Module 1

Lecture 2-4 → Essential Molecules

How do biologists investigate life?

Controlled experiments:
A single dependent variable is checked for by varying an independent variable, keeping
all other factors constant.

Comparative experiments:
We go to natural environments and study the effect of the previously taken independent
variable and its effect on the dependent, without ourselves varying any factor.

Atoms and elements

Mass of proton = 1 Dalton = 1.66 x 10^-24 g
Mass of electron = 0.0005 Da

Module 1 1
 A shell is a region where the probability of finding an electron is greater than 90%.
Chemical bonds; types and strengths:

Note these are ionic ‘attractions’ and not ionic bonds, making them weaker than
covalent bonds in this case.
Hydrogen bonds can be between two molecules, or even between two parts of the
same molecule.

Hydrophilic→ Water-loving, molecules attracted to water.

Hydrophobic → Water-hating, molecules attracted to themselves more than to water.

Molecules that make organisms

The composition of the type of molecules in our body are in the following order, highest
to lowest,
Proteins>Nucleic Acids>Carbohydrates>Lipis

Macromolecules

Module 1 2
 The formation of macromolecules releases a molecule, usually water and this is called a
condensation reaction.
The breakage of macromolecules required a molecule to be added, usually water, and
this is called a hydrolysis reaction.

Proteins 💪
Important:

Module 1 3
 Structural proteins → Actin etc.
Receptor proteins → Glycoproteins
Signalling proteins→ Hormones e.g. Oestrogen
Storage proteins(store metal ions as well as amino acids) → Ferritin(to store iron),
Albumin etc.
Transport proteins → Proteins that control flow of polar molecules etc. in the membrane
Gene regulatory proteins → Transcetylase

Each polypetide chain formed is linear, which is then folded due to different interactions.

Amino Acids
There are about 20 naturally occuring amino acids that make up all the proteins in our
body.
Structure:

Module 1 4
 Categories of Amino acids:

Enantiomers : Molecules having same chemical and stuctural formula but different
orientation in space.
Although Amino Acids could have both D and L Types due to them having a chiral
carbon, Proteins exclusively contain the L-Type Amino acid

Module 1 5
 [ NOTE : All amino acids have enantiomers except glycine since it only has Hydrogen in
its R-group, making the carbpn non-chiral ]
The NH3+ end of the amino acid is called the N-terminus while the COO- end is called
the C-terminus. a protein always runs in an N→C direction.

Two amino acids combine by condensation, releasing a water molecule and forming a
peptide bond.

Primary structure

Related to the number and sequence of the amino acids in a polypeptide. It is held by
the peptide linkages b/w the amino acids.

Secondary Structure

Related to coiling of the polypeptide chains.

1. α helices → The coiling results from hydrogen bonds that form between the δ+
hydrogen of the N—H of one amino acid and the δ– oxygen of the C=O of another.
When this pattern of hydrogen bonding is established repeatedly over a segment of the
protein, it stabilizes the coil
2. β - pleated sheets → formed from two or more polypeptide chains that are almost
completely extended and aligned.

Module 1 6
 Note: Proteins can have both types of secondary structures in different regions of a
same polypetide chain!

Alpha Helix clockwise Right Handed

Alpha Helix anticlockwise Left Handed

Secondary structure thus are maintained by Hydrogen bonds, but overall in secondary
structure both H-H and peptide bonds are present.

Tertiary structure

In many proteins, the polypeptide chain is bent at specific

sites and then folded back and forth, resulting in the tertiary
structure of the protein

Although α helices and β pleated sheets contribute to the tertiary structure, usually only
portions of the macromolecule have these secondary structures,
and large regions consist of tertiary structure unique to a particular protein.

Whereas hydrogen bonding between the N—H and C=O

groups within and between chains is responsible for secondary structure, the
interactions between R groups—the amino
acid side chains—and between R groups and the environment
determine tertiary structure.

