WEEK 2

Genetics is the scientific study of genes, heredity, and the variation of inherited characteristics in living
organisms.

Mitosis and Meiosis

Mitosis and meiosis are two types of cell division.
 Mitosis is a process where a single cell divides into two identical daughter cells. Each daughter cell has
the same number of chromosomes as the parent cell (diploid, 2n). This process is crucial for growth,
repair, and asexual reproduction.
 Meiosis is a special type of cell division that reduces the chromosome number by half, creating four
unique daughter cells, each with half the number of chromosomes of the parent cell (haploid, n). This
process produces gametes (sperm and eggs) for sexual reproduction.

Chromosomes
Chromosomes are thread-like structures located inside the nucleus of animal and plant cells. They are made of
protein and a single molecule of deoxyribonucleic acid (DNA). Chromosomes carry the genetic information
from parents to offspring. Humans have 23 pairs of chromosomes, for a total of 46.

DNA
Deoxyribonucleic acid (DNA) is the molecule that carries the genetic instructions for the development,
functioning, growth, and reproduction of all known organisms and many viruses. DNA is famous for its double
helix structure, resembling a twisted ladder. The "rungs" of the ladder are made of four chemical bases: adenine
(A), guanine (G), cytosine (C), and thymine (T).

Genetic Diversity
Genetic diversity refers to the total number of different genetic characteristics in the genetic makeup of a
species. It's the "raw material" for evolution and allows populations to adapt to changing environments. High
genetic diversity is generally beneficial for a population's long-term survival.

Genetic Drift
Genetic drift is a mechanism of evolution characterized by random fluctuations in the frequency of gene
variants (alleles) in a population. It happens by chance, not by natural selection. Its effects are strongest in small
populations, where random events can cause an allele to become much more or less common, or even
disappear entirely.

Genetic Variation
Genetic variation describes the differences in DNA sequences among individuals within a population. These
differences can result in different traits, such as eye color or blood type. The main sources of genetic variation
are mutation and genetic recombination (which occurs during meiosis).

Genome
The genome is the complete set of genetic material or DNA in an organism. It contains all the instructions
needed for an organism to grow, develop, and function. In humans, the genome consists of about 3 billion DNA
base pairs.

Heredity
Heredity, also known as inheritance, is the process by which traits are passed down from parents to their
offspring. You inherit genes from your parents, which is why you might have your mother's eyes or your father's
nose.

Mutation
A mutation is a permanent change in the DNA sequence. Mutations can arise from errors in DNA replication or
from exposure to mutagens like UV radiation. They can be beneficial, neutral, or harmful. Mutations are the
ultimate source of all genetic variation.
 WEEK 3

Mendelian genetics, named after the 19th-century Augustinian friar Gregor Mendel, forms the
foundation of our understanding of heredity.1 Through his meticulous experiments with pea plants,
Mendel uncovered the fundamental principles of how traits are passed from parents to
offspring.2 His work established that traits are inherited as discrete units, now known as genes,
and that their inheritance follows predictable patterns.

Key Terminology in Mendelian Genetics

Before diving into Mendel's laws, it's helpful to understand a few key terms:
 Allele: An allele is a specific version of a gene. For example, the gene for flower color in
pea plants has two alleles: one for purple flowers and one for white flowers.4
 Genotype: This refers to the genetic makeup of an organism, specifically the combination
of alleles it carries for a particular trait.
 Phenotype: This is the observable physical or biochemical characteristic of an organism,
which is determined by its genotype.5
 Homozygous: An organism is homozygous for a trait if it has two identical alleles for that
gene (e.g., two alleles for purple flowers).6
 Heterozygous: An organism is heterozygous for a trait if it has two different alleles for that
gene (e.g., one allele for purple flowers and one for white flowers).7

Mendel's Laws of Inheritance

Mendel's experiments led him to formulate three fundamental laws of inheritance:

1. The Law of Dominance

This law states that when an organism has two different alleles for a trait (is heterozygous), one
allele, the dominant one, will be expressed in the phenotype, masking the effect of the other
allele, the recessive one. The recessive allele is only expressed when the organism has two
copies of it (is homozygous).
For example, when Mendel crossed a purebred purple-flowered pea plant with a purebred white-
flowered pea plant, all the offspring had purple flowers. This is because the allele for purple
flowers is dominant over the allele for white flowers.

2. The Law of Segregation

This law states that during the formation of gametes (sperm or egg cells), the two alleles for a trait
separate, or segregate, from each other so that each gamete receives only one allele. This
means that an offspring inherits one allele from each parent for each trait.

