BB 101 HELP SESSION

Athul Viswam
Aerospace Engineering
 Prokaryotic and Eukaryotic cells
Prokaryotic cells
• Primitive
• No nuclear membrane , Hardly any membrane
bound organelles
• Nucleoid – Region of cytoplasm where Genetic
material can be found
• Majority are Unicellular
• Usually, a single circular DNA molecule is
present
Eukaryotic Cells
• Well defined nucleus and membrane bound
organelles
• Advanced, compared to prokaryotic cells
• Unicellular and Multicellular
• Multiple linear DNA molecules are present
 Organelles and Their Functions
Cell wall
• Only in plant cells, Fungi
• Tough, flexible, provide structural strength to
plant cells
• The composition is different for different
organisms, say for example, land plants have
cell wall made of cellulose, hemicellulose and
pectin.
Cell membrane / Plasma membrane
• In plant, fungal and animal cells
• Selectively permeable to ions / organic
molecules
• Lipid bilayer structure
• Cell adhesion, ion conductivity, cell signalling
• serve as the attachment surface for several
extracellular structures, including the cell wall
Cytoplasm
Nucleus  Read from lecture slides
Vacuole
Peroxisome
Endoplasmic Reticulum (ER)
• Two types – Soft endoplasmic reticulum (SER)
and Rough endoplasmic reticulum (RER)
• Found near Nucleus (why?)
• Absent in RBC!!
• Involved in post production processing and
transportation of Proteins, Lipids etc..
• interconnected network of flattened,
membrane-enclosed sacs or tube-like
structures known as cisternae
SER
• No ribosomes are attached
• Mainly helps in synthesis, transport of Lipids
• abundant in mammalian liver and gonad cells

RER
• Contains ribosomes – Involved in synthesis of
Proteins
Golgi apparatus / Golgi bodies
• Packages proteins into membrane bound
vesicles
• Send packages to different destination – Post
office
• series of compartments - Cisternae
• Two faces of golgi bodies - cis and trans
• Final products : Secretory vesicles
Mitochondria / Mitochondrion
• Power house
• Like plastids, Have own DNA!!!
• Double membrane structure
• Production of ATP, Regulate metabolism
• Major parts – Outer membrane, inner
membrane, cristae, inter membrane space,
matrix
Lysosome
• Present in most animal cells
• Spherical vesicles
• Called Suicide bags
• Stores enzymes involved in hydrolysis
• Digests unwanted materials – Waste disposal
system
CELL CYCLE
Terminology
• Somatic cells : Non reproductive cells
• Gametes / Sex cells : Reproductive cells
(sperm and egg/ovum)
• Genome : genetic material
• Chromosomes : Packed DNA
• Diploid Cells : Cells with 2 copies of each
chromosomes – Somatic cells
• Haploid cells : Cells with a single copy of each
chromosomes - Gametes
 Interphase
• G1 phase (Gap 1) – After cell division to start
of DNA replication. Cell is metabolically active
in G1 phase.
• S phase ( synthesis ) – DNA replication takes
place. DNA per cell doubles. NO INCREASE IN
CHROMOSOME NO. .
• G2 phase – proteins needed for mitosis are
made.
 Mitotic Phase
• Starts with nuclear division
• Separation of daughter chromosomes
(Karyokinesis)
• Division of cytoplasm (Cytokinesis)

***************************************
G0 phase : Some cells need not duplicate (for eg
heart cells, unless they are damaged). They
enter into a phase called G0 where cell is active,
but is not replicating
Mitosis
• Chromosome no is same for both parent cell
and daughter cells
• Somatic cells (animal cells)
• Somatic + reproductive cells (lower plant cells)
• Highly needed for repairing tissues, healing
wounds etc..
Mitotic Phase is divided into 4 stages
Prophase –
• Chromosomal material condenses to form
compact mitotic chromosomes. Chromosomes
are seen to be composed of two chromatids
attached together at the centromere.
• Initiation of the assembly of mitotic spindle,
the microtubules, the proteinaceous
components of the cell cytoplasm help in
theprocess.
Prometaphase
• Nuclear membrane fragments, microtubules
grow
• Each of the two chromatids have kinetochore
proteins at the centromere
• Cells at the end of prophase, when viewed
under the microscope, do not show golgi
complexes, endoplasmic reticulum, nucleolus
and the nuclear envelope.
Metaphase
• complete disintegration of the nuclear
envelope marks the start of metaphase
• Spindle fibres attach to kinetochores of
chromosomes.
