DNA Structure and Replication

• DNA stores genetic instructions for protein synthesis and is universal to all living organisms
• DNA is passed down through generations via replication

Molecular Structure of DNA

• DNA has a double-helix shape with two antiparallel strands twisted together
• Nucleotides consist of a phosphate group, deoxyribose sugar, and a nitrogenous base (A, T, C, G)
• Adenine (A) pairs with thymine (T), and cytosine (C) pairs with guanine (G) via hydrogen bonds

DNA in Different Cell Types

• Eukaryotic DNA is linear, bound to histone proteins, and located in the nucleus
• Prokaryotic DNA is circular, unbound, and found in the cytosol
• Mitochondria and chloroplasts possess their own circular DNA, supporting the endosymbiotic theory

DNA Replication

• DNA replication ensures genetic continuity, which allows cells to divide accurately
• Each new DNA molecule has one original and one new strand in a semi-conservative process
• Semiconservative replication ensures high fidelity of genetic information.

Enzymes and Steps in DNA Replication

• Helicase unwinds DNA by breaking hydrogen bonds between base pairs
• DNA polymerase adds complementary nucleotides in the 5’ to 3’ direction
• The leading strand is synthesized continuously, while the lagging strand is synthesized in Okazaki fragments
• Ligase seals gaps between Okazaki fragments

Importance of Complementary Base Pairing

• Complementary base pairing prevents mutations by ensuring accuracy, which reduces errors in DNA replication

Genes as DNA Sequences

• Genes contain instructions for making proteins
• Genes in eukaryotes have introns (non-coding) and exons (coding)

Transcription (DNA to RNA)

• In eukaryotes, transcription happens in the nucleus, while in prokaryotes, it happens in the cytoplasm
• RNA polymerase binds to the promoter region of DNA
• DNA strands separate, and one strand is copied
• RNA polymerase synthesizes a complementary mRNA strand, where adenine (A) pairs with uracil (U) instead of thymine (T)
• mRNA detaches and undergoes RNA processing, including splicing, and the addition of a cap and tail

Translation (mRNA to Protein)

• Translation takes place in ribosomes, which are in the cytoplasm or rough ER
• mRNA codons are groups of three nucleotides coding for an amino acid
• tRNA carries amino acids and matches its anticodon to the mRNA codon
• Ribosomal RNA (rRNA) forms ribosomes and catalyzes peptide bond formation

Process of Translation

• mRNA attaches to the ribosome
• tRNA brings amino acids according to the codon sequence
• Peptide bonds form between amino acids, which causes the polypeptide chain grow
• A stop codon signals the end of the process, which releases the protein to fold into its shape

Levels of Protein Structure

• Primary: Amino acid sequence
• Secondary: Alpha-helices and beta-pleated sheets formed by hydrogen bonds
• Tertiary: 3D folding from interactions between side chains like disulfide bonds and hydrophobic interactions
• Quaternary: Multiple polypeptides joining together

Protein Functions

• Structural proteins include collagen and keratin
• Enzymatic proteins catalyze chemical reactions, for example, amylase
• Hormonal proteins regulate body functions, for example, insulin
• Antibodies provide an immune response in defense mechanisms

Role of Enzymes

• Enzymes accelerate reactions by lowering activation energy
• In the induced-fit model, the enzyme’s active site molds around the substrate which enhances binding efficiency

Factors that Affect Enzyme Activity

• High temperatures denature enzymes, while low temperatures slow reactions
• Enzymes function best at their optimum pH levels
• Competitive inhibitors bind to the active site, blocking substrate binding
• Non-competitive inhibitors bind elsewhere, altering the enzyme shape
• More substrate or enzyme can increase reaction rates until saturation

Gene Regulation

• Genes can be switched on or off to control protein production, and are controlled by transcription factors

Epigenetics

• Epigenetics refers to changes in gene expression without changing the DNA sequence
• DNA methylation is the addition of methyl groups that silence genes
• Histone modification affects DNA accessibility for transcription

Epigenetics & Disease

• Changes in gene expression can lead to diseases such as cancer due to uncontrolled cell division
• Environmental factors influence epigenetics like diet, stress, and toxins
• Identical twins can have different traits because of epigenetic modifications

Types of Mutations

• Point mutations change one nucleotide (silent, missense, nonsense)
• Frameshift mutations happen when insertions or deletions shift the reading frame
• Chromosomal mutations include deletions, duplications, and translocations

Causes of Mutations

• Mutations can occur from spontaneous errors in DNA replication
• Mutagens include: ionizing radiation (UV, X-rays), chemicals, and viruses

Consequences of Mutations

• Germ cell mutations are passed to offspring and can drive evolution
• Somatic cell mutations can lead to cancer but are not inherited

DNA Extraction

• DNA extraction involves lysing cells to release DNA

Polymerase Chain Reaction (PCR)

• PCR rapidly amplifies DNA sequences
• Steps of PCR:
  • Denaturation, where heat breaks hydrogen bonds at 95°C
  • Annealing, where primers bind to the DNA at 50–65°C
  • Extension, where DNA polymerase adds nucleotides at 72°C

Gel Electrophoresis

• Gel electrophoresis separates DNA fragments by size, smaller fragments move faster through the gel
• Used for DNA fingerprinting and forensic analysis

DNA Sequencing & Genomics

• DNA sequencing determines exact nucleotide order
• They help in disease research, evolution studies, and personalized medicine