Download neutral mutation

Lecture 3
Proteins and Disease
Gene mutations
•  Proteins are coded for by genes.
•  A Mutation in our genes can
impact on the protein that gene
codes for.
•  Radiation, viruses, chemicals can
all cause mutations
•  Mistakes can occur during DNA
replication
mutagen
Damage to nucleotide
DNA molecule
G is now chemically similar to A
Incorrect base pairing
correct DNA molecule
incorrect DNA molecule
Impact of mutations in DNA
•  Impact on protein
sequence
• 
frameshift mutation –
caused by insertion or deletion of a
number of nucleotides that is not evenly
divisible by 3.
Due to the triplet nature of gene
expression by codons, the insertion or
deletion can disrupt the reading frame
resulting in a completely different
translation from the original.
Val
Glu
Cys
Ala
Impact of mutations in DNA
•  Impact on protein
sequence
• 
frameshift mutation –
caused by insertion or deletion of a
number of nucleotides that is not evenly
divisible by 3.
Due to the triplet nature of gene
expression by codons, the insertion or
deletion can disrupt the reading frame
resulting in a completely different
translation from the original.
Leu
Val
Ser
Glu
Val
Cys
His
Ala
Impact of mutations in DNA
•  Impact on protein sequence
• 
nonsense mutation results in a premature stop codon and a
truncated protein product. TGA
• 
Missense mutations are types of point mutations where a
single nucleotide is changed to cause substitution of a different
amino acid.
• 
neutral mutation is a mutation that occurs in an amino acid
codon which results in the use of a different, but chemically
similar, amino acid.
A Val
• 
Glu
Cys
Silent mutations are mutations that do not result in a change
to the amino acid sequence of a protein.
STOP
Impact of mutations in DNA
•  Impact on protein sequence
• 
nonsense mutation results in a premature stop codon and a
truncated protein product. TGA
• 
Missense mutations are types of point mutations where a
single nucleotide is changed to cause substitution of a different
amino acid.
• 
neutral mutation is a mutation that occurs in an amino acid
codon which results in the use of a different, but chemically
similar, amino acid.
T
Val
• 
Glu
Silent mutations are mutations that do not result in a change
to the amino acid sequence of a protein.
Val Cys
Impact of mutations in DNA
•  Impact on protein sequence
• 
nonsense mutation results in a premature stop codon and a
truncated protein product. TGA
• 
Missense mutations are types of point mutations where a
single nucleotide is changed to cause substitution of a different
amino acid.
• 
neutral mutation is a mutation that occurs in an amino acid
codon which results in the use of a different, but chemically
similar, amino acid.
G
Val
• 
Silent mutations are mutations that do not result in a change
to the amino acid sequence of a protein.
Val Glu
Cys
Impact of mutations in DNA
•  Inheritance?
•  Mutations can be
- germ line / inheritable:
mutation occurs in reproductive cell
can result in hereditary diseases
-somatic / acquired
not inheritable
present in all descendants of this cell in the same organism
Certain somatic mutations can cause cancer
Impact of mutations in DNA
•  Impact on “fitness” of the organism
harmful or beneficial ?
- neutral mutation
- deleterious mutation: negative effect
- advantageous mutation: positive effect
Mutations that change protein sequences are predominantly
harmful to an organism, Eg Cystic Fibrosis
On occasion, the effect can be neutral or positive in a given
environment. Eg. Sickle cell disease
Disease caused by deletion mutation
Cystic Fibrosis
As this dele,on that is evenly divisible by three is termed an in-­‐frame muta,on Point mutations- SNPs
-  single nucleotide polymorphisms (SNPs)
= variations in DNA sequence of genes
-  A single base change in the DNA of a gene can
lead to a single amino acid change
-  A single amino acid change can lead to a mutated
protein- conformational change
-  Conformation of a protein = function of protein
SNPs The order of bases
along the length of
the DNA= genetic code
instructs what protein
is to be made
DNA
T
Each set of three bases, or codon, specifies a par,cular amino acid. Amino acids are the building blocks of proteins. mRNA
Amino acid
Val
Glu
Glutamic acid codon = GAG
valine codon = GTG
Cys
Ala
} Single Nucleotide Polymorphism
Sickle-Cell Disease:
A Simple Change in Primary Structure
•  Sickle-cell anemia
–  Inherited blood disorder
–  Results from a single amino acid substitution in the protein hemoglobin
(glutamic acid-> valine)
–  Symptoms: sickle cell crises
•  Misshapen angular cells clog tiny blood vessels
•  Impede blood flow
•  Physical weakness, pain, organ damage and death
Hemoglobin function
•  Hemoglobin carries oxygen to
the cells of the body
•  All body cells require oxygen
for metabolism
-oxygen is non-polar and not
soluble in the aqueous blood.
