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CSIRNET
MIND MAPS SAMPLE EDITION

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Function
Transport of electrons
Through series of four protein
complexes
That couple redox reactions
Pumps hydrogen ions
Out of the matrix of the
mitochondria
And into the intermembrane space
Creates electrochemical gradient
That leads to ATP synthesis
Function
Collection of proteins arranged in
groups, called complexes
Embedded in the inner
mitochondrial membrane
NADH dehydrogenase
Made up of Eight iron-sulfur (Fe-S) clusters
Flavin mononucleotide (FMN)
2 electrons transferred from
NADH --> FMN --> Fe-S clusters
--> Coenzyme Q
Complex I (ubiquinone During this process, 4 hydrogen
oxidoreductase) ions pass from the mitochondrial
matrix to the intermembrane space
(NADH + H+) + CoQ + 4 H+
(matrix) -> NAD+ + CoQH2 + 4 H
+(intermembrane)
Flavin adenine dinucleotide (FAD)
Cofactors (prosthetic groups) Coenzyme Q
Heme bIron-sulfur (Fe-S) clusters
Second entry point to the ETC
When succinate oxidizes to
fumarate, 2 electrons are accepted
by FAD within complex II
FAD passes them to Fe-S
Complex II (succinate clusters and then to coenzyme
dehydrogenase) Q
No protons are translocated
across the membrane by complex
II
Succinate + FAD -> Fumarate +
2 H+(matrix) + FADH2
FADH2 + CoQ -> FAD + CoQH2
Cytochrome b
Rieske subunits (containing two
Electron Transport Chain Components 250 kD, 11 subunits, Made up of
Fe-S clusters)
Cytochrome c proteins
Ubiquinone (CoQ) transfers
electrons from Complex I and II
to commplex III
Electron transfer process occurs in
two steps (Q cycle)
Complex III (cytochrome c
reductase) Releases 4 protons into the
intermembrane space at the end
of a full Q cycle
2 CoQH2(site 1) + CoQ(site 2) +
2 Cyt c(ox) + 2 H+(matrix) -> 2
CoQ(site 1) + CoQH2(site 2) + 2
Cyt c(red) + 4 H+
(intermembrane)
Oxidizes cytochrome c and
transfers the electrons to
oxygen
Dimer of a multisubunit assembly
of 13 separate polypeptide chains
160 kD protein containing Cytochromes c and a3
cofactors: Copper ions
Hemes
Complex IV (cytochrome c
Free energy from the electron
oxidase)
transfer causes 4 protons to move
into the intermembrane space
2 cytochrome c(red) + ½O2 + 4
H+(matrix) -> 2 cytochrome
c(ox) + 1 H2O + 2 H+
(intermembrane)
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Enzyme classification

Act on many chemical groups to add or remove hydrogen atoms

Lactate dehydrogenase
e.g. sucrase catalyses hydrolysis of sucrose; Many enzymes named by adding "–ase" to substrate Oxidoreductase
name or to word describing their activity Glucose Oxidase
DNA polymerase catalyses polymerization
of nucleotides to form DNA Examples Peroxidase
e.g. oxidases catalyse oxidation reactions Some names describe function of enzyme Catalase
e.g. Pepsin (pepsis - digestion), lysozyme (lyse- Naming trends Phenylalanine hydroxylase
breakdown), trypsin (tryein - wear down) Some named after broad function
Transfer functional groups (methyl, phosphate etc) between donor & acceptor
e.g. alcohol dehydrogenase oxidizes ethanol Some names describe both substrate & function
Transferases Transaminases (ALT & AST)
Phosphotransferases(Kinases)
Examples
Transmethylases
Transacylases
Catalyse hydrolysis reactions where water is the acceptor of transferred group
Peptidases
Glycosidases
Hydrolases
Amylase
Maltase
Enzyme classes Examples Lactase
Lipase
Esterases
Deaminases
Phosphatases
Add Water, Ammonia or Carbon dioxide across double bonds, or remove these elements to produce double bonds
Fumarase
Lyases
Carbonic anhydrase
Examples Decarboxylase
Dehydrases
Deaminases
Catalyse isomerization changes/rearrangement of atoms within a single molecule
Isomerases L to D Isomerases
Examples
Mutase (Shifts of chemical groups)
Catalyse reactions in which two chemical groups are
joined (or ligated) with covalent bonds with use of energy
Formation of C-C, C-S, C-O and C-N bonds by
Ligases condensation reactions coupled to ATP cleavage
Acetyl-CoA Carboxylase
Examples
Glutamine synthetase
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Stages in embryogenesis
Zygote
2 celled stage (Diad)
4 celled stage (Quadrant)
8 Celled stage/Octant stage ( Globular
stage)
16 celled stage (Heart stage)
32 celled stage ( Torpedo stage)
Maturation stage
Seedling stage
Fusion of male and female gamete yields
one celled diploid zygote
Formation of 2 cell- Apex and basal cell
Further cell division gives to 4 celled stage
Apical cell forms an eight celled embryo to
a globular shaped embryo Outermost layer-
The center cells - SAM & cotyledons. The
epidermis,Next layer-Endodermis, cortex
apical region produces shoot apical
and central layer called procambium forms
meristem and cotyledons. The middle
vascular tissue and pericycle in the root.
region will form the hypocotyls, root, and
root meristem. The hypophysis region
gives rise to the root meristem.
Occur due to cell elongation throughout
the embryo and the cotyledon forms the
shoot apical meristem.
Embryo folds over within the seeds and the
seed starts to lose water to get into a
dormant stage.
Seedling takes place
 Modified shoot
Many genes involved in
conversion of vegetative
Copyright © 2022 Biotecnika meristem to floral meristem
Androecium ( group of stamens)
Reproductive whorls Essential whorls
Gynoecium ( group of carpels)
Flower Structure
Calyx ( group of sepals)
Accessory whorls Non essential whorls
Corolla ( group of petals)

