Transcript Introductory Biology Primer - A computational tour of the human

A Zero-Knowledge Based Introduction to Biology
Cory McLean
26 Sep 2008
Thanks to George Asimenos
Cells: Building Blocks of Life
cell, nucleus, cytoplasm, mitochondrion
© 1997-2005 Coriell Institute for Medical Research
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DNA: “Blueprints” for a cell
• Genetic information encoded in long strings of
double-stranded DNA
• DeoxyriboNucleic Acid comes in only four
flavors: Adenine, Cytosine, Guanine, Thymine
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Nucleotide
deoxyribose, nucleotide, base, A, C, G, T, purine, pyrimidine, 3’, 5’
purines
to previous nucleotide
O
O
P
O-
H
O
Thymine (T) Cytosine (C)
C
H
C
H
C
3’
to base
O
C
H
Adenine (A) Guanine (G)
5’
H
C
H
pyrimidines
H
to next nucleotide
Let’s write “AGACC”!
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“AGACC” (backbone)
5
“AGACC” (DNA)
deoxyribonucleic acid (DNA)
3’
5’
3’
5’
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DNA is double stranded
strand, reverse complement
5’
3’
3’
5’
DNA is always written 5’ to 3’
AGACC or GGTCT
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DNA Packaging
histone, nucleosome, chromatin, chromosome, centromere, telomere
telomere
centromere
nucleosome
DNA
chromatin
H1
~146bp
H2A, H2B, H3, H4
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The Genome
The genome is the full set of hereditary
information for an organism
 Humans bundle two copies of the genome into
46 chromosomes in every cell
 = 2 * (1-22 + X/Y)

