CYTOGENETICS PRELIMS FIRST SEM

MMLS 2-2

INTRODUCTION TO CYTOGENETICS

CYTOGENETICS

What is Cytogenetics?

 It is defined as the study of chromosomes, including their behavior, mechanics, and role in
inheritance.
 CYTOLOGY + GENETICS
 “Cytology- The medical and scientific study of cells. Cytology refers to a branch of
pathology, the medical specialty that deals with making diagnoses of diseases and
conditions through the examination of tissue samples from the body.
 “Genetics” study of heredity in general and of genes in particular. Genetics forms one of
the central pillars of biology and overlaps with many other areas, such as agriculture,
medicine, and biotechnology

BASIC TERMS TO REMEMBER:

Allele

 is a term coined to describe a specific copy of a gene. Each allele occupies a specific region on
the chromosome called a gene locus.

Gene

 A part of an organism’s DNA that is passed down from its parents and codes for a specific
function. It is the DNA sequences controlling our traits, are usually found in two copies in
eukaryotic genomes; each copy traits, are usually found in two copies in eukaryotic genomes;
each copy (allele) is inherited from one parent.

Dominant trait

 A trait caused by having either two dominant alleles or one dominant and one recessive allele. It
is allele that is expressed.

Recessive trait

 is a trait that is expressed when an organism has two recessive alleles, or forms of a gene. The
allele that is not expressed.
Chromosome

 A chromosome is an organized package of DNA found in the nucleus of the cell. Humans have 23
pairs of chromosomes--22 pairs of numbered chromosomes, called autosomes, and one pair of
sex chromosomes, X and Y.

Phenotype

 Is used to describe a visible trait. Phenotype can also be affected by the environment in many
real-life cases.

Genotype

 Is used to describe an organism’s set of alleles coding for each trait. Genotype determines
phenotype, an organism's observable features.

Homozygous genotype

 It means that the organism’s genome has two identical alleles for a specific gene. That means
both alleles contribute equally to the appearance of the trait. (YY or yy)

Heterozygous genotype

 In contrast, contains two different forms of a particular gene. (Yy)

BASIS OF CYTOGENETICS

 CHROMOSOME STRUCTURE
 CHROMOSOME BEHAVIOR DURING CELL DIVISION
 GENETIC CONSEQUENCES OF CHROMOSOMAL BEHAVIOR

Brief History of Cytogenetics

CELL DOCTRINE:

 MATTHIAS SCHLEIDEN
 THEODOR SCHWANN
 RUDOLF VIRCHOW
 “THE CELL IS THE FUNDAMENTAL UNIT OF STRUCTURE AND FUNCTION IN ALL LIVING
ORGANISMS”
“ALL FORMS OF LIFE ARE COMPOSED OF CELLS”

 THEODOR SCHWANN
 MATTHIAS SCHLEIDEN

“Cells arise only from pre-existing cells”

 RUDOLF VIRCHOW
UNIVERSALITY OF CELL DIVISION AS THE CENTRAL PHENOMENON IN REPRODUCTION

Fertilization:

CHROMOSOME THEORY OF INHERITANCE

 “THE CHROMOSOMES ARE THE PHYSICAL CARRIERS OF THE GENES”

 “THE BEHAVIOR OF THE CHROMOSOMES DURING MEIOSIS COULD EXPLAIN MENDELIAN
PRINCIPLES”.

CORRELATIONS BETWEEN MENDELIAN FACTORS AND CHROMOSOMES

  CHROMOSOMES EXISTS IN PAIRS
 MENDELIAN FACTORS EXIST IN PAIRS

Brief History of Cytogenetics

Carl Wilhelm von Nägeli (March 1817 – May 1891)

 He was a Swiss botanist. He studied cell division and pollination but became known as the man
who discouraged Gregor Mendel from further work on genetics.
 He first described thread-like structures in the nuclei of plant cells in the 1840s, and what he
called “transitory cytoblasts” are now known as chromosomes.
 Later, in 1888, Waldeyer coined the term “chromosome” after staining techniques had been
developed to make them more discernible (chromos = Greek for color; soma = Greek for body).

Grigorii Andreevich Levitsky (1878)

 First studies on cytology dealt with mitochondria in 1922–1923, Levitsky worked on the book
“The Material Basis of Heredity”.
 Levitsky introduced to karyology the term karyotype, which is fundamental for cytogenetics

Modern genetics began in 1900 with the rediscovery of studies of the monk Gregor Johann Mendel
(1822- 1884).

 He was known as “father of genetics” who formulated laws of inheritance by experimenting

garden pea.
 Mendel tracked the segregation of parental genes and their appearance in the offspring as
dominant or recessive traits.

Brief History of Cytogenetics

 Earlier in the 20th century, Russian biochemist Phoebus Levene (1863-1940) made the initial
steps towards discovering the components of genetic material. He is credited for discovering the
carbohydrate component of both DNA and RNA and how their components are connected, as
well as the structure of nucleotides in 1919 (Ray 2008).
 Oswald Avery (1877-1955) devised an ingenious experiment to find out that it was DNA that
carried the vital information needed for protein expression in the next generation of cells
(O'Connor 2008).
 In 1953, Francis Crick and his colleague James Watson came up with a model for the structure of
DNA (Deoxyribonucleic acid) based off of X-ray diffraction images.
History Timeline

 1842: Wilhelm von Nageli, a Swiss botanist, observed the plant cell.
 1866: Mendel’s research work published under the title of “experiments on plant hybridization.”
 1869: Friedrich Miescher discovered nucleic acid.
 1888: Waldeyer identified the chromosome present in the cell.
 1889: Richard Altmann purified DNA from the protein.
 1905: William Bateson coined the term “genetics”.
 1908: discovery of Hardy-Weinberg’s law.
 1910: Morgan T, explained that the genes are located on the chromosomes. Also, they
experimented on Drosophila Melanogaster and determined the nature of sex-linked traits.
 1923: Griffith F, experimented on bacteria and postulated that DNA is the genetic material.
 1953: Watson and Crick given the structure of DNA

FIELDS OF GENETICS
Molecular genetics

 is an interdisciplinary sub-branch of genetics dealing with the study of the structure and function
of DNA as well as genes (at a molecular level) using techniques such as Polymerase chain
reaction and DNA sequencing.
 Using molecular genetics techniques one can detect pathogenic mutations, SNPs (single
nucleotide polymorphism), minor deletion or duplication at a DNA level. Furthermore, those
techniques can study gene expressions too.

POLYMERASE CHAIN REACTION

 Is a process in which we can amplify millions of copies of a DNA segment of our interest in vitro.
The process is temperaturedependent, divided into three steps.

