Author: Admin

📌Definition Table

Term	Definition
Cell cycle	The series of stages a cell goes through from one division to the next.
Interphase	The phase between divisions, consisting of G1, S, and G2.
Checkpoints	Control mechanisms that ensure accuracy of cell cycle progression.
Cyclins	Regulatory proteins controlling progression through the cell cycle.
CDKs (cyclin-dependent kinases)	Enzymes activated by cyclins to phosphorylate target proteins.
Apoptosis	Programmed cell death triggered if errors cannot be corrected.

📌Introduction

The cell cycle is a tightly regulated process ensuring cells grow, replicate DNA, and divide accurately. Interphase makes up the majority of the cycle, preparing cells for mitosis or meiosis. Checkpoints safeguard against errors, preventing uncontrolled division and cancer. Cyclins and CDKs are key molecular regulators, ensuring the cycle proceeds only when conditions are favourable.

📌 Phases of the Cell Cycle

• G1 phase: cell grows, produces RNA, proteins, and organelles.
• S phase: DNA replication occurs; each chromosome duplicates.
• G2 phase: preparation for division; checks DNA integrity.
• M phase: nuclear division (mitosis/meiosis) and cytokinesis.
• Interphase dominates (~90% of cell cycle).

🧠 Examiner Tip: Don’t confuse interphase as a “resting” stage — it is metabolically active and essential for preparation.

📌 Checkpoints in Cell Cycle

• G1 checkpoint: assesses size, nutrients, DNA damage.
• G2 checkpoint: ensures DNA is fully replicated and undamaged.
• Metaphase (spindle) checkpoint: checks chromosome attachment to spindle fibres.
• If conditions fail, cycle halts for repair or apoptosis.
• Prevents propagation of mutations.

🧬 IA Tips & Guidance: Students can study onion root tips to calculate mitotic index as a measure of cell cycle activity.

📌 Cyclins and CDKs

• Cyclins rise and fall during cycle phases.
• Cyclins bind CDKs, forming active complexes.
• Complexes phosphorylate proteins, driving phase transitions.
• Example: cyclin D → G1 progression; cyclin B → mitosis entry.
• Dysregulation of cyclins → uncontrolled cell division (cancer).

🌐 EE Focus: An EE could investigate how environmental stressors affect checkpoint regulation, e.g., UV light and DNA repair.

📌 Consequences of Checkpoint Failure

• Uncontrolled cell division → tumours and cancer.
• Damaged DNA passed to daughter cells.
• Checkpoint mutations linked to p53 failure.
• Therapeutic target: drugs modulating cyclins/CDKs in cancer treatment.
• Balance between repair and apoptosis critical for survival.

❤️ CAS Link: Students could run awareness projects on cancer prevention, linking lifestyle choices to cell cycle regulation.

📌 Integration with Other Systems

• Cell cycle regulation tied to organism growth and repair.
• Endocrine signals (hormones) can influence proliferation.
• Immune cells rely on rapid cycling during infections.
• Stem cells demonstrate controlled cycling vs differentiation.
• Coordination prevents overgrowth and maintains tissue health.

🔍 TOK Perspective: The cell cycle is modelled as a linear series of phases. TOK issue: To what extent do such models capture the complexity of overlapping signals and feedback?

📝 Paper 2: Expect questions on phases, checkpoint roles, cyclins, or mitotic index data.

📌Definition Table

Term	Definition
Gene editing	Direct manipulation of an organism’s DNA to add, remove, or modify genes.
CRISPR-Cas9	A gene-editing tool derived from bacterial defense systems, using guide RNA and Cas9 nuclease to cut DNA at specific sites.
Guide RNA (gRNA)	Synthetic RNA molecule that directs Cas9 to the correct DNA sequence.
Cas9	Enzyme that makes double-strand cuts in DNA at gRNA-specified sites.
Off-target effects	Unintended DNA modifications caused by imprecise editing.

📌Introduction

Gene editing has revolutionized molecular biology, enabling precise modifications of DNA sequences. Among the various methods developed, CRISPR-Cas9 has emerged as the most powerful due to its accuracy, efficiency, and simplicity. Adapted from bacterial immune systems, CRISPR technology allows researchers to target virtually any gene for knockout, correction, or insertion, with wide-ranging implications in medicine, agriculture, and biotechnology.

📌 Mechanism of CRISPR-Cas9 Editing

• A synthetic guide RNA (gRNA) binds to a specific DNA sequence via complementary base pairing.
• The Cas9 enzyme introduces a double-strand break at the targeted site.
• The cell repairs the break using one of two mechanisms:
  • Non-homologous end joining (NHEJ): error-prone repair that often introduces mutations (useful for gene knockouts).
  • Homology-directed repair (HDR): precise repair using a supplied DNA template for accurate gene correction or insertion.
• The result is targeted gene disruption or modification with high specificity.

🧠 Examiner Tip: Always distinguish between NHEJ (mutagenic, knockouts) and HDR (precise, knock-ins) when explaining CRISPR mechanisms.

