Download Chapter 1: Bio Primer - Columbia CS

Chapter 1: Bio Primer
1.1 Cell Structure; DNA; RNA; transcription; translation; proteins
Prof. Yechiam Yemini (YY)
Computer Science Department
Columbia University
COMS 4761 --2007
Overview



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Cell structure and mechanisms
DNA; RNA; Transcription; Regulation
Translation; protein; sequence & structure
References:
 B. Alberts et al, “Molecular Biology of The Cell”, 4th edition, Garland
Science.
 R. Horton et al, “Principles of Biochemistry”, 3rd Edition, Prentice
Hall.
 J.D. Watson et al, “Molecular Biology of The Gene”, 5th edition,
Pearson Benjamin Cummings.
 NCBI Introductory overview:
http://www.ncbi.nih.gov/About/primer/index.html
 Animation sites:
o http://www.johnkyrk.com/
o http://vcell.ndsu.nodak.edu/~christjo/vcell/animationSite
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Organisms Are Made of Cells
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Prokaryotes & Eukaryotes Have Different Cells
 Prokaryotes: single cell organisms without nucleus
E.g., Bacteria: E-coli, H-Pylori
 Eukaryotes: single/multi-cell organisms with nucleus
E.g., Yeast, plants, drosophila, humans
Earth formed -4.5B yrs
Prokaryotic
bacteria
-3.5B yrs
-1.5B yrs
Nucleated
cells
Multi-cellular -0.5B yrs
eukaryotes
© Pearson; Benjamin
COMS
Cummings
4761 --2007
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Prokaryotes
Single cell; size 0.2-2µm
Eukaryotes
Single or multi cell; cell size 10-100µm
No nucleus
Nucleus
Structure
One membrane at cell boundary Multiple membranes/compartments
DNA
No organelles
No cytoskeleton
Organelles: mitochondria, Golgi, chloroplasts
Cytoskeleton
Single circular DNA
Two or more chromosomes
Genes code proteins
Genes have large non-coding regions (introns)
90% of DNA encodes proteins 95-97% non-coding DNA
Proteins
~105-6 base pairs
~107-9 base pairs
DNA is loosely organized
DNA is tightly packed (chromatin + histones)
Cell division through fission
1-2k protein species
Mitosis
5-20k protein species
~106 proteins per cell
~109 proteins per cell
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Cells Are Made of Macromolecules
Small molecules: 3%
Macromolecules: 26%
Sugars
Polysaccharides
Fatty Acids
Fats, Lipids, Membranes
Amino Acids
Proteins
Nucleotides
Nucleic Acids (DNA, RNA)
Molecules
% weight
Water
Inorganic ions
Sugars
Amino acids
Nucleotides
Fatty acids
Other small molecules
Macromolecules (proteins, DNA, RNA, polysaccharides)
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70%
1%
1%
0.4%
0.4%
1%
0.2%
26%
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DNA Structure
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The Central Dogma of Biology
DNA
Transcription
RNA
Translation
Protein
 DNA stores hereditary information
 DNA is transcribed into RNA
 RNA is translated into proteins
 Proteins perform the key functions of cells
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DNA Consists of Sequences of Nucleotides
 DNA strands are sequences of nucleotides
Backbone
T
+
T
Sugar Phosphate Base
Nucleotide
A
C
T
T
A
C
G
C
 Bases: Adenine, Guanine, Thymine, Cytosine
 DNA is organized in complementary double strands
 Hydrogen bonds hybridize complementary pairs: AT, CG
5’-end
Hydrogen bonds
3’-end
T
A
G
C
A
T
T
A
T
A
G
C
C
G
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G
C
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DNA Forms A Double Helix
Helix full turn: 10.5bp
Vertical hydrogen bonds
support the structure
Major and minor grooves
provide access by proteins
(e.g., transcription factors)
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DNA Is Tightly Packed
 DNA is 2m long; needs to fold
into 10-6m nucleus
 Chromatin beads fold around
4 histones
 Transcription needs to unpack
the DNA to copy it
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Sample Bioinformatics Challenges
Sequencing the genome
Discovering sequence similarity
Discovering genes
Analyzing evolutionary relationships
Discovering other important structures
Distinguishing exons from introns
Regulatory structures: (promoters & transcription factors)
Regions expressing micro RNA
….
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Transcription
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Schematics
DNA
Transcription
mRNA
Translation
Protein
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Overview
A. Assembling transcription complex
B. Transcribing DNA to mRNA
C. Removing introns
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Animation
The Transcription Process
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Transcription Details
http://cwx.prenhall.com/horton/medialib/
From PDB
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Transcription Factors
 TFs bind to promoters regions
and to RNA polymerases
 TFs regulate the rate of
transcription (up/down)
 Regulation is yet to be well
understood
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Transcription Is Regulated
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http://cwx.prenhall.com/horton/medialib/
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Example The Lac Operon
Lac consists of 3 genes; commonly transcribed
Used by bacteria to transport and metabolize lactose
cAMP activates
transcription to
initiate transport
& metabolism of
lactose
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Lac Activation
Low-level sugar  generate cAMP
 cAMP  binds with CRP; adjusts its alpha helix to fit the
DNA grooves and binds with it
CRP-cAMP  accelerates polymerase binding
Lac
Lac
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http://cwx.prenhall.com/horton/medialib/
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Splicing The Introns
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http://cwx.prenhall.com/horton/medialib/
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From Genes To
Networks
Regulation is organized in
networks
Top: gene network
regulating the body
development of sea urchin
Middle: a promoter region
Bottom: interaction of two
modules
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Regulatory Networks Can Be Complex
Genetic regulatory network controlling the development of the body plan of the sea urchin embryo
Davidson et al., Science, 295(5560):1669-1678.
