Water and inorganic ions

Water is a polar molecule: the oxygen is slightly negative and the hydrogens slightly positive, so water molecules hydrogen bond to each other and to other polar molecules. Consequences:

• Solvent — polar solutes and ions dissolve, so metabolic reactions can take place and substances can be transported in blood, xylem and phloem.
• High specific heat capacity — a large input of energy causes only a small temperature rise, buffering organisms against temperature change.
• High latent heat of vaporisation — evaporation (sweating, transpiration) has a powerful cooling effect.
• Cohesion and surface tension — allows the continuous column of water in the xylem.

Inorganic ions (1.1.2): Mg²⁺ is a component of chlorophyll; Fe²⁺ of haemoglobin; PO₄³⁻ of ATP, nucleic acids and phospholipids; Ca²⁺ forms calcium pectate in the middle lamella; NO₃⁻ supplies the nitrogen for amino acids and nucleotides. Ions also act in osmotic and buffering systems.

Carbohydrates and lipids

Monosaccharides: α- and β-glucose and fructose share the formula C₆H₁₂O₆. A condensation reaction joins two of them, forming a glycosidic bond and releasing water; hydrolysis reverses it.

• Maltose = glucose + glucose; sucrose = glucose + fructose.
• Starch and glycogen are storage polymers of α-glucose: coiled and branched, so compact, and insoluble, so they do not affect water potential. Glycogen is more highly branched than starch, so it can be hydrolysed even faster — which suits an animal.
• Cellulose is a structural polymer of β-glucose: alternate residues are inverted, giving straight chains hydrogen-bonded into microfibrils.
• Pentoses (ribose, deoxyribose) are components of nucleic acids and ATP.

Lipids: a triglyceride is glycerol + 3 fatty acids, joined by three condensation reactions forming three ester bonds. Saturated fatty acids have no C=C; unsaturated ones have one or more. A phospholipid has one fatty acid replaced by a phosphate group, making the head hydrophilic and the tails hydrophobic — which is why phospholipids spontaneously form a bilayer.

Protein structure — and prions

Amino acids have an amine group, a carboxyl group, a hydrogen and a variable R group. Condensation forms a peptide bond.

• Primary — the amino acid sequence (peptide bonds).
• Secondary — α-helix or β-pleated sheet, held by hydrogen bonds.
• Tertiary — the 3-D fold, held by hydrogen bonds, ionic bonds, disulfide bridges and hydrophobic interactions.
• Quaternary — more than one polypeptide chain (haemoglobin: four chains, each with a haem prosthetic group).

Fibrous vs globular: collagen is fibrous — three polypeptides wound into a triple helix, giving high tensile strength; it is insoluble and structural. Enzymes are globular — a compact, roughly spherical fold with hydrophilic groups outward, so they are soluble and have a precisely shaped active site. Conjugated proteins carry a prosthetic group: haemoglobin (haem) and glycoproteins (carbohydrate).

Prions (1.1.5): a prion is a protein — no nucleic acid at all. A change in its secondary structure creates a form rich in β-pleated sheet, which converts normal protein into the abnormal form. The result is a neurodegenerative disease: scrapie in sheep, BSE in cattle and CJD in humans. Infection can follow from eating prion-rich tissue.

Which bond, which level?

Tap a bond or feature, then tap the level of protein structure it belongs to.

Nucleic acids and semi-conservative replication

A nucleotide = pentose sugar + nitrogenous base + phosphate, formed by condensation. Nucleotides polymerise into a strand with a sugar–phosphate backbone.

DNA is a double helix of two antiparallel chains, held by hydrogen bonds between complementary bases: A–T (2 H-bonds) and C–G (3 H-bonds). RNA is single-stranded, has ribose, and uses uracil instead of thymine.

Replication (1.1.7) is semi-conservative:

• DNA helicase breaks the hydrogen bonds and unwinds the helix.
• Free nucleotides pair with the exposed bases on each strand.
• DNA polymerase catalyses the phosphodiester bonds, producing two identical helices, each with one original and one new strand.

Meselson and Stahl: E. coli grown in heavy ¹⁵N was transferred to ¹⁴N. After one generation, all the DNA was of intermediate density — which immediately disproves conservative replication. After two generations there were equal amounts of intermediate and light DNA — which disproves dispersive replication (that would have given a single band of ever-lighter DNA). Only semi-conservative replication fits.

Your turn — chromatography Rf

Enzymes and inhibition

Enzymes are globular proteins that act as biological catalysts by lowering the activation energy. The active site — whose shape derives from the tertiary structure — is complementary to the substrate, forming an enzyme–substrate complex. The induced fit model says the active site moulds itself around the substrate as it binds.

