Molecular Basis of Inheritance — NEET notes

DNA Structure

James Watson and Francis Crick (1953) proposed the double helix model of DNA based on X-ray crystallography data from Rosalind Franklin and Maurice Wilkins. DNA is a polymer of deoxyribonucleotides with two antiparallel strands held together by hydrogen bonds between complementary bases (A-T, G-C), following Chargaff's rules.

A = T, G = C A+G T+C = 1 (Chargaff's Rule)

Nucleotide

Each nucleotide has three components: a nitrogenous base, a pentose sugar (deoxyribose), and a phosphate group. Nucleotides are linked by 3'-5' phosphodiester bonds.

A nucleotide is the basic building block of DNA. It has three parts: (1) a nitrogenous base (purine or pyrimidine), (2) a pentose sugar (2'-deoxyribose in DNA, ribose in RNA), and (3) a phosphate group. A base + sugar alone (without phosphate) is called a nucleoside.

• Purines (double ring): Adenine (A), Guanine (G) — remember 'puRe As Gold' (R has 2 rings)
• Pyrimidines (single ring): Cytosine (C), Thymine (T) in DNA; Uracil (U) replaces T in RNA
• Nucleoside = base + sugar (e.g., adenosine, deoxyadenosine)
• Nucleotide = base + sugar + phosphate (e.g., deoxyadenosine 5'-monophosphate / dAMP)
• Nucleotides are joined by 3'→5' phosphodiester bonds — the phosphate connects the 3' carbon of one sugar to the 5' carbon of the next

Watson-Crick Double Helix

DNA is a right-handed double helix with two antiparallel polynucleotide strands. The sugar-phosphate backbone is on the outside; bases are on the inside, paired by hydrogen bonds.

Watson and Crick (1953) proposed the double helix model using Rosalind Franklin's X-ray diffraction data and Erwin Chargaff's base composition rules. Key features: two polynucleotide strands coil around a common axis in a right-handed helix, running antiparallel (one 5'→3', the other 3'→5').

• The two strands are antiparallel — one runs 5'→3', the other 3'→5'
• The sugar-phosphate backbone is on the outside (hydrophilic), bases are stacked on the inside (hydrophobic)
• Bases pair by hydrogen bonds: A=T (2 H-bonds), G≡C (3 H-bonds)
• One complete turn of the helix = 3.4 nm (34 Å), with 10 base pairs per turn
• Distance between adjacent base pairs = 0.34 nm (3.4 Å)
• The helix has a major groove and a minor groove — proteins bind here to read the genetic code
• The helix diameter is approximately 2 nm (20 Å)

Total base pairs = Total length of DNA 0.34 nm No. of turns = Total bp 10

Chargaff's Rules

Erwin Chargaff (1950) discovered that in any DNA molecule, the amount of adenine equals thymine (A=T) and guanine equals cytosine (G=C). This was crucial evidence for the Watson-Crick model.

Before Watson and Crick built their model, Erwin Chargaff (1950) analyzed DNA from multiple species and found a consistent pattern: the molar ratio of A to T is always 1:1, and G to C is always 1:1. This means A+G = T+C (total purines = total pyrimidines).

A T = 1, G C = 1, A+G T+C = 1 (Chargaff's Rule)

• Rule 1: A = T and G = C (complementary base pairing)
• Rule 2: A + G = T + C (total purines = total pyrimidines)
• The ratio (A+T)/(G+C) varies between species — this is the Chargaff's ratio and is species-specific
• Chargaff's rules apply to double-stranded DNA only — NOT to single-stranded DNA or RNA
• If one strand has 30% A, the complementary strand has 30% T — but the SAME strand need not have A = T

Quick recall

A DNA molecule has 20% adenine. What are the percentages of T, G, and C?

A = T = 20%. So A + T = 40%. Remaining 60% = G + C. Since G = C, each is 30%. Final: A = 20%, T = 20%, G = 30%, C = 30%.

Forms of DNA

DNA can adopt different structural forms. B-DNA (Watson-Crick) is the most common in living cells. A-DNA is a dehydrated form, and Z-DNA is a left-handed helix.

The Watson-Crick model describes B-DNA, the most common form under physiological conditions. But DNA can also exist as A-DNA (in dehydrated conditions) and Z-DNA (left-handed helix, found in regions rich in alternating G-C sequences).