1. Disulphide bonds(Strongest)

2. Hyrogen bonds (b/w R groups this time)

3. Hydrophobic interacion

4. Ionic attractions b/w +vely and -vely charged R groups, forming salt bridges.

Quartenary structure

Module 1 7
 Related to the structure formed after R-group interations between mutiple polypeptide
chains. It includes all types of bonds as tertiary as well.

Shape and chemistry

The precise shape of every protein, be it an enzyme or a signalling protein, is very
essential to its structure. Recent studies involve for example, studying active sites of
different enzymes which could then by inhibited by designing an inhibitor
complementary to the shape of the active site. Factors that can affect the protein
structure are the following:
1. Temperature→ Cause more rapid molecular movements and thus can break
hydrogen bonds and hydrophobic interactions

2. Alterations in pH→ affect pattern of ionization of exposed carboxyl and amino

groups, disrupting the pattern of ionic attractions and repulsions.

3. High concentrations of polar substances like urea can disurpt the H-bonding that is
crucial to protein structure

4. Nonpolar substances may also disrupt normal protein

structure in cases where hydrophobic interactions are essential to maintain the
structure

Denaturation can or cannot be reversible. Usually, if primary structure is broken(which is

the hardest to do so compared to weak bonds like H-H or ionic interactions of second,
tertiary or quartenary), denaturation becomes irreversible.

Lastly, proteins can change their shapes if needed in order to better bind to their
substrae.

Carbohydrates
Carbohydrates are composed of carbon, hydrogen, and oxygen in the general
ratio of 1:2:1.
General formula : CH2nOn → Cm (H2 O)n

Uses:

Module 1 8
 They are a source of stored energy that can be released in a form usable by
organisms.
They are used to transport stored energy within complex organisms.
They serve as carbon skeletons that can be rearranged to form new molecules.

Types:
Monosaccharides (mono, “one”; saccharide, “sugar”), glucose, ribose, and fructose.
Disaccharides (di, “two”) consist of two monosaccharides linked together by covalent
bonds. The most familiar is sucrose, which is made up of covalently bonded glucose
and fructose molecules.
Glucose+Glucose gives maltose. And galactose+glucose gives lactose.
Oligosaccharides (oligo, “several”) are made up of several (3–20) monosaccharides.
Polysaccharides (poly, “many”), such as starch, glycogen, and cellulose, are polymers
made up of hundreds or thousands of monosaccharides.

Structures of Glucose:

Ribose and Deoxyribose:

Module 1 9
 Disaccharides, oligosaccharides, and polysaccharides are all constructed from
monosaccharides that are covalently bonded together by condensation reactions that
form glycosidic linkages

B-glucose + B-glucose → Cellubiose

Module 1 10
 B-glucose + B-glucose (180o rotated) → Cellulose

a-glucose + a-glucose → Starch and glycogen

Starch is made up of amylopectin (containing alpha-1,4 and 1,6 bonds) and amylose
(containing alpha- 1,4 so a linear molecule) .
Note however, Glycogen is relatively much more branched than amylopectin.
Sucrose has alpha-1,2 bonds.

Parallel cellulose molecules form Hydrogen bonds b/w them, resulting in thin fibrils.
High amount of branching in gylcogen makes it more compact than starch.

Module 1 11
 While in starch, branching limits the number of H-bonds that can form, making it less
compact than cellulose.
MODIFIED SUGARS
Sugar phosphate (e.g., fructose 1,6 bisphosphate)
Amino sugars (e.g., glucosamine and galactosamine)
Chitin (polymer of N-acetyl glucosamine)

Nucleic Acids
Mainly, DNA and RNA.
Basic unit: Nucleotide, which then has 3 components :

1. Sugar (Ribose or Deoxyribose)

2. Base

i. Purines(Double ringed) → Adenine and Guanine

ii. Pyramidines(Single ringed) → Thymine(only in DNA), Uracil(only in RNA) and

Cytosine

3. Phosphate group

Polymers of nucleotides form polynucleotides, to usually form DNA or RNA.

DNA is a double helix, formed due to complementary base pairing between Adenine
and Thymine/Uracil (form 2-H bonds in b/w) and between Guanine and Cytosine (form 3
H-bonds in b/w).