📌 Applications in Medicine

• Correcting mutations responsible for genetic disorders (e.g., sickle-cell disease, cystic fibrosis).
• Engineering immune cells (CAR-T therapy) to fight cancers.
• Developing antiviral strategies by targeting viral DNA or RNA.
• Researching potential cures for polygenic diseases by editing multiple genes simultaneously.
• Advancing personalized medicine by tailoring gene edits to individual genomes.

🧬 IA Tips & Guidance: An IA could model CRISPR targeting using bioinformatics tools to identify PAM sequences in DNA, linking digital biology with molecular techniques.

📌 Applications in Agriculture and Biotechnology

• Creating crops resistant to pests, diseases, and environmental stress.
• Enhancing nutritional content (e.g., rice enriched with vitamins).
• Producing livestock with desirable traits such as faster growth or disease resistance.
• Industrial biotechnology uses gene editing to engineer microbes for biofuel or pharmaceutical production.
• Synthetic biology harnesses CRISPR to design novel organisms for environmental or medical use.

🌐 EE Focus: An EE could analyze ethical debates around CRISPR, investigating case studies such as gene-edited embryos, or explore agricultural applications and their impact on food security.

📌 Ethical, Safety, and Regulatory Issues

• Concerns about germline editing and heritable genetic modifications.
• Potential misuse in creating “designer babies.”
• Off-target mutations could cause unintended health risks.
• Ethical debates over editing animal and plant genomes for human benefit.
• Regulations vary worldwide, with stricter rules on human applications.

❤️ CAS Link: Students could hold a debate or awareness campaign on CRISPR ethics, engaging their peers in discussions about the balance between scientific progress and moral responsibility.

📌 Future Directions of Gene Editing

• Development of CRISPR variants (Cas12, Cas13) expands applications to RNA editing.
• Base editing and prime editing increase precision, reducing off-target risks.
• Potential for gene drives to alter wild populations, e.g., controlling malaria-spreading mosquitoes.
• Integration with AI and bioinformatics will improve guide RNA design.
• The challenge remains to balance medical promise with ethical safeguards.

🔍 TOK Perspective: CRISPR raises profound questions about the limits of human intervention. TOK reflection: If humans can rewrite the code of life, how do we determine what should or should not be changed? Does technological capability automatically justify its use?

📝 Paper 2: Be ready to explain CRISPR’s mechanism (gRNA, Cas9, NHEJ vs HDR), give examples of medical or agricultural applications, and evaluate ethical issues. Data questions may involve mutation frequencies with/without CRISPR, or success rates of targeted edits.

📌Definition Table

Term	Definition
Phenotype	Observable traits or characteristics of an organism resulting from genotype and environment.
Missense mutation	A base substitution that changes one amino acid in the polypeptide chain.
Nonsense mutation	A mutation that introduces a premature stop codon, producing truncated proteins.
Frameshift mutation	Mutation caused by insertion or deletion of bases, altering the reading frame.
Loss-of-function mutation	Mutation that reduces or abolishes a protein’s activity.
Gain-of-function mutation	Mutation that enhances or introduces a new protein function.

📌Introduction

Mutations affect proteins by altering amino acid sequences, folding, or regulation, which in turn changes phenotypes. While some mutations are silent with no observable effects, others disrupt critical functions and cause disease. Mutations can also create beneficial traits that drive adaptation. Studying these outcomes reveals the intricate link between genotype, protein function, and phenotype

📌 Impact on Protein Structure and Function

• Missense mutations can alter protein shape or stability (e.g., sickle-cell hemoglobin).
• Nonsense mutations truncate proteins, usually rendering them non-functional.
• Frameshifts completely disrupt amino acid sequences, often highly deleterious.
• Mutations in active sites or binding regions severely impair enzyme activity.
• Some mutations alter folding pathways, leading to aggregation and toxicity.

🧠 Examiner Tip: When linking mutations to proteins, always explain how amino acid changes affect structure (primary → tertiary) and function.

📌 Impact on Phenotypes

• Single-gene disorders: e.g., cystic fibrosis from CFTR gene mutations.
• Metabolic defects: enzyme deficiencies causing conditions like phenylketonuria.
• Morphological changes: mutations affecting developmental genes (HOX) altering body structure.
• Resistance traits: mutations conferring antibiotic resistance in bacteria or pesticide resistance in insects.
• Neutral effects: silent mutations or mutations in non-coding DNA with no observable phenotype.

🧬 IA Tips & Guidance: A lab investigation could track phenotypic changes in bacterial colonies under antibiotic stress, showing mutation-driven resistance.

📌 Beneficial vs. Harmful Effects

• Beneficial mutations increase survival or reproduction (e.g., lactase persistence in adults).
• Harmful mutations cause disease or lower fitness.
• Neutral mutations accumulate as genetic variation without obvious effects.
• The same mutation may be harmful in one environment but beneficial in another (e.g., sickle-cell trait).
• Evolution depends on the balance of these effects in populations.

🌐 EE Focus: An EE could explore how single-gene mutations manifest differently across populations, such as the protective effect of sickle-cell trait in malaria regions.