Type A- Sepals- dominant AP1

Type A
AP2
Type A+B- Petals AP3
Type B
PI Arabidopsis thaliana
Type B+ C- Stamens

Type c- Carpels- Dominant AG Type C ABC Genes Concept of ABC model: All
homeotic gene interact & forms
Type A and B are equally ABC Model floral organ
dominant Explains genetics behind the
B genes always express in Keypoints formation of whorl in flower
association with A & C
Determine the identity of tissue
during anatomical development
Plant Homeotic genes belong to
Homeotic gene
MADS Box( Floral identity gene)
Eg: Apetalla, agamous, Pistilata
Conserved motifs found in
1st whorl: Calyx( sepals) Wild type gene( MADS Box gene family)
2nd whorl: Corolla( petals) Encodes DNA binding MADS
3rd whorl: Androecium ( MADS Box domain
stamens) Length of MADS Box: 168-180
4th whorl: Gynoecium ( Carpels) bps
ABC model/floral organ M- MCM1 from budding
Mutation in AP1 & AP2 genes Homeotic genes & yeast,S.cerevisceae
Sepals and petals are not
identity genes
MADS Box A-AGAMOUS from Arabidopsis
formed thaliana
Controls organ identity in 1st & Type A activity encoded by 2 Origin of MADS Box D- DEFICIENS from Snapdragon
2nd whorl genes AP1 &AP2 ( Antirrhinum)
Loss of type A function ( S- SRF (Serum Response
AP1& AP2 mutated) Factor) from Homo sapiens
Male & female gametophyte
Forms stamens instead of
petals floral identity
Forms carpels instead of sepals embryo development
MADS-Box gene Controls Development
seed development
Mutation in AP3 & PI genes
Fruits, flower & root
Petals and stamens are not development
formed
Controls organ identity in Type B activity encoded by 2 Homeotic genes / Floral
2nd(petal) & 3rd whorl(stamen) genes AP3 & PI 1) APETALA 1 ( AP1)
Loss of type B function organ identity genes 2) APETALA 1 ( AP2)
(mutated AP3 & PI) 3) APETALA 1 ( AP3)
4) PISTILATA (P1)
Forms sepals instead of petals 5) AGAMOUS (AG)
Forms carpel instead of
stamens

Mutation in AG genes
Carpels and stamens will not be
formed
Controls organ identity in 3rd
whorl(stamen) & 4th whorl ( Type C activity encoded by AG
Carpel) Gene
Loss of type c function
(mutated AG)

Forms petals instead of

stamens
Forms sepas instead of carpels
Copyright © 2022 Biotecnika Adaptive radiation

Examples Definition
Adaptive radiation is a rapid
increase in the number of species
with a common ancestor,
Darwin's Finches characterized by great ecological
and morphological diversity.

Reason for Adaptive radiation

Adaptive radiation appears more
The fifteen species of finches
found at the Galápagos islands common during periods of major
was all descended from an environmental change.
ancestral species found in the
main land. Extinction produces empty
adaptive zones, which provide new
opportunities for species that
Mammals remain. Thus, deversifying rapidly.

They had existed mainly as small

nocturnal insectivores (insect
eaters) for millions of years.

Mammals diversified and exploited

a variety of adaptive zones
after the extinction of the
dinosaurs.
Copyright © 2022 Biotecnika Chemical Classes of Hormones

