MICROSCOPY
 IMAGING TECHNIQUES (MICROSCOPY eukaryotes.
 History of Microscope
 1.2.1 Principles of Microscopy{ Magnification, Resolution}
 1.2.2 Light Microscopy.-> • Simple light microscope->•
Compound light microscope Parts of a microscope, Objective
- dry, apochromats ->Eyepiece-> Body Tube-> Arm->->Stage.->
Nosepiece ->Condenser Lens.-> Diaphragm.->iIluminator.->
Specialized optical microscope-> Inverted microscope..->
Stereoscopic microscopes (Dissecting microscope. -
>Metallographic microscope.-> Reflecting microscope-
>Brightfield microscope->Darkfield microscope-
>Interference microscope
 .2.3 Phase Contrast Microscopy
 . 11.2.4 Fluorescence Microscopy
 1.2.5 Confocal Microscopy
 1.2.6 Polarization Microscopy Polarizer, Analyzer
 .3 ELECTRON MICROSCOPY (EM) Electron microscopy (EM)
Basic Components of an Electron Microscope
 1.3.1 Transmission Electron Microscopy (TEM Sample
Preparation, .-> An Ultramicrotome
 1.3.2 Scanning Electron Microscopy (SEM, Sample
preparation
 1.3.3 Scanning Transmission Electron Microscopy(STEM)
 . 1.3.4 Environmental Scanning Electron Microscopy (ESEM
 .3.5 Comparative Account of Different Types of Microscopes
 1.4 TECHNIQUES FOR PREPARING TISSUES FOR ELECTRON
MICROSCOPY
 1.4.1 Negative Staining
 4.2 Freeze-fracture
 1.4.3 Freeze-Etching
 1.4.4 Shadow Casting
DNA
10.2 STRUCTURE OF DNA
 10.2.1 Watson and Crick Double Helix Model
 10.2.2 Double Helix
 10.3 TYPES OF DNA.-> A-form of DNA, ->B-form DNA.-
> Z-form of DNA. ->Differences between A and B form of
nucleic, .-> Differences between Z-DNA and B-DNA i)
10.4 ORGANIZATION OF DNA IN VARIOUS CELLULAR
TYPES
 10.4.1 Prokaryotes
 10.4.2 Eukaryotes, DNA packaging,
 10.4.3 Viruses, . Flash field model
 10.5 MITOCHONDRIAL AND CHLOROPLAST DNA
Chloroplast DNA,-> Mitochondrial DNA
DNA REPLICATION
11.2 TYPES OF DNA REPLICATION
 11.2.1 Semi Conservative Replication, Meselson-Stahl
Experiment
-> 11.3 MODELS OF REPLICATION
-> 11.3.1 Theta (Ø) Model of Replication
-> 11.3.2 Uni and Bidirectional Replication
-> 11.3.3 Rolling Circle Replication
-> . 11.4 DNA REPLICATION IN PROKARYOTES
. -> 11.4.1 Initiation of Replication
 11.4.2 Unwinding of DNA
.-> 11.4.3 RNA Priming
-> 11.4.4 Elongation of DNA Chain, the leading strand, lagging
strand, Semidiscontinous replication
-> 11.4.5 Proof Reading
-> 11.4.6 Termination of Replication
■Various steps involved in DNA replication in prokaryotes can be
summarized as follows:
.-> 5 DNA REPLICATION IN EUKARYOTES
-> 11.5.1 Multiple Replicons
-> 11.5.2 Two or More DNA Polymerases
-> 11.5.3 Duplication of Nucleosomes at Replication Fork
.-> 5.4 Telomerase Enzyme, telomerase, “end-replication”
problem,The process of DNA replication in eukaryotes
can be summarized as follows
Comparative account of DNA replication in prokaryotes and
STRUCTURE AND TRANSCRIPTION
12.2 STRUCTURE OF RNA, ). Functionally RNA is more diverse
than DNA
12.3 TYPES OF RNA- a) Messenger RNA (mRNA), . b) Functional
RNA.
