Part 1: DNA Structure, Replication, and Function

DNA as the Genetic Material

• Genes: Hereditary "factors" associated with specific traits, carried on chromosomes

(composed of DNA and protein).

• One-gene-one-polypeptide hypothesis: Postulates that genes determine the structure of

proteins and other polypeptides.

• Discovery of Transformation (Griffith, 1928): Experiments in mice showed that an

extract from lethal S-strain Streptococcus pneumoniae could genetically transform non-
lethal R-strain cells, making the mice die. This demonstrated that the genetic material
could be transferred.

• Avery, MacLeod, and McCarty (1944): Confirmed that DNA is the hereditary
material because only the destruction of DNA (using DNase) prevented the transforming
principle from converting R-cells to S-cells .

• Hershey–Chase Experiment: Demonstrated that the genetic material of bacteriophages

(phages) is DNA, not protein, by using radioactive sulfur 35S to label the protein coat
and radioactive phosphorus 32P to label the DNA. Only the 32P entered the E. coli and
was found in new phages .
DNA's Essential Properties

• Faithful Replication: The structure must allow for accurate copying at every cell
division.

• Informational Content: Must encode the structures of all proteins expressed by the
organism.
• Ability to Change (Mutation): Must be stable but also able to change occasionally to
provide raw material for evolutionary selection8.
DNA Structure Key Concepts

• Nucleotides: Basic building blocks of DNA, composed of a phosphate group, a

deoxyribose sugar, and a nitrogenous base.
▪ Purines (double-ring): Adenine (A) and Guanine (G).

▪ Pyrimidines (single-ring): Cytosine (C) and Thymine (T).

• Chargaff’s Rules:

1. Amount of Purines (A + G) = Amount of Pyrimidines (T + C).

2. Amount of A = T and amount of C = G.

• X-ray Diffraction (Rosalind Franklin): Showed that DNA is long, thin, has two parallel
parts, and possesses a spiral (helical) shape

• Watson and Crick (1953): Co-discovered the double-helix structure of DNA .

▪ The two strands run antiparallel (one 5' to 3', the other 3' to 5').
▪ Bases pair via hydrogen bonds: A pairs with T (two H-bonds); G pairs with C
(three H-bonds).

▪ Sugar-phosphate backbone is on the outside .

DNA Replication

• Semiconservative Replication (Watson & Crick): Each new daughter DNA molecule
contains one original (parental) strand and one newly synthesized strand

• Meselson–Stahl Experiment (1958): Confirmed the semiconservative model using

heavy nitrogen 15N and light nitrogen 14N isotopes and density gradient centrifugation.

• Key Enzymes at the Replication Fork: Helicase: Unwinds the double helix by breaking
hydrogen bonds.

▪ Single-strand-binding (SSB) proteins: Stabilize the unwound DNA18.

▪ Topoisomerase/DNA Gyrase: Prevents the DNA ahead of the fork from

overwinding (supercoiling) by cutting and rejoining strands19.

▪ DNA Polymerase III (Pol III): Main enzyme for DNA synthesis; adds
nucleotides to the 3' end of a growing chain; is highly processive when held by
the beta clamp.

▪ Primase: Synthesizes short RNA primers to start DNA synthesis .

▪ DNA Polymerase I (Pol I): Removes RNA primers and fills the resulting gaps
with DNA .

▪ DNA Ligase: Connects adjacent DNA fragments (Okazaki fragments on the

lagging strand) .

• Leading Strand: Synthesized continuously in the 5' to 3' direction toward the
replication fork.

• Lagging Strand: Synthesized discontinuously away from the replication fork as short
Okazaki fragments, each starting with an RNA primer .

Telomere Shortening (Eukaryotes)

• The Problem: Due to the removal of the RNA primer for the last Okazaki fragment, the
lagging strand's end cannot be filled by conventional replication, resulting in a terminal
gap and a shortened chromosome after replication.
• Telomerase: An enzyme (abundant in germ cells, low/absent in somatic cells) that
lengthens the 3′ overhang of the telomere (chromosome end) .

• Senescence: Irreversible cell cycle arrest caused by progressive shortening of

chromosomes in proliferating somatic cells, linked to aging.

• Werner Syndrome: A premature aging disorder caused by a mutation in the WRN gene,
which is involved in maintaining the protective telomere cap structure.
 Part 2: RNA and Transcription
RNA Properties

• Ribose Sugar: Has a hydroxyl group (-OH) at the 2'-carbon, making it more reactive
than DNA's deoxyribose .

• Single-Stranded: Typically single-stranded, allowing for diverse 3D shapes and

catalytic activity (ribozyme).

• Uracil (U): Used instead of Thymine (T) .