Cytogenetics

 It is a sub-branch of genetics including the study of inheritance through chromosomal analysis

utilizing techniques such as:
 Karyotyping
 chromosomal staining and chromosomal banding
 Fluorescent in-situ Hybridization
 Structural and numerical chromosomal abnormalities can be screened using cytogenetic
techniques.
Human genetics

 The branch of genetics comprises the study of genetic alterations and its role in the
development of disease especially in humans.
 Using the cytogenetic, molecular genetics, phylogenetic, population genetics, and clinical
genetic methods, any mutation can be characterized which are involved in the development of
the disease.
 We can study,
 The inheritance pattern of disease.
 The severity of the disease.
 Possibility of inheritance in the consecutive generation

Preimplantation genetics

 It is characterizing or profiling the genetic composition of the embryo before implantation.

 Preimplantation genetic techniques are powerful enough to screen the genetic profile of oocyte
or sperm cells before fertilization.
 The major application of preimplantation genetic is to screen high-risk pregnancies.
Clinical genetics

 It involves the study of disease, finding the root of the disease, its adverse effects, and its
inheritance pattern.

Plant genetics

 The branch of genetics deals with the study of genetic variations and chromosomal
abnormalities in plants.
 It includes the study of plant genomes and genetically modified plant species using the
techniques such as karyotyping, PCR, and DNA sequencing. Genetically modified plant species
have tremendous economical value.

Microbial genetics

 It is an applied branch of genetics includes the study of the genes, genotypes ad gene expression
of microorganism for various genetic engineering applications. The study includes genetic
analysis of bacteria, viruses, archaea, protozoa and some fungi.
 The Novel coronavirus COVID-19 infecting people in recent times and causing respiratory
problems is detected accurately using the RT-PCR technique.

RT-PCR MACHINES

Metagenomics

 The branch of genetics that deals with the study and identification of different microorganisms
by processing the environmental samples using modern genetics techniques.
 Shotgun sequencing and PCR direct sequencing are commonly used for metagenomic analysis.
  Shotgun sequencing is a method involves breaking the genome into a collection of small DNA
fragments that are sequenced individually.

Metagenomics

 A powerful sequencing tool can even identify any unknown organism or new microbe or strains
of microorganisms.

Population genetics

 It includes the study of genetic differences within and between the population or individual.
 By doing mathematical calculations, statistical analysis, fieldwork and genetic analysis one can
calculate the genetic frequency, allelic frequency, and other factors with respect to the
population.
 We can also determine how natural selection, mutation, genetic drift, and gene flow can
influence the phenotype and genotype in the population.
 The Hardy-Weinberg’s equation is the basis of the population genetics, H-W equation: P2 + 2pq
+ q2 = 1
Epigenetics

 Put simply, epigenetics is the study of gene expression.

 It investigates gene expression profiles but not gene mutations.

Biochemical genetics

 The branch of genetics studying the chemistry of DNA, gene, chromosome, RNA and related
biomolecules.

Physiological genetics

 Deals with the study of physiological characteristics such as sex differentiation and sex
determination, blood group factor and sickle cell anemia like physiological conditions.

Quantitative genetics

 It is actually a branch of population genetics that studies the continuously varying phenotypes.
The correlation between phenotype and related genotype is the basis for quantitative genetics.

Conservation genetics

 It is a subfield of population genetics in which, using the genetic tools and by understanding the
dynamics of genes and their expression profile, researchers study the endangered species of
plants, animals and other organisms.

Behavioral genetics

 Studying the behavioral phenotypes of an organism at the genetic level is conducted in

behavioral genetics. The behavior of an organism is influenced by the interaction between the
environment and genetic composition.

LESSON 2
BASIC CONCEPTS OF GENETICS

HEREDITY

 It refers to the genetic heritage passed down by our biological parents

 It is the transmission of traits from one generation to the next
 - These traits can be physical, such as eye color, blood type or a disease, or behavioral

GREGOR JOHANN MENDEL (1822-1884)

 He was known as “father of genetics” who formulated laws of inheritance by experimenting

garden pea.
 Mendel tracks the segregation of parental genes and their appearance in the offsprings as
dominant or recessive traits.
 The genetic experiments mendel did with pea plants took him eight years (1856-1863) and he
published his results in 1865. During this time, Mendel grew over 10,000 pea plants, keeping
track of progeny number and type.

MENDEL’S LAW OF HEREDITY

 Gregor Mendel recognized the mathematical patterns of inheritance from one generation to the
next.

The Law of Segregation

 Each inherited trait is defined by a gene pair. Parental genes are randomly separated to the sex
cells so that sex cells contain only one gene of the pair. Offspring therefore inherit one genetic
allele from each parent when sex cells unite in fertilization

The Law of Independent Assortment

 Genes for different traits are sorted separately from one another so that the inheritance of one
trait is not dependent on the inheritance of another

The Law of Dominance

 An organism with alternate forms of a gene will express the form that is dominant

GENES COME IN PAIRS

 To follow the inheritance of genes from parent to child, Mendel first needed to be sure which
genes each parent carried.
 Since pea plants are naturally self-fertilizing, “pure-bred” strains were readily available. Each
strain contained only one form of the gene that determined a trait.
 Pure-bred plants with yellow seeds only produced offspring with yellow seeds. Pure-bred plants
with green seeds only produced offspring with green seeds.
 From the results of further experiments, Mendel reasoned that pure-bred plants must have to
copies of the same gene for each trait.
 He realized that each plant must have two traits, one inherited from each parent (Mawer 2006).
By crossing Aa with Aa we would achieve three different varations: AA (25%), Aa (50%), and aa
(25%).
  Mendel also reasoned that in order for such crossing to occur, the pairs of traits (later called
alleles) would need to separate from each other and be recombined during fertilization in order
to make new combinations, a principle he called the law of segragation.

PUNNETT SQUARE

 This diagram, called a Punnett square, shows what happened when Mendel crossed his purple
pea plants. Since the parents had the alleles for the dominant and recessive traits,
approximately one-fourth of their offspring showed the recessive white flower trait.
 Reginald C. Punnett, is the one who devised the approach in 1905.
 The Punnett square is a tabular summary of possible combinations of maternal alleles with
paternal alleles.

 Alleles are designated by letters to describe genotypes.

 The purple color’s allele (referred to as P) can naturally express the purple pigment while the
white color allele (referred to as p) cannot. Hence, the resulting genotype is written as Pp.
 Other genotypes that can be found for this trait are PP (Purple flower) and pp (white flower).
However, one P allele can produce enough pigment to make the flower purple color in this
particular example.
 Therefore, plants with either PP or Pp genotypes will have purple flowers, and only plants with
the pp genotype have white flowers.
DIFFERENCE BETWEEN MONOHYBRID AND DIHYBRID CROSS

Monohybrid Cross

 It is defined as the cross happening in the F1 generation offspring of parents differing in one trait
only. It is useful in determining the dominance of genes.

Dihybrid Cross

 It is a cross happens in F1 generation offspring of differing in two traits. It is used to create a

specimen with desirable traits. It is useful in studying the assortment of the offspring.

PUNNET SQUARE: MONOHYBRID CROSS

A homozygous cat with blue eyes mates with a heterozygous cat with brown eyes.