📌 Molecular Basis of Mutation Effects

• Loss-of-function mutations disrupt normal gene activity; often recessive.
• Gain-of-function mutations create hyperactive proteins; often dominant.
• Mutations in regulatory regions alter gene expression levels.
• Splicing mutations can exclude essential exons, producing dysfunctional proteins.
• Expanded trinucleotide repeats (e.g., Huntington’s disease) cause protein aggregation.

❤️ CAS Link: Students could design community outreach activities on genetic screening, raising awareness of how early detection of mutations can inform health choices.

📌 Mutations and Evolutionary Significance

• Mutations provide the raw material for adaptation and natural selection.
• Evolutionary novelties often trace back to mutations in developmental regulatory genes.
• Comparative genomics identifies conserved vs. mutated regions across species.
• Mutation rates vary across organisms, shaping evolutionary trajectories.
• Human variation and personalized medicine rely on identifying specific mutations.

🔍 TOK Perspective: Classifying mutations as “harmful” or “beneficial” depends on context and human values. TOK reflection: How do cultural, medical, or environmental perspectives influence our judgment of genetic change?

📝 Paper 2: Be prepared to explain mutation effects on proteins and phenotypes, with examples like sickle-cell anemia. Expect data questions on enzyme activity, genetic disorders, or inheritance patterns, linking genotype to phenotype.

📌Definition Table

Term	Definition
Mutation	A permanent change in the nucleotide sequence of DNA.
Point Mutation	Change affecting a single base (substitution, insertion, or deletion).
Frameshift Mutation	Caused by insertion/deletion of bases that shift the reading frame.
Mutagen	An external factor (e.g., radiation, chemicals) that increases mutation rate.
Silent Mutation	A base change that does not alter the amino acid sequence due to degeneracy of the genetic code.

📌Introduction

Mutations are the ultimate source of genetic variation and can occur spontaneously or be induced by mutagens. They affect protein synthesis by altering the genetic code, potentially changing amino acid sequences and impacting protein structure and function. While many mutations are harmful or neutral, a minority may be beneficial, driving evolutionary processes.

📌 Types of Mutations

• Substitution mutations may be silent, missense, or nonsense, with varying impacts on the resulting protein.
• Insertions and deletions can cause frameshift mutations, altering the reading frame of mRNA and drastically changing the polypeptide.
• Large-scale mutations include duplications, inversions, and translocations, which affect chromosomal structure.
• Germline mutations are heritable, affecting gametes and passed to offspring, while somatic mutations are confined to body cells.
• Spontaneous mutations arise during DNA replication errors, whereas induced mutations result from exposure to mutagens like UV light, X-rays, or chemicals in tobacco smoke.

🧠 Examiner Tip: Always distinguish between point mutations and chromosomal mutations, and specify whether a mutation leads to a silent, missense, or nonsense outcome.

📌 Causes of Mutations

• Spontaneous errors in DNA replication when proofreading fails.
• Physical mutagens like UV radiation causing thymine dimers, or X-rays inducing double-strand breaks.
• Chemical mutagens such as nitrosamines, benzopyrene (tobacco smoke), or mustard gas.
• Biological mutagens including viral insertions (retroviruses).
• Mutation hotspots (e.g., CpG islands) are regions of higher mutation frequency.

🧬 IA Tips & Guidance: Mutation frequency can be investigated with bacterial cultures exposed to UV light or mutagenic chemicals, linking lab work to DNA repair and variation.

📌 Mutations and Genetic Variation

• Mutations introduce new alleles into populations, fueling natural selection.
• Some are neutral, others deleterious, and a few advantageous (e.g., sickle-cell allele conferring malaria resistance).
• In sexually reproducing organisms, mutations combine with meiosis and fertilisation to enhance genetic diversity.
• In asexual organisms, mutation is the primary driver of variation and evolution.

🌐 EE Focus: An EE could investigate mutation rates in different organisms or the effect of environmental mutagens (e.g., UV intensity) on DNA damage.

📌 Consequences of Mutations

• Silent mutations do not alter amino acid sequence due to redundancy of the code.
• Missense mutations change one amino acid, potentially altering protein function (e.g., sickle-cell anemia).
• Nonsense mutations introduce a premature stop codon, truncating proteins (e.g., cystic fibrosis).
• Frameshift mutations often render proteins non-functional due to widespread sequence disruption.
• Mutations in oncogenes or tumour suppressor genes can initiate cancer.

❤️ CAS Link: Students could run a community awareness campaign about mutagens in daily life (UV exposure, smoking) and their link to cancer, connecting classroom learning to public health.

📌 Mutations in Medicine and Evolution

• Cancer progression often involves multiple accumulated mutations.
• Viral pandemics (e.g., COVID-19 variants) demonstrate real-time mutation effects.
• Mutations provide raw material for adaptive evolution across species.
• Biotechnology uses controlled mutations for protein engineering.