Transcription (DNA to RNA)

• Transcription Direction: RNA is synthesized in the 5' to 3' direction, using the 3' to 5'
DNA template strand .

• RNA Polymerase: Enzyme complex that scans DNA for a promoter sequence.

▪ Includes the core enzyme (alpha, beta, omega subunits) and the sigma factor.
▪ Sigma subunit recognizes and binds to promoter sequences (e.g., -35 and -10
regions).

• Elongation: RNA polymerase synthesizes the RNA strand, unwinding DNA ahead and
rewinding it behind.

• Termination (Intrinsic): RNA synthesis ends and the RNA transcript is released when
the newly formed RNA strand folds into a hairpin loop (a GC-rich self-complementary
region) followed by a run of Uracils.
 Part 3: Protein Synthesis
Proteins and Amino Acids

• Amino Acid Structure: Central alpha carbon bonded to an amino group , a carboxyl
group COOH, a hydrogen atom, and a unique R group (side chain) .

• Peptide Bond: Covalent bond linking the carboxyl group of one amino acid to the amino
group of the next, releasing water .

• Protein Structure Levels: * Primary: Sequence of amino acids.

▪ Secondary: Local structures like the alpha helix or beta pleated sheet, held by
hydrogen bonds.
▪ Tertiary: Overall 3D folding of a single polypeptide chain.
▪ Quaternary: Arrangement of multiple polypeptide subunits (e.g., hemoglobin.

Translation (RNA to Protein)

• Genetic Code: Nonoverlapping code where three mRNA bases (codon) specify one
amino acid .
• Ribosome: Molecular machine (rRNA and protein) responsible for protein synthesis. It
facilitates the interaction between tRNA (with anticodon) and mRNA (with codon). *
Ribosome Sites for tRNA Progression:

▪ A Site (Aminoacyl-tRNA): Entry point for the charged tRNA carrying the next
amino acid.

▪ P Site (Peptidyl-tRNA): Holds the tRNA with the growing polypeptide chain;
peptide bond formation is catalyzed here.

▪ E Site (Exit): Where the uncharged tRNA sits before exiting the ribosome.
 Part 4: Chromosomal Aberrations and Genetic Disorders
Chromosome Aberrations

• Aneuploidy (Numerical Aberrations): Loss or gain of one or a few chromosomes.

▪ Nondisjunction: Failure of chromosomes or chromatids to separate properly,

causing aneuploidy.

▪ Monosomy (2n-1): Missing one chromosome (e.g., Turner syndrome).

▪ Trisomy (2n+1): Extra chromosome (e.g., Down syndrome (Trisomy 21)).

• Structural Aberrations: Changes in chromosome structure due to breakage,

rearrangement, or loss of segments.

▪ Deletion: Loss of a segment (e.g., Cri-du-chat syndrome - deletion on

chromosome 5p).

▪ Duplication: A segment is copied, leading to extra genetic material.

▪ Translocation: Exchange of segments between non-homologous chromosomes

(e.g., Translocation Down Syndrome).

• Karyotyping: Technique used to study chromosome number, size, shape, and banding
pattern (chromosomes arrested at metaphase)
 Disorder Cause/Gene Type of Mutation Key Symptoms
Fragile X FMR1 gene (X Repeat Expansion Intellectual disability, autism
Syndrome chromosome) (>200 repeats) leads spectrum disorders, abnormal
(FXS) to gene silencing facial features (prominent
forehead/jaw, large ears). Lack
of FMRP disrupts synaptic
plasticity.

Huntington’s Huntingtin gene CAG Repeat Involuntary jerky movements

Disease (Autosomal Expansion in the (chorea), cognitive decline,
Dominant) gene severe psychiatric symptoms.
Progressive and fatal.

Wilson’s ATP7B gene Mutation impairs Copper buildup in liver/brain.

Disease (Chromosome copper transport Symptoms include liver
13) damage, neurological
problems (tremors, difficulty
speaking), and psychiatric
changes.

Lesch–Nyhan HGPRT gene (X Deficiency of Uric acid buildup

Syndrome chromosome) HGPRT enzyme (hyperuricemia), involuntary
muscle movements, spasticity,
and severe self-injurious
behaviors (lip/finger biting).

Tay–Sachs HEXA gene Absence of Buildup of GM} ganglioside in

Disease (Chromosome Hexosaminidase A nerve cells. Leads to neuron
15) enzyme 7676 destruction, motor weakness,
seizures, and cognitive decline.

Familial Early- APP, PSEN1, Mutations lead to Progressive memory loss,

Onset PSEN2 genes abnormal protein cognitive decline, and
Alzheimer’s (Dominantly processing behavioral changes due to
Disease inherited) buildup of beta-amyloid
plaques and tau protein
tangles.