 What is the probability that they will produce a cat with brown eyes?
 Calculate the genotrype ratio and phenotype ratio.
 BB = brown eyes; Bb = brown eyes; bb = blue eyes

PUNNETT SQUARE: DIHYBRID CROSS

 When Mendel did this cross and looked at the offspring, he found that there were four different
categoris of pea seeds: yellow and round, yellow and wrinkled, green and round, and green and
wrinkled.
 These phenotypic categories appeared in a ratio of approximately 9:3:3:1
DIHYBRID CROSS

 To make the square, we first put the four equally probable gamete types along each axis. (YR, Yr,
Yr, yr)
 Then we joined gametes on the axes in the boxes of the chart, representing fertilization events.
 The 16 equal-probability fertilization events that can occur among the gametes are shown in the
16 boxes.
 Suppose you cross a black-coated dog with blue eyes (Ffbb) to a white-coated dog with brown
eyes (ffBb)
 If coat color and color of the eyes are controlled by two genes that assort independently,
a. What is the probability that the puppy will have black fur and brown eyes
b. What is the probability that the puppy will have white fur and blue eyes?
c. What is the probability that the puppy will have homozygous dominant one trait?
d. Heterozygous in both traits?
e. Calculate the genotype and phenotype ratio.
PEDIGREE

 It is a family tree or chart made of symbols and lines that represent a patient’s genetic family
history.
 It is a visual tool for documenting biological relationships in families and the presence of
diseases.

PEDIGREE ANALYSIS

 Pedigree analysis is assessment made by a medical professional about genetic risk in a family.
 It can help identify a genetic condition running through a family, aids in making a diagnosis, and
aids in determining who in the family is at risk for genetic conditions.
 The first affected family member who seeks medical attention for a genetic disorder is called
Proband.

AUTOSOMAL DOMINANT INHERITANCE

 In an autosomal dominant disease, if you get the abnormal gene from only one parent, you can
get the disease. Often, one of the parents may also have the disease.
 A single abnormal gene on one of the first 22 non-sex chromosomes from either parent can
cause an autosomal disorder.
 Dominant inheritance means an abnormal gene from one parent can cause disease. Even the
gene from the other parent is normal, the abnormal gene may still be pass on. (eg. FF/Ff)
 A parent with an autosomal dominant condition has a 50% chance of having a child with the
condition. This is true for each pregnancy.
 It means that each child’s risk for the disease does not depend on whether their sibling has the
disease.
 It is often called vertical inheritance because of the transmission from parent to offspring
 The proportion of affected males should be equal to those of affected females
 The parents of those who were diagnosed with autosomal dominant disease should also be
tested for the abnormal gene.
AUTOSOMAL RECESSIVE INHERITANCE

 It means two copies of an abnormal gene must be present in order for the disease or trait to
develop
 One gene from the mother and father must be present to have this kind of inheritance
 Recessive inhertance means both genes in a pair must be abnormal to cause disease
 People with only one defective gene in the pair are called carries.
- These people are most often not affected with the condition. However, they can pass the
abnormal gene to their children.
 The proportion of affected males should be equal to the proportion of affected femails in a given
population.
 Examples include sickle cell anemia and cystic fibrosis.
 A child born to a couple who both carry the gene (but do not have signs of disease), the
expected outcome for each pregnancy is:
- A 25% chance that the child is born with two normal genes (normal)
- A 50% chance that the child is born with one normal and one abnormal gene (carrier,
without disease)
- A 25% chance that the child is born with two abnormal genes (at risk for the disease)
X-LINKED DOMINANT

 The inheritance of a trait by the presence of a single gene on the X chromosome in a male or
female
 If a male inherits a changed X chromosome then this would be enough to cause the condition
because males only have one X chromosome
 An affected female has a 50% (1 in 2) chance of having affected children. An affected male will
have all daughters affected but all sons will be unaffected.
- No male-to-male transmission
 Females may experience less severe symptoms of the disorder than males.

X-LINKED RECESSIVE INHERITANCE

 Two copies of a disease allele on the X chromosome are required for an individual with two X
chrosomes to be affected with an X-linked recessive disease.
 Since males are hemizygous (have a single X chromosome) for X-linked genes, any male with one
copy of an X-linked recessive disease allele is affected
 The female is usually a healthy carrier of the X linked condition
 A carrier means you do not have the condition, but carry a changed copy of the gene.
 Some examples include hemophilia, Duchenne muscular dystrophy and fragile X.

How X linked recessive conditions are passed on by female carriers

How X linked recessive conditions are passed on affected males

The following information must be included on the pedigree

 First name or initials of relatives

 Affected status (i.e who in the family has disease) for eacah individual in the family
 Age of all family members, or age at death
 Whether individuals are living or deceased. The cause of death, if known, should be indicated
below the symbol
 Residence for all the family members (City, State)
 Willingness to participate in the study (indicate with an asterisk)
 Key to shading of symbols
 Adoption status
 Consanguinity (i.e parents are related)
 Race and ethnicity
 Date pedigree obtained
BASIC PEDIGREE SYMBOLS

 Living unaffected female: clear cicle

 Living unaffected male: clear square
 Unknown gender (during pregnancy): clear diamond

PREGNANCY SYMBOLS

 Use a diamond if the gender is not yet known, a circle or a square of the gender is known.
 A triangle is used for any pregnancy not carried to term
 Include gestational age, or estimated date of delivery (EDD) for all pregnancies
 Pregnancy (P), stillbirth (SB), spontaneous abortion (SAB), termination of pregnancy (TOP),
ectopic pregnancy (ECT)

BASIC PEDIGREE SYMBOLS

 Living affected female: black circle

 Living affected male: black square
 Adoption, place brackets around the adopted individual
- A dashed offspring line indicates the individual was adopted into the family, and a solid line
indicates the individual was adopted out of the family.
  Deceased: symbol with a diagonal line

 Individual with multiple diagnoses

BASIC PEDIGREE LINES

 Marriage/Mating Line: horizontal line connecting 2 symbols at the center of each symbol

 Separated, divorce, relationship no longer exists Line: horizontal line connecting 2 symbols with
2 diagonal hash marks.

 Offspring Line: vertical line from the center of the mating line to the center of the offspring
symbol or to the sibling line.
 Children from a previous partner (stepchildren)
 Mike and Jane have one son, and Jane has a daughter from a previous marriage.

 Sibling Line: Horizontal line above the offspring and connected by vertical lines. Example:
brother and sister siblings.
 Brother and sister siblings with two parents.

 No children: a vertical line with 2 hash marks at the end. Indicate if an adult does not have
children by choice ©, infertility (i).

 Dizygotic Twins (non-identical): indicated by two diagonal vertical lines originating from the
same point.
  Monozygotic twins (identical): indicated by two diagonal vertical lines originating from the same
point.

GENERAL GUIDELINES WHEN DRAWING A PEDIGREE

 It is helpful to start in the middle of the page when drawing a pedigree.

