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Gene expression
Have you ever wondered how a frog grows?
http://www.teara.govt.nz/en/frogs
Native male frogs sit on the eggs and the young froglets hatch
almost fully formed.
http://www.erodent.co.uk/GardenPond/PondPhotos/Tadpole3w.jpg
Why are their parts where they are?
The answers lie in their cells.
In particular – the answer can be found in their genetic material.
A right handed
helix
Let’s revisit how we know that DNA is important.
Streptococcus pneumoniae
S: smooth
(virulent)
R: rough
(avirulent)
DNA is the genetic material - Griffith 1928
Avery, MacLeod & McCarty 1944
 Chemically characterised the ‘transforming extract’ from virulent
cells observed by Griffith
 Removed the protein from ‘transforming extract’
 and it still transformed
 Removed RNA
 extract still transformed
 Removed DNA
 prevented transformation
 Therefore transforming substance was DNA
 Biochemically characterised the transforming extract, all its
properties were consistent with DNA:
 High Mw (centrifugation)
 High charge (electrophoresis)
 Characteristic UV absorbance
 Chemical analysis, ratio of nitrogen to phosphorus
Hershey-Chase 1952
 Left, T2 virus protein
radioactively labelled 35S
 Radioactivity outside
 Right: T2 virus DNA
radioactively labelled 32P
 Radioactivity inside
 THEREFORE genetic
material infecting E.coli
was DNA and not protein
 Genes are made from
DNA (except some RNA
viruses)
Genes are encoded within DNA
What is a gene?
Classical molecular gene: “A stretch of DNA sequence that codes
for a particular protein that has a particular function”.(10,11) This can
be an interrupted sequence within a chromosome.
Other definitions of a gene
Evolutionary gene: “any portion of chromosomal material
that potentially lasts for enough generations to serve as a unit
of natural selection”.(39) As such a gene is an inherited unit
which is somewhere between a nucleotide and a chromosome.
Systemic Concept: The gene is a combination of (one or
more) nucleic acid (DNA or RNA) sequences, defined by the
system (the whole cell, interacting with the environment, or the
environment alone, in sub-cellular or pre-cellular systems), that
gives origin to a product (RNA or polypeptide).(57)
14
The central dogma
DNA Precursors
(deoxyribonucleotides)
Replication
DNA
RNA Precursors
(ribonucleotides)
Transcription
(Genotype)
RNA
Protein Precursors
(amino-acids)
Translation
Protein
(Phenotype)
Transcription is the first step in the process.
http://vcell.ndsu.nodak.edu/animations/transcription/advanced.htm
How many genes does it take to make a person?
20,00025,000
26,000
19,000
13,000
6,000
4,000
DSCAM: one gene 38,016 mRNAs
An immunoglobulin (Ig) superfamily member
an axon guidance receptor
Drosophila melanogaster Dscam gene contains 115 exons spanning ~60,000 bp
20 exons are constitutively spliced (open boxes) and 95 exons are alternatively spliced
(shaded boxes).
Alternatively spliced exons are orgnized into 4 clusters (exons 4,6, 9, 17) that contain
12, 48, 33 and 2 alternative exons each.
Exons in each cluster are spliced in a mutually exclusive manner.
Celotto & Graveley 2001 Genetics 159:599-608
18
Immunoglobulin genes recombine within the DNA.
19
So what if nuclei are the wrong shape?
249250621 bp
85 mm
48129895 bp
16 mm
More or less matters!
Patau
Klinefelters
(XXY)
Edwards
Down
Turners
(X)
Albert Einstein (1955)
22
30-35% of cells are aneuploid
~4% aneusomy
for chr 21
Affects survival, proliferation potential, and
protein imbalances
23
Copy number affects your weight
Falchi et al. (2014) Nat Genetics 46:492-498
24
How big is a vertebrate cell?
~6 µm
http://medicalpicturesinfo.com/human-cell/
Progeria (Hutchinson-Gilford progeria)
Children with this disease typically have a stroke or heart attack
caused by severe atherosclerosis at an average age of 13 years.
26
Nuclei in Progeria are the wrong shape.
Treating progeria cells with remodelin results in the nuclei
reverting to the ‘normal’ shape.
Shape directly affects the genes that are turned
on.
31 of the altered genes
affect vasculature and
atherosclerosis
22 of the altered genes
affect skeletal, limb
and cartilage
Defects in transcription can cause problems.
Who amongst us is lactose intolerant?
Lactase is encoded by a single gene
LCT gene 17 exons Chr 2q21
-24 Kb G-A
-14 Kb C-T
A single mutation (C changes to T) causes lactase persistence
The frequency of lactase persistence varies dramatically in
different populations.
Swallow; Annu Rev Genet 2003:37197-219
Pastoralists and milk drinkers tend to have higher frequencies of lactase
persistence than nonpastoralists
Swallow; Annu Rev Genet 2003:37197-219
Translation is important too.
tRNA: the adapter
What is the genetic code?
Redundant codons are all
synonyms for the same protein
building block.
Degenerate codons differ in their
third positions; e.g. both GAA and
GAG code for the amino acid
glutamic acid.