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Building an Organism
DNA
cell
Every cell has the same sequence of DNA
Subsets of the DNA sequence
determine the identity and
function of different cells
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From DNA To Organism
?
Proteins do most of the work in biology, and
are encoded by subsequences of DNA, known
as genes.
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RNA
ribose, ribonucleotide, U
purines
to previous ribonucleotide
O
O
P
O-
H
O
Uracil (U)
C
H
Cytosine (C)
C
H
C
3’
to base
O
C
H
Adenine (A) Guanine (G)
5’
H
C
OH
to next ribonucleotide
H
pyrimidines
TU
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Genes & Proteins
gene, transcription, translation, protein
Double-stranded DNA
5’
3’
TAGGATCGACTATATGGGATTACAAAGCATTTAGGGA...TCACCCTCTCTAGACTAGCATCTATATAAAACAGAA
ATCCTAGCTGATATACCCTAATGTTTCGTAAATCCCT...AGTGGGAGAGATCTGATCGTAGATATATTTTGTCTT
3’
5’
(transcription)
Single-stranded RNA
AUGGGAUUACAAAGCAUUUAGGGA...UCACCCUCUCUAGACUAGCAUCUAUAUAA
(translation)
protein
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Gene Transcription
promoter
5’
3’
G A T T A C A . . .
C T A A T G T . . .
3’
5’
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Gene Transcription
transcription factor, binding site, RNA polymerase
5’
3’
G A T T A C A . . .
C T A A T G T . . .
3’
5’
Transcription factors: a type of protein that
binds to DNA and helps initiate gene
transcription.
Transcription factor binding sites: Short
sequences of DNA (6-20 bp) recognized and
bound by TFs.
RNA polymerase binds a complex of TFs in
the promoter.
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Gene Transcription
5’
3’
3’
5’
The two strands are separated
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Gene Transcription
5’
3’
3’
5’
An RNA copy of the 5’→3’ sequence is
created from the 3’→5’ template
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Gene Transcription
5’
3’
pre-mRNA 5’
G A T T A C A . . .
3’
5’
C T A A T G T . . .
G A U U A C A . . .
3’
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RNA Processing
5’ cap, polyadenylation, exon, intron, splicing, UTR, mRNA
5’ cap
exon
poly(A) tail
intron
mRNA
5’ UTR
3’ UTR
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Gene Structure
introns
5’
3’
promoter
5’ UTR
exons
3’ UTR
coding
non-coding
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How many?
(Human Genome)
• Exons per gene:
~ 8 on average (max: 148)
• Nucleotides per exon:
170 on average (max: 12k)
• Nucleotides per intron:
5,500 on average (max: 500k)
• Nucleotides per gene:
45k on average (max: 2,2M)
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From RNA to Protein
• Proteins are long strings of amino acids joined
by peptide bonds
• Translation from RNA sequence to amino acid
sequence performed by ribosomes
• 20 amino acids  3 RNA letters required to
specify a single amino acid
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Amino acid
amino acid
H
N
H
O
C
C
H
R
OH
Alanine
Arginine
Asparagine
Aspartate
Cysteine
Glutamate
Glutamine
Glycine
Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Proline
Serine
Threonine
Tryptophan
Tyrosine
Valine
There are 20 standard amino acids
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Proteins
N-terminus, C-terminus
to previous aa
N
H
O
C
C
to next aa
H
R
H
N-terminus
(start)
from 5’
OH
C-terminus
(end)
3’ mRNA
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Translation
ribosome, codon
P site
A site
mRNA
The ribosome (a complex of protein and
RNA) synthesizes a protein by reading the
mRNA in triplets (codons). Each codon is
translated to an amino acid.
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Translation
A site
P site
mRNA
U
C
A
G
U
C
A
G
UUU Phenylalanine (Phe)
UCU Serine (Ser)
UAU Tyrosine (Tyr)
UGU Cysteine (Cys)
U
UUC Phe
UCC Ser
UAC Tyr
UGC Cys
C
UUA Leucine (Leu)
UCA Ser
UAA STOP
UGA STOP
A
UUG Leu
UCG Ser
UAG STOP
UGG Tryptophan (Trp)
G
CUU Leucine (Leu)
CCU Proline (Pro)
CAU Histidine (His)
CGU Arginine (Arg)
U
CUC Leu
CCC Pro
CAC His
CGC Arg
C
CUA Leu
CCA Pro
CAA Glutamine (Gln)
CGA Arg
A
CUG Leu
CCG Pro
CAG Gln
CGG Arg
G
AUU Isoleucine (Ile)
ACU Threonine (Thr)
AAU Asparagine (Asn)
AGU Serine (Ser)
U
AUC Ile
ACC Thr
AAC Asn
AGC Ser
C
AUA Ile
ACA Thr
AAA Lysine (Lys)
AGA Arginine (Arg)
A
AUG Methionine (Met) or START
ACG Thr
AAG Lys
AGG Arg
G
GUU Valine (Val)
GCU Alanine (Ala)
GAU Aspartic acid (Asp)
GGU Glycine (Gly)
U
GUC Val
GCC Ala
GAC Asp
GGC Gly
C
GUA Val
GCA Ala
GAA Glutamic acid (Glu)
GGA Gly
A
GUG Val
GCG Ala
GAG Glu
GGG Gly
G
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Translation
5’
...AUUAUGGCCUGGACUUGA...
UTR
Met
Start
Codon
Ala
Trp
3’
Thr
Stop
Codon
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Translation
5’
...AUUAUGGCCUGGACUUGA...
3’
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Translation
Met
5’
Trp
Ala
...AUUAUGGCCUGGACUUGA...
3’
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Errors?
mutation
• What if the transcription / translation machinery makes
mistakes?
• What is the effect of mutations in coding regions?
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Reading Frames
reading frame
G C U U G U U U A C G A A U U A G
G C U U G U U U A C G A A U U A G
G C U U G U U U A C G A A U U A G
G C U U G U U U A C G A A U U A G
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Synonymous Mutation
synonymous (silent) mutation, fourfold site
G
G C U U G U U U A C G A A U U A G
G C U U G U U U A C G A A U U A G
Ala
Cys
Leu
Arg
Ile
G C U U G U U U G C G A A U U A G
Ala
Cys
Leu
Arg
Ile
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Missense Mutation
missense mutation
G
G C U U G U U U A C G A A U U A G
G C U U G U U U A C G A A U U A G
Ala
Cys
Leu
Arg
Ile
G C U U G G U U A C G A A U U A G
Ala
Trp
Leu
Arg
Ile
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Nonsense Mutation
nonsense mutation
A
G C U U G U U U A C G A A U U A G
G C U U G U U U A C G A A U U A G
Ala
Cys
Leu
Arg
Ile
G C U U G A U U A C G A A U U A G
Ala
STOP
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Frameshift
frameshift
G C U U G U U U A C G A A U U A G
G C U U G U U U A C G A A U U A G
Ala
Cys
Leu
Arg
Ile
G C U U G U
U A C G A A U U A G
Ala
Tyr
Cys
Glu
Leu
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Gene Expression Regulation
Regulation, signal transduction
• When should each gene be expressed?
• Regulate gene expression
Examples:
– Make more of gene A when substance X is present
– Stop making gene B once you have enough
– Make genes C1, C2, C3 simultaneously
• Why? Every cell has same DNA but each cell expresses
different proteins.
• Signal transduction: One signal converted to another
– Cascade has “master regulators” turning on many proteins,
which in turn each turn on many proteins, ...
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Gene Regulation

Gene expression is controlled at many levels:

DNA chromatin structure

Transcription

Post-transcriptional modification

RNA transport

Translation

mRNA degradation

Post-translational modification
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Transcription Regulation
• Much gene regulation occurs at the
level of transcription.
• Primary players:
– Binding sites (BS) in cis-regulatory modules
(CRMs)
– Transcription factor (TF) proteins
– RNA polymerase II
• Primary mechanism:
– TFs link to BSs
– Complex of TFs forms
– Complex assists or inhibits formation of the
RNA polymerase II machinery
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Tx Factor Binding Sites
• Short, degenerate DNA sequences recognized
by particular TFs
• For complex organisms, cooperative binding of
multiple TFs required to initiate transcription
Binding Sequence Logo
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Transcription Regulation Mechanisms
enhancer, silencer, insulator
Transcription Factor Specificity:
Enhancer:
Silencer:
Insulator:
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Unicellular vs. Multicellular
unicellular
multicellular
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Non-coding RNAs
• RNAs transcribed from DNA but not translated
into protein
• Structural ncRNAs: Conserved secondary
structure (A-U, C-G, G-U)
• Involved in gene regulation
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Summary
• All hereditary information encoded in doublestranded DNA
• Each cell in an organism has same DNA
• DNA  RNA  protein
• Proteins have many diverse roles in cell
• Gene regulation diversifies protein products
within different cells
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The end?
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