 Male partners are to the left of female partners
 Sibligns are drawn from oldest to youngest with the oldest listen on the left and the youngest on
the right,
 If there are multiple disorders or diseases use quadrants or different shading (solid, cross-
hatching) to indicated each disease.
WEEK 3
BASICS OF CYTOLOGY

What is a cell?
 It is the smallest, basic unit of life that is responsible for all of life’s processes
 It is structural, functional, and biological untis of all living beings
 It can replicate itself independently. Hence, they are known as the buiding blocks of life
Cytology
 The study of cells as fundamental units of living things, their origin, structure, function,
and pathology
 It uses light or electron microscopin methods for the study of morphology, and as a
means to diagnose or test for cancer and other diseases

CELL DISCOVERY
Robert Hooke (1965)
 Robert Hooke observed a piece of bottler cork under a compound microscope and
noticed mini structures that reminded him of small rooms. He named these “rooms” as
cells.
 Due to limited maginificatioon of his microscope, he could not see any details in the
structure that’s why concluded that these were non-living entities.

Anton Van Leeuwenhoek

 Observed cells under another compound microscope with higher magnification. This
time, he had noted that the cells exhibited some form of movement (motility) – he
named it as animalcules.

Robert Brown (1883)

 A scottish botanist who provided the very first insights into the cell structure. He
described the nucleus present in the cells of orchids.

Characteristics of Cells
1. Cells provide structure and support to the body of an organism
2. The cell interior is organized into different individual organelles surrounded by a separate
membrane.
3. The nucleus (major organelle) holds genetic information necessary for reproduction and cell
growth.
4. Every cell has one nucleus and membrane-bound organelles in the cytoplasm
5. Mitochondria, a double membrane-bound organelle is mainly responsible for the energy
transactions vital for the survival of the cell.
6. Lysosomes digest unwanted materials in the cell.
 7. Endoplasmic reticulum plays a significant role in the internal organization of the cell by
synthesizing selective molecules and processing, directing and sorting them to their appropriate
locations.

FUNCTIONS OF THE CELL

1. Cell metabolism and human body - energy released during metabolism is used for cell, activities
such as the synthesis of new molecules, muscle contraction, and heat production, which helps
maintain body temperature
2. Synthesis of molecules - cells synthesize various types of molecules, including proteins, nucleic
acids, and lipids.
3. Communication - cells produce and receive chemical and electrical signals that allow them to
communicate with one another.
Ex. Nerve cells communicating with one another and with muscle cells causing it to contract.
4. Reproduction and inheritance - each cell contains a copy of the genetic information of the
individual.

TYPES OF CELLS
 Various types of cells perform different functions. There are two types of cells based on cellular
structure:
 Prokaryotes
 Eukaryotes

PROKARYOTES
 Prokaryotes are one of the most ancient groups of living organisms on earth, with fossil records
dating back to almost 3.5 billion years ago.
 It does not possess membrane-bound cell organelles such as a nucleus. Reproduction happens
through the process of binary fission.
 Prokaryotes have a capsule enveloping its entire body, and it functions as a protective coat. This
is crucial for preventing the process of phagocytosis.
 All members of Kingdom Monera are prokaryotes.
PROKARYOTIC CELL

PROKARYOTIC CELL STRUCTURES

Flagella
 whip like structures made of protein and provide motility to the cell.
Fimbriae and pili

 Fimbriae are proteinaceous, sticky, projected structure used by cells to attach to each other and
to objects around them.
 Pili are tubules that are used to transfer DNA from one cell to another cell
Cell wall

 It is present outside the plasma membrane. It provides rigidity to the cell shape and structure
and protects the cell from its environment.

Cytoplasmic Membrane

 It is a membrane that provides a selective barrier between the environment and the cell’s
internal structures.

Cytoplasm

 It is a thick, aqueous, semitransparent, and elastic semifluid present inside the prokaryotic cell.
Nucleoid

 This is where the DNA of the cell is located

Ribosomes

 They are composed of a complex of protein and RNA, and are the site of protein synthesis in the
cell.

Inclusion bodies

 These contain organic compounds such as starch, glycogen or lipid and act as food reserves
Endospore

 It develop within vegetative bacterial cells and are extraordinarily resistant to environmental
stresses such as heat, UV radiation, gamma radiation, chemical disinfectants, and desiccation.

EXAMPLES OF PROKARYOTIC CELLS

Bacterial Cells

 These are unicellular organisms found everywhere on earth from soil to the human body.
 The cell wall is composed of peptidoglycan that provides structure to the cell wall.
 Bacteria have some unique structures such as pili, flagella and capsule.
 They also possess extrachromosomal DNA known as plasmids

Archaeal Cells

 Archaebacteria are unicellular organisms similar to bacteria in shape and size.

 They are found in extreme environments such as hot springs and other places such as soil,
marshes, and even inside humans.
 They have a cell wall and flagella. The cell wall of archaea does not contain peptidoglycan.
 Just like bacteria, archaea have one circular chromosome. They also possess plasmids

EUKARYOTES

 “good or true nuclei”

 Eukaryotes are more complex and much larger than the prokaryotes. They include almost all the
major kingdoms except kingdom monera.
 Eukaryotes possess a cell wall, which supports and protects the plasma membrane. The cell is
surrounded by the plasma membrane and it controls the entry and exit of certain substances.
 Eukaryotes include almost every unicellular organism with a nucleus and all multicellular
organisms.
EUKARYOTIC CELL

 Eukaryotic cells contain a variety of intracellular compartments, each of which has a unique
function within the cell.
 Membranes are lipid structures that separate the contents of the compartment they surround
from its environment.
 Plasma membranes separate the cell from its environment.
 Organelles have membranes that separate the internal compartment of the organelle
from the cytoplasm.

Lysosomes

 The lysosomes are the intracellular organelles of digestion, which are enclosed by a single
membrane.
 Enzymes contained by lysosomes include nucleases, phosphatases, glycosidases, esterase and
proteases, with pH optima about 5.5 (acidic pH)

Mitochondria

 Contain most of the enzymes for the pathways of fuel oxidation and oxidative phosphorylation,
and, thus, generate most of the ATP required by mammalian cells.
 Inherited mutations in mitochondrial DNA lead to muscle, nerve and renal problems
 Mitochondrial disorders are maternally inherited, and all children who inherit defective
mitochondria will express some component of the disease
 (depends on the distribution of normal and mutant mitochondria to the egg when it was
produced)

Peroxisomes

 Are cytoplasmic organelles that are involved in oxidative reactions using molecular oxygen, in
many cases producing hydrogen peroxide.
 When the peroxisomes are not produced properly certain enzymatic reactions cannot take
place, including the appropriate formation of myelin in the nervous system.

Nucleus

 The nucleus is the largest subcellular organelle, and houses the genome of the cell. DNA
replication, transcription, and ribosome assembly occur within the nucleus.
 The nuclear envelope surrounds the nucleus, and consists of an outer and inner membrane
joined by pores
 The outer membrane is continuous with the rough endoplasmic reticulum.
 The inner nuclear membrane provides more of a permeability barrier.
RNA and other material that must be exported from the nucleus leave through the
pores.
 The nucleolus, a substructure of the nucleus, is the site of rRNA transcription and processing of
ribosome assembly.