•  Hemoglobin has a group called
"heme", which is at the heart of
the protein structure.
•  At the center of the heme
group is the iron +2 metal ion.
•  The oxygen molecule will
ultimately bind to this iron ion
Globular structure
•  Hemoglobin structure and sickle-cell disease
Primary
structure
Normal hemoglobin
Val His Leu Thr Pro Glul Glu 1 2 3 4 5 6 7
Secondary
and tertiary
structures
Red blood
cell shape
Val His Leu Thr Pro α
β
Molecules do
not associate
with one
another, each
carries oxygen.
β
α
Quaternary
structure
Glutamic acid codon = GAG
valine codon = GTG
...
α
β
β
α
10 µm
Red blood
cell shape
Exposed hydrophobic region β subunit
Function
10 µm
Normal cells are
full of individual
hemoglobin
molecules, each
carrying oxygen
Val Glu structure 1 2 3 4 5 6 7
Secondary
β subunit and tertiary
structures
Quaternary Hemoglobin A
structure
Function
Sickle-cell hemoglobin
. . . Primary
Hemoglobin S
Molecules
interact with
one another to
crystallize into a
fiber, capacity to
carry oxygen is
greatly reduced.
Fibers of abnormal
hemoglobin
deform cell into
sickle shape.
} Single Nucleotide Polymorphism
Sickle cell anemia
•  1/10 Africans have this trait
•  Selective advantage for the disease trait in
malarial regions
•  The malarial parasite remains at a lower density
in cells with sickle hemoglobin
•  Trade off
-Fewer malarial symptoms
vs
-sickle cell symptoms
Gene Mutations causing SNPs
-­‐ single nucleo,de polymorphisms (SNPs) varia,ons in DNA sequence of genes -­‐ A single base change in the DNA of a gene can lead to a single amino acid change Disease Cause Trait Re,ni,s Pigmentosa Muta,on in gene for transducin blindness Spina Bifida Muta,on in gene for Neural tube defect Methylene Tetra Hydra Folate Reductase (MTHFR) This enzyme MTHFR uses a nutrient called folic acid to help form the neural tube.
The mutant variant requires more folic acid:
Normal MTHFR
Folic acid
Building blocks for neural tubes
Variant MTHFR
Protein Folding
•  Unique shape confers unique function
•  What are the key factors determining shape?
-primary structure - sequence
effects
-secondary structure – bonds in polypeptide backbone
-tertiary structure
- bonds between side chains
•  Is this the whole story? –NO!
-we don’t know all the rules
Chaperones
•  Protein folding occurs
spontaneously in vitro
•  Physical and chemical conditions
of the cellular environment can
affect “native” conformation
• 
Hydrophilic environment
inside
pH changes / salt changes / temperature
changes
•  Chaperone proteins assist protein
folding in vivo
-protect a new protein from the
external environment
-provide hydrophilic environment
for proper folding
Cylindrical in shape
Chaperones
Disease due to misfolded proteins
- Many diseases are diseases of protein conformation.
- A good example are prion diseases, transmissible
spongiform encephalopathies (TSEs) (eg Creutzfeld
Jacob Disease, CJD)
- Prions = “infectious proteins”, virtually indestructible
- There is no known cure for prion diseases
- Prion proteins build up in the brain, ultimately causing
death
Brain Tissue infected with Prion
Prions- misfolded proteins
•  How can a protein which can not replicate itself be infectious?
•  Prions are mis-shapen versions of normal brain proteins
– once a prion gets into the brain they interact with the normal
version of the protein and convert it to the misfolded prion
version
•  This way Prions trigger a chain reaction which increase their
numbers
•  These Prions then polymerise and are toxic to normal cells
Normal
Disease-causing
Prions stacking to form fibrils
The mechanism: PrPsc interacts with PrPc PrPc turned into PrPsc PrPsc infects
Symptoms begin and accelerate Causing polymerisa,on PrPsc Neuronal death occurs