Chemical make-up of a cell
Living tissue and a lump of soil have the same kinds of elements (carbon, hydrogen, oxygen, nitrogen…), but living tissue has far more carbon and hydrogen. To find the carbon compounds, we do a simple analysis:
- Grind living tissue with trichloroacetic acid (Cl₃CCOOH) into a slurry.
- Strain it through cloth or cotton.
- The liquid that passes = acid-soluble pool (filtrate): small molecules like amino acids, sugars, nucleotides.
- What stays behind = acid-insoluble pool (retentate): proteins, nucleic acids, polysaccharides and lipids.
Burning (ashing) tissue removes all carbon compounds; the ash left has inorganic elements (Ca, Mg) and compounds like sulphate and phosphate.
Micromolecules have a molecular weight of 18–800 Da and are in the soluble pool. Macromolecules (biomacromolecules) are above 10,000 Da: proteins, nucleic acids and polysaccharides. Lipids are under 800 Da, yet they come in the insoluble pool because, on grinding, broken membranes form insoluble vesicles.
Typical cell by weight: water 70–90%, proteins 10–15%, nucleic acids 5–7%, carbohydrates 3%, lipids 2%, ions 1%.
Proteins: chains of amino acids
An amino acid has a central carbon (α-carbon) holding four groups: hydrogen, an amino group (–NH₂), a carboxyl group (–COOH) and a variable R group. The R group decides the amino acid: R = H is glycine, R = CH₃ is alanine, R = CH₂OH is serine. Based on amino and carboxyl groups they are acidic (glutamic acid), basic (lysine) or neutral (valine); some are aromatic (tyrosine, phenylalanine, tryptophan). In solution the amino acid carries both + and – charges at a certain pH: a zwitterion.
Amino acids join by peptide bonds (–CO–NH–), losing water, to form polypeptides. A protein is a heteropolymer of up to 20 kinds of amino acids. Essential amino acids must come from food; non-essential ones the body makes.
Four levels of structure
- Primary: the sequence of amino acids, from the N-terminal (first) to the C-terminal (last) end.
- Secondary: parts of the chain coil into a right-handed helix (or form sheets).
- Tertiary: the chain folds on itself like a ball of wool – the 3D shape needed for work.
- Quaternary: two or more chains fit together. Human haemoglobin = 2 α + 2 β subunits.
Jobs: collagen (most plentiful protein in animals) and RuBisCO (most plentiful protein in the biosphere); trypsin (enzyme), insulin (hormone), antibodies (defence), GLUT-4 (carries glucose into cells), receptors (sense smell, taste, hormones).
Carbohydrates (polysaccharides)
Sugars are made of C, H and O. Glucose and ribose are monosaccharides. Two join by a glycosidic bond to make a disaccharide (sucrose, lactose, maltose). Long chains are polysaccharides, found in the acid-insoluble pool.
- Starch – plant food store; its coils (helices) hold iodine and give a blue colour.
- Cellulose – a homopolymer of glucose in plant cell walls (cotton, paper); no helices, so no blue colour with iodine.
- Glycogen – animal food store, highly branched.
- Inulin – a polymer of fructose.
- Chitin – a complex polysaccharide of amino-sugars (like glucosamine) in insect exoskeletons and fungal walls.
In a polysaccharide chain, the right end is the reducing end and the left end is the non-reducing end.
Lipids
Lipids do not dissolve in water. A fatty acid is a carboxyl group joined to a carbon chain (R group); palmitic acid has 16 carbons including the carboxyl carbon, arachidonic acid 20. With no double bonds it is saturated; with one or more it is unsaturated. Glycerol (trihydroxy propane) carries up to three fatty acids: mono-, di- and triglycerides (fats and oils – oils melt at lower temperature, e.g. gingelly oil). Phospholipids such as lecithin have a phosphate group and form cell membranes. Nerve tissue has more complex lipids. Lipids are not strictly macromolecules or polymers.
Nucleic acids
A nucleotide has three parts: a nitrogen base, a pentose sugar and a phosphate. Base + sugar only = nucleoside (adenosine, guanosine, thymidine, uridine, cytidine).
- Purines (two rings): adenine, guanine. Pyrimidines (one ring): cytosine, thymine, uracil.
