Lecture 16- Mutation and Genetic Variation Flashcards
The Importance of Genetic Variation
Genetic Variation
genetic differences that exist
among individuals in a population at a particular
point in time
Mutations
mutations result in _____ ________? Mutations that occur in the germ line can be passed on
some mutations are? other have? and some are?
over time thru evolution these mutations increase or decrease in frequency in the population
Mutations result in genetic variation!
Mutations that occur in the germ line can be passed on
* Some mutations are harmful; others have no effect; some are beneficial
* Over time, through evolution, these mutations
increase or decrease in frequency in the
population
Gene Pool
– All alleles present in all individuals in a species
- Genotype
– the genetic makeup of a cell or organism
Alleles
- the different forms of any gene
Alleles correspond to different DNA sequences in the genes
– Homozygous vs. heterozygous
- Polymorphism
Any genetic difference that is present in multiple individuals in a population
Phenotype
an individual’s observable characteristics (i.e., height, eye color,
lactose intolerance, weight, color blindness, etc.)
Alleles
Different forms of any genes are called
Homozygous
An individual with two copes of the same allele of a gene
Heterozygous
Individuals with two different alleles of a gene
Genotype vs. Phenotype
Genotype
– the genetic makeup of a cell or organism
Phenotype
– an individual’s observable characteristics (i.e., height, eye color,
lactose intolerance, weight, color blindness, etc.)
Harmful Genetic Differences
E.g. Emphysema risk:
Normal
a1AT gene encodes
enzyme that inhibits
elastase function
Normal lung elasticity
maintained (balanced
elastin production and
destruction)
Smoking
Smoking reduces
a1AT activity;
increased elastin
breakdown, enzyme that inhibits elastase function is not inhibited Emphysema results
Mutant
Individuals
homozygous for PiZ
allele produce a1AT
with reduced activity
Individuals who never smoke can also develop emphysema
* mutation in the gene encoding alpha-1-antitrypsin (a1AT)
* Mutant allele = PiZ.
* Homozygous individuals produce a1AT with reduced activity and
therefore have reduced elastase inhibition
* Individuals with the mutant gene and that smoke are far more
susceptible to developing emphysema and also lung cancer
Harmful Genetic Differences
smoking and PiZ mutation
Smoking
- reduces a1AT activity–>emphysema results
* 80% of all emphysema cases are associated with smoking PiZ mutation
– PiZ/PiZ non smokers –>reduced a1AT activity–> emphysema results (life
expectancy 65 yrs)
– PiZ/PiZ smokers-> increases severity and progression of disease (life expectancy 40 yrs)
* This is an example of a genetic risk factor i.e. a mutation that increases the risk of a disease
– A risk factor does not cause the disease, but makes the disease more likely to occur
Harmful Genetic Differences
Example 2: Huntington’s Disease and HTT (called huntington) gene on pp. 270-271
– You must know this example – testable content!