Module 1 12
 DNA → double stranded, contains deoxyribose RNA, Thymine instead of Uracil, forms
H-bonds b/w strands→ single stranded(mostly), contains ribose, Uracil instead of
Thymine, no H-bonds since a single strand.
Ribose/Deoxyribose + Nitrogenous base forms a Nucleoside. Adding a phosphate
group then makes it a nucleotide.
Structure:

A polynucleotide always runs in a direction 5’ to 3’, where 5’ bein the carbon to which
the phosphate group is attatch, and 3’ the bottom left carbon.
The complementary nucleotide strand in a DNA always runs anti-parallel, from 5’ to 3’
direction again.

Module 1 13
 Sequence of nucleotides in DNA carries the informaion used by RNA to specify primary
protein structure.

The total DNA content of a body is known as Genome.

DNA undergoes a semi-conservative repilcation, where the parent strands (also called
the sense-strands) separate from each other and new nucleotides join to form a new
strand(also called the anti-sense strand) complementary to the parent, making the 2
new DNA molecules having 50% content of the original parental strand(i.e. 1 original
and 1 new strand for each DNA)

Nucleotides, like ATP are used for energy.

Lipids
Substances such as a fat, oil or wax that dissolves in alcohol but not in water.
Lipids contain carbon, hydrogen and oxygen but have far less oxygen proportionally
than carbohydrates.
Functions:

Module 1 14
 Triglycerides (made up of glycerol + fatty acid)

Each CH2-OH of Glycerol, and the terminus of fatty acids of CO-OH undergo
condensation to yield a water molecule and form an ester linkage
Fatty acids can saturated, meaning there is no C=C and so the resulting chain is
straight. Thus, they are easily packed. Due to this high density, they usually exist as
solids. They come from animal fats.
Unsaturated fatty acids on the other hand have C=C bonds, which causes a kink in the
chain, making it harded for them to pack together. Due to this density, they usually exist
as liquids. Come from plant fats.
Phospholipids

Module 1 15
 These have 1 polar chain unlike the triglycerides, making one side of it polar. Thus they
are used to form bilayers in cell membranes where the polar head faces towards the
water while the hydrophobic tail faces away from water.

Carrots that we eat are rich in Cartenoids which contain β Carotene, a good source of
Vitamin A which is necessary for cis-retinal, important for our vision.
Other forms of Lipids include Steroid e.g. Cholestrol which are simple organic molecules
with multiple rings and forms an essential component of the membrane.
Fat-soluble vitamins like Vitamin A that form part of rhodopsin (required for vission),
Vitamin-D which regulates absorption of calcium from small intestine, Vitamin-E which
protects cells from damaging effects of redox reactions, or Vitamin-K which is involved
in blood clotting.

Lecture 4 → Cell-Theory
Cells are fundamental units of life
All organisms are composed of cells
All cells come from pre-existing cells (hmm don’t confuse with evolution though)
All cells are similar in chemical composition
Complete sets of genetic information are replicated and
passed on during cell division
Viruses lack cellular structure but remain dependent on

Module 1 16
 cellular organisms
Require energy
Cells can either be

i. Prokaryotic, meaning they lack nucleus in their cells. For example, bacteria. Their
size is 1-10 micrometres. Infact, the don’t have any organelle (membrane bounded
compartments inside a cell).
A bacterial cell for instace, has an outermost capsule, cytoplasm, ribosomes(70S),
Nucleois(region having Chromosomes, but not membrane bound), and a flagellum.
Their Cell surface membrane is covered by cell wall, which in this case is made up
of peptidoglycan.

1. Or Eukaryotic, meaning they do have a nucleus. For example, plant and animal
cells. Their size os 10-100 micrometres. They contain Organelles e.g. Endoplasmic
reticulum, Golgi bodies, lysosomes, mitochondria, chloroplasts, peroxisomes etc.
Animal cells don’t have a cell wall but plant cells do. Animal cells also have much
smaller and only temporary vacuoles compared to plant cells.