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Sample Bioinformatics Challenges
 Discovering and analyzing transcription factors
Evolutionary analysis; motifs finding
Discovering the structure of regulatory networks
Analyzing the operations of regulatory networks
Designing synthetic regulatory networks
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Translation
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RNA Encodes Protein Sequences
DNA
Transcription
RNA
Translation
Protein
 Proteins are sequences of amino-acids (AA)
 Translation uses RNA sequence as a template to construct AA sequence
 The coding problem:
 Code sequence of 20 amino-acids using 4 nucleic acids
 2 nucleic acids can code only 42=16 amino-acids
 Codon: sequence of 3 nucleic acids; encodes amino acid
 Translation: translate mRNA codons to amino acids
 Start/Stop codons define an open reading frame(ORF)
 Translation requires reading/identifying codons and forming a respective protein
sequence
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The Genetic Code
U
U
C
A
A
G
UUU Phenylalanine
UUC Phe
UUA Leucine
UUG Leu
UCU Serine
UCC Ser
UCA Ser
UCG Ser
UAU Tyrosine
UAC Ty
CUU Leu
CUC Leu
CUA Leu
CUG Leu
CCU Proline
CCC Pro
CCA Pro
CCG Pro
CAU Histidine
CAC His
CAA Glutamine
CAG Gln
CGU Arginine
CGC Arg
CGA Arg
CGG Arg
AAU Asparagine
AAC Asn
AAA Lysine
AAG Lys
AGU Serine
AGC Ser
AGA Arg
AGG Arg
GAU Aspartate
GAC Asp
GAA Glutamate
GAG Glu
GGU Glycine
GGC Gly
GGA Gly
GGG Gly
AUU Isoleucine
AUC Ile
AUA Ile
AUG
G
C
ACU Threonine
ACC Thr
ACA Thr
Methionine ACG Thr
GUU Valine
GUC Val
GUA Val
GUG Val
GCU Alanine
GCC Ala
GCA Ala
GCG Ala
UAA Stop
UAG Stop
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UGU Cysteine
UGC Cys
UGA Stop
UGG Tryptophan
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tRNA Provides Translation Units
 Anticodon 3’ CGA 5’ binds to
codon
5’ GCU 3’ of mRNA
 It translates GCU to Alanine
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http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.html
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Translation Basics
 Initiation:
 Ribosome binds to mRNA; moves
in 5’3’ until it finds Start codon
AUG
 Elongation
 Ribosome recruits tRNA to match
next codon
 tRNA binds its AA into peptide
bond with protein
 Ribosome releases tRNA and
moves to next codob
 Termination
 Until a Stop codon is reached
 Release factor releases
polypeptide from ribosome
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http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.html
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Animation
Translation of RNA into proteins
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Proteins Are Sequences of Amino Acids
 Proteins are constructed through peptide bonds
 Proteins are folded into complex conformations
 Proteins perform functions by binding
Transcription factors and polymerase bind to DNA
Enzymes bind to molecules to accelerate their reactions
Globins bind to oxygen to transport it
Antibodies bind to pathogens
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Example: Hemoglobin
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Sickle-Cell Anemia: A Single Nucleotide Change
Codon 6 in β-globin
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Sickle structure
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Evolution of β-Globin
(α-globin cluster is coded
by chromosome 16 )
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The Evolution of α-Globin Across Species
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Protein Structures
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Protein Structure Is Of Central Importance
 Structure is found through complex crystallography
 X-ray diffraction; NMR
 The holy-grail: compute structure from sequence
 Ab-initio: compute structure directly from sequence
 Homology techniques: use similarity to known proteins
 Structure is conserved across wide variations
 Small number of fold families (α-helix, β-sheets…)
 There are rules (e.g., hydrophobic AA are packed inside)
 Nature folds proteins very fast
 So why is it so difficult to predict structure?
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SwissProt vs. PDB Statistics
PDB ~30k structures
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Proteins Interact Via Active Sites
 Protein interactions are defined by active sites
E.g., antibody with pathogen
E.g., drug design
 Proteins use geometry: ligands latch with holes
 Proteins use physics: electrical fields
 How can protein-protein interactions be computed?
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Sample Bioinformatics Challenges
Analyzing protein sequence similarity
Evolutionary conservation/changes
Computing structure from sequences
Analyzing structure homologies
Analyzing protein-2-protein interactions
Inferring function from structure
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The Cell Cycle
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Cells Operate In Cycles
 G0 Phase
 cell is at rest
 G1 Phase (4hrs)
 Cell either progresses into synthesis or
 leaves cell cycle to differentiate
 S Phase (10hrs)
 DNA Synthesis
 Checkpoint determines integrity of DNA
 G2 Phase (4hrs)
 Cell prepares for Mitosis
 Checkpoint determines integrity of DNA
 DNA is repaired or cell dies (Apoptosis)
 Mitosis (2hrs)
 Chromosomes are separated
 Cell divides
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The Cell Cycle is Regulated
 Transition among
phases is controlled by
a regulatory network
 Checkpoints are used
to assure quality
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Evolution
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Optimizing Functionality
 DNA is substantially conserved through evolution
 Evolution = mutation + selection
Mutation = single nucleotide polymorphism (SNP);
duplication of entire DNA segments
mating; recombination
Selection = optimize fitness of species
 Examples
Metabolic nets learn to optimize energy budget (Alon 05)
 Functional similarity Sequence similarity
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