CSIR-NET LIFE SCIENCES

Unit 3: Fundamental Processes

Complete Topic-Wise Syllabus

DNA Replication • DNA Repair • Recombination • Transcription • RNA Processing • Translation • Protein Processing • Gene Regulation

A. DNA Replication, Repair and Recombination

🧬 1. Unit of Replication

Replicon
Origin of replication
Replication unit
Replication fork
Bidirectional replication
Unidirectional replication
Leading strand
Lagging strand
Okazaki fragments

🧬 2. DNA Replication in Prokaryotes

Replication origin in bacteria
Initiation of replication
DNA unwinding
Helicase
Single-strand DNA-binding proteins
DNA gyrase
DNA topoisomerases
Primase
DNA polymerase III
DNA polymerase I
DNA ligase
Primer removal
Okazaki fragment processing

🧬 3. DNA Replication in Eukaryotes

Multiple origins of replication
Origin recognition complex (ORC)
Replication licensing
MCM helicase
DNA polymerase α
DNA polymerase δ
DNA polymerase ε
PCNA
RFC
Replication fork progression

🧬 4. Telomeres and Telomerase

Telomere structure
End-replication problem
Telomerase
RNA component of telomerase
Telomerase reverse transcriptase
Telomere shortening
Telomeres and cellular aging

⚙️ 5. Fidelity of DNA Replication

Base selection
Proofreading
3′ → 5′ exonuclease activity
Mismatch repair
DNA polymerase accuracy
Replication fidelity

🦠 6. Extrachromosomal Replicons

Plasmids
Bacterial plasmids
F plasmid
R plasmids
Copy number
Plasmid replication
Phage DNA
Viral replicons

⚠️ 7. DNA Damage

Depurination
Deamination
Oxidative damage
Alkylation
UV-induced damage
Thymine dimers
Single-strand breaks
Double-strand breaks
Replication-associated damage

🛠️ 8. DNA Repair Mechanisms

Direct repair
Photoreactivation
Base excision repair
Nucleotide excision repair
Mismatch repair
Double-strand break repair
Homologous recombination repair
Non-homologous end joining
Translesion synthesis

🔄 9. Homologous Recombination

Homologous DNA sequences
DNA strand invasion
RecA
Rad51
Holliday junction
Branch migration
Resolution of Holliday junction
Double-strand break model

🎯 CSIR-NET High-Yield:
Replication fork, DNA polymerases, Okazaki fragments, leading and lagging strand, telomerase, proofreading, BER, NER, mismatch repair, homologous recombination and Holliday junctions are extremely important.

B. RNA Synthesis, Processing and Regulation

🧬 1. Transcription

Definition of transcription
Template strand
Coding strand
Promoter
Transcription start site
Initiation
Elongation
Termination

🔬 2. RNA Polymerases

Bacterial RNA polymerase
Core enzyme
Sigma factor
Promoter recognition
Eukaryotic RNA polymerase I
Eukaryotic RNA polymerase II
Eukaryotic RNA polymerase III
Functions of different RNA polymerases

🧬 3. Transcription Machinery

General transcription factors
TFIIA
TFIIB
TFIID
TFIIE
TFIIF
TFIIH
TATA-binding protein
Mediator complex

🔄 4. Transcription Regulation

Transcription activators
Transcription repressors
Enhancers
Silencers
Promoter elements
Operator sequences
DNA-binding domains
Transcriptional regulation

💊 5. Transcriptional Inhibitors

Actinomycin D
α-Amanitin
Rifampicin
Mechanisms of transcription inhibition
Effects on RNA polymerases

🧢 6. RNA Capping

5′ cap structure
7-methylguanosine cap
5′–5′ triphosphate linkage
Functions of 5′ cap
mRNA stability
Translation initiation
Nuclear export

✂️ 7. RNA Splicing

Introns and exons
Spliceosome
snRNPs
5′ splice site
Branch point
Polypyrimidine tract
3′ splice site
Lariat formation
Alternative splicing

🧬 8. RNA Processing

Pre-mRNA processing
5′ capping
Splicing
3′ polyadenylation
Cleavage and polyadenylation
RNA stability

🔤 9. RNA Editing

RNA sequence modification
Base substitution
Insertion and deletion
RNA editing enzymes
Biological significance

🧬 10. Types of RNA

mRNA
tRNA
rRNA
snRNA
snoRNA
miRNA
siRNA
piRNA
lncRNA
circRNA

🚚 11. RNA Transport

RNA export from nucleus
mRNA transport
RNA localization
RNA-binding proteins
Nuclear pore complex

🧪 12. Ribozymes

Catalytic RNA
Self-splicing RNA
RNase P
Ribosomal catalytic activity
RNA world hypothesis

🔀 13. Riboswitches

Definition
RNA-based regulation
Ligand binding
Structural switching
Transcriptional regulation
Translational regulation

🧬 14. Non-Coding RNA

Regulatory RNA
miRNA
siRNA
piRNA
lncRNA
snRNA
snoRNA
Gene silencing

💡 Remember:
RNA polymerase II → mRNA
RNA polymerase I → Major rRNAs
RNA polymerase III → tRNA and 5S rRNA
snRNA → RNA splicing
miRNA / siRNA → Gene silencing

C. Protein Synthesis, Processing and Degradation

🧬 1. Ribosome Structure

Ribosomal subunits
Prokaryotic 70S ribosome
30S and 50S subunits
Eukaryotic 80S ribosome
40S and 60S subunits
rRNA
Ribosomal proteins
A site
P site
E site