Endoplasmic reticulum (ER)

 The ER is a network of membranous materials within the cell consisting of smooth ER (SER),
which lacks ribosomes, and rough ER (RER), which is studded with ribosomes.
 The SER has many functions, including being the site of synthesis for many large lipids, and the
site of cytochrome P450 oxidative enzymes that are used for detoxification and the synthesis of
hydrophobic molecules.
 The RER is involved in the synthesis of secreted and certain intracellular organelle-targeted
proteins and also the site of the initiation of posttranslational modifications to the newly
synthesized proteins.

Golgi complex

 The Golgi complex is involved in modifying the proteins produced in the RER and in sorting and
distributing these proteins to the lysosomes, secretory vesicles, or to the plasma membrane.

Cytoskeleton

 The structure of the cell, the shape of the cell surface, and the arrangement of subcellular
organelles are organized by three major protein components, all considered part of the
cytoskeleton.
 Microtubules are responsible for movement of vesicles and organelles.

ANIMAL CELL AND PLANT CELL STRUCTURE

Animal Cells versus Plant Cells

 Animal cells have centrioles, centrosomes and lysosomes, whereas plant cells do not.
 Plant cells have a cell wall, chloroplasts, plasmodesmata, and plastids used for storage, and a
large central vacuole, whereas animal cells do not.

HUMAN CELL STRUCTURE

HUMAN CELL STRUCTURES AND FUNCTIONS

ORGANELLES

NUCLEI - It is bounded by nuclear envelop,

consists of outer and inner
membranes with a narrow space
between them
- Human cells contain 23 pairs of
chromosomes which consist of
DNA and proteins
- Nucleoli – diffuse bodies with no
surrounding membrane, found
within the nucleus
- They are usually one to several
nuclei. Ribosomes (a type of
cytoplasmic organelle) are formed
within nucleolus
RIBOSOMES - This is where proteins are
produced. They may be attached
to other organelles, such as
endoplasmic reticulum

ROUGH AND SMOOTH ENDOPLASMIC - ER is series of membranes forming

RETICULUM (ER) sacs and tubules that extends
from the outher nuclear
membrane into the cytoplasm
- Rough ER – with ribosomes
attached to it. Larger RER
indicates synthesizing large
amounts of proteins
- Smooth ER – a site for lipid
synthesis and participates in
detoxification of chemiacls within
cells
GOLGI APPARATUS - It is also Golgi complex. It collects,
modifies, packages, and
distributes proteins and lipids
manufactured by the ER
SECRETORY VESICLES - A vesicle is a small-membrane-
bound sac that transports or
stores materials within cells.
- The membrane of a secretory
vesicle then fuses with the cell
 membrane, and the contents of
the vesicle are released to the
exterior of the cell
- Ex: insulin remains in the
cytoplasm of pancreatic cells until
rising blood glucose levels
stimualte its secretion
LYSOSOMES AND PEROXISOME - Membrane-bound vesicles formed
from the Golgi apparatus. They
contain a variety of enzymes that
function as intracellular digestive
systems. Ex: WBC phagocytize
bacteria
MITOCHONDRIA - Small organelles with inner and
outer membranes separated by a
space.
- Major sites of adenosine
triphosphate (ATP) production
within cells.
- Carry out aerobic respiration- a
series of chemical reactions that
require O2 to break down food
molecules to produce ATP
- ATP is the main energy source for
most chemical reactions within
the cell. Ex: muscles require larger
amounts of ATP for muscle
contraction
CYTOSKELETON - Acts as the internal framework of
the cell. It consists of protein
structures that support the cell,
hold organelles in place, and
enable the cell to change shape.
- Microtubules – hollow structures
formed from protein subunits that
structurally support cytoplasm,
determining the cell shape
- Intermediate filaments – fibrils
formed from protein subunits that
are smaller in diameter that
microtubules but larger in
diameter than microfilaments,
provides mechanical support to
the cell (Keratin is one specific
 type)
CENTRIOLES - Centrosome is specialized area of
cytoplasm close to the nucleuls
where microtubule formation
occurs
- Contains two centrioles –
normally oriented perpendicular
to each other
- They play an important role in cell
division “mitosis”
CILLA, FLAGELLA, AND MICROVILLI - Cillia – project form the surface of
cells, cylindrical structures that
extend from the cell and are
composed of microtubules,
organized in a pattern similar to
the centriole. Numerous on
surface cells that line the
respiratory tract. Helps in
transporting mucus
- Flagella – similar to cillia but much
longer, and only occur one per
cell. Ex: sperm cells each have one
flagellum, which prospers the
sperm cell
- Microvilli – specialized extensions
of the cell membrane that are
supported by microfilaments, but
not actively move as cilia and
flagella. Abundant on the surface
of cells that line the intestine,
kidney and other areas involving
absorption

Examples of Eukaryotic Cells

 Eukaryotic cells are exclusively found in plants, animals, fungi, protozoa, and other complex
organisms.

Plant Cells

 The cell wall is made up of cellulose, which provides support to the plant. The plant cell contains
chloroplast, which aids in the process of photosynthesis.
Fungal Cells

 The cell wall is made of chitin. Some fungi have holes known as septa which allow the organelles
and cytoplasm to pass through them.

Animal Cells

 These do not have cell walls. Instead, they have a cell membrane. That is why animals have
varied shapes. They have the ability to perform phagocytosis and pinocytosis.

Protozoa

 Protozoans are unicellular organisms. Some protozoa have cilia for locomotion. A thin layer
called pellicle provides supports to the cell.

Prokaryotes Eukaryotes
Type of Cell Always unicellular Unicellular and multi-cellular
Cell size Ranges in size from 0.2 μm – 2.0 Size ranges from 10 μm – 100
μm in diameter μm in diameter
Cell wall Usually present; chemically When present, chemically
complex in nature simple in nature
Nucleus Absent. Instead, they have a Present
nucleoid region in the cell
Ribosomes Present. Smaller in size and Present. Comparatively larger in
spherical in shape size and linear in shape
DNA arrangement Circular Linear
Mitochondria Absent Present
Cytoplasm Present, but cell organelles Present, cell organelles present
absent
Endoplasmic reticulum Absent Present
Plasmids Present Very rarely found in eukaryotes
Ribosome Small ribosomes Large ribosomes
Lysosome Lysosomes and centrosomes Lysosomes and centrosomes are
are absent present
Cell division Through binary fission Through mitosis
Flagella The flagella are smaller in size The flagella are larger in size
Reproduction Asexual Both asexual and sexual
Example Bacteria and Archaea Plant and Animal cell

WEEK 4
CELL DIVISION: MEIOSIS AND MITOSIS

MITOSIS

 Mitosis is used for almost all of your body’s cell division needs. It adds new cells during
development and replaces old and worn-out cells throughout your life
 The term ‘mitosis’ was coined by Walther Flemming in 1882.
a. Example: Healing of wounds, where damaged cells are replaced and repaired by forming
new cells
 Mitosis happens in all cell types such as skin, bone, blood, and structural cells, among others,
except the germ cells.
 In actively dividing animal cells, the whole process takes about one hour and half or two hours.