🔍 TOK Perspective: Mutations are random yet interpreted as meaningful in evolution and medicine. This raises epistemological questions: how can chance processes generate order? And to what extent does our classification of mutations (silent, harmful, beneficial) depend on human value judgments?

📝 Paper 2: Expect questions requiring identification of mutation types, explaining their effects on amino acids, or linking mutagens to outcomes. Graph/data interpretation may involve mutation frequency, genetic diseases, or mutagenic experiments.

📌Definition Table

Term	Definition
Post-translational modification (PTM)	Chemical or structural changes to a polypeptide after translation that alter its function.
Phosphorylation	Addition of phosphate groups to proteins, often regulating enzyme activity or signaling.
Glycosylation	Attachment of carbohydrate chains to proteins, important for stability and cell recognition.
Proteolytic cleavage	Cutting of polypeptide chains to activate or mature proteins.
Ubiquitination	Addition of ubiquitin tags marking proteins for degradation by proteasomes.
Chaperones	Proteins that assist proper folding of newly synthesized polypeptides.

📌Introduction

Once polypeptides are synthesized by ribosomes, they are rarely functional in their raw form. Post-translational modifications (PTMs) refine protein structure, regulate activity, and target proteins to specific locations. These modifications expand the diversity of the proteome far beyond what is encoded by the genome and are central to nearly all cellular processes.

📌 Folding and Chaperones

• Polypeptides must fold into precise 3D structures to function.
• Chaperone proteins prevent misfolding and aggregation during folding.
• Incorrect folding can cause diseases such as Alzheimer’s, Parkinson’s, or prion diseases.
• Protein disulfide isomerases catalyze disulfide bond formation, stabilizing structure.
• Folding often occurs in the endoplasmic reticulum (ER) for secretory proteins.

🧠 Examiner Tip: Always mention that correct folding is essential for protein function; misfolding usually results in loss of activity or toxicity.

📌 Chemical Modifications

• Phosphorylation adds phosphate groups (via kinases), switching enzymes or receptors “on” or “off.”
• Glycosylation attaches carbohydrate chains, crucial for protein stability, signaling, and immune recognition.
• Acetylation modifies histones, regulating gene expression by altering chromatin structure.
• Methylation can regulate protein interactions and epigenetic gene control.
• These modifications create dynamic regulation of protein activity.

🧬 IA Tips & Guidance: A possible IA could examine enzyme activity under conditions that mimic phosphorylation (using activators/inhibitors), linking PTMs to enzyme regulation.

📌 Proteolytic Processing

• Some proteins are produced as inactive precursors (zymogens or pro-proteins).
• Proteolytic cleavage activates them, e.g., pepsinogen → pepsin in the stomach.
• Hormones like insulin are produced as prohormones, requiring cleavage for activation.
• Viral proteins often rely on host proteases for activation, a target for antiviral drugs.
• Cleavage ensures proteins are only active at the right time and place.

🌐 EE Focus: An EE could investigate how glycosylation affects protein stability in biopharmaceuticals, or how phosphorylation regulates cell signaling in cancer biology.

📌 Protein Targeting and Degradation

• Signal peptides direct proteins to their proper cellular destinations (ER, mitochondria, nucleus).
• Ubiquitination tags damaged or unneeded proteins for degradation in proteasomes.
• Proteasome-mediated degradation maintains protein quality control.
• Autophagy recycles entire organelles and protein aggregates when necessary.
• Balance between synthesis and degradation maintains proteostasis.

❤️ CAS Link: Students could develop awareness projects showing how lifestyle choices (diet, toxins, stress) impact protein health and folding, linking cell biology to personal well-being.

📌 Integration with Protein Function

• PTMs expand protein diversity beyond genetic coding.
• Dynamic modifications allow rapid adaptation to cellular conditions.
• Misregulation of PTMs is a hallmark of many diseases, especially cancer and neurodegeneration.
• PTMs connect directly to signaling, metabolism, gene regulation, and immunity.
• Studying PTMs provides insight into systems biology and proteome complexity.

🔍 TOK Perspective: PTMs are invisible molecular events studied using indirect methods like mass spectrometry. TOK reflection: How do we decide when indirect evidence is strong enough to establish knowledge, and does the complexity of PTMs challenge the idea of a simple central dogma?

📝 Paper 2: Be prepared to describe examples of PTMs such as phosphorylation, glycosylation, and proteolytic cleavage. Exam questions may ask you to link PTMs to protein function, analyze data on enzyme activity under modifications, or explain how PTMs create proteome diversity.

📌Definition Table

Term	Definition
Translation	Process of synthesizing a polypeptide chain from mRNA using ribosomes.
Codon	Sequence of three nucleotides in mRNA that codes for a specific amino acid.
Anticodon	Complementary triplet sequence on tRNA that pairs with an mRNA codon.
tRNA (transfer RNA)	Molecule that carries specific amino acids to ribosomes during translation.
Ribosome	Cellular structure (made of rRNA and proteins) that catalyzes peptide bond formation.
Polysome	Cluster of multiple ribosomes translating a single mRNA simultaneously.