• B-DNA is the standard Watson-Crick form — right-handed, 10 bp/turn, 3.4 nm pitch
• A-DNA is wider and shorter — found when DNA is dehydrated; RNA-DNA hybrids adopt A-form
• Z-DNA is the only left-handed form — zigzag backbone, 12 bp/turn, found in alternating purine-pyrimidine stretches
• NCERT primarily discusses B-DNA — but NEET can ask about Z-DNA being left-handed

DNA Packaging

The 2-metre-long DNA of a human cell must be packed into a 6 μm nucleus. This is achieved through multiple levels of compaction: DNA wraps around histone octamers to form nucleosomes, which coil into solenoids, then loop into chromatin fibres, and finally condense into chromosomes during cell division.

DNA (2 nm) nucleosome 10 nm solenoid 30 nm loops 300 nm chromosome 700 nm

Histones & Nucleosomes

DNA wraps around histone protein octamers (2 copies each of H2A, H2B, H3, H4) to form nucleosomes — the 'beads on a string' structure visible under electron microscope.

In eukaryotes, DNA is packaged with the help of positively charged histone proteins (rich in lysine and arginine). The basic unit of packaging is the nucleosome: ~147 bp of DNA wraps 1.65 turns around a histone octamer (8 histone molecules). Adjacent nucleosomes are connected by linker DNA (~50-70 bp), giving the classic 'beads on a string' appearance.

• Histone octamer = 2 copies each of H2A, H2B, H3, and H4 (total 8 molecules)
• H1 (linker histone) sits OUTSIDE the nucleosome, sealing the DNA entry/exit points
• Histones are positively charged (rich in lysine and arginine) — they attract negatively charged DNA (phosphate backbone)
• ~147 bp of DNA wraps around each histone octamer in 1.65 turns
• Nucleosomes reduce DNA length by about 7-fold (first level of compaction)
• The 'beads on a string' structure = 10 nm chromatin fibre

Chromatin to Chromosome

Nucleosomes coil further into 30 nm solenoid fibres, then form looped domains (300 nm), and finally condense into the maximally compacted metaphase chromosome (700 nm).

The 10 nm 'beads on a string' fibre coils into a 30 nm solenoid (or chromatin fibre), with about 6 nucleosomes per turn. This further forms looped domains (~300 nm) attached to a non-histone protein scaffold. During cell division, maximum condensation produces the metaphase chromosome visible under a light microscope.

• 10 nm fibre → 'beads on a string' (nucleosomes + linker DNA)
• 30 nm fibre → solenoid (6 nucleosomes per turn, stabilized by H1)
• 300 nm fibre → looped domains attached to a protein scaffold
• 700 nm → metaphase chromosome (maximum compaction, ~10,000-fold total)
• Total packaging ratio: DNA is compacted approximately 10,000-fold to fit into the nucleus

Euchromatin vs Heterochromatin

Chromatin exists in two forms: loosely packed euchromatin (transcriptionally active) and densely packed heterochromatin (transcriptionally inactive). The balance between them controls gene expression.

Not all chromatin is packaged equally. Euchromatin is loosely packed, lightly stained, and transcriptionally active — genes here are accessible to RNA polymerase. Heterochromatin is densely packed, darkly stained, and mostly transcriptionally inactive — the DNA is so tightly wound that transcription machinery cannot access it.

• Euchromatin = gene-rich, loosely packed, actively transcribed
• Heterochromatin = gene-poor, tightly packed, transcriptionally silent
• The Barr body (inactive X chromosome in females) is an example of facultative heterochromatin
• Constitutive heterochromatin remains condensed in all cells (e.g., centromeric regions)
• Facultative heterochromatin can switch between active and inactive states depending on cell type

DNA Replication

DNA replication is semiconservative — each new double helix has one old strand and one new strand. Meselson and Stahl (1958) proved this using heavy nitrogen (¹⁵N) and density gradient centrifugation. Replication involves multiple enzymes including DNA polymerase, helicase, primase, and ligase.

Semiconservative: each daughter DNA = 1 2 old strand + 1 2 new strand

Semiconservative Replication

Each daughter DNA molecule has one parental (old) strand and one newly synthesized strand. Meselson and Stahl (1958) used ¹⁵N/¹⁴N labelling in E. coli to prove this elegantly.

