Central Dogma
Basic Biology Related to
Technology for Measuring
Gene Expression
DNA contains genes that code for proteins.
DNA
(transcription)
1/11/2011
RNA
Copyright © 2011 Dan Nettleton
(translation)
protein
Proteins perform essential biological functions.
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2
A VERY Simplified Eukaryotic Cell
Deoxyribonucleic Acid (DNA)
P
...
chromosome
nucleus
DNA strands
cytoplasm
...
P
P
S
S
S 3’
T
T
A
A
C
G
G
A
A
T
T
G
C
C
3’ S
S
S
S
S
S
S 5’
P
P
...
P
P
P
P
5’ S
S
S
S
S
S
S 3’
T
T
A
A
C
G
A
A
T
T
G
3’ S
S
S
S
S
P
P
P
P
P
P
P
P
hydrogen
bonds
...
P
The two DNA strands are twisted in
the famous double helix shape (base
pairs like rungs in a spiraling ladder).
pyrimidines
4
P
...
...
P
P
P
P
P
P
P
5’ S
S
S
S
S
S
S 3’
G
T
T
A
A
C
G
G
C
C
A
A
T
T
G
C
C
S
S 5’
3’ S
S
S
S
S
S
S 5’
P
...
Sequence of bases holds instructions for
manufacturing proteins
Nucleotide=Phosphate-Sugar-Base
P
P
Bases
A=adenine
C=cytosine
G=guanine
T=thymine
purines
P
P
S
3
P
P
S
DNA contains thousands of genes.
P
P
S
S=deoxyribose sugar
P=phosphate
P
P
5’ S
P
...
P
...
...
P
P
5
P
P
P
P
P
P
...
Coding
Sequence
...
P
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1
RNA Polymerase
Transcription
• An enzyme is a protein that catalyzes
chemical reactions.
P
...
• RNA polymerase is the enzyme
responsible for transcribing DNA to RNA.
...
P
P
P
P
P
P
P
5’ S
S
S
S
S
S
S 3’
T
T
A
A
C
G
G
A
A
T
T
G
C
C
3’ S
S
S
S
S
S
S 5’
P
P
P
P
P
P
P
...
...
P
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8
Transcription
P
...
...
P
P
P
P
Ribonucleic Acid (RNA)
P
P
P
5’ S
S
S
S
S
S
S 3’
U
U
A
A
C
G
G
A
A
T
T
G
C
C
3’ S
S
S
S
S
S
S 5’
P
P
P
P
P
P
P
P
...
...
...
P
P
P
P
P
5’ S
S
S
S
S
S
S 3’
U
U
A
A
C
G
G
S=ribose sugar
P=phosphate
P
P
P
Bases
A=adenine
C=cytosine
G=guanine
U=uracil
...
The product of transcription
is known as the
primary transcript.
9
Posttranscriptional Modifications
to Primary Transcript
10
Expression Levels
Primary transcript
5’ UTR
3’ UTR
Intervening sequences corresponding to introns
that are removed through splicing
Primary transcript after modification: messenger RNA (mRNA)
G
5’ cap
5’ UTR
3’ UTR
Coding portions of RNA sequence
corresponding to exons
AAAAAA...AAAA
• The amount of messenger RNA (mRNA)
produced by a gene is known as the gene's
expression level.
• This course focuses on the design and analysis
of experiments that involve the simultaneous
measurement of gene expression levels for
thousands of genes.
poly-A tail
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2
Translation
Transcription takes place inside the nucleus.
Ribosome
chromosome
mRNA
nucleus
DNA strands
cytoplasm
amino acid sequence
folds to become a protein
Translation takes place outside the nucleus.
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During translation transfer RNA (tRNA)
translates the genetic code
...
U
A
U
A
U
A
U
C
G
G
C
tRNA
anticodon
leu
U
C
G
A
U
UUU
UUC
UUA
UUG
phe
phe
leu
leu
UCU
UCC
UCA
UCG
ser
ser
ser
ser
UAU
UAC
UAA
UAG
tyr
tyr
STOP
STOP
UGU
UGC
UGA
UGG
cys
cys
STOP
trp
C
CUU
CUC
CUA
CUG
leu
leu
leu
leu
CCU
CCC
CCA
CCG
pro
pro
pro
pro
CAU
CAC
CAA
CAG
his
his
gln
gln
CGU
CGC
CGA
CGG
arg
arg
arg
arg
A
AUU
AUC
AUA
AUG
ile
ile
ile
met
ACU
ACC
ACA
ACG
thr
thr
thr
thr
AAU
AAC
AAA
AAG
asn
asn
lys
lys
AGU
AGC
AGA
AGG
ser
ser
arg
arg
G
GUU
GUC
GUA
GUG
val
val
val
val
GCU
GCC
GCA
GCG
ala
ala
ala
ala
GAU
GAC
GAA
GAG
asp
asp
glu
glu
GGU
GGC
GGA
GGG
gly
gly
gly
gly
...
G
amino
acid
Second Base
codon
A
mRNA
codon
The Genetic Code
First Base
codon
14
thr
amino acids
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Miscellaneous Comments
• The biology is more complicated than I described.
• It is amazing!
• Humans have somewhere around 30,000 genes. (The
exact number is a subject for debate.)
• Much of the variation is created by differences in how
cells use the genes they have.
• Microarrays and Next Generation Sequencing are tools
that can help us understand how cells of various types
use their genes in response to varying conditions. This
helps us to understand gene function.
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