Water-Soluble Hormones Lipid-Soluble Hormones

Amine hormones are synthesized Steroid hormones are derived from
by decarboxylating cholesterol
and otherwise modifying certain
amino acids Two thyroid hormones (T3 and T4)
are synthesized by attaching
The catecholamines— iodine to the amino acid tyrosine
epinephrine,norepinephrine, and The gas nitric oxide (NO) is both a
dopamine—are synthesized by hormone and a neurotransmitter
modifying the amino acid tyrosine
Histamine is synthesized from the
amino acid histidine
Serotonin and melatonin are
derived from tryptophan
Peptide hormones and protein
hormones are amino acid
polymers
Antidiuretic hormone and oxytocin
Protein hormones include human
growth hormone and insulin
The eicosanoid hormones like
prostaglandins and leukotrienes
are derived from arachidonic acid
 Chromosome Banding
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Study of chromosome number and structure
by staining the dividing cells with certain
dyes and then examining them under
microscope for cytogenetic analysis is called
chromosome banding.
Most frequently used technique for chromosome
staining
Proteolytic enzyme trypsin is used for
pretreatment
After pretreatment, it is subjected to Giemsa stain.
G-banding
Banding pattern observed under light microscope.
Dark region tends to be
heterochromatic, late
Series of lightly and darkly replicating and AT rich
stained bands are seen Light region tends to be
euchromatic, early
replicating and GC rich
It is the simplest and the first chromosomal
banding method
Q banding used quinacrine stain
Because quinacrine is a DNA intercalating agent
Q-banding and a fluorescent compound, the bands appear only
when the chromosomes are exposed to ultraviolet
(UV) light
Types of Chromosome Fluorescence of quinacrine is enhanced along AT
Banding rich sequence and appear bright than GC rich
sequence.
R-banding is called Reverse
chromosome banding
Band pattern produced in Dark regions are euchromatic, GC
chromosome is reversed to rich regions
R-banding
the band produced by G- Bright regions are heterochromatic,
banding and Q-banding AT rich regions
Telomeres are stained well
with this banding
C-banding is called Centromeric heterochromatin
staining
In this technique, before using Giemsa stain the cell
is pretreated with alkali.
C-banding Centromeric heterochromatin and distal part of Y
chromosome containing highly repetitiveDNA
sequence (satellite DNA) is used to stain by C-
banding technique.
After staining, banding is viewed by bright-field
microscope
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Low blood glucose
(hypoglycemia) stimulates alpha
cells to secrete
Control of secretion of glucagon
and insulin
High blood glucose
(hyperglycemia) stimulates beta
cells to secrete
Convert glycogen into glucose
Glucagon acts on liver cells to:
Form glucose from lactic acid and
certain amino acids
Glucose released by liver cells
GLUCAGON raises blood glucose level to
normal
If blood glucose continues to rise,
hyperglycemia inhibits release of
glucagon
Accelerate facilitateddiffusion of
glucose into cells
Speed conversion of glucose into
Insulin acts on various body cells
glycogen
to:
Increase uptake of amino acids
Increase protein synthesis speed
synthesis of fatty acids
INSULIN
Blood glucose level falls
If blood glucose continues to fall,
hypoglycemia inhibits release of
insulin
 High cytokinin: Shoot
development
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Low cytokinin: Root
development 1. Morphogenesis
Auxin=Cytokinin: Callus
formation
Basic in nature
2. Vascular tissue development;
xylem formation Derivatives of either amino
purine or phenyl urea
3. Shoot Apical Meristem (SAM)
rescue Promote cytokinesis (cell
division)
axillary bud formation
4. Lateral growth 1. Introduction First cytokinin disovered:
Anatgonist to apical dominance 6. Functions Kinetin (6-furfuryl amino-
In dicot plants purine); synthetic hormone
Help Agrobacterium tumifaciens 5. Crown gall formation Natural cytokinin: Zeatin (from
in the process unripe maize); present in
enhances cell division coconut milk

formation of functional female 6. Delay in leaf senescence

Are adenine derivatives
gametophhyte: megaspore
Pathway: Isoprenoid Pathway
7. Nodule formation
Most abundant cytokinin in
Inactivation: by cytokinin plants: Zeatin
glycosylation Location: Plastids
Cleavage: by cytokinin Examples: Isopentenyladenine
5. Regulation
oxidases; AtCKX1 and AtCKX2 (iP) and Dihydrozeatin (DHZ)

Ligand: Cytokinin CYTOKININ

1. CRE1 (CYTOKININ
RESPONSE 1); transmembrane 2. Biosynthesis
2. AHK2 Receptor:
3. AHK3
Siganling Pathway: derived from Process:
bacterial two component
phosphorelay system
membrane-bound histidine
kinase sensor protein
Histidine phosphotransfer
protein (Hpt): mediate Players:
phosphotransfer between
sensor kinases and response Synthesis: mainly in the root
regulators
4. Signaling Mechanism Translocation: acropetally to the
3. Transport
shoot in the xylem

Process:
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The production of
Ovum/egg(n) from
oogonia (2n) is called as
oogonia
Oogenesis is a
discontinuous process
Occurs in the germinal
epithelium of the foetal
ovary
All the stages takes
place in the ovary
except the formation of
ovum from secondary
oocyte will takes place
in the Fallopian tube
(oviduct)
Production of ova takes
place only in a month
Produces large non-
motile gametes Ovum/egg
Unequal cytokinesis
occurs during
oogenesis producing
one large ovum and tiny
polar bodies Cytokinesis
Only one ovum is
released per month. Production rate
The growth phase is
extended.
No nuclear
condensation Nuclear Condensation
Primary Oocyte
undergoes meiosis I to
form one secondary
oocyte and 1 polar body Primary Oocytes
The production of
sperms(n) from
spermatogonia (2n) is
called Spermatogenesis
Oogonia Continuous process
Spermatogenesis
occuring after puberty
till death
Occurs in the germinal
Location epithelium of
seminiferous tubule of
Location testis
All the stages take place
Stages in the testis
Production of Sperms
Duration take place everyday
Stages
Produces small motile
Sperm(n) gametes
Duration
Equal cytokinesis
Gametogenesis- occurs during the
Oogenesis Difference between Spermatogenesis
spermatogenesis
Spermatogenesis and producing four haploid
oogenesis Cytokinesis sperms
The production of
sperms is in millions
Production rate every day.
The growth phase is
Growth short.
Nuclear Condensation It takes place in sperm
Growth
Primary spermatocytes
divide by meiosis I
resulting in the
formation of 2
secondary
Primary Spermatocyte spermatocytes

Copyright © 2022 Biotecnika Occurs on day 14 of a 28-day
cycle
In the ovaries, rising estrogen
levels stimulate GnRH and LH
secretion (positive feedback)
LH causes rupture of mature
ovarian follicle (Graafian follicle)
and release of secondary oocyte
Ovulation
Lasts for 14 days after ovulation
In the ovaries, LH stimulates
formation of corpus luteum from
the ruptured ovarian follicle and
secretion of progesterone from
corpus luteum
Degeneration of corpus luteum
begins the next cycle of
menstruation
If fertilization does not occur, the
corpus luteum degenerates after 2
weeks forming corpus albicans
Progesterone and estrogen
secreted by corpus luteum induce
growth of endometrial glands,
vascularization and thickening of
endometrium
If fertilization occurs, the corpus
luteum persists for longer time
under the influence of HCG
produced by the embryo
Luteal/Secretory phase
Female reproductive cycle
Lasts from day 6 to 13
In the ovaries, a secondary ovarian
follicle becomes dominant over all
other growing follicles and
secretes estrogen and inhibin
These hormones inhibit FSH
secretion (negative feedback),
causing atresia of other less
mature follicles
In the uterus, estrogen (secreted
by ovarian follicles) stimulate the
proliferation of endometrial
epithelial cells
Proliferative/ Follicular phase
Lasts for about 5 days
Under FSH influence, primordial
follicles develop into primary and
secondary follicle
In uterus, declining progesterone
and estrogen levels stimulate
prostaglandins to constrict the
uterine arterioles leading to
decrease in blood flow and death
of endometrial cells
Endometrial cells are shed causing
menstrual flow
Menstruation
 Copyright © 2022 Biotecnika