Three models were proposed for DNA replication: conservative (old DNA stays intact, new DNA is entirely new), semiconservative (each daughter has one old + one new strand), and dispersive (old and new segments scattered in both strands). Meselson and Stahl (1958) proved replication is semiconservative.

• Organism used: *E. coli* grown in medium with heavy nitrogen ¹⁵N (¹⁵NH₄Cl)
• After DNA was fully labelled with ¹⁵N (heavy), bacteria were transferred to ¹⁴N (light) medium
• DNA was extracted after each generation and separated by CsCl density gradient centrifugation
• Generation 0: one heavy band (¹⁵N-¹⁵N)
• Generation 1: one intermediate band (¹⁵N-¹⁴N) — rules out conservative model
• Generation 2: one intermediate + one light band — confirms semiconservative model
• Taylor et al. later confirmed semiconservative replication in eukaryotes (*Vicia faba*) using radioactive thymidine

Quick recall

After 3 generations in ¹⁴N medium, what fraction of DNA molecules will be intermediate (hybrid)?

After n generations, there are 2ⁿ DNA molecules total, but only 2 have a ¹⁵N strand. So after 3 generations: 2/2³ = 2/8 = 1/4 are hybrid, 3/4 are light.

Replication Machinery

DNA replication requires a coordinated set of enzymes: helicase (unwinds), topoisomerase (relieves tension), primase (makes RNA primer), DNA polymerase III (synthesizes new strand), and ligase (joins Okazaki fragments).

DNA replication is not just 'unzip and copy'. It requires a team of enzymes working at the replication fork — the Y-shaped region where the two parental strands are being separated. The process begins at specific sites called origins of replication (ori).

• Helicase — unwinds the double helix by breaking hydrogen bonds between base pairs
• Topoisomerase (DNA gyrase in prokaryotes) — relieves the supercoiling tension ahead of the replication fork
• Single-strand binding proteins (SSBs) — prevent the separated strands from re-annealing
• Primase — synthesizes a short RNA primer (needed because DNA polymerase cannot start from scratch)
• DNA polymerase III — the main enzyme; adds nucleotides in the 5'→3' direction only
• DNA polymerase I — removes RNA primers and replaces them with DNA (nick translation)
• DNA ligase — joins the gaps (nicks) between Okazaki fragments on the lagging strand

Leading & Lagging Strand

Since DNA polymerase works only 5'→3', one strand (leading) is synthesized continuously while the other (lagging) is made in short Okazaki fragments that are later joined by ligase.

DNA polymerase can ONLY synthesize in the 5'→3' direction. But the two template strands run antiparallel. So one new strand (the leading strand) is synthesized continuously toward the replication fork, while the other (the lagging strand) is synthesized discontinuously as short fragments called Okazaki fragments, moving AWAY from the fork.

• Okazaki fragments: ~1000–2000 nucleotides in prokaryotes, ~100–200 in eukaryotes
• Each Okazaki fragment starts with an RNA primer laid by primase
• DNA Pol I removes the RNA primers and fills in with DNA
• DNA ligase seals the nicks between Okazaki fragments to create a continuous strand
• The replication fork is asymmetric — leading and lagging strand synthesis occur simultaneously but by different mechanisms

Quick recall

If a DNA molecule has 10 Okazaki fragments on its lagging strand, how many RNA primers were needed in total for replication?

10 primers for 10 Okazaki fragments + 1 primer for the leading strand = 11 primers total. Each Okazaki fragment needs its own primer, and the leading strand needs one primer at the origin.

Transcription

Transcription is the process of copying genetic information from one strand of DNA (template strand) into mRNA by RNA polymerase. In prokaryotes, a single RNA polymerase handles all RNA synthesis. In eukaryotes, three RNA polymerases exist (I, II, III), and the primary transcript (hnRNA) undergoes processing — 5' capping, 3' polyadenylation, and splicing.

DNA (template strand) RNA polymerase mRNA (3' 5' template read, 5' 3' mRNA made)

Transcription Unit

A transcription unit consists of a promoter (binding site for RNA polymerase), the structural gene (template for RNA), and a terminator (signal to stop transcription). The template strand is read 3'→5'.

A transcription unit in DNA has three components: (1) Promoter — located upstream (towards 5' end of coding strand), where RNA polymerase binds and transcription starts; (2) Structural gene — the DNA sequence that is actually transcribed; (3) Terminator — located downstream, signals the end of transcription.