• The plane of alignment of the chromosomes
at metaphase is referred to as the metaphase
plate
• Chromosomes are moved to spindle equator
and get aligned along metaphase plate
through spindle fibres to both poles.
Anaphase
• each chromosome arranged at the metaphase
plate is split simultaneously and the two
daughter chromatids, now referred to as
chromosomes of the future daughter nuclei,
begin their migration towards the two
opposite poles
• A protein “cohesin” helps in cleavage process
Telophase
• Chromosomes cluster at opposite spindle
poles and their identity is lost as discrete
elements.
• Nuclear envelope assembles around the
chromosome clusters.
• Nucleolus, golgi complex and ER reform
Cytokinesis
• Mitosis accomplishes not only the segregation
of duplicated chromosomes into daughter
nuclei (karyokinesis), but the cell itself is
divided into two daughter cells by a separate
process called cytokinesis at the end of which
cell division is complete
• In an animal cell, this is achievedby the
appearance of a furrow in the plasma
membrane.The furrow gradually deepens and
ultimately joins in the centre dividing the cell
cytoplasm into two.
 Meiosis
• The production of offspring by sexual
reproduction includes the fusion of two
gametes, each with a complete haploid set of
chromosomes
• Gametes are formed from specialised diploid
cells
• This specialised kind of cell division that
reduces the chromosome number by half
results in the production of haploid daughter
cells. This kind of division is called meiosis
 Meiosis
• Meiosis involves two sequential cycles of
nuclear and cell division called meiosis I and
meiosis II but only a single cycle of DNA
replication.
• Meiosis I is initiated after the parental
chromosomes have replicated to produce
identical sister chromatids at the S phase.
• Meiosis involves pairing of homologous
chromosomes and recombination between
them.
 Meiosis I
Prophase I
• During leptotene stage the chromosomes
become gradually visible under the light
microscope.
• During zygotene stage chromosomes start
pairing together and this process of
association is called synapsis. Such paired
chromosomes are called homologous
chromosomes.
• Pachytene is characterised by the appearance of
recombination nodules, the sites at which
crossing over occurs between non-sister
chromatids of the homologous chromosomes.
Crossing over is the exchange of genetic material
between two homologous chromosomes.
Crossing over is also an enzyme-mediated
process and the enzyme involved is called
recombinase. Crossing over leads to
recombination of genetic material on the two
chromosomes. Recombination between
homologous chromosomes is completed by the
end of pachytene, leaving the chromosomes
linked at the sites of crossing over.
• The beginning of diplotene is recognised by
the dissolution of the synaptonemal complex
and the tendency of the recombined
homologous chromosomes of the bivalents to
separate from each other except at the sites of
crossovers. These X-shaped structures, are
called chiasmata.
• The final stage of meiotic prophase I is
diakinesis. This is marked by terminalisation
of chiasmata. During this phase the
chromosomes are fully condensed and the
meiotic spindle is assembled to prepare the
homologous chromosomes for separation.
Metaphase I:
• The bivalent chromosomes align on the
equatorial plate. The microtubules from the
opposite poles of the spindle attach to the
pair of homologous chromosomes.

Anaphase I
• The homologous chromosomes separate,
while sister chromatids remain associated at
their centromeres
Telophase I
• The nuclear membrane and nucleolus
reappear, cytokinesis follows and this is called
as diad of cells
Meiosis II
 Gram staining
• Gram staining is a common technique used to
differentiate two large groups of bacteria
based on their different cell wall constituents.
The Gram stain procedure distinguishes
between Gram positive and Gram negative
groups
• Gram-positive bacteria have a thick mesh-like
cell wall made of, and as a result are stained
purple by crystal violet, whereas gram-
negative bacteria have a thinner layer.
CELL CYCLE REGULATION
Contact Inhibition
• The property of cells to stop multiplying once
it is in contact with other cells
• regulatory mechanism that functions to keep
cells growing into a layer one cell thick.
• Cancer cells lack this property!!!
Stages of embryo development
• The process of fusion of a sperm with an
ovum is called fertilisation.
• During fertilisation, a sperm comes in contact
with the zona pellucida layer of the ovum and
induces changes in the membrane that block
the entry of additional sperms. Thus, it
ensures that only one sperm can fertilise an
ovum.
• The mitotic division starts as the zygote moves
through the isthmus of the oviduct called
cleavage towards the uterus and forms 2, 4, 8,
16 daughter cells called blastomeres.