3. The Law of Independent Assortment

Mendel's third law states that the alleles for different traits are inherited independently of one
another. For instance, the inheritance of flower color does not influence the inheritance of seed
shape. This independent assortment of genes leads to a greater variety of genetic combinations in
offspring.
These foundational principles, while having exceptions and further complexities discovered in
modern genetics, remain a cornerstone of biology and explain the basic mechanics of how we
inherit our traits.
 WEEK 4

Chromosome mapping determines the position and relative distances of genes on

a chromosome. The methods used differ significantly between complex eukaryotes
and simpler organisms like bacteria and their viruses, bacteriophages.

Chromosome Mapping in Eukaryotes

In eukaryotes, mapping is primarily approached in two ways: genetic mapping
and physical mapping.

 Genetic Mapping (or Linkage Mapping): This method uses recombination

frequencies to determine the relative positions of genes.

o Principle: During meiosis, crossing over can occur between

homologous chromosomes, leading to the recombination of linked genes
(genes on the same chromosome). The farther apart two genes are on a
chromosome, the higher the probability that a crossover event will occur
between them.

o Method: By performing genetic crosses (like a three-point test cross)

and analyzing the phenotypes of the offspring, scientists can calculate
the recombination frequency between genes.

o Unit of Measurement: The distance is measured in map

units or centiMorgans (cM). One map unit is equal to a 1%
recombination frequency.

 Physical Mapping: This approach determines the actual physical distance

between genes, measured in nucleotide base pairs.

o Principle: It involves directly examining the DNA molecule.

o Methods: Techniques have evolved from using restriction enzymes to

cut DNA at specific sites (restriction mapping) to modern high-throughput
DNA sequencing. Sequencing the entire genome is the most detailed
physical map possible, providing the precise location of every gene.

Genetic Analysis and Mapping in Bacteria and Bacteriophages

Because bacteria and bacteriophages reproduce differently than eukaryotes
and have much smaller genomes, their mapping techniques rely on different
mechanisms of gene transfer.

Mapping in Bacteria
Bacteria transfer genetic material horizontally (from one cell to another), and
these processes can be exploited for mapping.
  Conjugation Mapping: Conjugation is the transfer of DNA through direct cell-
to-cell contact via a pilus. In Hfr (high-frequency recombination) cells, the
fertility factor (F factor) is integrated into the bacterial chromosome.

o Method: An Hfr strain is mixed with a recipient (F-) strain. The transfer of
the Hfr chromosome into the F- cell is sequential. By interrupting the
mating at different time intervals (e.g., in a blender), researchers can
determine the order in which genes are transferred. The longer the time
allowed, the more genes are transferred. This creates a map based on
"minutes" of transfer.

 Transformation Mapping: Transformation is the uptake of naked DNA from

the environment by a bacterial cell.
o Method: If two genes are close together on the chromosome, they are
likely to be on the same small fragment of DNA that is taken up by the
recipient cell. The frequency of this co-transformation is used to
determine the relative distance between genes; a higher frequency
means the genes are closer together.

 Transduction Mapping: Transduction involves the transfer of bacterial DNA

by a bacteriophage (a virus that infects bacteria).

Method: During viral assembly, a phage can mistakenly package a

piece of the host bacterium's DNA. When this phage infects a new
bacterium, it injects the previous host's DNA. The frequency of co-
transduction (two genes being transferred together) indicates how
close they are on the bacterial chromosome.

Mapping in Bacteriophages
Bacteriophage genomes can be mapped by analyzing the results of mixed
infections.

 Method: A single bacterial host cell is simultaneously infected with two

different mutant strains of a bacteriophage. Inside the host, the phage DNA
can undergo recombination. The resulting progeny phages are analyzed for
recombinant phenotypes.

 Principle: Similar to eukaryotic mapping, the recombination

frequency between two phage genes is calculated. A lower frequency
indicates that the genes are closer together on the phage's chromosome.
 WEEK 5

Sex is most often determined by specific sex chromosomes that carry genes influencing the
development of sexual characteristics. Changes affecting the number or structure of these, or any
other chromosomes, are known as chromosome mutations.

Sex Determination and Sex Chromosomes

Sex determination is the biological system that establishes the development of sexual
characteristics.2 In many organisms, this is controlled by sex chromosomes.3

 XX/XY System: This is the system found in humans, most mammals, and some
insects.4 Females have two X chromosomes (XX), while males have one X and one Y
chromosome (XY).5 The Y chromosome in humans contains the SRY gene (Sex-
determining Region Y), which triggers male development.6
 ZZ/ZW System: This system is found in birds, some reptiles, and some insects.7 Males
have two Z chromosomes (ZZ), and females have one Z and one W chromosome (ZW). In
this case, the female determines the sex of the offspring.8
 XX/X0 System: In some insects like grasshoppers, females have two X chromosomes
(XX), but males have only one (X0). The "0" indicates the absence of a second sex
chromosome.9

Chromosome Mutations: Variation in Number

This type of mutation involves a change in the total number of chromosomes. 10 It's often
caused by nondisjunction, the failure of chromosomes to separate properly during meiosis.