🧬 2. Translation

mRNA recognition
Initiation
Initiation factors
Start codon
tRNA charging
Aminoacyl-tRNA synthetases
Elongation
Peptide bond formation
Translocation
Termination
Release factors

🔬 3. Genetic Code

Triplet nature of genetic code
Codons
Anticodons
Start codon
Stop codons
Degeneracy
Universality
Wobble hypothesis

🔄 4. Regulation of Translation

Translational control
Initiation regulation
RNA-binding proteins
miRNA-mediated regulation
uORFs
Ribosome availability
mRNA stability

💊 5. Translational Inhibitors

Tetracycline
Chloramphenicol
Streptomycin
Puromycin
Erythromycin
Cycloheximide
Mechanisms of translation inhibition

🧪 6. Post-Translational Modification

Protein folding
Phosphorylation
Acetylation
Methylation
Glycosylation
Ubiquitination
SUMOylation
Lipidation
Disulfide bond formation
Proteolytic cleavage

🚚 7. Protein Trafficking

Signal peptides
Signal recognition particle
ER targeting
Co-translational translocation
Nuclear localization signals
Mitochondrial targeting signals
Peroxisomal targeting signals
Protein transport to Golgi
Lysosomal targeting

📦 8. Protein Transport

Cytosolic protein targeting
Nuclear import and export
Mitochondrial protein import
ER protein import
Peroxisomal protein import
Vesicular protein transport

♻️ 9. Protein Degradation

Ubiquitin-proteasome pathway
Ubiquitin activation
E1 enzyme
E2 enzyme
E3 ligase
26S proteasome
Lysosomal degradation
Autophagy-mediated degradation
Protein quality control

🎯 CSIR-NET High-Yield:
Ribosome structure, genetic code, wobble hypothesis, translation initiation/elongation/termination, aminoacyl-tRNA synthetases, antibiotics, protein targeting and ubiquitin-proteasome pathway are essential topics.

D. Control of Gene Expression at Transcription and Translation Level

🦠 1. Gene Regulation in Prokaryotes

Lac operon
Trp operon
Catabolite repression
Positive regulation
Negative regulation
Attenuation
Regulatory proteins

🧬 2. Gene Regulation in Phages

Phage gene regulation
Early and late genes
Phage developmental pathways
Regulatory switches
Lambda phage regulation
Lysogenic and lytic pathways

🦠 3. Gene Regulation in Viruses

Viral promoters
Viral transcription factors
Immediate-early genes
Early genes
Late genes
Viral gene expression strategies

🧬 4. Gene Regulation in Eukaryotes

Promoter regulation
Enhancers
Silencers
Insulators
Transcription factors
Mediator complex
Chromatin remodeling
DNA methylation
Histone modification

🧬 5. Chromatin and Gene Expression

Nucleosome organization
Chromatin remodeling complexes
ATP-dependent chromatin remodeling
Histone acetylation
Histone methylation
Histone phosphorylation
Histone ubiquitination
Chromatin accessibility

🔇 6. Gene Silencing

Transcriptional gene silencing
Post-transcriptional gene silencing
RNA interference
miRNA
siRNA
Heterochromatin formation
DNA methylation

🧬 7. Epigenetic Regulation

Definition of epigenetics
DNA methylation
Histone modifications
Chromatin remodeling
Genomic imprinting
X-chromosome inactivation
Epigenetic inheritance
Histone code

🔄 8. Translational Gene Regulation

Control of translation initiation
mRNA stability
miRNA-mediated repression
RNA-binding proteins
Iron-responsive elements
Riboswitch-mediated regulation

🧠 Three Major Levels of Gene Regulation:

Transcriptional level → Promoters, enhancers, repressors and transcription factors
Post-transcriptional level → RNA processing, splicing, editing and RNA stability
Translational level → Translation initiation, miRNA and mRNA stability

🎯 CSIR-NET High-Yield:
Lac operon, Trp operon, phage λ regulation, enhancers and silencers, chromatin remodeling, DNA methylation, histone modifications, RNA interference and epigenetic regulation should be studied thoroughly.

📚 CSIR-NET Unit 3 – Quick Revision Map

A → DNA Replication, Repair & Recombination

B → RNA Synthesis & Processing

C → Protein Synthesis & Processing

D → Gene Expression & Epigenetics

🎯 Most Important CSIR-NET Topics

DNA replication fork and replication enzymes
Leading and lagging strand synthesis
DNA polymerases and proofreading
Telomerase and telomere replication
BER, NER and mismatch repair
Homologous recombination and Holliday junction
RNA polymerases and transcription machinery
Transcription factors and promoter regulation
RNA capping, splicing and polyadenylation
Alternative splicing and RNA editing
Ribozymes and riboswitches
Non-coding RNA and RNA interference
Ribosome structure and translation
Genetic code and wobble hypothesis
Translation inhibitors
Post-translational modifications
Protein trafficking and signal sequences
Ubiquitin-proteasome pathway
Lac and Trp operons
Phage and viral gene regulation
Chromatin remodeling
DNA methylation and histone modification
Gene silencing and epigenetic regulation

📖 Recommended Study Sequence:

🧬 DNA Replication → 🛠️ DNA Repair → 🔄 Recombination → 📝 Transcription → ✂️ RNA Processing → 🧬 Translation → 📦 Protein Processing → ♻️ Protein Degradation → 🔬 Gene Regulation → 🧬 Epigenetics

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Saturday, 8 August 2026