📌Introduction

Translation is the second step of protein synthesis, where ribosomes decode the mRNA sequence into a polypeptide chain. This process occurs in the cytoplasm in both prokaryotes and eukaryotes, with ribosomes acting as molecular machines that align tRNAs with codons and catalyze peptide bond formation.

📌 Mechanism of Translation

• Initiation
  • Small ribosomal subunit binds to mRNA near the start codon (AUG).
  • Initiator tRNA carrying methionine binds to AUG codon.
  • Large ribosomal subunit attaches, forming the complete ribosome.
• Elongation
  • Incoming tRNAs bind to the A site with anticodon–codon pairing.
  • Peptide bond forms between amino acids in P and A sites.
  • Ribosome shifts (translocation), moving tRNA to the P site, freeing the A site.
• Termination
  • Stop codon (UAA, UAG, UGA) is reached.
  • Release factors bind, causing the ribosome to disassemble and release the polypeptide.
  • Polypeptide undergoes folding or further modification.

🧠 Examiner Tip: Always identify the ribosomal sites (A, P, and E) when describing translation. This is a common exam requirement.

📌 Role of Ribosomes

• Ribosomes are made of rRNA and proteins, with large and small subunits.
• They catalyze peptide bond formation via peptidyl transferase activity (rRNA acting as a ribozyme).
• In prokaryotes, ribosomes are 70S; in eukaryotes, 80S.
• Ribosomes can be free (producing cytoplasmic proteins) or bound to ER (producing secretory or membrane proteins).
• Polysomes increase efficiency by producing multiple polypeptides from one mRNA simultaneously.

🧬 IA Tips & Guidance: An IA could involve modeling codon–anticodon matching using color-coded cards or beads to simulate translation, or analyzing how inhibitors like antibiotics affect bacterial protein synthesis.

📌 Genetic Code and Fidelity

• The genetic code is universal, degenerate, and non-overlapping.
• Degeneracy means multiple codons code for the same amino acid, reducing mutation impact.
• Specificity comes from anticodon–codon pairing and aminoacyl-tRNA synthetase enzymes charging tRNAs with correct amino acids.
• Stop codons ensure proper termination, preventing faulty proteins.
• Errors in translation can result in misfolded proteins and disease.

🌐 EE Focus: An EE could investigate ribosome structure differences between prokaryotes and eukaryotes, analyzing how antibiotics selectively target bacterial translation.

📌 Efficiency and Regulation of Translation

• Initiation is the main regulatory step of translation.
• Polysomes enable rapid protein production in response to demand.
• Translation can be upregulated under growth signals (e.g., insulin) or suppressed during stress.
• Ribosome pausing helps coordinate protein folding.
• mRNA stability directly affects protein output.

❤️ CAS Link: Students could create classroom workshops demonstrating translation with role-play (students acting as mRNA, tRNA, and ribosome components), linking active learning with complex processes.

📌 Integration with Protein Synthesis

• Translation links genetic information to functional proteins.
• Errors in translation compromise cell function and health.
• Ribosome structure and function are highly conserved across species, highlighting evolutionary importance.
• Regulation of translation ensures proteins are made only when needed.
• Combined with transcription, translation determines the proteome of a cell.

🔍 TOK Perspective: Ribosomes were discovered through electron microscopy and biochemical studies, revealing molecular machines at a scale invisible to the naked eye. TOK reflection: How does reliance on technology to “see the unseen” affect the certainty of scientific claims?

📝 Paper 2: Expect questions on codon–anticodon pairing, ribosomal sites, differences between free and bound ribosomes, and antibiotic action. Data questions may involve translation rates or effects of inhibitors.

📌Definition Table

Term	Definition
Transcription	Process of synthesizing mRNA from a DNA template strand.
RNA polymerase	Enzyme that catalyzes the synthesis of RNA from DNA.
Promoter	Non-coding DNA sequence where RNA polymerase binds to initiate transcription.
Intron	Non-coding sequence in pre-mRNA that is removed during RNA processing.
Exon	Coding sequence of pre-mRNA that remains in mature mRNA after splicing.
Splicing	Process of removing introns and joining exons to form mature mRNA.

📌Introduction

Transcription is the first step of protein synthesis, converting the genetic code of DNA into a complementary RNA sequence. In eukaryotes, this occurs in the nucleus, where RNA polymerase synthesizes pre-mRNA that undergoes post-transcriptional modifications such as capping, polyadenylation, and splicing. These modifications protect RNA from degradation, regulate export from the nucleus, and increase proteome diversity through alternative splicing.

📌 Mechanism of Transcription

• DNA double helix unwinds and hydrogen bonds break at the gene region.
• RNA polymerase binds to the promoter and synthesizes RNA in a 5′→3′ direction using the template strand.
• Complementary base pairing occurs, with uracil replacing thymine.
• Transcription is divided into initiation, elongation, and termination phases.
• The resulting pre-mRNA contains both introns and exons.

🧠 Examiner Tip: Do not confuse RNA polymerase (used in transcription) with DNA polymerase (used in replication).