Occurs in: yeast and

Aerobic respiration: in
several bacterial
the presence of oxyen
species
Anaerobic respiration: in 1. Fate of Pyruvate
1. Pyruvate is
the absence of oxygen
decarboxylated to form
acetaaldehyde (catalyzed
Takes place in the absence of by Pyruvate
Oxygen Conversion of Pyruvate decarboxylase)
4. Alcoholic into Ethanol (two-step
NAD+ is regenerated from 2. Reduction of
NADH by transferring Fermentation process)
acetaldehyde into Ethanol
electrons to organic molecules (Alcohol dehydrogenase)
2. Fermentation
On the basis of
substrates fermented
Alcoholic acid Process:
fermentation Classification
Lactic acid fermentation On the types of
fermentation products
Propionic acid formed Growth condition:
Fermentation Reactions
fermentation Aerobic
Butyric acid Aerobic Respiration: Final electron acceptor:
fermentation Molecular oxygen
Occurs in: muscle cells Growth condition:
and certain bacterial 5. Comparison between Aerobic Anaerobic
species Respiration, Anaerobic Final electron acceptor:
respiration and Fermentation Anaerobic respiration: Inorganic substrate such
Conversion of Pyruvate
into Lactate (called as Nitrate, Sulfate but not
Lactic acid oxygen
fermentation) Growth condition:
Production of NAD+ Aerobic/Anaerobic
3.Lactic acid
Fermentation: Final electron acceptor:
Catalyzed by Lactate fermentation
Dehydrogenase enzyme An inorganic substance
(LDH)

Process:
Copyright © 2022 Biotecnika
Definition
Gene mutations
Mutations where the size of the
DNA lesion is relatively small that
affects a single gene only.
Causes
Types
Base Substitution
A nitrogen base in the DNA is
substituted by a different base.
Changes a single codon, if
occurred in the coding region of
the gene.
Insertion
One or a few nucleotides are
inserted in the DNA.
Changes the reading frame, if
occurred in the coding region of
the gene.
Deletion
One or a few nucleotides are
deleted from the DNA.
Changes the reading frame, if
occurred in the coding region of
the gene.
DNA replication error
Mutagens like base analogues and
intercalating agents
 Glycogen metabolism Glycogenesis
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Anabolic process
Stores glucose by converting
excess glucose into
glycogen
Takes place in the muscles
and the liver
Occurance
Operates when high levels
of glucose-6-phosphate are
formed
Does not operate when
energy stores (glycogen) are
full
Process initiated by insulin
signaling;
(insulin becomes active
when blood glucose level is
high)
Stimulated in well fed state
Process inhibited by
glucagon (liver) and
epineprine (muscle)
Regulation
Catalyzed by the enzyme
glycogen synthase
Glycogen synthase gets
activated upon getting
dephosphorylated
Pathway
Glucose is initially
converted to glucose-6-
phosphate using ATP
Glucose-6-phosphate is
converted to glucose-1-
phosphate
UTP activates glucose-1-
phosphate to form UDP-
glucose and pyrophosphate
(PPi)
UTP is required to transfer
glucose into existing
glycogen chain
Glucose in UDP-glucose
adds to glycogen
UDP-Glucose + glycogen --
> glycogen-glucose + UDP
UDP reacts with ATP to
regenerate UTP
UDP + ATP --> UTP +
ADP
Glycogen de-branching
enzyme transfers glucose
chains from branch points to
non reducing ends by
breaking alpha 1->6 bonds
at branch points
Glycogenolysis
Hydrolytic process
Formation of glucose by
breaking down glycogen
molecules stored in the liver
Glucose molecules are
removed one by one from
the end of the glycogen
chain to yield glucose-1-
phosphate
Increases the blood sugar
level
Takes place in the liver
Plays an important role in
the adrenaline-induced
fight-or-flight response;
Less ATP consumed
Occurance
Stimulated by fasting,
between meals physical
exercise
Process is activated during
low blood glucose level
By glucagon in liver and
epinephrine in muscle
Process inhibited by insulin
Regulation
Catalyzed by the enzyme
glycogen phosphorylase
Glycogen phosphorylase
gets activated upon getting
phosphorylated
Pathway
Bonds glucose to phosphate
to form glucose-1-phosphate
glycogen-glucose + Pi -->
glycogen + glucose-1-
phosphate
No UTP required. End
product G-6-P enters either
gluconeogenesis or
glycolysis
Glucose-6-phosphate not
utilized by brain and skeletal
muscle
Because they lack
glucose-6-phosphatase
G-6-P hydrolyzed to glucose
in the liver and kidney
Where glucose-6-
phosphatase is available
providing free glucose to
brain & skeletal muscle
 Most Popular tool of
genetic engineering Genetic Engineering
Used to obtain structural
Copyright © 2022 Biotecnika information of DNA
fragment
DNA Mapping/ Restriciton
Mapping
DNA molecule to be
sequenced is digested Applications
with restriciton enzyme Gene Sequencing
Gene expression &
mutation studies
Examination of population
polymorphisms