An Eukaryotic cell looks like:

Module 1 17
 Cell Surface Membrane
Thickness- 7nm
Composed of phospholipid bilayer and a variety of proteins, acting as a selectively
permeable barrier which helps cells to maintain a constant internal environment.
Contains receptors which are specific which then help with commincation and lastly, has
a structural role to maintain the cell’s shape.

Nucleus

Module 1 18
 Contains DNA
DNA is bound to proteins
Careful packaging!
Chromosomes
Has a nuclear envelope which has spaces between them called nuclear pores. The
envelope is continuous with endoplasmic reticulum

The nuclear lamina is a network of filaments just inside the nuclear envelope which
interact with chromatin and helps support the envelope to which it is attatched. An
octagon of protein complexes surrounds each nuclear pore. Protein fibrils on the
nuclear side form a cagelike structure.
The nuclear envelope is a double membrane.
Nucleolus is a compartment inside nucleus which is the site of assembaly for
ribosomes.
The nuclear pore too is selective.
Endoplasmic Reticulum
Interconnected membranes branching throughout the cytoplasm, forming tubes and
flattened sacs.
1/10th of its volume is occupied by its Lumen(inside area). Its surface area is many
times greater than plasma membrane.
There are two types of ER, rough and smooth.

Module 1 19
 The rough ER has 80S ribosomes which are sites of protein synthesis. It modifies the
proteins and packages them to Golgi apparatus in a vesicle. Also responsible for
Glucosilation of proteins such as forming Glycoproteins!
While smooth ER has no ribosomes but is a site for lipid synthesis(and other small
mlecules), chemical modification of proteins, degrade glycogen, store Calcium, and
detoxify harmful chemicals by making them more polar so they dissolve in water.

Golgi Apparatus
it almost always consists of two components: flattened membranous sacs called
cisternae (singular
cisterna) that are piled up like saucers, and small membrane enclosed vesicles.
Receives proteins from ER for further modification
Concentrates and packages proteins to destinations within and outside the cell

Module 1 20
 It also ‘targets’ where the final packaged protein has to go.
Lysosomes
1 micrometer diameter, single membrane. Contain digestive enzymes and and are the
sites where macromolecules are broken down into their monomers.
Primary Lysosomes originate from Golgi apparatus. It acts on phagocytosed stuff like
food,other cells or foreign objects which have been packaged into a vesicle. The
Lysosome combines with this vesicle, releasing its enzymes which then break down the
content.
(Phagocytosis is the process by which the extracellular contents enter inside the cell by
forming a vesicle)
All lysosomal enzymes ae active at the acidic pH(about 5) which is maintained inside
the lysosome.
Misfunctioning of these can lead to fatal diseases like Hurle’s and Inclusion cell disease.

Mitochondria

Module 1 21
 Assumed to have a bacterial origin?
Has a double membrane system, inner is called cristae. Cristae is extensively folded to
increases the SA:V ratio allowing maximum rate of respiration.
Inner region is called matrix, which contains the ribosomes, mtDNA etc.
1.2 μm diameter. 2-8μm length
Involved in energy production through cellular respiration.
They have their own ribosomes and DNA, which means they are self sufficient to make
their own proteins and are able to replicate themselves.
They contain mtDNA, which surprisingly is only maternally inherited.
Not that sperms don’t have mitochondria but only their nucleus enters the egg.
An average liver cells contains more than 1,000 mitochondria. Mostly, regions of body
that are most active and so require alot of energy have alot of mitochondria to
synthesize ATP.

More onto respiration later.

Chloroplasts
Double membraned, site of photosynthesis since they contain chlorophyll.

Module 1 22
 5-10 μm in length
Consider size of chloroplast>mitochondria generally.

More onto photosynthesis later.

Peroxisomes

Degrade hydrogen peroxide produced

as by-product of biochemical reactions
• 0.2 – 1.7 micrometer in diameter
• Single membrane
• Zellweger syndrome
Hydrogen peroxide makes reactive oxygen species which can go wreck havoc by
reacting with everything.