📌 RNA Processing and Gene Expression

• Pre-mRNA undergoes modification before leaving the nucleus.
• Addition of a 5′ methyl cap protects mRNA from degradation.
• Addition of a poly-A tail at the 3′ end enhances stability and transport.
• Splicing removes introns and joins exons; alternative splicing allows a single gene to produce multiple proteins.
• Processed mRNA leaves the nucleus through nuclear pores for translation.

🧬 IA Tips & Guidance: An IA could investigate how transcription inhibitors (e.g., antibiotics like rifampicin) affect bacterial growth, linking molecular processes to observable outcomes.

📌 Gene Regulation via Transcription

• Not all genes are expressed in all cells; transcription is the main control point.
• Transcription factors regulate RNA polymerase binding to promoters.
• Enhancers and silencers modulate gene activity, enabling cell specialization.
• Epigenetic modifications such as DNA methylation influence transcription levels.
• Misregulation of transcription is linked to diseases like cancer.

🌐 EE Focus: An EE could explore alternative splicing and its role in expanding the proteome, or investigate how transcription errors contribute to genetic diseases.

📌 RNA Processing and Proteome Diversity

• Alternative splicing creates different proteins from a single gene.
• Example: tropomyosin gene generates distinct isoforms in muscle vs. non-muscle cells.
• RNA editing can chemically alter nucleotides, changing the resulting protein.
• Regulation at this stage increases adaptability and complexity in eukaryotes.
• Defects in splicing machinery can cause genetic disorders (e.g., spinal muscular atrophy).

❤️ CAS Link: Students can create models of transcription and RNA processing using colored beads or string to demonstrate how exons and introns are rearranged, linking molecular biology to classroom creativity.

📌 Integration with Genetic Expression

• Transcription and RNA processing are tightly coupled with gene expression.
• Control at this level ensures that proteins are produced only where and when needed.
• RNA modifications also impact translation efficiency and protein stability.
• These processes highlight the complexity of the central dogma beyond the simple DNA → RNA → Protein pathway.
• Research into RNA regulation has expanded into RNA interference (RNAi) and microRNAs.

🔍 TOK Perspective: Much of transcription and RNA processing is studied indirectly using molecular markers, gels, or sequencing. TOK reflection: To what extent can we claim certainty about unseen molecular events, and how does technological interpretation shape our knowledge?

📝 Paper 2: Be prepared to describe transcription, splicing, and RNA modifications. Exam questions may ask you to compare prokaryotic and eukaryotic transcription, label diagrams of mRNA processing, or explain how alternative splicing contributes to protein diversity.

📌Definition Table

Term	Definition
Proofreading	Activity of DNA polymerases that detects and corrects mismatched bases during replication.
Mutation	Permanent change in DNA sequence due to replication error or DNA damage.
Mismatch repair	Post-replication correction system that identifies and fixes base mispairings missed by proofreading.
Excision repair	Mechanism that removes damaged bases or nucleotides and replaces them with correct ones.
Mutagen	Agent (chemical, radiation, virus) that increases mutation rate.
Genome stability	Maintenance of DNA sequence integrity across generations.

📌Introduction

DNA replication must be highly accurate to preserve genetic information. Despite the enormous number of nucleotides copied in every cell division, the error rate is remarkably low (about 1 mistake per 10⁹–10¹⁰ nucleotides). This fidelity results from multiple error-prevention mechanisms, including polymerase proofreading and specialized DNA repair systems. When these systems fail, mutations accumulate, contributing to cancer, aging, and genetic diseases.

📌 Accuracy of DNA Replication

• DNA polymerase has intrinsic proofreading activity (3′→5′ exonuclease function) that removes incorrectly paired nucleotides.
• Complementary base-pairing ensures most nucleotides are added correctly in the first place.
• Error rate before proofreading = ~1 in 10⁵ nucleotides; after proofreading, reduced to ~1 in 10⁷.
• Post-replication repair mechanisms reduce the overall error rate further to ~1 in 10⁹–10¹⁰.
• High fidelity is essential for genetic stability and faithful inheritance.

🧠 Examiner Tip: Always mention proofreading by DNA polymerase and mismatch repair together for maximum marks.

📌 Sources of Errors and DNA Damage

• Replication errors: mismatched bases, insertions, or deletions.
• Chemical damage: oxidation, alkylation, cross-linking of bases.
• Radiation: UV light causes thymine dimers; ionizing radiation creates strand breaks.
• Mutagens and carcinogens: increase likelihood of errors (e.g., tobacco smoke, asbestos).
• Endogenous factors: reactive oxygen species (ROS) from metabolism damage DNA.

🧬 IA Tips & Guidance: A model IA could explore how environmental conditions (UV exposure, chemical treatments) affect DNA integrity in bacterial cultures, linking experimental outcomes to repair mechanisms.

