Introduction to DNA, RNA, and Chromosomes

1. Prokaryotes vs. Eukaryotes

Organisms are divided into prokaryotes and eukaryotes based on cellular complexity and internal structural organization.

• Prokaryotic Cells:

  • Found in simple single-celled organisms such as bacteria.

  • Lack membrane-bound organelles and a membrane-enclosed nucleus.

  • Contain a nucleoid region where genetic material floats freely in the cytoplasm.

  • DNA structure: Consists of one circular piece of double-stranded DNA per cell.

• Eukaryotic Cells:

  • Found in complex single-celled and multicellular organisms (fungi, plants, animals).

  • Contain membrane-bound organelles and a distinct membrane-enclosed nucleus.

  • DNA structure: Consists of multiple linear pieces of DNA organized into chromosomes.

2. Nucleic Acid Structure: DNA vs. RNA

Both DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are nucleic acid polymers made of monomer building blocks called nucleotides.

Nucleotide Composition

Every nucleotide monomer consists of three components:

1. A phosphate group.

2. A five-carbon pentose sugar (deoxyribose in DNA; ribose in RNA).

3. A nitrogenous base.

Key Structural Differences Between DNA and RNA

Historical Discovery of the DNA Structure

• Watson and Crick (1950s–1960s) formulated the double helix model of DNA.

• Rosalind Franklin (1953) captured Photo 51 using X-ray diffraction, revealing the key structural features of DNA (helical shape, double sugar-phosphate backbone on the outside, and nitrogenous bases oriented perpendicularly in the center).

• Maurice Wilkins shared Franklin's X-ray image with Watson and Crick, which enabled them to solve the full physical structure.

Base Pairing Rules & Chemical Orientation

• Complementary Base Pairing Rules:

  • Adenine ($A$) pairs with Thymine ($T$) via $2$ hydrogen bonds.

  • Cytosine ($C$) pairs with Guanine ($G$) via $3$ hydrogen bonds.

  • In RNA, Uracil ($U$) substitutes for Thymine ($T$) and pairs with Adenine ($A$).

• Ring Structures:

  • Purines (Adenine and Guanine) contain a two-ring chemical structure.

  • Pyrimidines (Thymine, Cytosine, and Uracil) contain a single-ring chemical structure.

  • Pairing always joins a purine with a pyrimidine ($ ext{Two-ring} + ext{One-ring}$), maintaining a uniform width along the DNA double helix and preventing structural distortions.

• Antiparallel Configuration:

  • DNA backbones run parallel to each other but in opposite directions: one strand runs $5' \rightarrow 3'$, while the complementary strand runs $3' \rightarrow 5'$.

  • The $5'$ end corresponds to the position of the terminal phosphate group, and the $3'$ end corresponds to the hydroxyl group on the sugar.

3. DNA Base Composition Percentages (Chargaff's Rules)

Because nitrogenous bases pair specifically ($A$ with $T$ and $C$ with $G$), the proportion of adenine equals thymine, and cytosine equals guanine:

$\%A = \%T \quad \text{and} \quad \%C = \%G$

$\%A + \%T + \%C + \%G = 100\%$

• Example Percentage Calculation: If an organism's DNA contains $24.7\%$ Adenine ($A$):

  1. $\%T = 24.7\%$

  2. $\%A + \%T = 24.7\% + 24.7\% = 49.4\%$

  3. $\%C + \%G = 100\% - 49.4\% = 50.6\%$

  4. $\%C = \%G = \frac{50.6\%}{2} = 25.3\%$

• Experimental Variations: Minor deviations from exact equality can occur due to random DNA mutations or environmental factors.

• Biotechnology Applications: Modern DNA sequencing uses fluorescent dyes to label bases ($A$, $C$, $T$, $G$) with specific colors. Spectrophotometry output peaks indicate the exact sequence of base pairs along a fragment.

4. DNA Replication

Human somatic cells divide every $24\,\text{hours}$, requiring complete copying of cellular DNA, a process taking approximately $6\text{--}8\,\text{hours}$.

Models of Replication

• Conservative Replication: The original parent molecule remains intact while an entirely new copy is produced (rejected).

• Dispersive Replication: Parental and newly synthesized segments are scattered throughout both strands (rejected).

• Semi-Conservative Replication (Watson & Crick - Proven): The parental strands separate, and each acts as a template. Each daughter DNA molecule contains $50\%$ original parental DNA and $50\%$ newly synthesized DNA.

Enzymatic Machinery and Process

1. Unzipping (Helicase): The enzyme helicase breaks the weak hydrogen bonds holding complementary base pairs together at the origin of replication.

2. Priming (Primase): Primase synthesizes short RNA primers to provide a free $3'$ end for DNA extension.

3. Elongation (DNA Polymerase): DNA polymerase incorporates free floating nucleotides complementary to the template strand ($A$ to $T$, $C$ to $G$).

   • Constraint: DNA polymerase can only synthesize new DNA strands in the $5' \rightarrow 3'$ direction (adding nucleotides exclusively to the $3'$ end).

4. Ligation (DNA Ligase): RNA primers are removed and replaced with DNA. DNA ligase seals gaps in the sugar-phosphate backbone.

5. Origins of Replication: Eukaryotic DNA contains multiple origins of replication, allowing replication to occur simultaneously at multiple points to speed up synthesis and limit copying mistakes.

5. Chromosomes, Chromatin, and Genes

DNA Packaging

• Chromatin: DNA complexed with histone proteins.

• Long strands of double-stranded DNA wrap around histone proteins to form compact structural units.

• During cell division (metaphase), chromatin condenses tightly into distinct visible structures called chromosomes.

Relationships Between DNA, Genes, and Chromosomes

• DNA: The individual base pair sequence ($A$, $C$, $T$, $G$), acting like letters.

• Gene: A specific segment of DNA along a chromosome that codes for a specific protein or trait, acting like a word.

• Chromosome: The complete condensed structure containing many genes, acting like a story.

Karyotypes and Chromosomes Sets

• Karyotype: A visual display of an individual's complete set of condensed chromosomes isolated during cell division.

• Somatic Cells vs. Gametes:

  • Somatic Cells (body cells): Diploid ($2n$), containing two full sets of homologous chromosomes.

  • Gametes (egg/sperm): Haploid ($n$), containing one single set of chromosomes.

• Human Chromosome Complement:

  • Humans have $23$ pairs ($46$ total chromosomes, $2n = 46$).

  • $22$ pairs are homologous autosomes (carrying genes for the same traits at matching locations, one inherited from each parent).

  • $1$ pair of sex chromosomes: Females have $XX$; Males have $XY$ (the $Y$ chromosome is significantly smaller than the $X$ chromosome).

• Species Specificity:

  • Chromosome numbers are unique to species and do not reflect organismal complexity.

  • Examples:

  • Humans: $2n = 46$

  • Dogs: $2n = 78$

  • Goats: $2n = 60$

  • Fruit Flies: $2n = 12$

  • Kingfishers: $2n = 84$ or $94$ (Birds use $Z$ and $W$ sex chromosome systems)