GENETICS LECTURE - “Fittest” – survived because of series of mutation making

FINALS REVIEWER them adapt.

LECTURE 4: MUTATIONS - Mutations occur because of its benefits:
o Vestigial structures – non-functional structures to
be removed (tail=coccyx)
[Mutations]

Mutation: Type of Molecular Change

*Chromatin Modification on Cancer
- Changes in genetic sequence
- For gene expression to push through, relaxing of histone
protein must be done (HATs or histone acetylases).
- Cancer is expressed as gene expression for cell differentiation
and senescence are inhibited.
- HDAC (histone deacetylases) prevents relaxation of genes,
preventing gene expression for differentiation and senescence.
- DNA methylation – regulation (alteration of patterns of HDACs
on cancer cells).

1. Frameshift Mutation
Gene Mutations – changes in the gene level, more
o Insertion and deletion of nucleotide – tendency
encompassing (highly affects all genetic components including
to move the sequence to the left or right.
chromosomes)
o Its occurrence changes the “frame” to be
Chromosomal Mutations – changes in number and/or location translated – change how tRNA reads the mRNA.
of chromosomes o Change in genes – change in proteins
2. Point Mutation
o Change in one of the nucleotide bases –
Mutations and Evolution substitution (change in a single base)
o Example: Sickle Cell Anemia – change in one
- Speciation – formation of new species, due to base, changed the translated protein, resulting to
development of new organism where their genomes are mutant β-globin (sickle-shaped hemoglobin).
different.
 o Types of Point Mutation: 2. Gain-of-Function – possible switch from non-coding to a
a. Missense – change of one base, changes the coding region. Introduction of new function and also
amino acid product. enhance an existing function.
b. Nonsense – change of one base, it encodes a 3. Suppressor Mutation – reverse mutation, lose of
stop codon, terminates translation (premature function (first mutation) then gain of function (second
gene – protein can be changed). mutation)
c. Silent – change of one base, but encoded to o Example: IRGM gene
same amino acid.
d. Neutral – nothing to do with amino acid
sequence. Changes in non-coding regions of the
gene (ex. introns)
e. Transition – change a purine with another purine
(A to G or G to A), also applies with pyrimidines
(T to C or C to T)
f. Transversion – changes from purine to
pyrimidines and vice versa (A to T / G to C)

Mutation: Effect on Function

Mutation: Location
- Changes in coding regions of the genes.
- More on chromosomes than genes
1. Loss-of-Function – reduction of function, mutation
1. Somatic – mutation on somatic cells, not dictated on the
inhibits gene expression.
offspring, affects only the individual.
a. Recessive – expression of wild type phenotype
2. Germ-line – mutation on sex cells, affect also the
(natural), mutation targets the recessive alleles
offspring (changes are passed through generations).
(dominant alleles are still expressed)
o CRISPR-Cas9 – targeted genetic engineering
b. Dominant – mutation on dominant allele, changes
tool, involves somatic cells (not germ-line) to
the expressed phenotype (mutant)
evade ethical issues.
c. Dominant negative – mutated gene produces
o Genetic engineering on germ line – inherited by
product that interferes to wild type product
offspring
(enzymatic activity), changes in bioactivity
3. Autosomal – autosomes are not the sex chromosomes,
▪ Haploinsufficiency – lack of gene, single
no sex-dependent effects
copy of mutant gene is insufficient to
4. X- or Y- linked – mutations of X or Y chromosomes
induce changes in phenotype expressed
 o XY (males), XX (females) – males can express Induced Mutations – exposure to mutagens, agents that cause
X-linked recessive mutations (sex-dependent mutations.
mutations).
- Ames Test – determines mutagens, mutagens allow
reverse mutation (presence of histidine).
Spontaneous Mutations – naturally occurring, it is because of
mistakes in genetic mechanisms.
- Mutation rate – likelihood of genes to have mutation
- Mutation hotspots – regions in genome highly
susceptible to mutations
o Tandem Repeats – repeats in the sequence
o Microsatellites – repeats in the genome
- Slippage – Nascent strand (growing strand) creates
looping
o Backward Slippage – looping on template strand
o Loops are not read or skipped by enzymes
(polymerases) – creates gaps
- DNA Replication Errors – mispairing of bases
o Tautomeric Shifts – tautomers (isomers of Types of Mutagens
specific compound) changes in the position of
protons and electrons affects affinity of the 1. Base Analogs – structure analogous with nucleotide
molecules with another compound. bases; it is possible that other with bind due to same
o Depurination – loss of purine, cleaves glycosidic structures.
bonds (purines are broken – apurinic site) – 2. Alkylating – provide alkyl group (CH3), nucleotide with
create gap alkyl group changes the structure – changes on base
o Deamination – removal of amino group in pairing.
cytosine or adenine – cytosine will be uracil and 3. Intercalating – ethidium bromide allows to visualize the
adenine will be a compound similar to guanine. DNA; it is intercalating agent as it penetrates to DNA that
Changes in base pairing. produce change and stains the DNA.
o Oxidative Damage – production of reactive- 4. Adduct-Forming Agents – structurally bind to DNA which
oxygen species (ROS) that targets the DNA. changes the DNA (ex. acetaldehyde)
Oxidase+ degrade H2O2, an ROS.
 5. UV Light – adjacent base pairs exposed to UV light
creates covalent bonds in between (dimers) – changes
in the structure of DNA.
6. Ionizing radiation – able to transform molecules in the
cells, stable cells are ionized by radiation (e.g. x-ray) to
unstable cells (free radicals). Changes in binding
compounds.
Scientific Reports: Microbial communities evolve faster in
extreme environments (Li, et.al)
- Checked the relative evolutionary rates
- Checked dN/ds ratio – ratio between non-synonymous
and synonymous substitution between orthologs
(common gene from ancestor)
- Checked transposase – enzyme involved in
transposons (jumping genes)
o Mutation – higher amounts of transposase
- Bacterial species in normal/stable environments does
not normally mutate.
- Microbes in extreme environments (acid drainage)
o Have higher relative evolutionary rates.
o Have higher dN/ds ratio, beneficial orthologs
exist in microbial species.
o Have higher copies transposase gene,
transposons are important mechanism to mutate
therefore more transposase (enzyme) are
needed.
Nature Genetics: Diet and the evolution of human amylase gene
copy number variation (Perry, et.al)
- Looked at the copy numbers of amylase gene, amylase
is responsible for breakdown of starch.
- Samples are Europeans, Americans, and Japanese.
- More copies of human amylase gene on Europeans and
Japanese.
- Diet of the two groups is more on starchy foods (rice,
pasta, potatoes, etc.). Different diet produces different
number of copies of amylase gene.
- Copy number – based on the genome, not on the
expression of genes and proteins.
Transposable Elements
- DNA elements of the genome that can be transferred
from one region to another (jumping genes).
1. Transposons – DNA as is
o Autonomous – ITR (Inverted terminal repeats),
ORF (Open reading frame) encodes for
transposase gene, ITR are intact and have
functional transposase
o Nonautonomous – cannot move as is due to lack
of functional transposase, needs to wait for
available transposons to move.
o Examples: Maize transposons: Ac-Ds system
▪ Ac – activator
▪ Ds – dissociation
▪ In absence of Ac, Ds is not transposable.
▪ When Ac is present, Ds may be
transposed.
▪ Ds can move into and out of another
gene.