• Temperature: rate rises with kinetic energy, then falls steeply past the optimum as bonds holding the tertiary structure break: denaturation.
• pH: extremes of pH disrupt the ionic and hydrogen bonds of the tertiary structure, so the active site changes shape.
• Substrate concentration: rate rises until all active sites are occupied — then the enzyme concentration becomes limiting and the rate plateaus.
• Competitive inhibitor — similar shape to the substrate; binds the active site; the effect is overcome by more substrate.
• Non-competitive inhibitor — binds elsewhere and changes the shape of the active site; not overcome by more substrate.

Immobilised enzymes (e.g. in alginate beads) can be recovered and reused, do not contaminate the product, and are more stable to changes in temperature and pH.

Identify the inhibitor

Viruses and cell ultrastructure

Viruses are non-cellular: nucleic acid (DNA or RNA) inside a protein capsid, sometimes with a lipid envelope carrying attachment proteins. They have no cytoplasm, no ribosomes and no metabolism, so they are obligate intracellular parasites — they can only replicate by taking over a host cell.

Eukaryotic ultrastructure: nucleus (with nuclear envelope, pores and nucleolus), rough ER (protein synthesis and transport), smooth ER (lipid synthesis), Golgi (modification and packaging), mitochondria (cristae, matrix), lysosomes, 80S ribosomes.

• Plant cells — cellulose cell wall, chloroplasts, a large vacuole, and the middle lamella of calcium pectate.
• Fungal cells — protoplasm (often multinucleate) bounded by a wall of chitin. No chloroplasts.
• Animal cells — no cell wall, no chloroplasts, but they do possess centrioles.
• Prokaryotic cells — circular DNA, plasmids, 70S ribosomes, murein wall, no membrane-bound organelles.

Your turn — graticule calibration

Your turn — actual cell size

Membranes, transport and water potential

The fluid-mosaic membrane is a phospholipid bilayer with intrinsic (channel and carrier) and extrinsic proteins, cholesterol regulating fluidity, and glycoproteins and glycolipids for recognition. Transport across it: simple diffusion, facilitated diffusion (channel/carrier, passive), osmosis, active transport (carrier + ATP, against the gradient) and bulk transport (endocytosis / exocytosis).

Water moves by osmosis from a higher (less negative) water potential to a lower (more negative) one.

• Plant cell in a dilute solution: water enters, the vacuole swells, the wall pushes back — ψ_p rises. The cell becomes turgid.
• Plant cell in a concentrated solution: water leaves, the protoplast shrinks away from the wall — plasmolysis. At incipient plasmolysis ψ_p = 0, so ψ = ψ_s — which is exactly how the practical measures the solute potential of the cells.
• Animal cells have no wall, so in pure water they burst (lysis); in a concentrated solution they crenate.

Your turn — water potential

Which way does water move?

The cell cycle, mitosis, meiosis and cancer

Interphase (G1 → S → G2) occupies most of the cycle; DNA is replicated in S phase. Then mitosis — prophase (chromosomes condense, nuclear envelope breaks down, spindle forms), metaphase (chromosomes align on the equator), anaphase (centromeres divide; chromatids pulled to the poles), telophase (nuclear envelopes re-form) — then cytokinesis. Two genetically identical diploid cells.

Meiosis has two divisions and produces four haploid, genetically different cells. Variation arises from chiasma formation (crossing over) in prophase I and from independent assortment in metaphase I.

Cancer: a disruption of the cell cycle. Mutations in proto-oncogenes (which become oncogenes, permanently stimulating division) or in tumour suppressor genes (which normally halt the cycle at checkpoints and trigger apoptosis) lead to uncontrolled mitosis and a tumour. Many anticancer drugs work precisely by disrupting rapidly dividing cells — for example by preventing spindle formation, which arrests the cell in metaphase.

Match the process to its bond or enzyme

Tap a process on the left, then the correct answer on the right.

The ileum as a mammalian organ

A tissue is a group of similar cells performing the same function; an organ contains several tissues working together.

The ileum has five tissue layers: mucosa, muscularis mucosa, submucosa, muscularis externa and serosa.

• The mucosa is folded into villi, hugely increasing the surface area for absorption. Its columnar epithelium carries a brush border of microvilli — increasing the area again — and contains goblet cells secreting mucus.
• The epithelial cells have numerous mitochondria, because absorption of glucose and amino acids uses active transport (co-transport with Na⁺) alongside diffusion and pinocytosis.
• Each villus contains blood capillaries (which absorb monosaccharides and amino acids) and a lacteal (which absorbs fats). The rich blood supply maintains the concentration gradient.
• Crypts of Lieberkühn contain the dividing stem cells that continually replace the epithelium, protected by the antimicrobial Paneth cells at the base.

Why so many mitochondria?

The big ideas to know

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