• The strand that serves as template is read 3'→5' and is called the template strand (antisense strand)
• The other strand (5'→3') is called the coding strand (sense strand) — it has the same sequence as mRNA (except T instead of U)
• mRNA is synthesized in the 5'→3' direction (same polarity as the coding strand)
• The promoter is at the 5' end of the coding strand (upstream of the structural gene)
• The terminator is at the 3' end of the coding strand (downstream of the structural gene)
• RNA polymerase binds to the promoter and moves along the template strand 3'→5'

RNA Polymerase

Prokaryotes have a single RNA polymerase (with sigma factor for initiation and rho factor for termination). Eukaryotes have three: RNA Pol I (rRNA), RNA Pol II (mRNA), and RNA Pol III (tRNA, 5S rRNA, snRNA).

In E. coli (prokaryote), a single RNA polymerase performs all transcription. The core enzyme (α₂ββ'ω) needs the sigma factor (σ) to recognize the promoter and initiate transcription. Rho factor (ρ) helps terminate transcription at specific sites. In eukaryotes, three different RNA polymerases exist, each transcribing different RNA types.

• Prokaryotic RNA polymerase: single enzyme; holoenzyme = core enzyme (α₂ββ'ω) + sigma factor (σ)
• Sigma factor (σ) — required ONLY for initiation; recognizes the promoter; dissociates after ~10 nucleotides
• Rho factor (ρ) — involved in termination of transcription at rho-dependent terminators
• Eukaryotic RNA Pol I → transcribes rRNA (28S, 18S, 5.8S) in the nucleolus
• Eukaryotic RNA Pol II → transcribes mRNA (and some snRNAs) — sensitive to α-amanitin (mushroom toxin)
• Eukaryotic RNA Pol III → transcribes tRNA, 5S rRNA, and snRNA

Steps of Transcription

Transcription proceeds in three stages: initiation (RNA polymerase binds to promoter), elongation (RNA chain grows 5'→3'), and termination (RNA polymerase reaches terminator and releases the transcript).

Transcription involves three stages, analogous to DNA replication but with key differences. RNA polymerase does NOT need a primer, uses ribonucleotides (NTPs), and incorporates uracil (U) instead of thymine (T). Only a short stretch of DNA is unwound at any time — forming the transcription bubble.

• Initiation: RNA polymerase (with sigma factor in prokaryotes) binds to promoter → DNA unwinds locally → first nucleotide is laid down → sigma factor released after ~10 nt
• Elongation: RNA polymerase moves along template strand (3'→5'), adding ribonucleotides in 5'→3' direction → transcription bubble travels along DNA
• Termination: RNA polymerase reaches the terminator → RNA transcript is released → DNA re-winds
• Prokaryotes: termination is either rho-dependent (rho factor chases polymerase) or rho-independent (palindromic sequence forms hairpin loop)
• Unlike DNA replication, transcription copies only ONE strand of a gene, and only a SMALL segment of the total DNA

Quick recall

Given a DNA template strand: 3'-ATGCCG-5'. What is the mRNA sequence?

RNA polymerase reads template 3'→5' and synthesizes mRNA 5'→3'. So: template 3'-ATGCCG-5' gives mRNA 5'-UACGGC-3'. (A→U, T→A, G→C, C→G, but using ribonucleotides with U instead of T.)

Post-Transcriptional Processing

In eukaryotes, the primary transcript (hnRNA/pre-mRNA) undergoes three modifications before becoming functional mRNA: 5' capping, 3' polyadenylation, and splicing to remove introns.

In eukaryotes, the primary RNA transcript is called hnRNA (heterogeneous nuclear RNA) or pre-mRNA. It contains both exons (expressed sequences) and introns (intervening sequences that do NOT code for protein). Three processing steps convert it into mature mRNA.

• 5' Capping: a methylated guanine cap (7-methylguanosine / m⁷G) is added to the 5' end — protects mRNA from degradation and aids ribosome binding
• 3' Polyadenylation: a poly-A tail (100–200 adenine nucleotides) is added to the 3' end — stabilizes mRNA and aids export from nucleus
• Splicing: introns are removed and exons are joined together by spliceosomes (made of snRNPs)
• Exons = expressed sequences (code for protein); Introns = intervening sequences (removed during splicing)
• In prokaryotes, there is NO post-transcriptional processing — mRNA is used directly (no introns!)
• Prokaryotic mRNA is polycistronic (codes for multiple proteins); eukaryotic mRNA is mostly monocistronic (one protein)

Genetic Code

The genetic code is a triplet code — three consecutive nucleotides (a codon) on mRNA specify one amino acid. There are 64 codons: 61 code for amino acids and 3 are stop codons. The code is degenerate, non-overlapping, universal, comma-less, and unambiguous. George Gamow proposed the triplet nature; Marshall Nirenberg and Har Gobind Khorana deciphered the code.