Bifunctional enzyme
Structure
Immunoblotting
Three different subunits Subunits
ATP, Mg2+, S-
adenosylmethionine Cofactors
Bipartite & asymmetric Recognition site Type I
Nonspecific>1000 bp
from recognition site Cleavage site
EcoAI, EcoKI
Examples
Unifunctional enzyme
Either with endonuclease/ Structure
methylase activity Also Known
as"Restriction
Two identical subunits Subunits Endonuclease/Molecular
Mg2+ Cofactors Scissors"
4-6 bp sequence, often Type II Classification Belong to larger class of
palindromic Recogntiton site enzymes called
Same as or close to “Nucleases”
recognition site Cleavage site Introduction
Recognizes specific base
EcoRI, BamHI Example pair sequence in DNA
Bifunctional enzyme called “Restriction site”
Endonuclease & Structure Cleaves DNA within
methylase activity sequence

Two different subunits Subunits

ATP, Mg2+ Cofactors
5-7 bp Asymmetric Type III
sequence Recognition site
24-26 bp downstream of RESTRICTION
recognition site Cleavage site ENZYMES (RE)
HinfIII, EcoPI Examples

Both strands of DNA

Cut at same place in
middle of recognition site Blunt ends
Produces "Blunt ends/
Flush ends"
Both strands of DNA
Not cut at same position Examples
Cleavage staggered,
usually by two or four
nucleotides
Sticky Ends
Resulting DNA fragments
have short single-
stranded overhangs at Cleavage Pattern
each end Produces “Sticky/
Stick back by transient Cohesive ends”
base pairing

Named according to
organism in which they
were discovered
Using system of letters &
numbers
First three letters of the
name are italicized
Abbreviate genus &
species names of the Nomenclature
organism
"H": First letter of Genus
name (Haemophilus)
"in": First two letters of the
species name (influenza)
"d" : strain type Example: HindIII
"III" : Third enzyme
discovered in that
organism (Roman
numerals used)

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Mechanism of Cyclic
4.
Photophosphorylation
Mechanism of Non- Comparison between Cyclic
3. Cyclic
Photophosphorylation Photophosphorylation
Refers to the synthesis of ATP,
coupling to a cyclic passage of
electrons from P700
Occurs in isolated chloroplasts
and photosynthetic bacteria
Electrons move in a
cyclic fashion
Only Photosystem I is
involved
Electrons are first excited
from the reaction center of
PS I
Electrons return to P700
Cyclic after passing throuh
1.
Photophosphorylation ETS
Final electron acceptor
is P700
No photolysis of water
No oxygen evolution
Only ATP produced
Mainly occurs in
anaerobic conditions
Cannot be inhibited by
Diuron
Occurs in anoxygenic
photosynthesis
Refers to the synthesis of ATP in which
and Non-cyclic an electron donor is required and oxygen
produces as a byproduct
Occurs in plants, algae
and cyanobacteria
Electrons move in a
linear fashion
Both Photosystems I
and II are involved
ELectrons are first excited
from the reaction center of
PS II
Electrons return to P700
Non-cyclic and accepted by NADP+
2.
Photophosphorylation
Final electron acceptor
is NADP+
Photolysis occur
Evolution of oxygen
Both ATP and reduced
co-enzymes are
produced
Mainly occurs in
aerobic conditions
Inhibited by Diuron
Occurs in oxygenic
photosynthesis
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Auxin, particularly 2, 4-D, is generally necessary to induce

embryogenesis
Requirement of exogenous auxin for induction of SEs dependson
Induction
nature of explants used with relative concentration of auxin

Competent cells have the ability to develop somatic embryos

when auxin is removed from medium
Stages of Somatic Rapid cell division occurs in cell clusters leading to the formation
Embryogenesis of globular stage somatic embryos
Plantlets develop from globular embryos via heart, cotyledonary
and torpedo shaped somatic embryos
As soon as the embryo reaches torpedo stage, it will quickly
germinate so external stress is provided to prevent germination.
Development and Maturation
sucrose concentration can be raised to 6%
To overcome this problem OR

Transfer to the medium that contains ABA

Signs of tissue differentiation become apparent at globular stage
and apical meristem are apparent in heart shaped embryo
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Types of Somatic embryogenesis

Indirect SE Direct SE

When explants produced undifferentiated mass of cells(callus) When embryos are formed directly from explant tissue creating an
which is maintained or differentiated into embryo identical clone without production of intervening callus.

Specific growth regulators and culture conditions are required for The explants capable of direct embryogenesis seem to carry
callus formation and the redetermination of embryogenic competent or “pre-embryonic determined cells”(PEDCs).
development pattern called “induced embryogenic determined
cells”(IEDCs). These cells are committed to Embryo development and need only
to be released.
After this step, cells transform into “induced embryogenic pre-
determined cells” (IEDs) that are equivalent to PEDCs.
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Summary of signal
sequences with their
respective organelles

Import into Endoplasmic reticulum Import into nucleus

Core of 6–12 hydrophobic amino acids, often preceded by one or Common motif includes a short segment rich in Lys and Arg
more basic amino acids (Arg, Lys) residues

Soluble resident proteins will have -Lys-Asp-Glu-Leu-(KDEL) -Pro-Pro-Lys-Lys-Lys-Arg-Lys-Val