Harmful mutations are exemplified by alleles of a gene HTT, which encode the protein HTT or huntingtin, although the function or functions of huntingtin remain unknown, the protein is important in maintaining nerve cells, mutant forms of HTT result in huntingtins disease, the disease is associated with characteristic changes in brain morphology including enlarges ventricles and atrophy of cerebral nerve tissue, and basal ganglia, the result is incurable and relentless degeneration of the nervous system usually beginning sometime in middle age and progressing rapidly
The HTT gene encodes a protein of more than 3000 amino acids, and the gene is expressed in various cell types, especially in the brain, near its amino end, the protein contains a sequence of consecutive glutamines, the run of glutamine results from repeats of codon CAG, in the messenger RNA. . Nonmutant forms of the gene contain 6-35 CAG repeats and therefore 6-35 glutamines in the protein. The CAG repeats are genetically unstable, however and can undergo a process called trinucleotide expansion that increases the number of CAG repeats, resulting in 36-250 glutamines in the protein, the excessive number of glutamines in turn results in huntingtins disease
Huntingtins Disease
Nonmutant vs Mutant
Nonmutant: The HTT gene encodes a large protein that is expressed in many cell types but is highly expressed in brain –>HTT gene (expression of nonmutant HTT protein)–>Different nonmutant alleles code for a protein containing 6-35 consecutive glutamine (Q) amino acids (KSFQQ…QQQPPP)–>Ventricle, Basal ganglia
Mutant: Mutant HTT genes produce an mRNA that contains excessive repeats of the codon CAG, which increases the number of successive Q’s in the protein–> Mutant HTT gene (expression of mutant HTT protein)–>Different mutant alleles code for a protein containing 36-250 consecutive glutamine (Q) amino acids (KSFQQQQQQ…QQQQQQPPP) –>enlarged ventricles, atrophy of cerebral tissue and basal ganglia
Huntingtins Disease
Harmful Mutations
(a) Nonmutant forms: of the HTT gene encode a protein that includes a consecutive run of the amino acid glutamine (Q).
(b) Mutant forms: of HTT encode proteins with longer runs of Q’s, which result in Huntington’s disease and characteristic brain abnormalities.
Neutral Genetic Differences
* Neutral Mutations
No effect on organism or have effects not associated with reproduction and survival
– Often found in noncoding DNA
– Sometimes occur in coding sequences but still harmless
* E.g. PTC tasting (phenylthiocarbamide, gene=TAS2R38=Taste receptor, PAV/PAV=Tasters of PTC, AVI/AVI or AVi/PAV=nontasters of PTC)
Beneficial Genetic Differences
Example: Mutation that protects against aids by means a glycoprotein
Some mutations are beneficial
1) An example of such a mutation is one that protects against AIDS.
2) By means of a glycoprotein, a product of the env region in the HIV genome,
3)HIV combines with a cell-surface receptor CD4 to gain entry into T cells.
* Interaction with CD4 alone does not enable the virus to infect the T cell.
4) The surface glycoprotein must also interact with another receptor (CCR5) co receptor, in the early stages of infection
* Cells that lack it (CCR5) are more difficult to invade.
*For HIV to invade a T cell, it must interact with a CD4 receptor and a CCR5 co-receptor
Beneficial Genetic Differences
of a mutation called 🔼32 in CCR5
how was it discovered
The mutation has a 32 nucleotide deletion that shifts ?
The beneficial effect of a mutation (called Δ32) in CCR5 was
discovered in studies focusing on patients who did not develop AIDS for 10+ years
* The mutation has a 32 nucleotide deletion that shifts the reading
frame and results in a defective CCR5 protein
- Patients with HIV that are homozygous(Δ32CCR5/Δ32CCR5) for this allele rarely progress to AIDS, and even those heterozygous (Δ32CCR5/CCR5) for Δ32 have a delay in the progression of AIDS by about 2 years
Types of Mutations
Broad categories of mutations:
A. Small-scale Mutations
-Nucleotide substitution or point mutation
- Synonymous (silent) mutations
-Nonsynonymous (missense) mutations
- Nonsense mutations
-Insertion/Deletion of small number of nucleotides
-Frameshift
B. Chromosomal Mutations (large scale)
- Duplications/Deletions
- Inversion
- Translocation
Small-scale Mutations
* Nucleotide Substitution or
Point Mutation
Error incorporated during replication can become?
Effect of point mutation depends partly on? (non-coding region or coding region)
functions of non-coding DNA known or not known?
functions of coding DNA known or not known?
Mutations in DNA coding regions have?