 Aneuploidy: The gain or loss of one or more individual chromosomes.11

o Monosomy (122n−1): The loss of a single chromosome.13 An example is Turner
Syndrome in humans, where an individual has only one X chromosome (45, X0)
and is phenotypically female.14
o Trisomy (152n+1): The gain of an extra chromosome.16 A common example is Down
Syndrome, which results from an extra copy of chromosome 21 (Trisomy
21).17 Another example is Klinefelter Syndrome (47, XXY), where a male has an
extra X chromosome.18
 Polyploidy: The condition of having more than two complete sets of chromosomes (e.g.,
triploidy 193n, tetraploidy 204n).21 Polyploidy is common and often beneficial in plants,
leading to larger and more robust individuals.22 It is rare and typically lethal in animals.23

Chromosome Mutations: Variation in Arrangement

These mutations alter the structure of a single chromosome.

 Deletion: A segment of a chromosome is lost or deleted.24 Cri-du-chat syndrome is

caused by a deletion on the short arm of chromosome 5.25
 Duplication: A segment of a chromosome is repeated, resulting in extra genetic
material.26
 Inversion: A chromosome segment breaks off, flips 180 degrees, and
reattaches.27 While the genetic information is still present, the change in order can affect
gene expression.
 Translocation: A segment of one chromosome breaks off and attaches to a different,
non-homologous chromosome.28 A well-known example is the Philadelphia
chromosome, a translocation between chromosomes 9 and 22 associated with chronic
myeloid leukemia.29
 WEEK 6

DNA structure and analysis.

The Nature and Structure of DNA and Genes

 Early experiments, like the Avery–MacLeod–McCarty experiment, deduced that DNA
(deoxyribonucleic acid)is the molecule of heredity.1 DNA has a double helix structure,
resembling a twisted ladder.2 The sides are made of a sugar-phosphate backbone, and the
rungs are pairs of four nitrogenous bases: adenine (A), guanine (G), cytosine (C),
and thymine (T).3 These bases pair in a specific way: A always pairs with T, and C always
pairs with G.
 A gene is a specific segment of DNA that provides instructions for building a protein or
functional RNA molecule.4 In eukaryotes, genes are composed of coding regions
called exons and non-coding intervening sequences called introns.5 The genome is the
complete set of an organism's DNA.6

Genome and Chromosome Structure

The organization of the genome varies between organisms.
 Prokaryotes (like bacteria) typically have a single, circular chromosome located in a region
called the nucleoid.7
 Eukaryotes (like plants and animals) have multiple, linear chromosomes housed within a
nucleus.8
In eukaryotes, the immense length of DNA is compacted to fit inside the nucleus. The DNA double
helix wraps around proteins called histones, forming structures called nucleosomes.9 This DNA-
protein complex, known as chromatin, coils and condenses further to form the
visible chromosomes seen during cell division.10

The Central Dogma: From DNA to Protein

The genetic information in DNA is expressed in a two-step process.11
1. Transcription: The information from a gene is copied into a molecule of messenger RNA
(mRNA).12This process is governed by the genetic code, where three-base sequences of
DNA (codons) correspond to specific amino acids.13
2. Translation: The mRNA molecule travels to a ribosome, where its code is read to
assemble a chain of amino acids, forming a protein.14

DNA Replication and Recombination

 DNA Replication: Before a cell divides, it must copy its entire genome.15 DNA replication
is semi-conservative, meaning each new DNA molecule consists of one original strand
and one new strand.16This ensures accurate duplication of genetic information.
 Genetic Recombination: This process shuffles genetic material to create new
combinations of alleles.17The most common form is crossing over, which occurs during
meiosis when homologous chromosomes exchange segments.18

DNA Analysis and Technology

 Recombinant DNA Technology: This involves combining DNA from different sources to
create a new, artificial DNA molecule.19 Key tools include restriction enzymes to cut DNA
at specific sites and DNA ligase to join fragments together.20 This technology is used to
create genetically modified organisms (GMOs) and to produce therapeutic proteins like
insulin.21
 DNA Forensics: This field uses unique variations in an individual's DNA for
identification.22 The primary method is DNA fingerprinting, which analyzes highly variable
regions called Short Tandem Repeats (STRs). By comparing the STR profiles from
forensic evidence to suspects, law enforcement can link individuals to crime scenes.23 It is
also used for paternity tests and identifying disaster victims.24
 WEEK 7

The Central Molecular Dogma describes the fundamental flow of genetic information within a
biological system, typically summarized as DNA 1→ RNA 2→ Protein.3 While DNA replication and
transcription (DNA to RNA) are crucial initial steps, the process culminates in translation, where
the genetic code carried by mRNA is used to synthesize proteins.4