• The embryo with 8 to 16 blastomeres is called
a morula
• After the 7th cleavage has produced 128 cells,
the embryo is called a blastula.
• The blastula transforms into blastocyst as it
moves further into the uterus.
• The blastomeres in the blastocyst are arranged
into an outer layer called trophoblast and an
inner group of cells attached to trophoblast called
the inner cell mass.
• The trophoblast layer then gets attached to the
endometrium and the inner cell mass gets
differentiated as the embryo.
• After attachment, the uterine cells divide rapidly
and covers
• the blastocyst. As a result, the blastocyst
becomes embedded in the endometrium of the
uterus. This is called implantation and it leads to
pregnancy.
• After implantation, finger-like projections appear
on the trophoblast called chorionic villi which are
surrounded by the uterine tissue and maternal
blood.
• The chorionic villi and uterine tissue become
interdigitated with each other and jointly form a
structural and functional unit between
developing embryo (foetus) and maternal body
called placenta.
• The placenta facilitate the supply of oxygen and
nutrients to the embryo and also removal of
carbon dioxide and excretory/waste materials
produced by the embryo.
• The placenta is connected to the embryo through
an umbilical cord which helps in the transport of
substances to and from the embryo.
• Immediately after implantation, the inner cell
mass (embryo) differentiates into an outer layer
called ectoderm and an inner layer called
endoderm. A mesoderm soon appears between
the ectoderm and the endoderm. It needs to be
mentioned here that the inner cell mass contains
certain cells called stem cells which have the
potency to give rise to all the tissues and organs.
Biotechnology
Recombinant DNA technology
• plasmid - autonomously replicating circular
extra-chromosomal DNA
• The cutting of DNA at specific locations became
possible with the discovery of the so-called
molecular scissors– restriction enzymes
• The cut piece of DNA was then linked with the
plasmid DNA. These plasmid DNA act as vectors
to transfer the piece of DNA attached to it.
• The linking of antibiotic resistance gene with
the plasmid vector became possible with the
enzyme DNA ligase, which acts on cut DNA
molecules and joins their ends.
• This makes a new combination of circular
autonomously replicating DNA created in vitro
and is known as recombinant DNA.
• When this DNA is transferred into a bacterium
• Multiple copies of recombinant DNAs are
generated when bacterium multiply
 Plant cloning
• Totipotency is the ability of a single cell to
divide and produce all of the differentiated
cells in an organism.(eg Morula)
Stem cells
• Undifferentiated cell of a multicellular
organism which is capable of giving rise to
indefinitely more cells of the same type, and
from which certain other kinds of cell arise by
differentiation.
• Example : Bone marrow, Umbilical cord blood
cells
Mendelian Principles
• Based on these observations, Mendel proposed
that something was being stably passed down,
unchanged, from parent to offspring through the
gametes, over successive generations. He called
these things as ‘factors’. Nowadays, we call them
as genes.
• Genes, therefore, are the units of inheritance.
They contain the information that is required to
express a particular trait, in an organism.
• Genes which code for a pair of contrasting traits
are known as alleles, i.e., they are slightly
different forms of the same gene.
Law of dominance :
i) Characters are controlled by discrete units called
factors.
(ii) Factors occur in pairs.
(iii) In a dissimilar pair of factors one member of
the pair dominates (dominant) the other
(recessive).

The law of dominance is used to explain the

expression of only one of the parental characters
in a monohybrid cross in the F1 and the expression
of both in the F2. It also explains the proportion of
3:1 obtained at the F2.
Law of Segregation
• This law is based on the fact that the alleles do
not show any blending and that both the
characters are recovered as such in the F2
generation though one of these is not seen at
the F1 stage.
• Two alleles for a heritable traits separate from
each other during gamete formation and form
different gametes
Test cross
In a typical test cross an organism (pea plants
here) showing a dominant phenotype (and
whose genotype is to be determined) is crossed
with the recessive parent instead of self-
crossing. The progenies of such a cross can
easily be analysed to predict the genotype of
the test organism.

HOW??
Law of Independent Assortment
• The law states that ‘when two pairs of traits
are combined in a hybrid, segregation of one
pair of characters is independent of the other
pair of characters’.
• Co dominance – ABO Blood grouping
Incomplete dominance
• occurs when the phenotype of the
heterozygous phenotype is distinct from and
often intermediate to the phenotypes of the
homozygous phenotypes.