Cytoskeleton
It is involved in:

1. Maintaining the shape of cell

2. Holds positions of cell organelles in their places.

3. Forms a network of transport for molecules within the cell.

4. Plays a part in cell divison.

5. Involved in movements of cytoplasm

Module 1 23
 6. Interacts with extracellular structures, helping anchor the cell in its place.

i. Microfilaments. made of actin. 7nm in width, mostly towards the periphery of the
cell. Change cell shape and drive cellular motion.

ii. Intermediate filaments ,made of fibrous proteins 8-12 nm in width, scattered

around everywhere. Maintain cell’s shape, help to hold neighbouring cells together
while some make nuclear lamina.

iii. Microtubules. 25nm in width, Long and extensive, stretched throughout the cell.
long, hollow cylinders made up of many molecules of the protein tubulin. Help in
transport within the molecule, while their shortening moves chromosomes.

Cells - Summary

Require energy for their functions

Are surrounded by membranes

Module 1 24
 Contain informational(DNA and RNA) and non-informational(Proteins,
Polysacharides, lipids)
macromolecules

Need to sense and communicate with their environment

Depend on pathways for processing nutrients and waste,

and synthesis/breakdown of small/large molecules

Life-begets-life!

Cell communication
Different types of extracellular signals to regulate cell fate →

1. Cells always need signals to survive. For instance even in our cultured mediums we
use mediums that ensure the healthy cell receives the signal to survive.

2. Signals telling it to undergo cellular divison.

3. Signals to differentiate.

4. Signal telling the cell to die by the process apoptasis, for instance if its a bacteria, or
a cancerous cell etc.

Essential things for cell signalling are

Module 1 25
 a. Signal

b. Receptor for that signal

Types of signalling:
Local → Autocrine, Juxtacrine and Paracrine
Distal → Endocrine(mostly hormones), Synaptic(Since neurones are very long)

A signal transduction pathway is a sequence of molecular events and chemical

reactions that lead to a cell’s response to a signal (Note: AFTER the signal has been
received)
The signal can be either chemical or physical. Chemically, it can be the hormones,
neurotransmitters or the fragrances the take the signal(or macromolecules even like
Proteins, Nucleic acids or Lipoproteins). Physically it can be mechanical, light or
something like injury,damage or stress.
These signals are detected by receptors which are very specific. Different types of
receptors include Membrane receptors→ ion channels, protein kinase receptors, G-
protein couple receptors
Intracellular receptors
Changes in the receptor due to signals can be chemical or physical.
It can happen that after a signal the receptor protein changes its location. For example
from cytoplasm to nucleus.

Module 1 26
 G Proteins are essential signal carriers. In their case its GDP which completly detatches
after which GTP is attatched. But in the reverse proess from GTP to GDP, GTPase
simply removes a phosphate.

Phosphorylation
Is a process through which a certain residue in a particular protein (namely serene,
threonine, tyrosine) a phosphate group Named ATP’s gamma phosphate(terminal
phosphate) is added by an enzyme kinase. The result is that in most cases it makes it
active.
Protein phosphatases as opposed to protein kinases remove the Phosphate group from
the protein.

Receptor Tyrosine Kinases

The signal arrives and attahces to the receptor which then activates and changes it
shape such that it now has a cytoplasmic facing region which can bind to ATP. ATP
binds and phosphorlyzes the receptor, leaving itself as ADP(It can also phosphorylyze
itself!). It can also phosphorlyze other molecules which can then relay the signals.
These molecules are rightly called the xyz-response substrates.

Ion channels,

Module 1 27
 The plasma membranes of many types of cells contain gated ion
channels that allow ions such as Na+, K+, Ca2+, or Cl– to enter or leave the cell. The
gate-opening mechanism is an alteration in the three-dimensional shape of the channel
protein upon interaction with a signal. Pay close attention to the diagram.

We can go from ATP to cAMP using adenylyl cyclase, and then to AMP from cAMP
using phosphodiesterase

G-protein coupled receptors

or Nuclear receptors like steroid hormone receptors.