📌 DNA Repair Mechanisms

• Proofreading (DNA polymerase): immediate correction during synthesis.
• Mismatch repair: detects distortions in helix due to base-pair mismatches; excises error and resynthesizes correct DNA.
• Base excision repair (BER): removes damaged bases (e.g., uracil misincorporation) and replaces them with correct bases.
• Nucleotide excision repair (NER): removes bulky lesions like thymine dimers caused by UV light.
• Double-strand break repair: uses homologous recombination or non-homologous end joining (NHEJ) to repair severe breaks.
• Telomere maintenance: telomerase prevents loss of important sequences at chromosome ends.

🌐 EE Focus: An EE could investigate links between defective repair systems (e.g., xeroderma pigmentosum from NER failure) and disease, or analyze mutation rates under different environmental conditions.

📌 Consequences of Replication Errors

• Silent mutations: do not change amino acid sequence, little to no effect.
• Missense mutations: change one amino acid, potentially altering protein function.
• Nonsense mutations: create premature stop codons, truncating proteins.
• Frameshift mutations: insertions or deletions shift reading frame, usually highly damaging.
• Large-scale errors: chromosomal rearrangements, duplications, or deletions.
• Accumulation of mutations contributes to cancer, aging, and heritable diseases.

❤️ CAS Link: Students could organize awareness activities on how lifestyle factors (smoking, UV exposure, diet) increase DNA mutation rates and cancer risk, linking biology to community health education.

📌 Integration with Genome Stability and Evolution

• Repair systems ensure continuity of genetic information across generations.
• Controlled mutation provides raw material for evolution and adaptation.
• Balance between fidelity and flexibility is key: too many errors cause disease; too few limit evolution.
• Epigenetic modifications and chromatin remodeling also influence repair efficiency.
• Genome stability is a central theme in cancer biology and developmental genetics.

🔍 TOK Perspective: DNA repair mechanisms are largely inferred from indirect evidence (gel assays, radioactive labeling, sequencing). TOK reflection: To what extent can unseen molecular processes be considered “certain knowledge,” and how does reliance on indirect evidence shape scientific confidence?

📝 Paper 2: Be prepared to explain proofreading, mismatch repair, and types of mutations. Expect data questions involving mutation frequency under mutagens, or diagrams showing repair pathways (e.g., thymine dimer excision).

📌Definition Table

Term	Definition
Semi-conservative replication	DNA replication mechanism where each new double helix has one parental strand and one newly synthesized strand.
Replication fork	Y-shaped structure formed during unwinding of DNA where new strands are synthesized.
Leading strand	DNA strand synthesized continuously in the 5′→3′ direction toward the replication fork.
Lagging strand	DNA strand synthesized discontinuously in short Okazaki fragments away from the replication fork.
Okazaki fragments	Short DNA fragments synthesized on the lagging strand that are later joined by ligase.
Origin of replication	Specific sequence where replication begins.

📌Introduction

The semi-conservative mechanism of DNA replication ensures that each daughter cell receives one original (template) strand and one newly synthesized strand. This method preserves genetic continuity across generations while allowing occasional mutations that fuel evolution.

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📌 Evidence for Semi-Conservative Replication

• Proposed by Watson and Crick based on complementary base-pairing.
• Confirmed by Meselson–Stahl experiment (1958):
  • Used E. coli grown in heavy nitrogen (¹⁵N) then transferred to light nitrogen (¹⁴N).
  • DNA after one generation showed hybrid density (¹⁵N/¹⁴N), ruling out conservative replication.
  • After two generations, both hybrid and light bands appeared, proving semi-conservative replication.
• Widely regarded as one of the most elegant experiments in biology.

🧠 Examiner Tip: Always state that Meselson–Stahl proved semi-conservative replication by density-gradient centrifugation using ¹⁵N/¹⁴N. This detail often earns marks.

📌 Steps in Semi-Conservative Replication

• Initiation
  • Replication begins at origins of replication, often AT-rich regions (easier to unwind).
  • Helicase unwinds DNA and forms replication forks.
  • Single-stranded binding proteins (SSBs) stabilize open strands.
• Elongation – Leading strand
  • DNA polymerase III adds nucleotides continuously in the 5′→3′ direction.
  • Requires only one primer.
  • Synthesis proceeds smoothly toward the replication fork.
• Elongation – Lagging strand
  • DNA polymerase III synthesizes discontinuously away from the fork.
  • Multiple primers are laid down by primase.
  • Okazaki fragments form, later joined by DNA ligase.
• Termination
  • DNA polymerase I removes RNA primers and replaces them with DNA.
  • Ligase seals nicks in the sugar–phosphate backbone.
  • Two identical DNA molecules are formed, each with one old and one new strand.

🧬 IA Tips & Guidance: A model-building IA could recreate replication forks with paper/DNA kits to demonstrate leading vs lagging strand synthesis, reinforcing understanding of semi-discontinuous replication.

📌 Directionality and Strand Differences

• DNA polymerases can only extend in the 5′→3′ direction.
• This creates asymmetry: one strand continuous (leading) and one discontinuous (lagging).
• The antiparallel nature of DNA explains why replication is semi-discontinuous.
• Okazaki fragments ensure the lagging strand is eventually completed.
• Proofreading by polymerases minimizes errors during elongation.