Most frequent type of mutation
* Error incorporated during
replication can become
permanent change to
genome
* Effect of point mutation
depends partly on where in
genome it occurs
* i.e. in coding or non-coding region
In most multicellular eukaryotes, most of the DNA in
genome doesn’t code for proteins or RNA
* Function of noncoding DNA regions not known
* May explain why many mutations in noncoding DNA
have no detectable effect on organism
* Not the case for mutations in the coding regions
* Mutations in DNA coding regions have predictable
effects…
Small-scale Mutations
* Nucleotide Substitution and Point Mutation
Synonymous (silent) and Nonsynonymous (missense)
mutations:
DNA to RNA to AA
A. Nonmutant- the nonmutant gene expresses normal B-globin
B. Synonymous Mutation- A nucleotide substitution that does not change the amino acid is a synonymous (silent) mutation
C. Nonsynonymous mutation- A nucleotide substitution that changes the amino acid is nonsynonymous (missense) mutation
*: DNA sequence that codes for b-globin (a subunit in hemoglobin)
Small-scale Mutations is
Nucleotide Substitution and Point Mutation
Nonsense Mutations
A point mutation can change an amino acid into a stop codon that terminates translation this is called nonsense mutation
What is the result?
A point mutation can change an amino acid to a stop codon that terminates translation
* Result: truncated
polypeptide – most
are nonfunctional
and unstable
*a nucleotide substitution that creates a stop codon is called a nonsense mutation
Sickle-cell anemia is caused by a point mutation
Sickle-cell anemia is caused by a
change in only a single amino
acid:
– Glu is replaced by Val or Lys.
* Result: misfolding of the
hemoglobin subunit β-globin.
* Individuals who inherit two
copies of the mutant β-globin
gene (either S or C) have sickle- cell anemia.
* In this condition:
-hemoglobin crystallizes in low levels of oxygen, causing the cell to collapse.
-oxygen is not carried through the body effectively, causing anemia.
-Sickled cells block capillary vessels, causing pain and low oxygen levels.
Small-scale Mutations:
Small Insertions and Deletions
Insertion/deletion of small number of nucleotides is
another common small-scale mutation
– Little effect in noncoding DNA
– In protein coding regions of DNA, effect depends on
size
* Insertion or deletion that is an exact multiple of three
nucleotides can result in a polypeptide with more or fewer
amino acids as there are codons inserted or deleted.
3nt=1 codon=AA
Small-scale Mutations
Example: Cystic Fibrosis
How is it characterized?
Results in?
Characterized by a faulty protein
CFTR (cystic fibrosis
transmembrane conductance
regulator)
* Deletion of 3 nucleotides
* Mutant CFTR protein is a result of an in-frame deletion of amino acid
* Resulting protein does not fold properly
* Results in: abnormal secretions in
the lungs, liver, pancreas ,and
other gland
Nonmutant CFTR vs Mutant CFTR
Nonmutant CFTR:
Mutant CFTR:
Nonmutant CFTR: The CFTR transporter pumps chloride ions out of the cell
Mutant CFTR: missing amino acid (PHE) in the most common mutant proteins, three nucleotides are deleted in the CFTR gene, resulting in a missing amino acid at position 508
The mutant CFTR protein is unstable and is degraded before reaching the membrane
Small-Scale Mutations
Frameshift Mutations
– Insertion or deletion of 1 or 2 bases results in
disruption or shifting of the reading frame.
1 codon=3nt=1AA
THE BIG BOY SAW THE CAT EAT THE BUG
TH(E) BIG BOY SAW THE CAT EAT THE BUG
TH(B) IGB OYS AWT HEC ATE ATT HEB UG
Small-scale Mutations
Frameshift Mutations (2)
-Single base insertion shifts the reading frame
-When the transcript is translated, the shift in reading
frame results in a very different amino acid sequence
from the nonmutant sequence
Chromosomal Mutations (Large Scale)
Duplications and Deletions
- Segment of chromosome present in two copies
(duplication) or missing (deletion) - Deletion can result from an error in replication or from
joining breaks in chromosome on either side of a deleted region
Duplications and Deletions
* Although deletion may eliminate a gene essential for
survival, deletion can persist in population because
chromosomes exist in homologous pairs
* Deletions or duplications involving a centromere are rare
– Abnormal chromosomes without centromeres or with two
centromeres are lost within a few cell divisions
Chromosomal Mutations (Large Scale)
Gene Duplication and Evolutionary Divergence
Small duplications important in origin of new genes in
evolution
* When a mutation in the extra copy of the gene is
beneficial to survival, the extra copy can become a new
gene
* Process is known as duplication and divergence
– the formation of new genes from duplicates of old ones
Many rounds of duplication and divergence can give
rise to a gene family = a group of genes with related
functions
– Largest gene family in human genome: odour detectors
Many rounds of duplication and divergence can give
rise to a gene family
A gene family is?