4^3 = 64 codons (61 sense + 3 stop: UAA, UAG, UGA)

Triplet Code

Since there are 20 amino acids and only 4 bases, a doublet code (4² = 16) is insufficient. A triplet code (4³ = 64) provides more than enough codons. Gamow proposed this, and Nirenberg/Khorana cracked it experimentally.

The genetic code must specify 20 amino acids using only 4 bases (A, U, G, C in mRNA). A singlet code (4¹ = 4) can code for only 4 amino acids. A doublet code (4² = 16) can code for 16 — still not enough. A triplet code (4³ = 64) gives 64 combinations — more than enough for 20 amino acids. George Gamow proposed the triplet nature.

• George Gamow (physicist) proposed that the genetic code must be a triplet code (3 bases per amino acid)
• Marshall Nirenberg and Heinrich Matthaei (1961) — used cell-free translation system; poly-U mRNA → polyphenylalanine → proved UUU = Phenylalanine (first codon deciphered)
• Har Gobind Khorana — synthesized artificial mRNAs with known sequences to decipher remaining codons
• Severo Ochoa's enzyme (polynucleotide phosphorylase) was used to synthesize artificial RNA polymers
• Nirenberg and Khorana shared the 1968 Nobel Prize for deciphering the genetic code

The Codon Table

Of 64 codons, 61 code for amino acids (sense codons) and 3 are stop/termination codons (UAA, UAG, UGA). AUG is the start codon and also codes for methionine.

The codon table maps all 64 triplet codons to their corresponding amino acids. AUG serves a dual role — it is the universal start codon AND codes for methionine (Met). Three codons — UAA (ochre), UAG (amber), and UGA (opal) — do NOT code for any amino acid; they signal termination of translation.

• Start codon: AUG — codes for methionine; also called the initiator codon
• Stop codons: UAA (ochre), UAG (amber), UGA (opal) — also called nonsense codons or termination codons
• Stop codons do NOT code for any amino acid — no tRNA recognizes them
• Instead, release factors (proteins) bind to stop codons and trigger release of the polypeptide
• 61 sense codons code for 20 amino acids → most amino acids have more than one codon (degeneracy)
• Tryptophan (UGG) and Methionine (AUG) — the only amino acids with a SINGLE codon each

Quick recall

How many codons code for leucine?

6 codons — Leucine is the most degenerate amino acid with 6 codons (UUA, UUG, CUU, CUC, CUA, CUG). Serine also has 6 codons. Arginine also has 6. Tryptophan and methionine have only 1 each.

Properties of the Genetic Code

The genetic code is: (1) triplet, (2) degenerate, (3) non-overlapping, (4) comma-less/non-ambiguous, (5) universal, and (6) has polarity (read 5'→3'). Each property has been experimentally verified.

The genetic code has several remarkable properties that NEET tests frequently. Understanding each property is critical — questions often present statements and ask you to identify which property is being described.

• Triplet — 3 nucleotides code for 1 amino acid
• Degenerate (redundant) — most amino acids are coded by more than one codon (e.g., leucine has 6 codons). BUT each codon specifies only ONE amino acid (unambiguous)
• Non-overlapping — each nucleotide belongs to only ONE codon; codons are read sequentially without sharing bases
• Comma-less (no punctuation) — there are no gaps or spacers between codons; reading is continuous from start to stop
• Universal — the same codon specifies the same amino acid in almost ALL organisms (bacteria, plants, animals). Exceptions: mitochondria, some protozoans
• Polarity — the code is read in the 5'→3' direction on mRNA

Translation

Translation is the process of synthesizing a polypeptide chain from an mRNA template on ribosomes. tRNA acts as the adaptor molecule, carrying amino acids to the ribosome and matching codons via its anticodon. The process occurs in three stages: initiation, elongation, and termination. Polysomes (polyribosomes) allow multiple copies of a protein to be made from a single mRNA simultaneously.

mRNA codon + tRNA anticodon ribosome polypeptide chain

tRNA

Francis Crick proposed the adaptor hypothesis. tRNA has a cloverleaf structure with an anticodon loop (reads mRNA) and a 3' CCA acceptor end (carries amino acid). Aminoacyl-tRNA synthetase charges the tRNA.