12.3.2 Transfer RNAs
12.3.3 Ribosomal RNA
12.3.4 Small RNA Molecules-Classes of small RNA molecules: : i)
Small nuclear RNAs (snRNAs, ii) MicroRNAs (miRNAs) and Small
interfering RNAs (siRNAs, Argonaut
12.4 TRANSCRIPTION
12.4.1 DNA Template and Transcription Apparatus- Central Dogma
of Molecular Biology, The idea that RNA is involved as an
intermediate molecule in the process of information
flow between DNA and protein is suggested by
following observations, DNA template->. The raw materials
(Substrates], -> BACTERIAL RNA POLYMERASE, ->
EUKARYOTIC RNA POLYMERASE, Table: 12.2:Eukaryotic RNA
polymerases..► The promoter of genes transcribed by
RNA polymerase II contains several different
sequence elements surrounding their transcription
sites. These sequences are categorized into two
groups:, 1) Core promoter 2) Regulatory sequences =proximal
control elements. ,,enhancers and silencers, open complex., Table
12.3: General transcription factors needed for transcription initiation
by polymerase II.-> Elongation and Termination of transcription,
►Table 12.4: Basic differences between prokaryotic and eukaryotic
transcription.
12.5 PROCESSING AND MODIFICATION OF RNA
12.5.1 Addition of the 5_ Cap
12.5.2 Addition of Poly (A) Tail at 3_ End
2,5.3RNA SPLICING-SPLIT GENES,INTRONS,EXONS
. 12.5.4 RNA Editing
. 12.6 GENETIC CODE- Features of genetic code ->The genetic
code is a triplet code, . ->Genetic code is nonoverlapping and
commaless-> The genetic code is nearly universal
TRANSLATION
13.2 TRANSLATION IN PROKARYOTES
13.2.1 The Cast of Characters-The cellular machinery involved in
translating mRNAs into polypeptides includes five major components:
1) Ribosomes, 2) tRNA molecules, 3) aminoacyl tRNA synthetases, 4)
mRNA molecule, and 5) Protein factorsprocess of translation
13.2.2 Initiation of Translation[STEP]
13.2.3 Chain Elongation
13.2.4 Termination of Polypeptide Synthesis
.3 TRANSLATION IN EUKARYOTES
13.3.1 The Cast of Characters
13.3.2 Initiation of Translation-13.3.3 Chain Elongation
13.3.4 Termination of Polypeptide Synthesis
13.4 POST TRANSLATIONAL MODIFICATION OF PROTEINS
1313.4.2 Protein Cleavage
.4.1 Polypeptide Folding
13.4.3 Glycosylation
13.4.4 Attachment of Lipids Protein Modification by Lipids
i) N-myristoylation, ii) Prenylation). iii) Palmitoylation
13.4.5 Protein Modification by Small Molecules.-> Acetylation of
lysine residues->Methylation of lysine and arginine residues.
-> Nitrosylation to cysteine residue
REGULATION OF GENE EXPRESSION
14.2 PRINCIPLES OF TRANSCRIPTIONAL REGULATION
. 14.3 GENE REGULATION IN PROKARYOTES
. 14.3.1 Catabolic Pathways and Substrate Induction
. 14.3.2 Anabolic Pathways and End-Product Repression
14.3.3 Mechanisms of Gene Regulation at Transcriptional Level
-> Operon Control
-> Operon Structure . -> Strategies of Gene Regulation
-> Negative Regulation: ->Positive Regulation
-> Positive control -> Inducible positive operon: -> Inducible operons: -> Inducible operons: -> Negative
-> Repressible positive operon: 14.3.4 Model Systems for Gene repressible operons: -> When the level of the product U is high:
Regulation in Prokaryotes . -> When the product U is absent:
->The lac operon of E. coli: An example of a negative inducible ■Isotacho-electrophoresis or isotachophoresis (ITP) –
operon ■Isoelectric focusing (IEF) –
->Lactose metabolism and regulation of lac operon: ■Gel Electrophoresis
->The trp operon model of E. coli: An example of a negative ■Denaturing gel electrophoresis
repressible operon ■Polyacrylamide
->Attenuation in the trp Operon in E. coli: ■Agarose
->High tryptophan levels: ■Pulsed-field Gel Electrophoresis (PFGE
->Low tryptophan levels: ■Capillary Electrophoresis (CE)
14.4 GENE REGULATION IN EUKARYOTES ■ eukaryotic cells ■Affinity Electrophoresis
and bacteria have many features of gene regulation
■Set up for Electrophoresis
14.4.1 Gene Regulation by Chromatin Modification ■Principle of gel electrophoresis
Methylation of histones  Acetylation of histones ■Procedure
ii) Chromatin Remodelling iii) DNA Methylation ■Polyacrylamide gel electrophoresis (PAGE)
14.4.2 Gene Regulation by Transcription Factors and ■Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-
Transcriptional Regulator Proteins PAGE)-
-> Transcriptional Activators and Coactivators; ■Two-dimensional gel electrophoresis
14.4.3 Coordinated Gene Regulation ■Applications
14.5 GENE SILENCING
14.5.1 Transcriptional Gene Silencing
CELL
-> Genomic Imprinting:
4.2 DISCOVERY OF CELL AND CELL THEORY
-> On the paternal chromosome: ■Schleiden and Schwann proposed the unified cell
14.5.2 Posttranscriptional Gene Silencing ■RNA Silencing theory and summarized their observations into three
■Mechanism of Gene Silencing by RNA Interference tenets about cells.
Genetic material ■ three tenets of classical Cell Theory
9.2 TYPES OF GENETIC MATERIAL 4.3 CELL-SHAPE, SIZE AND NUMBER
■Structure of Nucleic Acids (Polynucleotides) l. 4.4 PROKARYOTIC AND EUKARYOTIC CELLS
9.3 DEOXYRIBONUCLEIC ACID (DNA) 4.4.1 Prokaryotic Cell Structure
. 9.3.1 Discovery of DNA 4.4.2 Eukaryotic Cell Structure
9.3.2 Structure of DNA 4.4.3 Plant Cell Versus Animal Cell
.4 RIBONUCLEIC ACID (RNA) Table 4.1: Eukaryotic cell organelles and their functions
->Genetic RNA ->Non-genetic RNA ->Messenger RNA (mRNA) - - 4.5 EUKARYOTIC CELL ORIGIN (THE ENDOSYMBIOTIC
THEORY)
>Ribosomal RNA (rRNA) ->Transfer RNA (tRNA) –
■Small Nuclear RNA ■Small nucleolar RNA ■MicroRNAs CELL WALL AND CELL MEMBRANE
9.5 TRANSFORMATION EXPERIMENTS 5.2 CELL WALL
FORCONFIRMATION OF DNA AS GENETIC MATERIAL 5.2.1 Chemical Nature of Cell Wall
9.5.1 Griffith’s Experiment 5.2.2 Structure of Cell Wall
9.5.2 Avery’s Experiments
5.2.3 Functions of Cell Wall
9.5.3 Hershey-Chase Bacteriophage Experiment
5.2.4 Bacterial Cell Wall
■biochemical evidence due to certain facts such as
5.3 CELL MEMBRANE
those given below confirmed that DNA is the genetic
5.3.1 Various Models for the Structure of Cell
material
Membrane
CHROMATOGRAPHY i) Overton’s Lipid Layer Model
■Two major components in the chromatography
ii) Lipid Bilayer Model
technique are:
iii) Sandwich Model or Lipid Protein Model
2.2.2 Thin Layer Chromatography
iv) Robertson’s Unit Membrane Model
2.2.3 Adsorption Chromatography