Membrane proteins will have KKXX Location of Sequence Within Protein varies

Location of Sequence Within Protein is N terminus

Import into lysosome
Import into Mitochondria No aminoacid sequence as Motif

Amphipathic helix, 20–50 residues in length, with Arg and Lys Mannose-6-phosphate is the signal sequence
residues on one side and hydrophobic residues on the other

Met-Leu-Ser-Leu-Arg-Gln-Ser-Ile-Arg-Phe-Phe-Lys-Pro-Ala-Thr- Import into Plastid

Arg-Thr-Leu-Cys-Ser-Ser-Arg-Tyr-Leu-Leu

Location of Sequence Within Protein is N terminus Motif rich in Ser, Thr, and small hydrophobic residues and poor in
Glu and Asp

Met-Val-Ala-Met-Ala-Met-Ala-Ser-Leu-Gln-Ser-Ser-Met-Ser-Ser-
Import into Peroxisome Leu-Ser-Leu-Ser-Ser-Asn-Ser-Phe-Leu-Gly-Gln-Pro-Leu-Ser-Pro-
Ile-Thr-Leu-Ser-Pro-Phe-Leu-Gln-Gly
PTS1 signal (Ser-Lys-Leu; SKL) at extreme C-terminus
Location of Sequence Within Protein is N terminus
PTS2 signal at N-terminus
 Chemical composition of membrane
Copyright © 2022 Biotecnika
Glycerophospholipids - Glycerol Backbone
Phosphatidic acid
Phosphatidylethanolamine
Phosphatidyl choline
Example
Phospholipids - Phosphate group attached Phosphatidyl serine
Phosphatidylglycerol
Cardiolipin

Phosphosphingolipids - Sphingosine Backbone

Membrane lipids
Example Sphingomyelin

Glycosphingolipids -Sphingosine Backbone

Cerebrosides
Example Gangliosides
Glycolipids - Sugar attached Globosides

Galactolipids - Glycerol Backbone

Monogalactosyldiacyglycerol (MGDG)
Example
Digalactosyldiacyglycerol (DGDG)

Proteins that are attached to either surface of the bilayer

Associated with the polar head groups of lipid bilayer by non covalent
Peripheral membrane proteins interactions (electrostatic interactions, H bonding)
Extracted by mild treatment

Membrane Proteins Very firmly associated with lipid bilayer

Held to membrane by hydrophobic interactions between membrane lipids and
hydrophobic domains of the protein
Removable by agents that interfere with hydrophobic interactions eg.
Detergents, organic solvents, denaturants etc.
Integral membrane proteins Type I - have only one transmembrane helix; amino-terminal domain is outside
the cell
Type II - have only one transmembrane helix; amino-terminal domain is inside
the cell
Type III - proteins have multiple transmembrane helices in a single polypeptide
Types of Integral membrane proteins
Type IV - proteins, transmembrane domains of several different polypeptides
assemble to form a channel through the membrane.
Type V - proteins are held to the bilayer primarily by covalently linked lipids
Type VI - proteins have both transmembrane helices and lipid anchors.

Predominantly glycoproteins
Cerebrosides and gangliosides
prominent in epithelial cells that line the mammalian digestive tract and
endothelial cells that line blood vessels
Sugars on the surface make up the glycocalyx - Keeps cells moist and slippery
composed of glycosaminoglycans, proteoglycans and other glycoproteins
bearing acidic oligosaccharides and terminal sialic acids.
Membrane Carbohydrates
Cell signalling
Function of Glycocalyx in Eucaryotes Protecting the cell
Adhesion with other cells
Condensed form - tightly associated with the underlying cell wall
Glycocalyx in Procaryotes -2 types
Loosely attached - removed from the cell easily by mild treatment
Enable bacteria to become harder for phagocytic uptake
Function of Glycocalyx in Procaryotes
Becomes more invisible to the immune system of a host.
Copyright © 2022 Biotecnika

Membrane Proteins Attached To

Lipids

Type I
Palmitoyl group attached by thioester linkage to a Cys residue

Type II
N-myristoyl group attached to an amino-terminal Gly

Type III
Farnesyl and geranyl groups attached to carboxyl-terminal Cys
residue

Type IV
GPI-linked, Glycosyl phosphatidyl Inositol; short oligosaccharide
covalently joined to the carboxyl terminal residue of a protein
through phosphoethanolamine
 Copyright © 2022 Biotecnika

Type of protein refers to local of some part of

secondary structure conformation polypeptide
Discovered by Pauling &
run in same direction Adjacent β Strands Corey
adjacent strands match N to C terminal Because it is second
INTRODUCTION
have 12 atoms structure elucidated
Hydrogen bonded ring Named β
less stable Alpha helix been first
buried inside protein Extended conformation rather than tightly
7.0 Å between pleats on Found of polypeptide chains coiled as in α helix
sheet
Parallel β-sheet with amide bonds
3.47 Å Rise per residue coplanar
Linear arrangement of
amino acids side chains alternating plane of peptide
above & below backbone
Usually found hydrogen forming Beta-sheet
bonded in pairs structures
β STRAND No intramolecular between amino acid
hydrogen bonds residues
run in opposite direction Adjacent β Strands Distance between
adjacent amino acids
adjacent strands
along β strand approximately 3.5 Å
doesn’t match N to C terminal
atoms no. alternate by linking two/more β
between 14 & 10 BETA (β) SHEET strands by hydrogen
withstand greater Hydrogen bonded rings FORMATION bonds
exposure to solvent More stable TYPES OF β-SHEET Polypeptide chain extended into zigzag
6.5 Å between pleats on BETA (β) SHEET
AntiParallel β-sheet backbone rather than helical
sheet Found
structure
3.25 Å Rise per residue
form structure
Zigzag polypeptide resembling series of
chains arranged side by side pleats
between adjacent
segments of polypeptide
Hydrogen bonds formed chain
STRUCTURE
R groups adjacent amino from zigzag structure creating alternating
Having both parallel &
acids protrude in opposite directions pattern
antiparallel
Many strands, typically come together in β
4/ 5 or 10 or more sheets
β sheets structurally
diverse than α helices
Mixed
β sheets relatively flat
Adopt twisted shape