THE CELL CYCLE

 It is the series of growth and development steps a cell undergoes between its “birth”—
formation by the division of a mother cell and reproduction (division to make two new daughter
cells)
PHASES OF THE CELL CYCLE

G0 (Gap) Phase

 The G0 phase is the resting phase of the cell. The amount of time a cell spends in G0 is variable
and depends on how actively a cell is dividing.

G1 Phase.

 The G1 phase is the gap of time between mitosis (M phase) and DNA synthesis (S phase).
 The G1 phase is the phase where RNA, protein, and organelle synthesis occurs. The G1 phase
lasts about 5 hours in a typical mammalian cell with a 16-hour cell cycle

S (Synthesis) Phase

 The S phase is the phase where DNA synthesis occurs.

 The S phase lasts about 7 hours in a typical mammalian cell with a 16-hour cell cycle.

G2 Phase

 The G2 phase is the gap of time between DNA synthesis (S phase) and mitosis (M phase).
 The G2 phase is the phase where high levels of ATP synthesis occur. The G2 phase lasts about 3
hours in a typical mammalian cell with a 16-hour cell cycle.

M (Mitosis) Phase

 The M phase is the phase where cell division occurs.

 The M phase is divided into six stages called prophase, prometaphase, metaphase, anaphase,
telophase, and cytokinesis.
 The M phase lasts about 1 hour in a typical mammalian cell with a 16-hour cell cycle.

PHASES OF MITOSIS
INTERPHASE OF MITOSIS

 It is the preparatory growth phase of mitosis when the DNA (the genetic material) gets copied.
 It is the most active phase of the cell cycle involving a series of metabolic changes.
PROPHASE OF MITOSIS
 It is the first and the longest of all phases of mitosis.
 The chromatin condenses to form well-defined X-shaped chromosomes.
 Each chromosome has been duplicated during the S phase and has a specific DNA sequence
called the centromere that is required for proper segregation.
 The centrosome complex, which is the microtubule organizing center (MTOC), splits into two
and each half begins to move to opposite poles of the cell. The mitotic spindle (microtubules)
forms between the centrosomes
 On reaching the end of this phase, the nuclear envelope starts to breaks apart thus releasing the
chromosome
 The nucleolus gradually disintegrates. The chromosomes begin to migrate towards the center of
the cell, marking the end of prophase.

METAPHASE OF MITOSIS
 It is the second phase of mitosis and is marked with the complete disappearance of the nuclear
envelope that had started during prophase.
 The chromosomes, which are at their shortest and thickest stage with two sister chromatids, get
attached to the spindle fibers present at the opposite poles.
 They then align end to end along the middle of the cell. (metaphase plate)
 The spindle fibers then attach to each of the sister chromatids.
 The cells can be arrested in this stage by microtubule inhibitors (e.g., colchicine). The cells
arrested in this stage can be used for karyotype analysis.
ANAPHASE OF MITOSIS
 It starts by splitting each paired chromosome into two sister chromatids, now known as
daughter chromosomes.
 The daughter chromosomes are pulled towards the opposite end of the cell due to the
contraction of the spindle fibers.
 At the end of this phase, each pole contains a complete set of chromosomes.
TELOPHASE OF MITOSIS
 It is the last recognized phase of mitosis marked by the end of the daughter chromosome’s
migration to the opposite poles.
 Nuclear envelope redevelops around each group of chromosomes to form daughter nuclei.
 Mitotic apparatus disappears with a reduction in the viscosity of cytoplasm, followed by the
synthesis of RNA.
 The nucleolus reappears with the chromosomes becoming slender and extended

CYTOKINESIS OF MITOSIS
 This is the process where the cytoplasm gets divided to produce two independent daughter
cells, each containing a complete set of chromosomes.
 Cytokinesis begins at the anaphase stage and continues through telophase and into the
interphase.
 In the end, mitosis results in two genetically identical daughter cells, each having diploid (2n)
number of chromosomes
MEIOSIS

 Meiosis is used for just one purpose in the human body: the production of gametes—sex cells,
or sperm and eggs
 (germ cell division)
 Meiosis in humans is a division process that takes us from a diploid cell (one with two sets of
chromosomes) to haploid cells (ones with a single set of chromosomes).
 The term diploid is classically used to refer to a cell containing 46 chromosomes.
 The term “haploid” is classically used to refer to a cell containing 23 chromosomes.
 In humans, the haploid cells made in meiosis are sperm and eggs. When a sperm and an egg join
in fertilization, the two haploid sets of chromosomes form a complete diploid set: a new
genome.

PHASES OF MEIOSIS

 Meiosis is like mitosis in many aspects like their stages and strategies to organize and separate
chromosomes.
 Meiosis involves two successive stages or phases of cell division, meiosis I and meiosis II.
 Each stage includes a period of nuclear division or karyokinesis and a cytoplasmic
division or cytokinesis. Although not a part of meiosis, the cells before entering meiosis I
undergo a compulsory growth period called interphase.
INTERPHASE OF MEIOSIS
 During this phase, the nuclear envelope remains intact. The chromosomes exist in the form of
long, slender, and coiled chromatin fibers.

G1 phase

 The first gap phase or the preparatory phase of cell division. During this phase, the cell increase
in size by absorbing water from the cytoplasm and synthesize different types of RNA and
proteins.

S phase

 The period of DNA synthesis during which the genetic material present within the nucleus gets
copied. Each chromosome duplicates to become two identical sister chromatids attached at a
specific point, called the centromere. The centrioles get duplicated as well

G2 phase

 The second gap phase that happens after the DNA synthesis, but before prophase. During this
phase, the cell continues to increase in size with the synthesis of RNA and proteins.
PROPHASE I OF MEIOSIS
 It is the longest phase of meiotic division.
 The duplicated chromosomes condense, resembling an Xshaped structure with two sister
chromatids that become distinctly visible within the nucleus.
 The homologous chromosome pair comes closer and associate along the entire chromosome
length, forming a tetrad. Each tetrad is composed of four chromatids.
 The homologous chromosomes exchange parts of DNA with each other; this process is known as
crossing over.
 Crossover refers to the equal exchange of large segments of DNA between the maternal
chromatid and paternal chromatid (i.e., non-sister chromatids) at the chiasma.
 Chiasma is the location where crossover occurs forming an Xshaped chromosome
 Spindle fibers originate from the centrioles on either side of the cell, getting attached to each
chromosome’s centromere.
 The last step of prophase involves the breakdown of the nuclear envelope. The chromosomes
then start moving towards the middle of the cell

Take Note:

 During crossover, two other events may occur, which introduces variable number tandem
repeat (VNTR) polymorphisms, duplications, or deletions into the human nuclear genome.
 (Example: unequal crossover and unequal sister chromatid exchange)

METAPHASE I OF MEIOSIS
 Homologous chromosomes align along the center of the cell.
 The centrioles reach the opposite poles of the cell with the spindle fibers extending from them.
  The centromeres orient themselves towards the opposite poles of the cell.