Sickle-cell anaemia:
• This is an autosome linked recessive trait that
can be transmitted from parents to the
offspring when both the partners are carrier
for the gene (or heterozygous).
• The disease is controlled by a single pair of
allele, HbA and HbS. Out of the three possible
genotypes only homozygous individuals for
HbS (HbSHbS) show the diseased phenotype.
Chromosomal Basis of Inheritance
• Failure of segregation of chromatids during
cell division cycle results in the gain or loss of
a chromosome(s) is called aneuploidy.
• Down’s syndrome results in the gain of extra
copy of chromosome 21.
• Turner’s syndrome results due to loss of an X
chromosome in human females.
• Failure of cytokinesis after telophase stage of
cell division results in an increase in a whole
set of chromosomes in an organism and this
phenomenon is known as polyploidy.
• This condition is often seen in plants.
 Griffith’s Transformation Principle
• Streptococcus pneumoniae – bacterium
responsible for pneumonia
• When Streptococcus pneumoniae are grown on
a culture plate, some produce smooth shiny
colonies (S) while others produce rough
colonies (R).
• This is because the S strain bacteria have a
mucous (polysaccharide) coat, while R strain
does not.
• He concluded that the R strain bacteria had
somehow been transformed by the heat-killed S
strain bacteria.
• Some ‘transforming principle’, transferred from
the heat-killed S strain, had enabled the R strain
to synthesise a smooth polysaccharide coat and
become virulent.
• This must be due to the transfer of the genetic
material.
• However, the biochemical nature of genetic
material was not defined from his experiments.
DNA / Protein?
• The unequivocal proof that DNA is the genetic
material came from the experiments of Alfred
Hershey and Martha Chase (1952).
• They grew some viruses on a medium that
contained radioactive phosphorus and some
others on medium that contained radioactive
sulfur.
• Viruses grown in the presence of radioactive
phosphorus contained radioactive DNA but not
radioactive protein because DNA contains
phosphorus but protein does not.
• Similarly, viruses grown on radioactive sulfur
contained radioactive protein but not radioactive
DNA because DNA does not contain sulfur.
• Radioactive phages were allowed to attach to E.
coli bacteria.
• Then, as the infection proceeded, the viral coats
were removed from the bacteria by agitating
them in a blender.
• The virus particles were separated from the
bacteria by spinning them in a centrifuge.
• Bacteria which was infected with viruses that
had radioactive DNA were radioactive,
indicating that DNA was the material that
passed from the virus to the bacteria.
• Bacteria that were infected with viruses that
had radioactive proteins were not radioactive.
This indicates that proteins did not enter the
bacteria from the viruses.
• DNA is therefore the genetic material that is
passed from virus to bacteria
Composition of DNA
• A nucleotide has three components – a
nitrogenous base, a pentose sugar (ribose in
case of RNA, and deoxyribose for DNA), and a
phosphate group.
• There are two types of nitrogenous bases –
Purines (Adenine and Guanine), and
Pyrimidines (Cytosine, Uracil and Thymine).
• Cytosine is common for both DNA and RNA
and Thymine is present in DNA. Uracil is
present in RNA at the place of Thymine.
• A nitrogenous base is linked to the pentose
sugar through a N-glycosidic linkage to form a
nucleoside, such as adenosine or
deoxyadenosine, guanosine or
deoxyguanosine, cytidine or deoxycytidine
and uridine or deoxythymidine.
• When a phosphate group is linked to 5'-OH of
a nucleoside through phosphoester linkage, a
corresponding nucleotide (or deoxynucleotide
depending upon the type of sugar present) is
formed.
• Two nucleotides are linked through 3'-5‘
phosphodiester linkage to form a dinucleotide.
• More nucleotides can be joined in such a
manner to form a polynucleotide chain.
• A polymer thus formed has at one end a free
phosphate moiety at 5'-end of ribose sugar,
which is referred to as 5’-end of polynucleotide
chain.
• Similarly, at the other end of the polymer the
ribose has a free 3'-OH group which is referred
to as 3'- end of the polynucleotide chain.
• The backbone in a polynucleotide chain is
formed due to sugar and phosphates.
• The nitrogenous bases linked to sugar moiety
project from the backbone.
• In RNA, every nucleotide residue has an
additional –OH group present at 2'-position in
the ribose.
• Also, in RNA the uracil is found at the place of
thymine (5-methyl uracil, another chemical
name for thymine).
