Water, carbohydrates, lipids and proteins

Water is polar and hydrogen bonds to itself: hence its role as a solvent, its high specific heat capacity (temperature buffering), its high latent heat of vaporisation (cooling by evaporation), and its cohesion and surface tension.

Carbohydrates: monosaccharides join by condensation, forming a glycosidic bond. Starch and glycogen are branched, coiled, insoluble stores of α-glucose; cellulose is straight chains of β-glucose hydrogen-bonded into microfibrils.

Lipids: a triglyceride is glycerol + three fatty acids joined by three ester bonds. Saturated fatty acids have no C=C; unsaturated ones do. A phospholipid has a hydrophilic phosphate head and hydrophobic tails.

Proteins: amino acids join by peptide bonds (condensation). Primary → secondary (α-helix, β-pleated sheet; hydrogen bonds) → tertiary (hydrogen, ionic and disulfide bonds and hydrophobic interactions) → quaternary. Fibrous proteins (collagen) are structural and insoluble; globular proteins (enzymes, haemoglobin) are soluble and functional.

Qualitative reagents: iodine → blue-black for starch; Benedict’s (heated) → brick-red for a reducing sugar; Biuret → purple for protein; emulsion test → white emulsion for lipid.

Which bond?

Tap the molecules being joined, then the bond that joins them.

Your turn — peptide bonds

Cell structure, organisation and microscopy

Eukaryotic cells: nucleus (envelope, pores, nucleolus), rough ER (protein synthesis and transport), smooth ER (lipid synthesis), Golgi (modification and packaging; makes lysosomes), mitochondria (cristae, matrix), lysosomes, 80S ribosomes; plants also have a cellulose wall, chloroplasts and a vacuole.

Prokaryotic cells: circular DNA, plasmids, 70S ribosomes, a murein (peptidoglycan) wall, sometimes a capsule and flagellum — and no membrane-bound organelles.

Levels of organisation: organelle → cell → tissue → organ → organ system → organism.

Magnification vs resolution: magnification is how much bigger the image is; resolution is the smallest distance at which two points can still be distinguished. Resolution is limited by wavelength — which is why the electron microscope (resolving ~0.1 nm) beats the light microscope (~200 nm), and why simply magnifying a light image further just gives a bigger blur.

Your turn — magnification

The fluid-mosaic membrane, transport and water potential

The fluid-mosaic model: a phospholipid bilayer with intrinsic (channel and carrier) proteins, extrinsic proteins, cholesterol regulating fluidity, and glycoproteins and glycolipids for recognition.

• Diffusion — small non-polar molecules straight through the bilayer, down the gradient. Passive.
• Facilitated diffusion — polar molecules and ions through channel or carrier proteins, down the gradient. Passive.
• Osmosis — water down the water potential gradient through a partially permeable membrane (largely through aquaporins).
• Active transport — a carrier protein plus ATP, moving a substance against its gradient.
• Endocytosis / exocytosis — bulk transport in vesicles; both require ATP.

Plant cell: in a dilute solution it becomes turgid (the wall pushes back, so ψ_p rises); in a concentrated one, plasmolysed. An animal cell has no wall, so in pure water it bursts. This is why the practical determines water potential by finding the concentration at which there is no change in mass or length.

Your turn — water potential

Does it need ATP?

Tap a process, then tap the group it belongs to.

Enzymes and inhibition

Enzymes are globular proteins that lower the activation energy of a reaction. The active site is complementary to the substrate; its shape comes from the tertiary structure. The induced fit model says the active site changes shape slightly as the substrate binds, straining the substrate’s bonds.

• Temperature — rate rises with kinetic energy; past the optimum, the bonds holding the tertiary structure break and the enzyme is denatured.
• pH — extremes disrupt the ionic and hydrogen bonds of the tertiary structure, changing the active site.
• Substrate concentration — the rate rises, then plateaus when all the active sites are saturated.
• Competitive inhibitor — similar shape to the substrate; binds the active site; effect overcome by adding more substrate.
• Non-competitive inhibitor — binds elsewhere and distorts the active site; not overcome by more substrate.

Immobilised enzymes (trapped in alginate beads) can be reused, do not contaminate the product, and are more stable to changes in pH and temperature — which is why industry uses them.

Your turn — rate of reaction

Diagnose the inhibitor

DNA, RNA and replication

A nucleotide = pentose sugar + phosphate + nitrogenous base. Nucleotides join by phosphodiester bonds to form a sugar–phosphate backbone.

DNA — an antiparallel double helix. A–T (two hydrogen bonds) and C–G (three). RNA — single-stranded, ribose, uracil instead of thymine.

Semi-conservative replication: DNA helicase breaks the hydrogen bonds; free nucleotides pair with the exposed bases; DNA polymerase joins them, always working 5′→3′ (hence a leading and a lagging strand). Each new molecule has one original and one new strand — as Meselson and Stahl proved using ¹⁵N and ¹⁴N.

Transcription and translation

Transcription (nucleus): RNA polymerase reads the DNA template strand and builds a complementary mRNA. In eukaryotes the primary transcript is spliced: non-coding introns are removed and the coding exons joined. The mature mRNA leaves through a nuclear pore.

Translation (ribosome): each mRNA codon is recognised by the complementary anticodon of a tRNA carrying a specific amino acid. The ribosome catalyses peptide bond formation and moves along one codon at a time until it reaches a stop codon.

The genetic code is triplet, non-overlapping, degenerate (so some base substitutions are silent) and effectively universal — which is why a human gene can be expressed in a bacterium.

ATP is the universal energy currency: hydrolysis of ATP → ADP + P_i releases a readily usable quantity of energy, and the phosphate group can be transferred to another molecule to make it more reactive (phosphorylation). ATP is small, soluble, and easily and rapidly regenerated.

Where does it happen?

Membrane structure

The big ideas to know

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