles of Biochemistry

DNA RNA Protein

Information flow:Central Dogma

Genome:

The entire hereditaryinformation contentof an organism

10

Context (DNA)

Lehninger, Principles of Biochemistry

Darnell, Molecular Cell Biology

11

Chromatin fiber (30 nm)

DNA

Nucleosomes

Histones

Chromosome

Lehninger, Principles of Biochemistry

3.4 nm

Minor groove Major groove

The Double Helix

Brown, Genomes

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DNA backbone

Sugar

Phosphate

Base

Brown, Genomes

BASES

A

C

G

T

Brown, Genomes

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Darnell, Molecular Cell Biology

RNA

Lehninger, Principles of Biochemistry

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Proteins

Amino acids

H3N—C—H

COO

R

+

Lehninger, Principles of Biochemistry

15

Peptide bond

Polypeptide

Stryer, Biochemistry

Primary TertiarySecondary Quaternary

Amino acids α−helix Polypeptidechain

Assembledsubunits

Protein representations

Lehninger, Principles of Biochemistry

16

DNA RNA Protein

Central Dogma

Lehninger, Principles of Biochemistry

DNA RNA

ACTG

ACUG

Transcription

CODE:

Lehninger, Principles of Biochemistry

17

Promoter Coding region

Bacterial chromosome (5 x 106 bp)

Promoter

RNA Polymerase

Coding region

Bacterial chromosome (5 x 106 bp)

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Promoter

RNA Polymerase

Coding region

Bacterial chromosome (5 x 106 bp)

Promoter

RNA Polymerase

mRNA

Coding region

ACTG

ACUG

Bacterial chromosome (5 x 106 bp)

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Promoter

RNA Polymerase

mRNA

Coding region

ACTG

ACUG

Bacterial chromosome (5 x 106 bp)

RNA Protein

Translation

CODE:ACUG

A C D EF G H IK L M NP Q R ST V W Y

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AUG = methionine/startUUA = LeucineUUG = Leucine

UAA = StopUAG = StopUGA = Stop...

The Genetic Code

Stryer, Biochemistry

GATCTGGAATATACGTACCCATTGAGTACATACGCACTGCTAGACCTTATATGCATGGGTAACTCATGTATGCGTGAC5’ 3’

GACCUUAUAUGCAUGGGUAACUCAUGUAUGCGUGAC5’

Peptide1: Met—Gly—Asn—Ser—Cys—Met—Arg…..

Peptide2: Met—His—Gly—STOP

The importance ofreading frame (register)

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Brown, Genomes

Initiation of translation

Watson, Recombinant DNA

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mRNA

Promoter

RNA Polymerase

Coding region

polypeptide

Ribosome

Coupled transcription/translation (bacteria)

Translation in Proks. vs. Euks.

Watson, Recombinant DNA

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α−Tropomyosin mRNA splicing

Watson, Recombinant DNA

DNA RNA Protein

Interactions

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DNA RNA Protein

Interactions

DNA RNA

Protein

Prokaryote

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DNA RNA

Protein

Eukaryote

DNA RNA

Protein

Eukaryote

Stimulus

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DNA RNA

Protein

Eukaryote

Stimulus

DNA RNA

Protein

Eukaryote

Stimulus

Stim

ulus

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DNA RNA

Protein

StimulusSt

imul

us

Intracellular networks

DNA RNA

Protein

fn

DNA RNA

Protein

fn

DNA RNA

Protein

fn

DNA RNA

Protein

fn

DNA RNA

Protein

fn

DNA RNA

Protein

fn

Network of cells

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DNA RNA

Protein

Stimulus

Stim

ulus

DNA RNA

Protein

fn

DNA RNA

Protein

fn

DNA RNA

Protein

fn

DNA RNA

Protein

fn

DNA RNA

Protein

fn

DNA RNA

Protein

fn

Higher-level organization

Cells Network of cells Organism

DNA RNA

Protein

fn

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DNA RNA

Protein

fn

DNA RNA

Protein

fn

30

DNA RNA

Protein

fn

DNA RNA

Protein

fn

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DNA RNA

Protein

fn

fn

Scale of observations

~1011 sequence comparisons~107 observations

~108 possible interactions

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Technology Analysis

K-means clusteringIteration 1

Iteration 2

0) Randomly seed vectors1) Assign closest points to

each vector.2) Calculate new centers

for each vector.3) Iterate back to (2) until

vectors converge.

0 5 10 15 20 25 30 350

0.05

0.1

0.15

0.2

0.25

K = 20

P = 10-11

Eisen et al. Davidson et al.

Boone et al. O’dell et al.

Models