STRUCTURAL
ELEMENT IN Example: Fatty acid-
PROTEINS binding proteins
 Copyright © 2022 Biotecnika
processivity is a measure of
nucleotides added before
polymerase dissociates
polymerization rate number of
nucleotides added per unit time
due to high processivity and
high polymerization rate
priming of replication of both
strands
one subunit has primase activity
the largest subunit has
polymerization activity DNA polymerase α
elongation of lagging strand
has 3’-5’ proofreading
exonuclease activity
Eukaryotic
primers made by DNA DNA polymerase δ
polymerase α are extended by
DNA polymerase δ
Catalyze the synthesis of DNA
elongation of leading strand DNA polymerase ε require a DNA template to copy
the information
DNA repair DNA Polymerase β two central requirements for
replication of mitochondrial DNA DNA Polymerase γ DNA polymerization a free 3'-hydroxyl group to
which a nucleotide can
DNA Polymerases
removes and replaces primers DNA polymerase I be added
DNA repair , restarts replication
after damaged DNA halts several types of DNA
synthesis DNA polymerase II Polymerases in prokaryotes and
eukaryotes
main replicative enzyme
DNA polymerase III
Prokaryotic
elongates DNA during replication
DNA repair , Translesion
synthesis DNA Polymerase IV
DNA repair , Translesion
synthesis DNA Polymerase V
 RNA polymerases in Eukaryotes

Copyright © 2022 Biotecnika All are large enzymes with

multiple subunits

Each class of RNA polymerases

recognizes particular types of
genes

Synthesizes the precursor of

the large ribosomal RNAs (28S,
RNA polymerase I 18S and 5.8S)

Location –nucleolous
Synthesizes the precursors of
messenger RNA (m RNA)
also synthesizes small RNAs like
small nuclear RNAs (snRNAs),
microRNA(miRNA), small
interfering RNA (siRNAs)
Location- nucleus
A 550 kDa complex of 10-12
subunits
Yeast Pol II consists of 10
different peptides (RPB1 -
RPB10)
12 in humans (RPB1 - RPB12)
RNA polymerase II
RPB1 and RPB2 are homologous
to E. coli RNA polymerase β and
β'
RPB1 is the largest subunit of
Three distinct classes of RNA
RNA polymerase II
polymerases
composed of up to 52
heptapeptide repeats
(YSPTSPS) Tyr-Ser-Pro-Thr-
Ser-Pro-Ser that are essential
for polymerase activity

initiation of transcription
It contains a carboxy terminal capping of the RNA transcript
CTD involved in the:
domain (CTD)
attachment to the spliceosome
for rRNA splicing
CTD domain does not exist in
RNA Polymerase I or RNA
Polymerase III

Synthesizes transfer RNA

(tRNA), small 5S ribosomal
RNA(5s rRNA) ,other small
RNAs (including the small 5S
ribosomal RNA (5s rRNA),
snRNA U6-spliceosome, signal
recognition particle RNA (SRP
RNA) -signal sequences and
RNA polymerase III
other stable short RNAs
Location-nucleus (and possibly
the nucleolus-nucleopasm
interface)

found only in plants

RNA polymerases IV and V
transcribe small interfering
RNAs (siRNAs) involved in
transcriptional silencing
 Copyright © 2022 Biotecnika
Non-living: Prion, Viroid
Non-living/Living: Virus
Prokaryotic: Bacterium
Eukaryotic: microscopic fungi,
protozoa, helmenths
Host required
Obligate Parasite
eg. Virus
Host not required
Facultative Parasite
eg. Candida
Mutualism eg. Humans and Escherichia coli
Commensalism eg. Humans and Entamoeba gingivalis
Types of Interaction Parasitism eg. Humans and Plasmodium species
Amensalism eg. Penicillium and other bacterias
Types of Parasite
Parasite completes sexual
reproduction
Definitive/Primary Host
Host- Parasite Interaction eg. Plasmodium in mosquito
Parasite completes asexual
reproduction
Parasite Intermediate/secondary Host
eg. Plasmodium in humans
No parasitic development
Paratenic/ transport Host
Host eg. Alaria americana in tadpoles
Block transmission to the definitive
Dead-end, incidental, or accidental host
host
eg. West Nile virus in humans
Harbors a pathogen without infection
Reservoir host
eg. Bubonic plague and Black rats