DNA Replication – Meselson & Stahl Experiment
Molecular Biology Techniques
Polymerase Chain Reaction (PCR)
• In this reaction, multiple copies of the gene (or
DNA) of interest is synthesised in vitro using two
sets of primers (small chemically synthesised
oligonucleotides that are complementary to the
regions of DNA) and the enzyme DNA
polymerase.
• The enzyme extends the primers using the
nucleotides provided in the reaction and the
genomic DNA as template. If the process of
replication of DNA is repeated many times, the
segment of DNA can be amplified to
approximately billion times
• Such repeated amplification is achieved by the
use of a thermostable DNA polymerase
(isolated from a bacterium, Thermus
aquaticus), which remain active during the
high temperature induced denaturation of
double stranded DNA.
• The amplified fragment if desired can now be
used to ligate with a vector for further cloning
Gel Electrophoresis
• Since DNA fragments are negatively charged
molecules they can be separated by forcing
them to move towards the anode under an
electric field through a medium/matrix.
• Nowadays the most commonly used matrix is
agarose which is a natural polymer extracted
from sea weeds.
• The DNA fragments separate (resolve) according
to their size through sieving effect provided by
the agarose gel
• Hence, the smaller the fragment size, the farther
it moves.
• The separated DNA fragments can be
visualised only after staining the DNA with a
compound known as ethidium bromide
followed by exposure to UV radiation (you
cannot see pure DNA fragments in the visible
light and without staining).
• You can see bright orange/pink coloured
bands of DNA in a ethidium bromide stained
gel exposed to UV light
Sodium Dodecyl Sulfate Polyacrylamide Gel
Electrophoresis – for proteins
• Along with the addition of SDS to denature
(i.e., unfold, destroy native structure of) the
cellular proteins, a second reagent is added.
This reagent contains a soluble thiol (-SH)
group to reduce any inter-or intra-molecular
disulfide bonds
• This is important because disulfide bonds,
which can exist within as well as between
polypeptide chains, prevent the polypeptide
from fully unfolding.
• The horribly stinky β-mercaptoethanol is most
commonly used.
• that poly-acrylamide gels are run in a vertical
orientation, unlike agarose gels, which are
horizontal; and that SDS-coated protein are
negatively charged, regardless of the pH of the
buffer
EVOLUTION
Darwinian concept
• Branching descent and natural selection are
the two key concepts of Darwinian Theory of
Evolution
• Even before Darwin, a French naturalist
Lamarck had said that evolution of life forms
had occurred but driven by use and disuse of
organs.
HARDY-WEINBERG PRINCIPLE
• In a given population one can find out the
frequency of occurrence of alleles of a gene or
a locus.
• This frequency is supposed to remain fixed
and even remain the same through
generations.
• HW - Principle says that allele frequencies in a
population are stable and is constant from
generation to generation.
• The gene pool (total genes and their alleles in
a population) remains a constant.
• This is called genetic equilibrium. Sum total of
all the allelic frequencies is 1.
Domains of Life
• Bacterium
• Eukaryotes
• Archaebacterium
Archaebacterium
• Prokaryots – But similar to eukaryotes
• differ from other bacteria in having a different
cell wall structure and this feature is
responsible for their survival in extreme
conditions.
• live in some of the most harsh habitats such as
extreme salty areas (halophiles), hot springs
(thermoacidophiles) and marshy areas
(methanogens).
Plant Kingdom
Algae
• algae reproduce by vegetative, asexual and sexual
methods.
• The algae are divided into three main classes:
Chlorophyceae, Phaeophyceae and Rhodophyceae
• The members of chlorophyceae are commonly called
green algae
• The members of phaeophyceae or brown algae are
found primarily in marine habitats.
• Rhodophyta are commonly called red algae because
of the predominance of the red pigment, r-
phycoerythrin in their body.
BRYOPHYTES
• Bryophytes include the various mosses and
liverworts that are found commonly growing
in moist shaded areas in the hills
• Bryophytes are also called amphibians of the
plant kingdom because
these plants can live
in soil but are
dependent on water
for sexual reproduction.
PTERIDOPHYTES
• The Pteridophytes include horsetails and
ferns.
• Evolutionarily, they are the first terrestrial
plants to possess vascular tissues – xylem and
phloem.
GYMNOSPERMS
• The gymnosperms (gymnos : naked, sperma :
seeds) are plants in which the ovules are not
enclosed by any ovary wall and remain
exposed, both before and after fertilisation.
ANGIOSPERMS
• In angiosperms, the seeds are enclosed by
fruits.
All The Best!!!