Cambridge Biology Unit 1 CAPE Notes

Aspects of Biochemistry

Water as a Medium for Life

• Molecular Structure:

  • Formula is $H_2O$. Two hydrogen atoms are covalently bonded to one oxygen atom.

  • Dipole Nature: The shared electrons are distributed unequally; the oxygen atom attracts them more, gaining a small negative charge ($δ-$), while hydrogen atoms gain a small positive charge ($δ+$). This unequal distribution creates a dipole.

  • Hydrogen Bonding: Weak electrical attractions form between the $δ-$ oxygen of one molecule and the $δ+$ hydrogen of another. Each molecule can form hydrogen bonds with its four nearest neighbors.

• Physical States and Density:

  • Water is liquid at Earth's ambient temperatures due to hydrogen bonds holding molecules together.

  • Ice Density: In ice, molecules form a rigid lattice where they are held further apart than in liquid water. Consequently, ice is less dense and floats.

  • Ecological Significance: The maximum density of water occurs at $4\,°C$. Surface water cools, sinks to the bottom at $4\,°C$, and allows floating ice to insulate the liquid water below, preserving aquatic life in winter.

• Thermal Properties:

  • High Specific Heat Capacity: Water's value is $4.2\,J\,g^{-1} \,°C^{-1}$. Significant energy is required to break hydrogen bonds before the temperature rises, providing thermal stability for organisms.

  • Latent Heat of Vaporization: Evaporation requires breaking hydrogen bonds, which absorbs substantial heat energy. This provides a cooling mechanism (e.g., sweating in humans, transpiration in plants).

  • Latent Heat of Fusion: Changing water from liquid to solid requires significant heat loss ($300\,J/g$). This makes cytoplasm difficult to freeze, preventing ice crystal damage to cell membranes.

• Solvent Properties:

  • Water is an excellent solvent for ionic (e.g., $NaCl$) and polar covalent (e.g., glucose, amino acids) compounds.

  • Dipoles on water molecules attract charges on solutes, surrounding them in a "cloud" to keep them in solution.

  • This facilitates metabolic reactions, as reactants must be in solution to collide.

• Cohesion and Surface Tension:

  • Cohesion: Molecules stick together via hydrogen bonds, allowing mass flow in xylem and blood vessels.

  • Surface Tension: Molecules at the surface are pulled downward, creating a skin-like layer that allows insects (e.g., water striders) to walk on water.

• Chemical Reactivity and pH:

  • Hydrolysis: Water is used to break down polymers into monomers.

  • Photosynthesis: Water provides hydrogen ions to create sugars and releases oxygen as a byproduct.

  • pH Neutrality: Pure water dissociates into $H^+$ and $OH^-$, maintaining a neutral pH of 7, serving as a buffer medium.

Carbohydrates

Monosaccharides

• General formula: $(CH_2O)_n$. Monosaccharides are the simplest sugars, soluble and sweet.

• Trioses (3C): e.g., Glyceraldehyde (metabolic intermediate).

• Pentoses (5C): e.g., Ribose (RNA constituent), Deoxyribose (DNA).

• Hexoses (6C): e.g., Glucose, Fructose, Galactose.

  • Glucose: The primary respiratory substrate. It exists in ring forms: $α$-glucose (OH on carbon 1 is below the ring) and $β$-glucose (OH on carbon 1 is above the ring).

Disaccharides

• Formed by a condensation reaction between two monosaccharides, creating a glycosidic bond and releasing a water molecule.

• Maltose: $α$-glucose + $α$-glucose via an $α\,1-4$ glycosidic bond.

• Sucrose: $α$-glucose + $β$-fructose via an $α\,1-β2$ glycosidic bond. It is the transport sugar in plants.

• Hydrolysis: The addition of water, catalyzed by enzymes (e.g., maltase, sucrase), breaks the glycosidic bond.

Polysaccharides

• Giant polymers made of thousands of monosaccharide units. Insoluble and ideal for storage.

• Starch (Plant Storage): Mixture of two polymers of $α$-glucose:

  • Amylose: Unbranched, coiled spiral held by hydrogen bonds; contains $α\,1-4$ bonds.

  • Amylopectin: Branched structure with $α\,1-4$ and $α\,1-6$ bonds.

• Glycogen (Animal Storage): Similar to amylopectin but more highly branched ($α\,1-4$ and $α\,1-6$). Stored in liver and muscle.

• Cellulose (Structural): Linear polymer of $β$-glucose using $β\,1-4$ glycosidic bonds. Every alternate glucose is rotated $180\,°$. Chains form bundles called microfibrils, held by hydrogen bonds, providing high tensile strength for cell walls.

Biochemical Tests

• Benedict's Test: Detects reducing sugars (glucose, fructose, maltose). Heat with blue Benedict's reagent; a brick-red precipitate of copper(I) oxide indicates a positive result.

• Non-reducing Sugars (Sucrose): If Benedict's is initially negative, boil with $HCl$ to hydrolyze, neutralize with alkali, then re-test with Benedict's.

• Iodine Test: Detects starch. A blue-black color forms as iodine fits into the amylose coils.