Francis Crick proposed the adaptor hypothesis — there must be a molecule that reads the mRNA codon on one end and carries the correct amino acid on the other. This adaptor molecule is tRNA (transfer RNA). Each tRNA has a specific anticodon (complementary to mRNA codon) and carries a specific amino acid.

• tRNA has a cloverleaf secondary structure with 4 major arms/loops
• Anticodon loop — contains the 3-base anticodon that base-pairs with the mRNA codon
• Acceptor arm (3' end) — ends in CCA sequence; the amino acid attaches here (to the 3'-OH of terminal adenine)
• DHU arm (dihydrouridine loop) — helps in binding to aminoacyl-tRNA synthetase
• TψC arm — helps in binding to the ribosome
• Aminoacyl-tRNA synthetase — the enzyme that 'charges' tRNA by attaching the correct amino acid (uses 1 ATP → AMP + PPi)
• There are at least 61 types of tRNA (one for each sense codon, though wobble base pairing reduces the actual number needed)

Ribosome Structure

Ribosomes have two subunits: a large and a small subunit. In prokaryotes: 70S (50S + 30S). In eukaryotes: 80S (60S + 40S). The ribosome has three tRNA binding sites: A (aminoacyl), P (peptidyl), and E (exit).

Ribosomes are the molecular machines where translation occurs. Each ribosome has two subunits that come together during translation and dissociate afterward. The ribosome provides three binding sites for tRNA, facilitating the transfer of amino acids to the growing polypeptide chain.

• A site (aminoacyl) — where the incoming charged tRNA binds
• P site (peptidyl) — where the tRNA holding the growing polypeptide chain sits
• E site (exit) — where the uncharged tRNA exits after donating its amino acid
• The small subunit binds mRNA and helps match codons with anticodons
• The large subunit catalyzes peptide bond formation (the rRNA acts as a ribozyme)
• Svedberg coefficient (S) is NOT additive — 50S + 30S = 70S, not 80S (it depends on shape and mass)

Steps of Translation

Translation begins when the small ribosomal subunit binds mRNA at AUG. The initiator tRNA (carrying Met/fMet) occupies the P site. During elongation, peptide bonds form as tRNAs cycle through A→P→E sites. Termination occurs when a stop codon enters the A site.

Translation converts the nucleotide language of mRNA into the amino acid language of proteins. It occurs on ribosomes in three phases: initiation (ribosome assembles on mRNA at AUG), elongation (amino acids added one by one), and termination (release at stop codon).

• Initiation: small subunit binds mRNA → identifies AUG (start codon) → initiator tRNA (carrying fMet in prokaryotes / Met in eukaryotes) binds to P site → large subunit joins
• Elongation: charged tRNA enters A site → peptide bond forms (catalyzed by peptidyl transferase / ribozyme) → ribosome translocates one codon → tRNA moves from A→P→E → process repeats
• Termination: when a stop codon (UAA/UAG/UGA) enters the A site → no tRNA recognizes it → release factors bind → polypeptide is released → ribosome subunits dissociate
• Energy cost per amino acid added: 2 GTP for elongation (1 for tRNA binding, 1 for translocation) + 1 ATP equivalent for tRNA charging = roughly 4 high-energy phosphate bonds per amino acid
• Direction of translation along mRNA: 5'→3' (same as transcription direction)

Polysome (Polyribosome)

Multiple ribosomes can translate a single mRNA simultaneously, forming a polysome. This increases the rate of protein production. The ribosome closest to the 5' end has the shortest polypeptide; the one near the 3' end has the longest.

Once the first ribosome has moved along an mRNA far enough, a second ribosome can attach to the start codon and begin translation. Many ribosomes translating the same mRNA simultaneously form a polysome (polyribosome). This massively increases protein output from a single mRNA molecule.