ANAPHASE I OF MEIOSIS
 The chromosomes with two sister chromatids are separated, and they begin to migrate to the
opposite poles.
 This separation is achieved because of the contraction of the spindle fibers attached to
each chromosome’s centromere.
 The homologous chromosomes start to migrate to the opposite poles.

TELOPHASE I OF MEIOSIS
 The chromosomes stop migrating with each pole containing a haploid number of chromosomes.
 The nuclear envelope is formed around the chromosome, and the spindle fibers disappear
  The chromosomes uncoil and become less dense with the nucleolus appearing within the
nucleus.

CYTOKINESIS I OF MEIOSIS
 It involves the division of the cytoplasm to produce two individual daughter cells.
 At the end of cytokinesis I, two different daughter cells are formed, each with half the number
of chromosomes as the parent cell (having 23 chromosomes having 23 pairs of chromatids).
 Meiosis is thus also called the reduction division- number of chromosomes is reduced by half.
PROPHASE II OF MEIOSIS
 The daughter cells produced in meiosis I enters the second round of division called meiosis II.
 The nuclear membrane initiates to break down, and the spindle fibers appear again
 Each centriole divides, forming two pairs of centrioles.
 Chromosomes do not replicate any further in this phase of meiosis and begin migration towards
the center of the cell

METAPHASE II OF MEIOSIS
 Chromosomes arrange on the equator of the cell with the help of the spindle fibers.
 The centrioles are now at opposite poles in each of the daughter cells.
 Centromere divides, producing two sister chromatids, now known as daughter chromosomes,
with the spindle fibers attached to each chromosome
ANAPHASE II OF MEIOSIS
 The daughter chromosomes are pulled towards the opposite poles of the cells with the help of
the spindle fibers.
 At the end of anaphase II, each end of the cell contains a complete set of chromosomes.

TELOPHASE II OF MEIOSIS
 The nuclear membrane forms around each chromosome with the disappearance of the spindle
fibers.
 Nucleolus reappears as the cell prepares for the second round of cytoplasmic division
CYTOKINESIS II OF MEIOSIS
 This step is identical to cytokinesis I, involving the second cytoplasm division, resulting in the
formation of two individual daughter cells
 At the end of meiosis II, four non-identical, haploid daughter cells are formed, each having half
chromosome number as the original parent cell

MEIOSIS I VS MEIOSIS II

 In meiosis I, a pair of homologous chromosomes separate to produce two diploid daughter cells,
each having half the number of chromosomes as the parent cell.
 In contrast, during meiosis II, sister chromatids separate to produce four haploid daughter cells.
Also, unlike meiosis I, no genetic recombination by crossing over occurs in meiosis II.

PURPOSE OF MEIOSIS

 Maintaining chromosome number in organisms

 Creates genetic diversity
 Repairs genetic defects
WEEK 5
HUMAN GENETIC MATERIALS

HUMAN GENOME

 The human genome refers to the haploid set of chromosomes (nuclear plus mitochondrial),
which is divided into the very complex nuclear genome and the relatively simple mitochondrial
genome.
 The human nuclear genome consists of 24 different chromosomes (22 autosomes; X and Y sex
chromosomes).
 The human nuclear genome codes for 30,000 genes (precise number is uncertain) which make
up 2% of human nuclear genome.

In order to fully understand how heritable traits are passed down, it is important to understand three
aspects of the human nuclear genome:

 Protein-coding genes
 A mutation in a protein-coding gene caused the formation of an abnormal protein and
hence an altered trait or disease.
 RNA-coding genes
 RNA-coding genes produce active RNAs that can profoundly alter normal gene
expression and hence produce an altered trait or disease.
 Epigenetic control
 It involves chemical modification of DNA (e.g., methylation) and chemical modification
of histones (e.g., acetylation, phosphorylation, addition of ubiquitin), both of which can
profoundly alter normal gene expression and hence produce an altered trait or disease

NUCLEIC ACIDS

- A nucleoside consists of a nitrogenous base and a sugar.

- A nucleotide consists of a nitrogenous base, a sugar, and a phosphate group.
- DNA and RNA consist of a chain of nucleotides, which are composed of the following
components:

Nitrogenous Bases

Purines

a. Adenine (A)
 b. Guanine (G)
Pyrimidines

a. Cytosine (C)
b. Thymine (T)
c. Uracil (U), which is found in RNA
Base Pairing

a. Adenine pairs with thymine or uracil (A-T or A-U).

b. Cytosine pairs with guanine (C-G).

Sugars

- Deoxyribose, which is found in DNA

- Ribose, which is found in RNA

Phosphate

DISCOVERY OF DNA

Russian biochemist Phoebus Levene (1863-1940)

 He is credited for discovering the carbohydrate component of both DNA and RNA and how their
components are connected, as well as the structure of nucleotides in 1919

Oswald Avery (1877-1955)

 Had an experiment that it was DNA that carried the vital information needed for protein
expression in the next generation of cells.

Francis Crick and James Watson (1953

 They came up with a model for the structure of DNA based off on X-ray diffraction images.

Deoxyribonucleic acid (DNA)

 It is the central information storage system of most animals and plants, and even some viruses.
The name comes from its structure, which is a sugar and phosphate backbone which have bases
sticking out from it.

So that "deoxyribo" refers to the sugar and the nucleic acid refers to the phosphate and the bases.

The bases go by the names of:

 adenine, cytosine, thymine, and guanine

The observable traits like eye color or height of individuals come from individual proteins.

LEVELS OF DNA PACKAGING

Double Helix DNA

 The DNA molecule is two complementary polynucleotide chains (or DNA strands) arranged as a
double helix, which are held together by hydrogen bonding between laterally opposed base
pairs (bps).
 DNA can adopt different helical structures, which include:
a. A-DNA: a right-handed helix with 11 bp/turn
b. B-DNA: a right-handed helix with 10 bp/turn
c. Z-DNA: a left-handed helix with 12 bp/turn
 In humans, most of the DNA is in the B-DNA form under physiological conditions.

Nucleosome

 The most fundamental unit of packaging of DNA is the nucleosome. A nucleosome consists of a
histone protein octamer

Centromere

 It is a specialized nucleotide DNA sequence that binds to the mitotic spindle during cell division.
 Chromosomes have a single centromere that is observed microscopically as a primary
constriction, which is the region where sister chromatids are joined.

Heterochromatin
  It is condensed chromatin and is transcriptionally inactive. In electron micrographs,
heterochromatin is electron dense (i.e., very black).
 An example of heterochromatin is the Barr body, which can be seen in interphase cells from
females, which is the inactive X chromosome. Heterochromatin comprises 10% of the total
chromatin.

Constitutive heterochromatin is always condensed (i.e., transcriptionally inactive) and consists of

repetitive DNA found near the centromere and other regions.

Facultative heterochromatin

 It can be either condensed or dispersed (i.e., transcriptionally active).