a group of genes with related
functions
Chromosomal Mutations (Large Scale)
Inversions
When the normal order of a block of genes is reversed
* Typically form when the region between two breaks in
a chromosome is flipped before the breaks are repaired
* In large genomes, breaks likely to occur in noncoding
regions
Chromosomal Mutations (Large Scale)
Reciprocal Translocation
Reciprocal translocations join segments from nonhomologous chromosomes
* In large genomes, the breaks are likely to occur in
noncoding DNA, so the breaks themselves do not usually
disrupt gene function
DNA Damage - How Mutations Occur
- Spontaneous (most common)
- Mutagens – increase the probability of a mutation
(often by a factor of 100 or more!) - X-rays – sugar-phosphate backbone
- UV light – cross-linking of adjacent pyrimidines
- Chemicals - base losses; bulky side group additions
DNA Repair
DNA ligases?
Different types?
DNA polymerases?
DNA ligases – seal the breaks in the sugar-phosphate backbone
– uses energy in ATP to join the 3’ hydroxyl of one end to the 5’
phosphate of the other end
Many different types
– Some participate in DNA replication
– Some seal single-stranded breaks in DNA
– Others seal double-stranded breaks in DNA
DNA polymerases – proofread bases during DNA replication and correct mispairing
– 99% of mispaired bases corrected this way
– Missed mispairing errors are corrected by mismatch repair….
DNA Repair
Mismatch repair
Base Excision repair
Mismatch repair
-MutS recognizes mismatched bases in DNA and initiates the repair process
-MutL ans MutH proteins are recruited and MutH breaks the backbone some distance away
-An exonuclease removes successive nucleotides, including the one with the mismatched base
-A DNA polymerase fills in the missing nucleotides, and a DNA ligase joins the backbone
Base Excision repair
-Uracil in DNA signals the repair process
-DNA uracil glycosylase cleaves the uracil from the deoxyribose sugar
-AP endonuclease cleaves the backbone and removes the sugar
-Other enzymes close the gap by new DNA synthesis, using the intact nucleotide opposite the site as a template
Nucleotide excision repair
Nucleotide excision repair
* Similar to mismatch repair
but recognizes multiple
mismatched bases in a
region instead of just one
-one or more damaged bases signal the repair process
-Enzymes cleave the DNA backbone at sites flanking the damage
-The region with damaged bases is removed
-The gap is filled by new DNA synthesis, using the ungapped strand as the template
DNA Damage and repair reading
Mutations result from?
Mutations result from unrepaired errors in DNA replication or from damage to DNA that is not repaired. DNA is a fragile molecule, prone
to damage of many different kinds
Every day, in each cell in our bodies, the DNA is damaged in some way at tens of thousands of places
along the molecule. Fortunately, cells have evolved mechanisms for repairing various types of damage and restoring the DNA to its original condition, which helps explain the low mutation rate in most organisms
DNA damage can affect both DNA backbone and base
Most mutations, whether small-scale or chromosomal, are spontaneous and occur naturally. However, mutations can also be induced by
radiation or chemicals.
Mutagens are agents that increase the probability of mutation.