Proteins

Structure and Formation

• Amino Acids: Central carbon bonded to an amino group ($—NH_2$), a carboxyl group ($—COOH$), a hydrogen atom, and a variable R group (20 different types).

• Peptide Bonds: Formed by a condensation reaction between the amino group of one amino acid and the carboxyl group of another.

• Levels of Structure:

  1. Primary: The unique sequence of amino acids in a polypeptide chain, determined by genes.

  2. Secondary: Regular coiling or folding via hydrogen bonds between the —CO and —NH groups (e.g., $α$-helix or $β$-pleated sheet).

  3. Tertiary: Overall 3D shape held by hydrogen bonds, ionic bonds, disulfide bridges (between cysteines), and hydrophobic interactions.

  4. Quaternary: The assembly of multiple polypeptide chains (e.g., haemoglobin consists of four chains).

Examples and Classification

• Globular Proteins: Spherical, often soluble, and metabolically active. Haemoglobin has four subunits, each with a prosthetic haem group containing an $Fe^{2+}$ ion to bind oxygen.

• Fibrous Proteins: Long strands, insoluble, and structural. Collagen consists of three helical polypeptide chains wound like a rope. Every third amino acid is glycine. High tensile strength makes it ideal for tendons and skin.

• Biuret Test: Detects proteins by a purple color change when treated with copper(II) sulphate in alkaline solution.

Lipids

Triglycerides

• One glycerol molecule linked to three fatty acids via ester bonds (formed by condensation).

• Role: Energy storage (releases twice as much energy as carbohydrates). Provides thermal insulation and buoyancy.

• Saturated Fatty Acids: No double bonds in the carbon chain; maximum hydrogens.

• Unsaturated Fatty Acids: Contain one or more $C=C$ double bonds, causing a "kink" in the chain.

Phospholipids

• Two fatty acids and a phosphate group attached to glycerol.

• Amphipathic: Hydrophilic phosphate "head" and hydrophobic fatty acid "tails."

• Function: Arrange into a bilayer in water, forming the fundamental structure of cell membranes.

Emulsion Test

• Shake sample with ethanol to dissolve lipids, then pour into water. A milky white emulsion indicates the presence of lipids.

Cell Structure and Microscopy

Microscopy Concepts

• Magnification: Image size divided by real size.

  • $1\,\mu m = 10^{-3}\,mm$

  • $1\,nm = 10^{-3}\,\mu m$

• Resolution: The ability to distinguish between two close points. Determined by the wavelength of radiation.

  • Light Microscope: Limit is $200\,nm$ (blue light has the shortest wavelength).

  • Electron Microscope: Limit is $0.5\,nm$ (electron beams have much shorter wavelengths).

• Transmission Electron Microscope (TEM): Uses a beam passed through thin sections for internal detail.

• Scanning Electron Microscope (SEM): Bounces electrons off surface for 3D images.

Organelles and Functions

• Nucleus: Contains chromatin (DNA and histones). Surrounded by a double-membrane nuclear envelope with pores for mRNA transport. The nucleolus makes rRNA.

• Mitochondria: Double-membrane, inner folds (cristae), and space (matrix). Site of aerobic respiration and ATP production.

• Chloroplasts: Double-membrane, containing thylakoids stacked into grana in a fluid stroma. Site of photosynthesis.

• Endoplasmic Reticulum (ER):

  • Rough (RER): Studded with ribosomes; synthesizes and transports proteins.

  • Smooth (SER): No ribosomes; synthesizes lipids and steroids.

• Golgi Body: Modifies, packages, and secretes proteins into vesicles.

• Lysosomes: Vesicles containing digestive enzymes for destroying old organelles or pathogens.

• Ribosomes: Sites of protein synthesis (80S in eukaryotes, 70S in prokaryotes).

• Centrioles: Animal cells only; organize microtubules/spindle fibers during division.

• Cell Wall: Plant cells only; made of cellulose microfibrils in a pectin matrix. Joined to others via the middle lamella and plasmodesmata.

Prokaryotic vs. Eukaryotic Cells

• Prokaryotes (Bacteria): Lacks nucleus (circular DNA free in cytoplasm), lacks membrane-bound organelles, smaller ribosomes (70S), cell wall made of peptidoglycan.

• Endosymbiont Theory: Mitochondria and chloroplasts were once free-living prokaryotes that invaded larger cells. Evidence includes their own circular DNA, 70S ribosomes, and reproduction by binary fission.

Membrane Structure and Function

The Fluid Mosaic Model

• Fluid: Phospholipids and proteins can move laterally within the bilayer.

• Mosaic: Proteins are scattered in the surface like a mosaic pattern.

• Components:

  • Cholesterol: Regulates membrane fluidity.

  • Glycolipids/Glycoproteins: Carbohydrate chains for cell recognition and receptor sites (signalling).

  • Proteins:

    • Integral: Span the bilayer (transmembrane).

    • Peripheral: Attached to surface.

Movement Across Membranes

• Passive Processes:

  • Simple Diffusion: Small, uncharged or lipid-soluble molecules move down a concentration gradient.

  • Facilitated Diffusion: Large or charged particles pass through channel proteins or carrier proteins.