Euchromatin

 It is dispersed chromatin and comprises 90% of the total chromatin. Of this 90%, 10% is
transcriptionally active and 80% is transcriptionally inactive.

Ribonucleic Acid (RNA)

 RNA is single-stranded.
 An RNA strand has a backbone made of alternating sugar (ribose) and phosphate groups.
 Attached to each sugar is one of four bases:
 adenine (A), uracil (U), cytosine (C), or guanine (G)

Different types of RNA exist in the cell:

 messenger RNA (mRNA) - nucleic acid information molecule that transfers information from the
genome into proteins by translation.
 transfer RNA (tRNA) - are non-protein encoding RNA molecules that physically carry amino acids
to the translation site that allows them to be assembled into chains of proteins in the process of
translation.
 ribosomal RNA (rRNA) - forms part of the ribosome. It is exported to the cytoplasm to help
translate the information in mRNA into protein.
 More recently, some small RNAs have been found to be involved in regulating gene expression.

DNA AND RNA STRUCTURE

DNA RNA
Stores genetic information for the cell Uses the information stored in DNA to make
proteins
Contains the 5-carbon sugar deoxyribose Contains the 5-carbon sugar ribose
Double-stranded Single-stranded
Contains thymine Contains uracil
 Self-replicating Synthesized by transcription

Cell cycle of eukaryotic cells

1. During the G1 (first gap) phase, cells prepare to duplicate their chromosomes
2. During the S (synthesis) phase, synthesis of DNA (replication) occurs
3. During the G2 (second gap) phase, cells prepare to divide
4. During the M (mitosis) phase, cell division occurs.
5. Cells can traverse the cell cycle many times.
6. Cells can also leave the cycle never to divide again, or they can enter a phase (sometimes called
G0) in which they remain for extended periods. In response to an appropriate stimulus, these
cells reenter the cell cycle and divide again.
Mechanism of replication

Replication

 DNA replication is a semi-conservative process, because when a new double-stranded DNA

molecule is formed:
a. One strand will be from the original template molecule
b. One strand will be newly synthesized
 Each daughter molecule of DNA contains one intact parental strand and one newly synthesized
strand joined by base pairs.

Mechanism of replication

 This occurs because each nitrogenous base can only pair with its complementary partner
a. Adenine (A) pairs with thymine (T)
b. Cytosine (C) pairs with guanine (G)
 When DNA is replicated by the combined action of helicase and DNA polymerase:
a. Each new strand formed will be identical to the original strand separated from the template
b. The two semi-conservative molecules formed will have an identical base sequence to the
original molecule
c. The normal structure of our DNA when it is not being copied is a double helix. It looks very
similar to a winding staircase.
d. In its normal form, the DNA cannot be copied.

DNA helicase
  It is needed in order to open the DNA to expose the nucleotide bases that are used as the
template for replicating the DNA.

Replication fork

 Is the area of the DNA that is opened by DNA

The parental strands of DNA separate and the helix unwinds ahead of a replication fork

 Helicases unwind the helix, and single-strand binding proteins hold it in a single-stranded
conformation.
 Topoisomerases act to prevent the extreme supercoiling of the parental helix that would result
as a consequence of unwinding at a replication fork.
 DNA polymerase can only copy a DNA template in the 3′ to 5′ direction and produce the newly
synthesized strand in the 5′ to 3′ direction. It requires a primer (RNA serves as the primer).
 DNA ligase - form a phosphodiester bond, two adjacent DNA strands that are bound to the same
template.

REPLICATION PROCESS

1. The process starts when topoisomerase nicks (or breaks) a single strand of DNA, which causes
DNA unwinding.
2. Chromosome replication begins at specific nucleotide sequences located throughout the
chromosome called replication origins.
a. Eukaryotic DNA contains multiple replication origins to ensure rapid DNA synthesis.
Normally, the S phase of the mammalian cell cycle is 8 hours.
3. DNA helicase recognizes the replication origin and opens up the double helix at that site,
forming a replication bubble with a replication fork at each end. The stability of the replication
fork is maintained by single-stranded binding proteins
4. Replication fork
 Leading strand that is synthesized continuously by DNA polymerase delta.
 Lagging strand that is synthesized discontinuously by DNA polymerase alpha.
 DNA primase synthesizes short RNA primers along the lagging strand.
 DNA polymerase uses the RNA primer to synthesize DNA fragments called
Okazaki fragments. Okazaki fragments end when they run into a downstream
RNA primer.
 To form a continuous DNA strand from the Okazaki fragments, a DNA repair
enzyme erases the RNA primers and replaces it with DNA.
 DNA ligase subsequently joins all the DNA fragments together
Transcription

 It is the process of making an RNA copy of a gene sequence. This copy, called a messenger RNA
(mRNA) molecule, leaves the cell nucleus and enters the cytoplasm, where it directs the
synthesis of the protein, which it encodes.
 It's the process of turning DNA into RNA

Translation

 It is the process of translating the sequence of a messenger RNA (mRNA) molecule to a

sequence of amino acids during protein synthesis.
 The genetic code describes the relationship between the sequence of base pairs in a gene and
the corresponding amino acid sequence that it encodes

Components of Translation

The key components required for translation are mRNA, ribosomes, and transfer RNA (tRNA).

 During translation, mRNA nucleotide bases are read as codons of three base
 Each ‘codon’ codes for a particular amino acid.
  Every tRNA molecule possesses an anticodon that is complementary to the mRNA codon, and at
the opposite end lies the attached amino acid.
 tRNA molecules are therefore responsible for bringing amino acids to the ribosome in
the correct order ready for polypeptide assembly

The genetic code

 During translation, a cell “reads” the information in a messenger RNA (mRNA) and uses it to
build a protein. It always encodes a polypeptide, or chain of amino acids.

The genetic code

 There are 61 codons for amino acids, and each of them is "read" to specify a certain amino acid
out of the 20 commonly found in proteins.
 One codon, AUG, specifies the amino acid methionine and also acts as a start codon to signal the
start of protein construction.
 There are three more codons that do not specify amino acids. These stop codons, UAA, UAG,
and UGA, tell the cell when a polypeptide is complete.
 All together, this collection of codon-amino acid relationships is called the genetic code, because
it lets cells “decode” an mRNA into a chain of amino acids.
Steps of translation

Initiation

 The ribosome assembles around the mRNA to be read and the first tRNA (carrying the amino
acid methionine, which matches the start codon, AUG)
 This setup, called the initiation complex, is needed in order for translation to get started.
Elongation

 It is the stage where the amino acid chain gets longer. In elongation, the mRNA read one codon
at a time, and the amino acid matching each codon is added to a growing protein chain

Termination

 It is the stage in which the finished polypeptide chain is released.

 It begins when a stop codon (UAG, UAA, or UGA) enters the ribosome, triggering a series of
events that separate the chain from its tRNA and allow it to drift out of the ribosome.

After termination, the polypeptide undergo processing such as the removal of amino acids, get shipped
to the right place in the cell, or combine with other polypeptides before it can do its job as a functional
protein