Once the signal has reached a cekll, the intracellular signalling(e.g. enzymes, G
proteins or scaffold proteins) proteins take the message to the effector.

Module 1 28
 Membrane receptors: Large or polar ligands cannot cross the lipid bilayer e.g. Insulin
Intracellular receptors: Small or nonpolar ligands can diffuse across the nonpolar
phospholipid bilayer of the plasma membrane and enter the cell e.g. Estrogen

Module 1 29
 Signal Transduction is regulated with the help of phosphorylation. :

(only G-proteins are bound to GDP/GTP)

A protein kinase cascade

1. A growth factor signal attatches to a receptor

2. Receptor phosphorylates itself to become active

3. This activates receptor initates a series of events that allow RAS to bind to GTP
(note GDP is first removed and GTP added, not just an addition of a phosphate)

4. Activated RAS binds and activates RAF

5. Activated RAF is a protein kinsase that phosphorylates many molecules of MEK

6. MEK is a protein kinase that phosphorylates many molecules of MAPk

7. Activate (phosphorylates) MAPk can enter the nucleus.

A protein kinase cascade, where one protein kinase activates the next, and so on. Such
cascades are key to the external regulation of many cellular activities. The genomes of
complex eukaryotes, such as humans, typically encode hundreds of protein kinases.
Protein kinase cascades are useful signal transducers for four reasons:
• At each step in the cascade of events, the signal is amplified,
because each newly activated protein kinase is an enzyme
that can catalyze the phosphorylation of many target proteins.
• The information from a signal that originally arrived at the
plasma membrane is communicated to the nucleus where

Module 1 30
 the expression of multiple genes is often modified.
• The multitude of steps provides some specificity to the
process.
• Different target proteins at each step in the cascade can
provide variation in the response.

In cancer cells however, the abnormal form of RAS protein stays phosphorylated,
always stays active.

Epinephrine(Adrenaline) to glucose release

Module 1 31
 Second messengers
Small intracellular mediators; Small intracellular signaling molecules that are
formed or released for action in response to an extracellular signal and help to relay that
signal within the cell.
Types : cyclic AMP, cyclic GMP, IP3, Ca2+, diacylglycerol (remember)
Ca+2 can activate Protein Kinase C (PKC)

Cell Division

Module 1 32
 Events of cell divison

1. Reproductive Signal- either from inside or outside the cell

2. Replication of DNA

3. Segregation- Distribution of the replicated DNA into new cells

4. Cytokinesis- Physical separation of a cell into two

Cell Cycle -

A cell always needs a signal to know whether it has to divide or not, as otherwise it can
be cancerous. It also must make sure that the chromosome number doesn’t double in

Module 1 33
 every cycle.
n means hapolid, 2n diploid. Normally in our cells, there are 22 pairs of homologous
chromosomes and 1 pair of sex chromosomes. One chromosome of each pair comes
from a father and the other from a mother.
In bacteria, there is an origin of replication where the DNA replicates. The daughter
DNA are then segregated, after which cytokinesis occurs. This can occur is just about
20-40 mins in bacteria under favourable conditions!

While the cell is in G1, and the signal to replicate arrives, it crosses the restriction point
and then it always always undergoes cell divison. Otherwise if no signal comes, the cell
is arrested.
Then in Synthesis(S) , the 2n cell must double to 4n and then divide to 2n 2n again.

Cellular division occurs in cytokinesis.

Mitosis is only responsible for nuclear division.

Module 1 34
 Cyclin, Cdk at different stages ensure that everything is working properly
Basically, CDK is a protein that is normally present in our cell but not active. However,
cyclin proteins are made at only certain instance of the cell cycle. These cyclin
molecules when present go and bind to CDK, which causes conformational changes tp
CDK exposing CDK’s active site. Once this has happened, a specific protein substrate
along with an ATP are able to bind to the CDK protein, which results in the
phosphorylation of the protein substrate attached, now leaving it free to go on and
regulate the cell cycle as usual.
Note there are different types of CDKs for different parts of cell cycle with different
specific protein substrates attaching to them.