2.2.4 Column Chromatography v) Fluid Mosaic Membrane Model Fluid Mosaic
Liquid column chromatography Membrane Model
Gas chromatography 5.3.2 Chemical Composition of Cell Membrane
. 2.2.5 Ion Exchange Chromatography ■ Membrane Lipids
2.2.6 Gel Filtration Chromatography
■ Membrane Carbohydrates-
2.2.7 High Pressure Liquid Chromatography
5.4 CELL MEMBRANE FLUIDITY
. 2.3 COMPARATIVE ACCOUNT OF DIFFERENT TYPES OF
5.4.1 Importance of Membrane Fluidity
CHROMATOGRAPHY
5.4.2 Maintaining Membrane Fluidity
5.5 FUNCTIONS OF CELL MEMBRANE
TECHNIQUES IN MOLECULAR BIOLOGY
3.2 SPECTROPHOTOMETRY CELL ORGANELLES (I)
3.2.1 Principle of Spectrophotometer 6.2 MITOCHONDRIA
3.2.2 Working and Applications of Spectrophotometer
Applications 6.2.1 Structure and Composition
3.3 CENTRIFUGATION ► Functions
3.3.1 Density Gradient Centrifugation . 6.2.2 Semi Autonomous Nature
3.3.2 Differential Centrifugation 6.2.3 Proteins Synthesized within Mitochondria,
3.3.3 Ultracentrifugation
Mitochondrial DNA, and Marker Enzymes
3.4 X RAY DIFFRACTION
3.5 ELECTROPHORESIS ►Mitochondrial DNA
■Types of Electrophoresis ►Mitochondrial marker enzymes
■Moving boundary electrophoresis 6.2.4 Symbiont Hypothesis (The Endosymbiotic
■Zone electrophoresis (ZE) –
6.3.2 Semiautonomous Nature Theory)
Origin of chloroplast 6.3 CHLOROPLASTS
6.3.3 Chloroplast DNA 6.3.1 Structure and Composition ► Functions
6.4 OTHER ORGANELLES
6.4.1 Endoplasmic Reticulum
►Structure ► Function
6.4.2 Golgi Apparatus ► Functions
6.4.3 Lysosomes ►. Functions

CELL ORGANELLES (II)

7.2 PEROXISOMES Structure
7.2.1 Biogenesis/Origin of Peroxisomes
7.2.2 Functions
7.3 GLYOXYSOMES Structure
7.3.1 Biogenesis of Glyoxysomes
7.3.2 Functions
7.4 THE CYTOSKELETON
7.4.1 Microtubules
7.4.2 Microfilaments ►7.4.4 Functions
7.4.5 Structure of Cilia and Flagella
. 7.5 CELL INCLUSIONS
►Table 7.1 : Difference between ribosomes found in prokaryotes
and eukaryotes.
►Structural components of Nucleus
7.6 RIBOSOMES
). 7.7 Nucleus
Structural components of Nucleus
■Nuclear Membrane/Envelope
■Nuclear matrix and nuclear lamina
■Nucleoplasm
■Nucleolus
►. Four distinct zones are present in the nucleolus:
(i) granular zone (ii) fibrillar zone (iii) nucleolus
associated chromatin (iv) matrix or amorphous zone
(Fig. 7.17).
►Chromosomes
■Nuclear pore and Nuclear pore complex
■ nuclear pore complex (NPC → Functions
CELL CYCLE
8.2 OVERVIEW OF CELL CYCLE
Modern scientists divide cell cycle- i) Gap 1 (G1), ii)
Synthesis (S), iii) Gap 2 (G2) and iv) Mitotic (M) phase.
■Cytokinesis
8.3 REGULATION OF CELL CYCLE
8.3.1 Cell Cycle Checkpoints- The G1 Checkpoint
The G2 Checkpoint
. The M Checkpoint
8.3.2 Role of Regulator Molecules of the Cell Cycle
■Positive Regulation of the Cell Cycle
8.3.3 Regulation of Cell Cycle by Protein kinase
■Mechanism of Cdk Regulation
►Cyclin-dependent kinases
. You should remember the following important
points before proceeding further
8.4 MITOSIS
►Prophase ►Prometaphase (Metakinesis)
►Metaphase ►Anaphase ►Telophase
►Importance of Mitosis
8.5 MEIOSIS (REDUCTION DIVISION)
8.5.1 Meiosis I
►Leptotene
►Zygotene ► Diplotene ► Pachytene ►Diakinesis
8.5.2 Meiosis II
Biological significance of meiosis