• A polysome = multiple ribosomes on a single mRNA, each at a different stage of translation
• The ribosome nearest the 5' end of mRNA has the shortest polypeptide (just started)
• The ribosome nearest the 3' end has the longest (nearly complete) polypeptide
• Polysomes can contain 5–40+ ribosomes on a single mRNA
• Polysomes allow rapid, efficient protein production — many copies of the same protein made simultaneously
• Polysomes are found both free in cytoplasm (making soluble proteins) and bound to rough ER (making membrane/secretory proteins)

Gene Regulation: Lac Operon

The lac operon in E. coli is a model for gene regulation in prokaryotes, proposed by François Jacob and Jacques Monod (Nobel Prize 1965). It consists of structural genes (lacZ, lacY, lacA), a promoter, an operator, and a regulator gene (lacI). The operon is under both negative regulation (repressor protein) and positive regulation (CAP). Lactose (converted to allolactose) acts as the inducer.

Lactose (inducer) + Repressor arrow Inactive repressor Operon ON

The Operon Concept

An operon is a cluster of functionally related genes under the control of a single promoter and operator. Jacob and Monod proposed this model to explain how E. coli regulates lactose metabolism.

François Jacob and Jacques Monod (1961) proposed the operon model to explain gene regulation in *E. coli*. An operon is a unit of gene expression that includes structural genes (coding for enzymes), a promoter (RNA polymerase binding site), an operator (regulatory switch), and is controlled by a regulator gene that makes a repressor protein.

• The lac operon controls enzymes needed for lactose metabolism in *E. coli*
• Structural genes: lacZ (β-galactosidase), lacY (permease), lacA (transacetylase)
• Promoter — site where RNA polymerase binds to begin transcription
• Operator — short DNA sequence between promoter and structural genes; acts as the ON/OFF switch
• Regulator gene (lacI) — located upstream; constitutively produces the repressor protein
• The structural genes are transcribed as a single polycistronic mRNA (one mRNA, multiple proteins)

Negative Regulation

In the absence of lactose, the repressor protein (product of lacI gene) binds to the operator and BLOCKS RNA polymerase from transcribing the structural genes. The operon is switched OFF.

In the absence of lactose (the default state), the lacI gene continuously produces a repressor protein. This protein binds to the operator sequence and physically blocks RNA polymerase from moving past the promoter to transcribe the structural genes. Result: operon is OFF, no enzymes for lactose metabolism are made.

• The lacI gene is expressed constitutively — it's always ON, always making repressor
• The repressor protein is an allosteric protein — it can exist in active or inactive forms
• In its active form, the repressor binds tightly to the operator
• When repressor occupies the operator, RNA polymerase cannot transcribe the structural genes
• This is called negative regulation because the regulatory molecule (repressor) SHUTS OFF transcription

Induction by Lactose

When lactose is present, it is converted to allolactose (the actual inducer), which binds to the repressor protein and changes its shape. The inactive repressor falls off the operator, allowing RNA polymerase to transcribe the structural genes.

When lactose is available in the medium, a small amount enters the cell via existing (basal level) permease. Inside the cell, β-galactosidase converts lactose into allolactose, which is the actual inducer. Allolactose binds to the repressor protein, causing a conformational change that makes the repressor unable to bind the operator. The operator is now free, and RNA polymerase transcribes the structural genes.

• Lactose is the substrate, but allolactose (an isomer of lactose) is the true inducer
• Allolactose binds to the repressor at its allosteric site → changes shape → repressor CANNOT bind operator
• With operator free, RNA polymerase moves through and transcribes lacZ, lacY, lacA as polycistronic mRNA
• β-galactosidase (lacZ product) cleaves lactose into glucose + galactose
• Permease (lacY product) helps transport lactose into the cell
• Transacetylase (lacA product) function is less clear; may be involved in detoxification
• When lactose is used up, no more allolactose → repressor becomes active again → operon switches OFF

Quick recall

What is the inducer of the lac operon — lactose or allolactose?

The actual inducer is allolactose (an isomer of lactose). Lactose is converted to allolactose by the small amount of β-galactosidase always present at basal levels. NCERT says 'lactose is the inducer' for simplicity, but technically it's allolactose.

Human Genome Project & DNA Fingerprinting

The Human Genome Project (HGP, 1990–2003) was a mega-project that sequenced the entire human genome (~3.2 billion base pairs). Key findings: ~20,500 genes, <2% codes for proteins, >50% is repetitive sequences. DNA fingerprinting, developed by Alec Jeffreys (1984), exploits polymorphisms in satellite DNA (VNTRs) to create unique genetic profiles for forensics and paternity testing.