Module 1 35
 Retinoblastoma Protein
Retinoblastoma is attatched to a segment of E2F gene segment of DNA, not allowing
the genes encoded by that segment to be transcripted.
However, once a growth factor is reveived by the protein kinase receptor and it
undergoes a Ras pathway, activating a Cyclin-CDK complex which finally
phosphorylyzes the Retinoblastoma protein, which in this case deactivates the Rb’s
activity exposing the E2F elongation factor. The E2F section is then transcribed and
translated to essential proteins and enzymes needed to carry out the S-Phase of the
cell cycle.

Module 1 36
 (Phosphorylation can also deactivate something’s activity)
DNA is never naked inside the cell nucleus. It’s always wrapped around histone
proteins.
Each DNA wrapped around a histone protein forms a nucleosome. The Nucleosome
form ‘beads on a string, which altogether after coiling folding etc form a chromosome.

Nuclear divison happens in telophase

Interphase is basically the normal state of the cell.

Mitosis

Module 1 37
 1. Prophase
Chromatin condenses and becomes easily visible.
Centrosomes start moving towards opposite poles of the cell.
Nucleolus disintegrates

2. Prometapase
Nuclear envelope breaks down.
Kinetochore tubules appear from the centrosomes at the poles, attaching at the
centromeres of the chromosomes.

3. Metaphase
Centromeres become aligned in a plane at the cell’s equator.

4. Anaphase
The paired sister chromatid separate, and the new daughter chromosomes begin to
move toward the poles.

5. Telophase
The daughter chromosomes reach the poles.As telophase concludes, the
nuclearenvelopes and nucleoli re-form, the chromatin decondenses.

Cytokinesis is occurs after mitosis, and ends up dividing the cells themselves after
which the daughter cells enter interphase once again.

Module 1 38
 Meiosis
Meiosis 1
Meiosis-I is called reduction divison.

1. Prophase 1
Nucleolus disinitegrates, nuclear envelope breaks, homologous chromosome pair
up to form bivalents/tetrads. Centrosomes move towards the opposite ends and
spindle fibres are formed.
During this period, crossing over occurs between the two homologous
chromosomes i.e. certain segments of genes are exchanged between the two. The
points where the chromosomes overlap are called ‘chiasmata’. Also, pairing of
homologs to form a tetrad is called a synapsis.
Crossing over is essential for genetic variation.

2. Metaphase 1
Homologous chromosomes align at the centre of the cell, attatched by the
kinetochore tubules with their centromeres.

3. Anaphase 1
Sister chromatids remain attatched, while recombinant chromosomes are separated

4. Telophase and after cytokinesis (note cytokinesis isnt exactly a part of meiosis)
The two cells, each with 1 of the pair of chromosome are now present in each cell
i.e. 23 chromosomes in each of the two new cells formed.

Module 1 39
 Meiosis 2
Note that at this stage we have 2 resulting cells coming from the original cell, so both
the 2 cells undergo meiosis 2 from 1 original cell.

1. Prophase 2
Same as prophase 1, except no crossing over this time.

2. Metaphase 2
Same as metaphase 1

3. Anaphase 2
Same as anaphase 1. except this time both the sister chromatids are separated and
not the pair of homologous chromosomes.

4. Telophase 2

Module 1 40
 Essential chart, do note

Food Chain

Module 1 41
 Types of reactions in nature:

1. Endergenic → Reactions that require energy, for example active transport, cell
movement, anabolism etc.
When ATP is hydrolyzed to ADP + Pi (inorganic phosphate), energy is released,
while

2. Exergenic → Reactions that release energy, for example respiration, catabolism

When ATP is hydrolyzed to ADP + Pi (inorganic phosphate), energy is released, while

the reverse reaction requires energy.
Oxidation refers to losing electrons and reduction to gaining electrons.

Module 1 42
 Respiration
Oxidation of glucose to release energy.
It can either be aerobic or anaerobic.

Stage-I-Glycolysis
This stage is similar for both Aerobic or Anaerobic respiration.
Glucose is converted to two molecules of three-carbon pyruvate, and a small amount of
energy is captured in usable form. 4 ATPs are made while 2 ATPs are used in the
process. This reaction occurs in the cytoplasm.