Translation and Proteins

Translation is the sophisticated process by which the nucleotide sequence of a messenger
RNA (mRNA) molecule is decoded to produce a specific sequence of amino acids, forming a
polypeptide chain.5 This polypeptide chain then folds into a functional protein.6 This process
occurs in the cytoplasm, primarily on complex molecular machines called ribosomes.7

Key Players in Translation:

1. Messenger RNA (mRNA): Carries the genetic code from the DNA in the nucleus (or
nucleoid in prokaryotes) to the ribosomes in the cytoplasm.8 The code is in the form of
codons, each consisting of three consecutive nucleotides.9
2. Ribosomes: These are made up of ribosomal RNA (rRNA) and ribosomal proteins, forming
two subunits (large and small).10 They provide the site for mRNA binding and the catalytic
activity for peptide bond formation.
3. Transfer RNA (tRNA): Small RNA molecules that act as adaptors.11 Each tRNA molecule
has an anticodon loop that is complementary to a specific mRNA codon, and at its 3' end, it
carries the corresponding amino acid.12
4. Amino Acids: The building blocks of proteins.13 There are 20 common amino acids, each
specified by one or more codons.14
5. Enzymes and Protein Factors: Various enzymes (e.g., aminoacyl-tRNA synthetases) and
protein factors (e.g., initiation factors, elongation factors, release factors) are required to
facilitate and regulate the different stages of translation.15
6.
Stages of Translation:
Translation proceeds in three main stages:16
1. Initiation:
o The small ribosomal subunit binds to the mRNA molecule, typically at the 5' end in
eukaryotes (aided by the 5' cap) or at specific Shine-Dalgarno sequences in
prokaryotes.17
o The initiator tRNA, carrying methionine (or formylmethionine in prokaryotes), binds to
the start codon (AUG) on the mRNA.18
o The large ribosomal subunit then joins the complex, forming a complete functional
ribosome.19
2. Elongation:
o Codon Recognition: A new tRNA molecule, carrying its specific amino acid, enters
the A (aminoacyl) site of the ribosome, matching its anticodon with the next codon on
the mRNA.20
o Peptide Bond Formation: The ribosome catalyzes the formation of a peptide bond
between the amino acid on the tRNA in the A site and the growing polypeptide chain
attached to the tRNA in the P (peptidyl) site.21
o Translocation: The ribosome moves along the mRNA by one codon. The tRNA that
was in the P site (now uncharged) moves to the E (exit) site and is released. 22 The
tRNA that was in the A site (now carrying the growing polypeptide) moves to the P
site, making the A site available for the next incoming tRNA.23 This process repeats,
adding amino acids one by one to the polypeptide chain.24
3. Termination:
o Elongation continues until a stop codon (UAA, UAG, or UGA) is reached on the
mRNA.25
 o There are no tRNAs that recognize stop codons. Instead, release factors bind to the
stop codon in the A site.26
o This binding causes the hydrolysis of the bond between the polypeptide and the
tRNA in the P site, releasing the completed polypeptide chain from the ribosome.
o The ribosomal subunits then dissociate from the mRNA, ready to initiate another
round of translation.27

Proteins: The End Products

The polypeptide chain synthesized during translation is not yet a functional protein. It must
undergo foldingand often post-translational modifications to become biologically active.
 Folding: The linear sequence of amino acids dictates the unique three-dimensional
structure of a protein.28 This folding is often spontaneous, driven by interactions between
amino acid side chains, but can also be aided by chaperone proteins.29 The final 3D
structure (conformation) is critical for protein function.30
 Post-translational Modifications (PTMs): These are chemical modifications that occur to
a protein after its synthesis. PTMs can significantly alter a protein's function, stability,
localization, and interactions. Examples include:
o Phosphorylation: Addition of a phosphate group, often involved in signaling
pathways.31
o Glycosylation: Addition of carbohydrate chains, important for cell recognition and
protein stability.
o Acetylation: Addition of an acetyl group.
o Ubiquitination: Tagging with ubiquitin for protein degradation.32
o Cleavage: Proteolytic removal of specific peptide segments.