Human Genome: 3.2 10^9 bp 20 , 500 genes

Human Genome Project

HGP (1990–2003) was coordinated by the US Department of Energy and NIH. It used two approaches: the publicly funded hierarchical shotgun approach (BAC-by-BAC) and Craig Venter's whole-genome shotgun approach. Frederick Sanger's method was used for sequencing.

The Human Genome Project (HGP) was launched in 1990 and completed in 2003. It was a 13-year international effort coordinated by the US Department of Energy and the National Institutes of Health (NIH). The project aimed to sequence all ~3.2 billion base pairs of human DNA and identify all human genes.

• Goals of HGP: (1) Identify all ~20,000–25,000 genes, (2) Determine the sequence of 3.2 billion base pairs, (3) Store this information in databases, (4) Develop tools for data analysis, (5) Address ethical, legal, social issues (ELSI)
• Methodology: Two approaches were used — (a) Expressed Sequence Tags (ESTs) — sequencing only the coding regions; (b) Sequence Annotation — sequencing the entire genome then assigning functions
• BAC (Bacterial Artificial Chromosomes) and YAC (Yeast Artificial Chromosomes) were used as cloning vectors to handle large DNA fragments
• Sequencing method: Frederick Sanger's dideoxy chain termination method (Sanger sequencing)
• DNA fragments were separated by automated DNA sequencers using polyacrylamide gel electrophoresis
• Craig Venter (Celera Genomics) used the whole genome shotgun approach — faster but computationally demanding

HGP Findings

The human genome has ~3.2 billion bp but only ~20,500 protein-coding genes. Less than 2% of the genome codes for proteins. Over 50% is repetitive DNA. The average gene is 3000 bp long.

The HGP revealed several surprises about the human genome that challenged earlier assumptions. The genome is far larger than the number of genes would suggest, and most of it does NOT code for proteins.

• Total genome size: 3.2 × 10⁹ bp (about 3.2 billion base pairs)
• Total genes: estimated ~20,500 (far fewer than the 100,000 originally predicted)
• Less than 2% of the genome codes for proteins (the rest was initially called 'junk DNA')
• Average gene size: ~3000 bp (but sizes vary enormously — dystrophin gene is 2.4 million bp!)
• More than 50% of the genome consists of repetitive sequences (satellite DNA, transposons, etc.)
• Chromosome 1 has the most genes (~2968); the Y chromosome has the fewest (~231)
• 99.9% of nucleotide bases are identical in all humans — only 0.1% variation (SNPs) makes us unique

Quick recall

What percentage of the human genome codes for proteins?

Less than 2%. The remaining >98% includes introns, repetitive sequences, regulatory regions, telomeres, centromeres, and other non-coding sequences. Much of this 'non-coding' DNA has regulatory functions.

DNA Fingerprinting

DNA fingerprinting uses polymorphisms in repetitive DNA sequences (VNTRs/microsatellites) to create unique genetic profiles. Developed by Alec Jeffreys (1984), it uses restriction enzymes, Southern blotting, and VNTR probes.

DNA fingerprinting (also called DNA profiling) was developed by Alec Jeffreys (1984). It exploits the fact that repetitive DNA sequences (particularly VNTRs — Variable Number of Tandem Repeats) vary in length between individuals. Since each person has a unique pattern of VNTR lengths, this creates a 'fingerprint' as distinctive as a physical fingerprint.

• Satellite DNA — highly repetitive, non-coding DNA sequences; basis of DNA fingerprinting
• VNTR (Variable Number Tandem Repeats) — also called minisatellites; repeat units of 10–60 bp; the number of repeats varies between individuals
• STR (Short Tandem Repeats) — also called microsatellites; repeat units of 2–6 bp; used in modern forensics
• The non-coding repetitive sequences show high degree of polymorphism — which is what makes fingerprinting possible
• Polymorphism in satellite DNA is due to mutations accumulating in non-coding regions (no selection pressure to conserve them)

• Southern blotting (named after Edwin Southern) — DNA fragments transferred from gel to nylon/nitrocellulose membrane
• Each person inherits one set of VNTRs from each parent → bands in DNA fingerprint show inheritance pattern
• Identical twins have the same DNA fingerprint (they came from the same zygote)
• Applications: forensics (crime scene evidence), paternity/maternity disputes, immigration cases, evolutionary studies, identification of disaster victims