  • Osmosis: Diffusion of water down a water potential gradient ($\Psi$) through a partially permeable membrane.

    • $\Psi = \Psi_s + \Psi_p$ (Water Potential = Solute Potential + Pressure Potential).

    • Animal Cells: Higher $\Psi$ leads to bursting (lysis); lower $\Psi$ leads to shrinking (crenation).

    • Plant Cells: High $\Psi$ leads to turgidity; lower $\Psi$ leads to plasmolysis (cytoplasm pulls away from wall).

• Active Processes:

  • Active Transport: Moving substances against a concentration gradient using carrier proteins and ATP (e.g., Sodium-Potassium pump).

  • Endocytosis/Exocytosis: Bulk transport using vesicles to move materials into or out of the cell.

Enzymes

Mechanism of Action

• Biological Catalysts: Globular proteins that lower activation energy required for metabolic reactions.

• Active Site: A cleft in the enzyme where the substrate binds to form an enzyme-substrate complex.

• Specificity: The shape of the active site matches only one specific substrate (Lock and Key or Induced Fit models).

Factors Affecting Enzyme Rate

• Temperature: Rate increases with kinetic energy until the optimum temperature. Excess heat breaks bonds, causing irreversible denaturation.

• pH: Extreme pH values interfere with ionic charges on R-groups, leading to denaturation.

• Enzyme/Substrate Concentration: Rate increases with concentration until all active sites are saturated ($V_{max}$).

Inhibition

• Competitive Inhibitors: Similar shape to substrate; bind to the active site. Effects can be overcome by increasing substrate concentration.

• Non-competitive Inhibitors: Bind to an allosteric site, changing the enzyme's shape. Substrate concentration does not reverse the effect.

Nucleic Acids and Protein Synthesis

DNA and RNA Structure

• Nucleotides: Consist of a phosphate group, a pentose sugar, and an organic base.

• DNA: Deoxyribose sugar. Bases: Adenine (A), Guanine (G), Cytosine (C), Thymine (T). Composed of two anti-parallell strands in a double helix. Complementary base pairing: A pairs with T (2 H-bonds), C with G (3 H-bonds).

• RNA: Ribose sugar. Single-stranded. Bases: A, G, C, and Uracil (U) instead of Thymine.

DNA Replication

• Occurs during Interphase. Semiconservative replication means each daughter molecule contains one parental strand and one new strand.

• Enzymes: DNA Helicase unzips the strands; DNA Polymerase adds new nucleotides in a $5'$ to $3'$ direction.

Protein Synthesis

• Transcription: In the nucleus, RNA Polymerase creates mRNA using the DNA sense strand as a template.

• Translation: At the ribosome, tRNA molecules bring specific amino acids based on mRNA codons. Anticodons on tRNA pair with codons. A peptide bond forms between amino acids, building a polypeptide.

Cell Division

The Cell Cycle and Mitosis

• Interphase: G1 (growth), S (DNA replication), G2 (preparation).

• Mitosis (Division of Nucleus):

  • Prophase: Chromosomes condense, spindle forms, nuclear envelope breaks down.

  • Metaphase: Chromosomes align at the equator.

  • Anaphase: Centromeres split; sister chromatids move to opposite poles.

  • Telophase: Nuclear envelopes reform; chromosomes decondense.

• Cytokinesis: Division of cytoplasm to form two genetically identical daughter cells.

Meiosis

• Two-stage division producing four genetically different haploid cells from one diploid cell.

• Sources of Variation:

  1. Crossing Over: Exchange of genetic material between homologous chromosomes during Prophase I.

  2. Independent Assortment: Random alignment of homologous pairs at Metaphase I.

  3. Random Fertilization: Any male gamete can fuse with any female gamete.

Genetics and Evolution

Key Terms

• Gene: Length of DNA coding for a polypeptide.

• Allele: Different version of a gene. Dominant alleles show effect even in heterozygotes; Recessive only in homozygotes.

• Genotype: Genetic makeup (e.g., $Aa$).

• Phenotype: Physical characteristics.

• Codominance: Both alleles affect the phenotype (e.g., blood group AB).

• Epistasis: One gene masks the expression of another (e.g., mouse coat color).

Natural Selection

• Darwin's Theory: Overproduction leading to competition; variation among offspring; survival of the fittest; inheritance of advantageous traits.

• Types of Selection:

  • Stabilizing: Favors intermediate phenotypes.

  • Directional: Shift toward a new extreme (e.g., antibiotic resistance in bacteria).

  • Disruptive: Favors both extremes against the mean.

Genetic Engineering

• Recombinant DNA: DNA comprising sections from two different sources.

• Restriction Enzymes: Cut DNA at specific sequences, often leaving sticky ends.

• Vectors: Passages for foreign DNA into host cells (e.g., Plasmids, viruses).

• DNA Ligase: Joins DNA fragments together.

• Polymerase Chain Reaction (PCR): Rapidly clones DNA samples in a thermocycler using DNA polymerase and primers.

• Gene Therapy: Inserting functional alleles into cells to treat genetic disorders like Cystic Fibrosis (a recessive disorder affecting chloride channels).