Functions of Proteins:
Proteins are incredibly diverse and perform a vast array of essential functions within living
organisms, including:
 Enzymatic Catalysis: Enzymes are proteins that accelerate biochemical reactions (e.g.,
DNA polymerase, amylase).33
 Structural Support: Provide shape and support to cells and tissues (e.g., collagen,
keratin).34
 Transport: Carry molecules across membranes or throughout the body (e.g., hemoglobin,
membrane transporters).35
 Immune Defense: Identify and neutralize pathogens (e.g., antibodies).
 Signaling and Communication: Transmit signals within and between cells (e.g.,
hormones like insulin, receptors).
 Movement: Enable cellular and organismal motion (e.g., actin, myosin in muscle
contraction).
 Storage: Store ions and molecules (e.g., ferritin stores iron).36
 Regulation: Control gene expression and other cellular processes.37

In summary, translation is the crucial bridge that connects the genetic information encoded in
nucleic acids to the functional machinery of the cell – proteins.38 Without accurate and efficient
translation, the genetic blueprint would remain unexpressed, and life as we know it would not be
possible.
 WEEK 8

Genes are the fundamental units of heredity, segments of DNA that contain the instructions for
building and maintaining an organism.1 However, these instructions are not immutable.2 Changes
can occur in the DNA sequence, leading to variations that are critical for evolution but can also
cause disease.3 These changes are broadly categorized as gene mutations, and organisms have
evolved intricate DNA repair mechanisms to correct them. Additionally, certain DNA sequences,
known as transposable elements, have the remarkable ability to move within the genome, a
process called transposition, further contributing to genetic variation.4

A gene mutation is a permanent alteration in the DNA sequence that makes up a gene, such that
the sequence differs from what is found in most people. Mutations can range in size from a single
DNA building block (nucleotide) to a large segment of a chromosome that includes multiple
genes.5

Types of Gene Mutations:

Gene mutations can be broadly classified based on how they alter the DNA sequence:
1. Point Mutations (Base-Pair Substitutions): These involve a change in a single nucleotide
base pair.6
o Silent Mutation: A change in a nucleotide that does not alter the amino acid
sequence of the protein.7 This occurs because the genetic code is redundant
(multiple codons can code for the same amino acid).8
o Missense Mutation: A change in a nucleotide that results in a different amino acid
being incorporated into the protein.9 The effect on protein function can range from
neutral to severe, depending on the new amino acid's properties and its location in
the protein.
o Nonsense Mutation: A change in a nucleotide that converts a codon into a stop
codon, leading to premature termination of protein synthesis.10 This often produces a
truncated, non-functional protein.11
2. Insertions: The addition of one or more extra nucleotides into a DNA sequence.12
3. Deletions: The removal of one or more nucleotides from a DNA sequence.13
4. Frameshift Mutations: These occur when the number of inserted or deleted nucleotides is
not a multiple of three.14 Since codons are read in groups of three, a frameshift mutation
alters the reading frame of the genetic code, changing all downstream codons and usually
leading to a completely non-functional protein.15 Insertions and deletions that are not
multiples of three cause frameshifts.16
5. Duplications: A segment of DNA is copied and repeated, leading to extra copies of a gene
or a chromosomal segment.17 This can increase gene dosage, potentially affecting gene
expression.18
6. Inversions: A segment of DNA is reversed end-to-end within the chromosome.19 This can
disrupt gene function if the breakpoints occur within a gene or its regulatory regions. 20
7. Repeat Expansions: An increase in the number of times that a short DNA sequence (e.g.,
trinucleotide repeats like CAG) is repeated. If the number of repeats exceeds a certain
threshold, it can lead to genetic disorders (e.g., Huntington's disease).21

Causes of Gene Mutations:

 Spontaneous Mutations: Occur naturally due to errors during DNA replication,
recombination, or from chemical instability of DNA bases.22
 Induced Mutations: Caused by environmental factors called mutagens.23
o Chemical Mutagens: Certain chemicals can modify DNA bases, leading to
mispairing during replication.24
o Radiation:
 Ionizing Radiation (e.g., X-rays, gamma rays): Can cause double-strand
breaks in DNA and other types of damage.25
  Non-ionizing Radiation (e.g., UV light): Can cause the formation of
pyrimidine dimers (e.g., thymine dimers), which distort the DNA helix and
interfere with replication and transcription.26
DNA Repair
Given the constant threat of DNA damage from both endogenous and exogenous sources, living
organisms have evolved a sophisticated array of DNA repair mechanisms to maintain genomic
integrity.27 These systems detect and correct errors and damage in the DNA, preventing the
accumulation of harmful mutations.28

Major DNA Repair Mechanisms:

1. Direct Reversal: Some types of DNA damage can be directly reversed without cutting out
any part of the DNA strand.29
o Photoreactivation: (Not active in humans) An enzyme called photolyase uses
energy from visible light to directly break the covalent bonds in pyrimidine dimers
caused by UV radiation, restoring the original bases.30
o Methyltransferase Activity: Certain enzymes can remove alkyl groups (e.g., methyl
groups) directly from modified bases, restoring the original base.31
2. Excision Repair: This is a broad category where the damaged or incorrect DNA segment
is excised (cut out) and then replaced with newly synthesized DNA using the undamaged
strand as a template.32
o Base Excision Repair (BER): This pathway deals with small, non-helix-distorting
lesions, such as damaged or modified bases (e.g., oxidized bases, deaminated
bases, uracil incorporation).33
1. A DNA glycosylase recognizes and removes the damaged base, creating an
AP (apurinic/apyrimidinic) site.34
2. An AP endonuclease cleaves the phosphodiester bond at the AP site.35
3. DNA polymerase fills the gap with the correct nucleotide.
4. DNA ligase seals the nick in the sugar-phosphate backbone.36
o Nucleotide Excision Repair (NER): This pathway is crucial for repairing bulky,
helix-distorting lesions, such as UV-induced pyrimidine dimers and bulky chemical
adducts.37
1. Recognition of the distortion in the DNA helix.
2. The damaged segment (a stretch of about 12-30 nucleotides) is excised by
nucleases on both sides of the lesion.
3. DNA polymerase fills the gap using the undamaged strand as a template.
4. DNA ligase seals the remaining nick.38
3. Mismatch Repair (MMR): This system corrects errors that escape the proofreading activity
of DNA polymerase during replication (e.g., mismatched base pairs, small insertions or
deletions).39
o The MMR system identifies the newly synthesized strand (often by methylation
patterns in prokaryotes, or by nicks in eukaryotes) and selectively removes the
incorrect base(s) from that strand.40
o Exonucleases degrade the incorrect segment.41
o DNA polymerase fills the gap.
o DNA ligase seals the nick.42
4. Double-Strand Break (DSB) Repair: These are highly dangerous lesions that can lead to
chromosomal rearrangements and cell death if not repaired correctly.
o Non-Homologous End Joining (NHEJ): A "quick and dirty" repair mechanism that
ligates broken DNA ends together without a homologous template. It is often error-
prone but essential for preventing chromosome fragmentation.
o Homologous Recombination (HR): A more accurate repair pathway that uses a
homologous DNA sequence (e.g., sister chromatid after replication) as a template to
repair the broken DNA strands. This is a high-fidelity repair mechanism.
Transposition
Transposition is a process by which specific DNA sequences, known as transposable elements
(TEs) or "jumping genes," move from one location to another within a genome.43 TEs can insert
themselves into new positions, potentially disrupting genes, altering gene expression, or creating
new gene combinations.44

Types of Transposable Elements:

1. Class I Transposons (Retrotransposons): These elements transpose via an RNA
intermediate.
o They are transcribed into an RNA molecule.
o This RNA is then reverse-transcribed into DNA by a reverse transcriptase enzyme
(often encoded within the retrotransposon itself).46
o The newly synthesized DNA copy is then inserted into a new location in the genome.
o Retrotransposons often leave a copy of themselves at the original site, leading to an
increase in their copy number in the genome.47
o Examples include LINEs (Long Interspersed Nuclear Elements) and SINEs (Short
Interspersed Nuclear Elements), which make up a significant portion of the human
genome.
2. Class II Transposons (DNA Transposons): These elements move directly as DNA.48
o They typically use a "cut-and-paste" mechanism: the transposon DNA is excised
from its original location and inserted into a new target site.49
o This process is catalyzed by an enzyme called transposase, usually encoded within
the transposon.50
o Some DNA transposons can also use a "copy-and-paste" (replicative transposition)
mechanism, similar to retrotransposons, where a copy is made before insertion.51
Impact of Transposition:
 Mutagenesis:
o Insertional Mutagenesis: If a transposable element inserts into a gene's coding
region or a regulatory sequence (like a promoter or enhancer), it can disrupt gene
function, leading to a mutation.53
o Deletions/Rearrangements: When TEs excise, they can sometimes carry along
adjacent genomic DNA, causing deletions, or their activity can lead to larger
chromosomal rearrangements like inversions or translocations through
recombination between homologous TE copies.
 Genetic Variation and Evolution: While often mutagenic, TEs are a significant source of
genetic variation, which is the raw material for evolution.54 They can:
o Create new gene combinations.
o Alter gene expression patterns by inserting near genes and providing new regulatory
elements.55
o Contribute to genome evolution by acting as sites for recombination or by introducing
new genetic material.56
 Genome Size and Structure: TEs can significantly increase genome size, especially
retrotransposons, as they multiply and spread throughout the genome.57 They also
contribute to the complex structural organization of chromosomes.
 Gene Regulation: In some cases, TEs can contribute novel regulatory sequences, such as
promoters or enhancers, that can alter the expression of nearby genes.58
 Diseases: Transposon insertions have been implicated in various human genetic diseases,
including hemophilia, Duchenne muscular dystrophy, and some cancers.59

In summary, gene mutations are changes in the DNA sequence, ranging from single base pair
alterations to large chromosomal rearrangements.60 Organisms possess sophisticated DNA repair
mechanisms to correct these changes and maintain genomic integrity.61 Transposition, the
movement of mobile genetic elements, is another dynamic process that can cause mutations and
contribute significantly to genetic variation and genome evolution.62 The interplay between
mutation, repair, and transposition drives the continuous evolution of life.
WEEK 9

Gene Expression: From Bacteria to Biotech

Gene expression, the fundamental process by which information from a gene is used in the
synthesis of a functional gene product, is a tightly controlled mechanism essential for all life. 1 This
intricate regulation allows organisms to respond to environmental changes, differentiate into
specialized cells, and maintain cellular homeostasis.2 This overview will delve into the diverse
strategies employed by both prokaryotes and eukaryotes to control gene expression at various
stages, concluding with a discussion of the revolutionary CRISPR-Cas system for genome editing.