Copyright © 2022 Biotecnika
Single transmembrane
Receptor tyrosine kinases polypeptide chains
Receptor Enzymes
Non-receptor tyrosine
kinases
Receptor serine/threonine
kinase
Intracellular tyrosine kinase
domain
ligand causes dimerization
and autophosphorylation of
the tyrosine residues of the
cytoplasmic domain
Ligands - insulin and
growth factors.
Activation-
Effectors- phospholipase C
and Ras
Ras activates MAP kinase
embryonic development
Involved widely in- cell growth and
proliferation
Insulin receptor,
Vascular endothelial growth
factor receptor,
Example- Nerve growth factor
receptor,
Fibroblast growth factor
receptor
Do not have tyrosine kinase
activity
Janus kinase (JAK) family
proteins are associated with
the receptors
Ligand binding leads to
activation of STAT proteins
STAT proteins act as
transcription factors for
JAK-STAT regulated genes
Activation-
Ligands- growth hormones,
interferons, prolactin,
erythropoietin, and
thrombopoietin.
bind to transforming growth
factor-beta (TGF-beta)
cell-surface TGF receptors RI, RII, and RIII
Smads (R-Smads),
co-Smads,
types of Smad proteins
inhibitory or antagonistic
Smads (I-Smads).
 Concept
Copyright of Niche
© 2022 Biotecnika

used to indicate not only the habitat but also the role played by the organisms in the
environment

where it can live

What is Niche ?
the total requirements of a species, resources and physical conditions determine how abundant it can be at any one place within its range

these requirements are termed abstractly as the ecological niche

Habitat is the “address” of the organism

Niche is its “profession,”

1. food
includes all the factors that a species needs to survive, stay healthy, and reproduce 2. abiotic conditions

3. behavior
What all Niche includes?
Place in the food web
Physical conditions required to survive
Range of temperature organism needs to survive
Type of food organism eats
How it obtains food?
Who uses the organism for food?
When & how organism reproduces?

1. spatial or habitat niche- the physical space occupied by an organism

Aspects of Niche 2. the trophic niche its functional role in the community

its position in environmental gradients of temperature, moisture, pH, soil, and other
conditions of existence
3. the multidimensional or hyper-volume niche
 Population Growth Models
Copyright © 2022 Biotecnika
Two types of popula on growth
pa erns may occur depending on
specific environmental condi ons:
1. Exponential Growth
2. Logistic Growth
Exponential population growth is
population increase under
idealized conditions
under these conditions, the rate of
increase is at its maximum,
denoted as rmax
exponential growth cannot be
sustained for long in any
population
can be seen in populations that
are very small or in regions that
are newly colonised by a species
the equation of exponential
population growth is
J-shaped curve characterizes
exponential growth
a more realistic population model
limits growth by incorporating
carrying capacity
carrying capacity (K) is the
maximum population size the
environment can support
carrying capacity varies with the
abundance of limiting resources
logistic model starts with the
exponential model and adds an
expression that reduces per capita
rate of increase as N approaches
K
seen in any stable population
occupying a fixed geographic
space
sigmoid (S-shaped) curve
characterizes logistic growth
Graphs for exponential and logistic
growth

Copyright © 2022 Biotecnika
Optical & geometrical isomers
ortho, meta, para positions in
aromatic ring
that produce similar fragmented
ions
Where, p= peak in mass
spectrum
m= total mass of ion
z= total charge
Mr= average mass of protein
Peptide ion of interest passed
into collision cell
with “collision gas” (Helium/
Argon)
Analytical technique
WHAT IS IT?
Measures mass-to-charge (m/z)
ratio for ions in gas phas
Arthur Jeffrey Dempster &
Modern techniques devised by F.W. Aston
Production of charged molecular
species &
PRINCIPLE Separation by magnetic &
Identification of unknown
electric field based on mass to charge ratio
compounds
Determine isotopic composition
Direct infusion
of elements in molecule
Sample Inlet Example Gas / Liquid Chromatography
Determine compound structure
by observing its fragmentation Capillary electrophoresis
Applications
Quantify amount of compound in First ionization techniques
sample developed
Electron Ionizer (EI) Useful for organic compounds
Protein characterization &
sequencing (Mw below 600)
(i) Solution of macromolecules from capillary tube kept at high
sprayed voltage (4000 V)
Not distinguish between (ii) Fine, highly charged droplets
Positions of substituent formed
Limitations
Scope limited in identifying (iii) Solvent rapidly evaporates
hydrocarbons Electrospray Ionization (ESI) from it
Ion Source (iv) Yields gas phase have ionic charges (0.5 to 2 per
p=m/z macromolecular ions kilodalton)
MASS SPECTROMETER BASIC Useful for compounds with
p1=(Mr+z1 )/z1
Protein Molecular weight COMPONENTS molecular masses >100 kD
determination by MS in crystalline matrix (Eg:
(i) Macromolecule embedded Gentisic acid)
MASS SPECTROMETRY (MS)
(ii) Irradiated with intense short
p2=[Mr+(z1 -1)]/(z1 -1) pulses of laser light
Matrix Associated Laser
Desorption/Ionization(MALDI) (iii) Energy absorbed by matrix
ejects macromolecules from its surface into gas phase with charge of +1
Polypeptides of >400 kD have
Used to sequence Short been characterized
polypeptides (<25 residues)
Time taken by particle to reach
Two Mass Spectrometers detector at known distance measured
coupled in series
Mass Analyzer Time Of Flight (TOF) Velocity of ion depends on mass- Heavier particles moves with
First MS (MS-1), peptide to-charge ratio of particle lower speeds
mixture is sorted
Electron multiplier
Peptide further fragmented by
Faraday cup
high-energy impact
Detector Example Photomultiplier conversion
m/z for each fragment
dynode
measured in second MS (MS-2)
Tandem Mass
Array detector
Spectrometry(MS/MS)
Atom or molecule ionised
Stage 1: Ionisation By knocking one/more electrons
off to give a positive ion
Ions accelerated
Stage 2: Acceleration So that they all have same
kinetic energy
Ions deflected by magnetic field according to their masses
Stage 3: Deflection Lighter ions/ions with more
charge deflected mor
Beam of ions detected
HOW IT WORKS Stage 4: Detection electrically
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