Module 1 43
 Stage-II-Link reaction
NAD+ to NADH is reduction/hydrogenation.
Remember this reaction, Pyruvate→Acetyl CoA with the release of CO2, reducing
NAD+ to NADH in the process. Occurs in the matrix of Mitochondria.

Glucose converted into two 3-C Pyruvates from glycolsis enters this stage to be
converted to Acetyl CoA by the reduction of NAD+ to NADH and the release of a CO2
molecule. Notice this occurs twice for each molecule of glucose (since 2 pyruvates).

Module 1 44
 Stage III-Krebs cycle
Occurs in the matrix of mitrohondria.

1. Acetyl CoA (2-C) combines with Oxaloacetate(4-C) to form Citrate(6-C)

2. Citrate is converted to a 5-Carbon compound by the release of CO2 and reducing

NAD+ to NADH

3. step 2 occurs again except 5-C is converted to 4-C

4. Energy is utilized to convert GDP+Pi to GTP

5. FAD+ is reduced to FADH2

6. H20 is added

7. NAD+ is reduced to NADH

8. Oxalacetate is now ready to combine with another Acetyl CoA and the cycle repeats

Again, all this occurs twice for each molecule of glucose since there will be 2-Acetyl
CoA for each molecule of glucose.

Stage-IV-Electron Transport Chain

Module 1 45
 All the NADH and FADH2 formed in previous stages arrive at the cristae(inner
membrane of mitochondria) to oxidise and release electrons. These Electrons jump
from one Cytochrome protein to the next (NADH reductase(1) → Ubiquinone →
Cytochrome c reductase(2), → Cyctochrome c → Cytochrome oxidase(3)), (1, 2 & 3
are the sites where H+ are pumped into intermembrane space) in the process releasing
energy for these proteins to pump Protons from the matrix into the intermembrane
space of the mitochondria. Doing this creates a concentration as well as an
electrochemical gradient, with greater concentration of protons in the intemembrane
space (and more positive) than the matrix, hence protons move down back into the
matrix through a unit that contains ATP synthase. As protons move down the
electrochemical gradient, ATP synthase uses the energy released to convert ADP + Pi
into ATP.
The electrons on the other hand that were passing across the cytochrome proteins
combine with the H+ released and Oxygen to form an H20 molecule. 2H+ + 1/2 O2 +
2e- → H20

Thus in total, 32 ATPs are formed. 2 from Glycolsis, 2 from Krebs cycle, and 28 from
ETC.

Module 1 46
 Photosynthesis

Stage-I-The light reaction aka photophosphorelation.

To begin with, water is converted to + 1/2O2 + 2H+ + 2e- using sunlight.
Light is absorbed by the by antenna pigments of photosystem-II(680 nm) and passed
onto reaction centre, which using the electrons from the photolysis of water
photoactivates them to higher energy levels. These electrons are thus able to pass
down the gradient across the ETC, forming ATPs in the process.
Electron from photosystem 1 is at a higher energy level than 2.
Now the electron reaches photosystem-I (700nm) where it’s again photoactivated using
light energy, where these electrons along with the H+ released from photolysis of water
and NADP+(which was made by reducing ferredoxin) form NADPH.

These NADPH and ATP particularly are essential products from this stage to be used in
the Light indepedent stage/Calvin cycle.

Module 1 47
 In short:

Module 1 48
 Stage-II-The Light Independent Reaction

3CO2 combines with its acceptor RuBP (Ribulose bisphosphate) to to form 6-3PG
molceules. Which is then reduced to 6-Triose phosphate molecules using energy from 6
ATPs and electrons from 6 NADPH’s oxidation, both coming from the light reaction.
1 of these triose phosphates is used to form sugars, while the rest 5 are recycled to
RuBP using energy from ATP with the help of Rubisco enzyme (most abundant enzyme
in the world)h, to take part in the Calvin Cycle again.

Module 1 49
Module 1 50