2. Retrotransposons – DNA needed to be transcribed and
RNA will produce Integrase and RT.
o Long-terminal repeat (LTR)
o Non-LTR
Mutations and Diseases
1. Monogenic – to induce a disease, only a single gene is
needed to be affected.
2. Polygenic – before disease is expressed, many genes
must be affected.
Repair Mechanisms
- Proofreading – polymerases (exonuclease activity)
- Mismatch Repair – endonuclease cut the mismatch part
and exonuclease degrade that part, polymerase and
ligase acts to seal the gap
- Post-replication Repair – RecA protein direct
recombinational exchange due to lesions, gets donor
strand as a template to synthesize the gap
- SOS Repair – found in bacteria, activation or expression
of genes (20) with different functions – act on
lesions/gaps to proceed DNA replication.
o Prone to damages and mutations – very random,
it forces to resolve the gaps
- Photoreactivation – exposure of visible light will activate
photolyase that cleaves the dimers
- Base and Nucleotide Excision – correcting the base
pairing by removal of the base.
o Mismatch are recognized by glycosylases,
enzyme that cuts glycosidic bonds between base
and sugar – removal of pyrimidine (apyrimidinic
site)
o AP endonuclease enzyme removes
phosphodiester backbone to allow DNA
polymerase to insert new nucleotide sealed by
ligase.
- Double Stranded Break – both strands have errors
(over-hanging sequences)
o Homologous recombination repair – gets sister
chromatids to act as template to synthesize DNA
on the damaged regions.
o Non-homologous end-joining – joining of the two
broken strands which can still cause mutation.
Lab Applications
1. Mutation vs. Phenotypic Plasticity
Phenotypic Plasticity – changes in phenotype, expression of
genes due to exposure (varying temperatures)
Mutation – changes in genetic composition
 2. Antibiotic Resistance
Gradient Plate Method – agar with and without antibiotics,
gradient is due to concentration of antibiotics.
- Middle colonies are probably antibiotic resistance
microbes (in which mutation is induced)

Research Applications
Green tea extract inhibits biofilm formation in acyl homoserine
lactone-producing, antibiotic-resistant Morganella morganii
isolated from Pasig River, Philippines (Guzman, et.al)
- Looked for antibiotic-resistant microorganisms
- Made use of mutant strains – expressed the violet
pigments.
o It may be autoinducers are shared.
o Horizontal gene transfer.
Clinically relevant mutations in core metabolic genes confer
antibiotic resistance (Lopatkin, et.al)
- Interactions between two different genes. They can
affect one another despite having different functions and
away from each other.
- Mutation in metabolic genes develops resistance.
Improvement of Bacillus strains by mutation for overproduction
of exopolygalacturonases (Muzzamal & Latif, 2015)
- Mutation of genes (induced or targeted) changes
production of compounds.