What types of damage affects the structure of the DNA double helix
Some types of damage affect the structure of the DNA double helix, these include breaks in the sugar phosphate backbine, one of the main mutageinc effect of X-ray
Ultraviolet
light can cause cross-links between adjacent pyrimidine bases, especially thymine, resulting in the formation of thymine dimers that warp the backbone.
Another type of structural damage
is loss of a base from one of the deoxyribose sugars, resulting in a gap in one strand where no base is
present. Spontaneous loss of a purine base is one of the most common types of DNA damage, occurring at the rate of approximately 13,000
purines lost per human cell per day. Most of these mutations result from the interaction between DNA and normal metabolic by-products.
When does mutation rate increase?
The Mutation rate increases with age, and it can also be increase by exposure to oxidizing agents such as bleach or hydrogen peroxide
Other types of damage alter the chemical structure of the bases themselves, making them prone to mispairing. Chemicals that are highly
reactive also tend to be mutagenic, often because they add bulky side groups to the bases that hinder proper base pairing.
The main environment source of such chemical is tobacco smoke, other chemicals can perturb the DNA replication complex and cause the insertion or deletion of one or occasionally several molecules
Most DNA damage is corrected by specialized repair enzymes
Cells contain many specialized DNA repair enzymes that correct specicifc kinds of damage
Perhaps the simplest is the repair of breaks in the sugar-phosphate backbone, which are sealed by DNA ligase, an enzyme that can repair the
break by using the energy in ATP to join the 3′-hydroxyl group of one end to the 5′-phosphate group of the other end
Double-stranded breaks are less likely to be repaired correctly than single-stranded breaks,
ligases: allow DNA molecules from different sources to be joined to produce recombinant DNA
mispairing of bases during DNA replication leads to the incorporation of incorrect nucleotides that can
become?
mispairing of bases during DNA replication leads to the incorporation of incorrect nucleotides that can
become nucleotide substitutions in the next round of replication if they are not corrected. Approximately 99% of the mis paired bases are
corrected immediately by the proofreading function of DNA polymerase, in which the mis paired nucleotide is removed immediately after incorporation and relaced by the correct nucleotide
Second Chance mechanism for catching mismatches is known as?
mismatch repair
In mismatch repair, the segment of a DNA strand containing the mismatch is removed and then
resynthesized.
combined effect of proofreading by DNA polymerase and mismatch repair is increased fidelity of DNA replication
Repair DNA damage, even in nondividing cells
Cells have evolved many other systems that repair different types of DNA damage that can occur, even in nondividing cells such as those in the adult brain, heart, liver, and kidney, one example is base-exclusion repair, which correct abnormal or damaged bases
In the first step of base exclusion repair, an abnormal or damaged base is cleaved from the sugar in the DNA backbone, then the baseless sugar is removed from the backbone, leaving a gap of one nucleotide, finally a repair polymerase insert the correct nucleotide into the gap
To repair short stretches of DNA containing mismatched or damaged bases
known as?
nucleotide excision repair, which has a similar mechanism of action to mismatch repair but uses different enzymes, instead of degrading a DNA strand in a nucleotide-by-nucleotide fashion until the mismatch is removed, nucleotide exclusion repair removes an entire damaged section of a strand at once, nucleotide exclusion repair is also used to remove nucleotides with bulky side groups, as well as thymine dimers resulting from ultraviolet light
Nucleotide excision repair. In nucleotide excision repair, a damaged segment of a DNA strand is removed and resynthesized
using the undamaged partner strand as a template.
Importance of Nucleotide excision repair is illustatred by the disease
importance of nucleotide excision repair is illustrated by the disease xeroderma pigmentosum (XP), in which nucleotide excision repair is defective. People with XP are sensitive to the UV radiation in sunlight, because of the defect in nuelctiode excision repair, damaged to DNA resulting from UV light is not correct, leading to the accumulation of mutation in skin cell, the result is high rates of skin cancer, people with XP must minimize their exposure to sunlight and in extreme cases stay out of the sun altogether