🌐 EE Focus: An EE could analyze how different organisms initiate replication at multiple vs single origins, or compare replication rates in prokaryotes vs eukaryotes.

📌 Key Features of Semi-Conservative Replication

• Each new molecule retains one parental strand (template).
• Ensures genetic stability and faithful transmission of information.
• Allows mutations at low frequency, driving evolution.
• Involves coordinated enzyme action at replication forks.
• Is universal across all domains of life, highlighting its evolutionary importance.

❤️ CAS Link: Students could create an educational workshop or visual models demonstrating Meselson–Stahl’s experiment, linking scientific discovery to how evidence builds biological knowledge.

📌 Integration with Cell Cycle

• Replication occurs during the S-phase of interphase.
• Accurate replication ensures proper chromosome segregation during mitosis.
• Errors in replication can cause mutations, cancer, or genetic disorders.

🔍 TOK Perspective: Meselson–Stahl’s experiment is a case study in scientific proof. TOK reflection: How do simple, elegant experiments strengthen scientific knowledge, and what makes them more convincing than complex theoretical models?

📝 Paper 2: Be ready to describe Meselson–Stahl’s experiment, outline leading vs lagging strand synthesis, and explain the semi-conservative nature of replication. Diagram-based questions on replication forks are common.

📌Definition Table

Term	Definition
DNA (Deoxyribonucleic acid)	Double-helical molecule carrying genetic information in base sequences.
Nucleotide	Basic unit of DNA, consisting of a phosphate, deoxyribose sugar, and nitrogenous base.
Complementary base pairing	Specific hydrogen bonding between bases: A–T (2 bonds), C–G (3 bonds).
Helicase	Enzyme that unwinds DNA helix and breaks hydrogen bonds between strands.
DNA polymerase III	Main enzyme that synthesizes new DNA strand in 5′→3′ direction.
DNA polymerase I	Enzyme that removes RNA primers and replaces them with DNA.
Primase	Enzyme that synthesizes short RNA primers to initiate replication.
DNA ligase	Enzyme that joins Okazaki fragments by forming sugar–phosphate bonds.
Single-stranded binding proteins (SSBs)	Proteins that stabilize unwound DNA strands during replication.

📌Introduction

DNA replication is essential for genetic continuity in cell division. The double-helical structure, proposed by Watson and Crick, allows complementary base pairing to act as a template for accurate copying. Specialized enzymes coordinate the process, ensuring rapid and precise duplication of billions of nucleotides.

📌 Structure of DNA

• DNA consists of two antiparallel strands (5′→3′ and 3′→5′) forming a double helix.
• Nucleotides are linked via phosphodiester bonds between sugar and phosphate.
• Hydrogen bonds between complementary bases stabilize the helix: A–T (2 bonds), C–G (3 bonds).
• The antiparallel arrangement means replication requires different strategies for each strand.

🧠 Examiner Tip: In diagrams, always label 5′ and 3′ ends, and show hydrogen bonds as dotted lines between bases.

📌 Enzymes in DNA Replication

• Helicase unwinds DNA and breaks hydrogen bonds, creating the replication fork.
• SSBs prevent re-annealing of strands.
• Primase lays down short RNA primers as initiation points.
• DNA polymerase III elongates the new strand by adding nucleotides in the 5′→3′ direction.
• DNA polymerase I removes primers and replaces them with DNA nucleotides.
• DNA ligase joins Okazaki fragments on the lagging strand.

🧬 IA Tips & Guidance: A possible IA could involve modelling DNA replication with molecular kits or computer simulations, emphasizing enzyme roles and directionality.

📌 Importance of Enzymatic Coordination

• Helicase and polymerases must act simultaneously to replicate both strands.
• The coordination of primase, ligase, and proofreading enzymes ensures accuracy.
• Without these enzymes, replication would be error-prone and slow.

🌐 EE Focus: An EE might investigate how inhibitors of DNA replication enzymes (e.g., antibiotics like ciprofloxacin targeting bacterial DNA gyrase) affect cell survival, linking molecular biology to medicine.

📌 Enzymes and Disease Connection

• Malfunction in DNA polymerase proofreading can increase mutation rates.
• Cancer can result from uncontrolled mutations in cell cycle genes.
• Many chemotherapies target enzymes involved in DNA replication.

❤️ CAS Link: Students could design interactive workshops with DNA models, showing how enzymes function in replication, to educate younger students or communities about genetics.

📌 Integration with Genome Stability

• Precise DNA replication preserves genetic identity across cell generations.
• Errors in replication lead to mutations, some of which may drive evolution or disease.

🔍 TOK Perspective: Our knowledge of replication enzymes largely comes from indirect biochemical assays and models. TOK reflection: How do models and analogies (e.g., “unzipping a zipper” for helicase) influence our understanding of complex molecular processes?

📝 Paper 2: Expect questions requiring enzyme identification, explaining directionality (5′→3′), or describing base-pairing. Diagrams of replication forks are common, and markschemes emphasize enzyme roles.dn