Regulation of Gene Expression in Bacteria: The Operon Model

Bacteria, with their relatively simple cellular structure, primarily regulate gene expression at the
transcriptional level.3 The cornerstone of bacterial gene regulation is the operon, a cluster of
functionally related genes under the control of a single promoter and operator.4
 Operon Structure: An operon typically consists of:
o Promoter: The DNA sequence where RNA polymerase binds to initiate
transcription.5
o Operator: A regulatory DNA sequence located within or adjacent to the promoter, to
which a repressor protein can bind.6
o Structural Genes: Genes that code for proteins involved in a specific metabolic
pathway.7
o Regulatory Gene: A gene located elsewhere on the chromosome that codes for
aressor or activator protein.
 Negative Control (Repressible and Inducible Operons):
o Inducible Operons (e.g., lac operon): These operons are typically "off" and are
turned "on" in the presence of an inducer molecule.8 The lac operon, responsible for
lactose metabolism, is a classic example.9 In the absence of lactose, a repressor
protein binds to the operator, blocking RNA polymerase.10 When lactose is present, it
is converted to allolactose, which acts as an inducer by binding to the repressor,
causing it to detach from the operator and allowing transcription to proceed.11
o Repressible Operons (e.g., trp operon): These operons are typically "on" and are
turned "off" in the presence of a corepressor molecule.12 The trp operon, involved in
tryptophan synthesis, is an example.13 When tryptophan levels are low, the repressor
is inactive, and the genes are transcribed. When tryptophan is abundant, it acts as a
corepressor, binding to the repressor and enabling it to bind to the operator, thereby
halting tryptophan synthesis.14
 Positive Control (e.g., CAP-cAMP system): In addition to negative control, some bacterial
operons are also subject to positive control, which enhances gene expression.15 For
instance, the catabolite activator protein (CAP), when bound to cyclic AMP (cAMP), can
bind to the promoter region of the lac operon, increasing RNA polymerase's affinity for the
promoter and thus promoting transcription, especially when glucose (the preferred energy
source) is scarce.16

Transcriptional Regulation in Eukaryotes: A Multi-Layered Approach

Eukaryotic gene expression is vastly more complex than in bacteria, reflecting the greater
complexity of eukaryotic genomes and the need for cell-type specific expression.17 Transcriptional
regulation is the primary control point, involving a sophisticated interplay of DNA sequences and
proteins.18
 Chromatin Structure: Eukaryotic DNA is packaged into chromatin, a complex of DNA and
histone proteins.19 The accessibility of genes to transcriptional machinery is heavily
influenced by chromatin structure:
o Euchromatin: Loosely packed chromatin, generally transcriptionally active.
o Heterochromatin: Densely packed chromatin, generally transcriptionally inactive.
 o Histone Modification: Chemical modifications to histone tails (e.g., acetylation,
methylation, phosphorylation) can alter chromatin structure and influence gene
accessibility.20 For example, histone acetylation generally loosens chromatin,
promoting transcription, while deacetylation compacts it, repressing transcription.21
o DNA Methylation: The addition of methyl groups to cytosine bases, often in CpG
islands near gene promoters, is typically associated with gene silencing.22
 Transcription Factors: These are proteins that bind to specific DNA sequences and
regulate transcription.23
o General (Basal) Transcription Factors: Essential for the transcription of all protein-
coding genes, they bind to the promoter region (e.g., TATA box) and recruit RNA
polymerase II.24
o Specific (Regulatory) Transcription Factors: These bind to control elements,
which are regulatory DNA sequences that can be located far from the promoter. 25
 Enhancers: Distal DNA sequences that, when bound by activator proteins,
can significantly boost transcription rates. They can act over long distances
and are often tissue-specific.
 Silencers: DNA sequences that, when bound by repressor proteins, inhibit
transcription.26
 Mediator Complex: A large protein complex that acts as a bridge between transcription
factors bound at enhancers and the general transcription factors and RNA polymerase II at
theoter, facilitating the formation of a functional transcription initiation complex. 27