The genetic code is not always the same
First
position
(5’ end)
U
C
Ser
Candida
A
Nons.
Micrococcus
G
Third
position
(3’ end)
Second Position
U
UUU Phe
UUC Phe
UUA Leu
UUG Leu
CUU Leu
CUC Leu
CUA Leu
CUG Leu
AUU Ile
AUC Ile
AUA Ile
AUG Met
GUU Val
GUC Val
GUA Val
GUG Val
C
UCU Ser
UCC Ser
UCA Ser
UCG Ser
CCU Pro
CCC Pro
CCA Pro
CCG Pro
ACU Thr
ACC Thr
ACA Thr
ACG Thr
GCU Ala
GCC Ala
GCA Ala
GCG Ala
A
UAU Tyr
UAC Tyr
UAA Stop
UAG Stop
CAU His
CAC His
CAA Gln
CAG Gln
AAU Asn
AAC Asn
AAA Lys
AAG Lys
GAU Asp
GAC Asp
GAA Glu
GAG Glu
G
UGU Cys
UGC Cys
UGA Stop
UGG Trp
CGU Arg
CGC Arg
CGA Arg
CGG Arg
AGU Ser
AGC Ser
AGA Arg
AGG Arg
GGU Gly
GGC Gly
GGA Gly
GGG Gly
U
C
A
G
U
C
A
G
U
C
A
G
U
C
A
G
Cys
Euplotes
Trp
Mycoplasma
Spiroplasma
Gln: Ciliates
& Acetabularia
Nons.
Mycoplasma
Nons.
Micrococcus
Some people can’t use Glucose.
Typically they have mutations in GLUT1
These mutations occur because the codons are changed.
37
GLUT1 mutations are often in helix 4
R126H
R126L
R153L
38
Mitochondria in a mouse myoblast cell
Mitochondria
are red
Actin
filaments are
green
Nucleus is
blue
Image taken by James Markworth (Liggins Institute)
39
Differences in the human nuclear
and mitochondrial genetic codes
First
Second Position
position
(5’ end)
U
C
A
Met
G
U
UUU Phe
UUC Phe
UUA Leu
UUG Leu
CUU Leu
CUC Leu
CUA Leu
CUG Leu
AUU Ile
AUC Ile
AUA Ile
AUG Met
GUU Val
GUC Val
GUA Val
GUG Val
C
UCU Ser
UCC Ser
UCA Ser
UCG Ser
CCU Pro
CCC Pro
CCA Pro
CCG Pro
ACU Thr
ACC Thr
ACA Thr
ACG Thr
GCU Ala
GCC Ala
GCA Ala
GCG Ala
A
UAU Tyr
UAC Tyr
UAA Stop
UAG Stop
CAU His
CAC His
CAA Gln
CAG Gln
AAU Asn
AAC Asn
AAA Lys
AAG Lys
GAU Asp
GAC Asp
GAA Glu
GAG Glu
G
UGU Cys
UGC Cys
UGA Stop
UGG Trp
CGU Arg
CGC Arg
CGA Arg
CGG Arg
AGU Ser
AGC Ser
AGA Arg
AGG Arg
GGU Gly
GGC Gly
GGA Gly
GGG Gly
Third
position
(3’ end)
U
C
A
G
U
C
A
G
U
C
A
G
U
C
A
G
Trp
Stop
40
Protein structure is important as well.
41
Prions and Alzheimer’s disease are examples of
pathological protein misfolding
42
43
What’s different between these bears?
Polar bears and Brown
Bears
Divereged ~479-343
kya
Polar bears are adapted to high fat diets
• Lipids are the predominant energy source
• The polar bear has a lipid-rich diet (i.e. seals)
throughout life.
• Extreme cholesterol levels
• Humans <5.2 mmol/l
• Polar bear
female: 8.58±1.31 (n=20)
Male: 6.61 2.06 (n=20)
• Polar bear milk contains 27% fat
• Up to 50% of individual’s body weight is
adipose (subcutaneous and around organs)
Modified from Liu et al. Population genomics reveal recent speciation and rapid evolutionary adaptation in
Polar bears. Cell (2014): 157, 785-794 and Ombostad, I. (2012) Relationships between persistent organic
pollutants (POPs) and plasma clinical-chemical parameters in polar bears (Ursus maritimus) from Svalbard,
Norway. Student thesis (Trondheim, Norway: Norwegian University of Science and Technology).
The environment is affecting the genes that Polar bears have.
Basic unit of muscle
Polar bears have seven missense substitutions in the LYST gene
These mutations occur in
the same region as ones in
human disease
Chediak-Higashi syndrome
Autosomal recessive
Mutation of lysosomal trafficking regulator (LYST)
What do Chimo and a Polar bear have in common?
Lyst affects melanosome maturation
The organelle that is involved in synthesis, storage and transport
of melanin
White fur is common in the arctic:
beluga whales, polar bears, arctic hare, arctic fox – but not all
due to Lyst mutations.
Confers a selective advantage?
www.katoa.ac.nz
Hands on experience for you and
your students!
[email protected].