Posttranscriptional Regulation of Gene Expression in Eukaryotes: Fine-Tuning

and Rapid Response
Beyond transcription, eukaryotes employ numerous mechanisms to regulate gene expression at
posttranscriptional stages, providing additional layers of control and allowing for rapid adjustments
to protein levels.28
 RNA Processing:
o Alternative Splicing: A single pre-mRNA molecule can be spliced in different ways,
leading to the production of multiple distinct mRNA isoforms (and thus different
proteins) from the same gene. This significantly expands the coding capacity of the
genome.
o 5' Capping and 3' Polyadenylation: These modifications are crucial for mRNA
stability, transport from the nucleus, and efficient translation.29 Regulation of these
processes can impact gene expression.
 mRNA Stability: The lifespan of an mRNA molecule significantly influences the amount of
protein produced.30 mRNA stability is regulated by:
o Untranslated Regions (UTRs): Sequences at the 5' and 3' ends of mRNA that do
not code for protein but contain regulatory elements that can bind to proteins or
microRNAs, influencing mRNA degradation or stabilization.31
o RNA-binding Proteins (RBPs): Proteins that bind to specific sequences in mRNA
and can either stabilize or destabilize the mRNA.32
 Translational Control: The rate at which mRNA is translated into protein can be
regulated.33
o Initiation Factors: The availability and activity of translation initiation factors can be
regulated, affecting the overall rate of protein synthesis.
o microRNAs (miRNAs): Small non-coding RNA molecules that bind to
complementary sequences in mRNA, typically in the 3' UTR.34 This binding can lead
to either mRNA degradation or translational repression, effectively silencing gene
expression.
 Protein Processing and Degradation:
o Post-translational Modifications: After translation, proteins can undergo various
modifications (e.g., phosphorylation, glycosylation, ubiquitination) that alter their
activity, localization, or stability.35
 o Protein Degradation (Proteasome): The ubiquitin-proteasome system tags
proteins for degradation, providing a mechanism for rapid turnover of proteins and
control over their steady-state levels.36
CRISPR-Cas and Genome Editing: Precision Engineering of Life
The discovery of the clustered regularly interspaced short palindromic repeats (CRISPR) and
CRISPR-associated (Cas) protein system has revolutionized the field of genome editing, providing
a powerful and precise tool for modifying DNA sequences.37
 Natural Role in Bacteria: In bacteria, CRISPR-Cas serves as an adaptive immune system
against invading viruses and plasmids.38 Bacteria incorporate short fragments of foreign
DNA into their CRISPR loci. These CRISPR RNAs (crRNAs) then guide Cas proteins to
target and cleave complementary foreign DNA, thereby neutralizing the threat.39
 Mechanism of Genome Editing: The most widely used CRISPR-Cas system for genome
editing is CRISPR-Cas9:
1. Guide RNA (gRNA): A synthetic RNA molecule is engineered to contain a "spacer"
sequence that is complementary to the target DNA sequence to be edited, fused to a
"scaffold" sequence that binds to the Cas9 enzyme.40
2. Cas9 Enzyme: A nuclease that, when guided by the gRNA, creates a double-strand
break (DSB) at the specific target site in the DNA.41
3. DNA Repair Pathways: Once the DSB is created, the cell's natural DNA repair
mechanisms are activated:
 Non-Homologous End Joining (NHEJ): An error-prone pathway that ligates
the broken ends, often resulting in small insertions or deletions (indels) that
can disrupt a gene (gene knockout).42
 Homology-Directed Repair (HDR): A precise repair pathway that uses a
homologous DNA template (provided by researchers) to repair the break,
allowing for the precise insertion, deletion, or correction of specific DNA
sequences (gene correction/knock-in).43
 Applications of CRISPR-Cas:
o Basic Research: Studying gene function by creating gene knockouts or introducing
specific mutations in cell lines and model organisms.
o Gene Therapy: Correcting disease-causing mutations in genetic disorders (e.g.,
cystic fibrosis, sickle cell anemia) by excising or replacing faulty genes.44
o Agriculture: Engineering crops with improved traits such as disease resistance,
herbicide tolerance, or enhanced nutritional value.45
o Biotechnology: Creating genetically modified organisms for industrial production of
valuable compounds.
 Ethical Considerations: While CRISPR-Cas holds immense promise, its power
necessitates careful ethical consideration, particularly regarding its application in human
germline editing (modifications that would be heritable) and the potential for unintended off-
target effects.46

In conclusion, the regulation of gene expression is a fundamental aspect of biology, orchestrated

through a diverse array of mechanisms in both prokaryotes and eukaryotes.47 From the elegant
simplicity of bacterial operons to the multifaceted control in eukaryotes, these regulatory networks
ensure precise and adaptable gene activity.48 The advent of CRISPR-Cas technology has not only
deepened our understanding of these processes but also provided an unprecedented tool for
manipulating genomes, opening new frontiers in medicine, agriculture, and fundamental biological
research.