- DNA: deoxyribose sugar, bases A, G, C, T; double helix – A pairs with T by 2 hydrogen bonds, G with C by 3.
- RNA: ribose sugar, bases A, G, C, U; usually single-stranded.
In a nucleic acid, the phosphate joins the 3′ carbon of one sugar to the 5′ carbon of the next: a phosphodiester bond. The Watson–Crick (B-DNA) model: the two strands are antiparallel, one full turn has 10 base pairs, rise per base pair is 0.34 nm, and a turn is 3.4 nm long.
Enzymes: types, properties and action
Enzymes are biological catalysts – almost all are proteins; a few nucleic acids also act like enzymes and are called ribozymes. They speed up reactions and come out unchanged.
How they act
Each enzyme has an active site, a pocket where the substrate fits. E + S → ES (enzyme–substrate complex) → EP → E + P. Energy is needed to start any reaction – the activation energy. The enzyme lowers it, so the reaction goes much faster. Example: carbonic anhydrase makes CO₂ + H₂O → H₂CO₃ about 10 million times faster (about 600,000 molecules per second instead of about 200 per hour).
Factors affecting enzyme activity
- Temperature and pH: each enzyme has an optimum. Low temperature keeps it inactive for a while; high temperature denatures it (destroys the shape).
- Substrate concentration: the rate rises and then levels off at Vmax when all active sites are busy. Km = substrate concentration at half Vmax.
- Inhibitors: a competitive inhibitor looks like the substrate and blocks the active site – e.g. malonate blocks succinic dehydrogenase. Such inhibitors are used to control bacterial germs.
Six classes
- Oxidoreductases/dehydrogenases – move H or electrons between two substrates.
- Transferases – move a group (not H) between substrates.
- Hydrolases – break ester, ether, peptide, glycosidic, C–C or P–N bonds using water.
- Lyases – remove groups without water, leaving double bonds.
- Isomerases – change one isomer into another.
- Ligases – join two compounds (e.g. C–O, C–S, C–N, P–O bonds).
Co-factors
The protein part is the apoenzyme. Many need a non-protein helper: a prosthetic group (tightly bound, e.g. haem in peroxidase and catalase), a co-enzyme (loosely bound, often from vitamins, e.g. NAD and NADP contain niacin) or a metal ion (e.g. zinc for carboxypeptidase). Remove the co-factor and the enzyme stops working.
Try it: see an enzyme at work
Chew a small piece of plain roti or boiled rice for two minutes without swallowing – it starts to taste sweet, because amylase in saliva breaks starch into sugar. Now test the effect of heat: put a drop of iodine on a slice of raw potato (blue-black = starch). Then cut a raw potato and a boiled potato, add a drop of hydrogen peroxide (from a chemist) to each – the raw one fizzes because its catalase enzyme works; the boiled one hardly fizzes because heat denatured the enzyme. Match this with step 6 of the 3D.
Key formulas and definitions
- Acid-soluble pool: micromolecules (18–800 Da); acid-insoluble pool: proteins, nucleic acids, polysaccharides (> 10,000 Da) + lipids
- Amino acid: α-carbon + H + –NH₂ + –COOH + R group
- Peptide bond: –CO–NH–; glycosidic bond (sugars); ester bond (fats); phosphodiester bond (nucleic acids)
- Protein structure: primary → secondary → tertiary → quaternary
- Nucleotide = base + pentose sugar + phosphate; nucleoside = base + sugar
- E + S ⇌ ES → EP → E + P
- Enzyme classes: oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases
- Holoenzyme = apoenzyme + co-factor (prosthetic group / co-enzyme / metal ion)
Worked examples
1. Liver tissue is ground in trichloroacetic acid and filtered. In which fraction will you find (a) glucose, (b) DNA, (c) phospholipids?
(a) Glucose is small → filtrate (acid-soluble pool). (b) DNA is a macromolecule → retentate (acid-insoluble). (c) Phospholipids are small, but broken membranes form vesicles, so they also stay in the acid-insoluble pool.
2. A DNA segment has 20 base pairs. How many full turns of the double helix does it make, and how long is it?
One turn = 10 bp, so 20 ÷ 10 = 2 turns. Length = 20 × 0.34 nm = 6.8 nm.
3. A DNA molecule has 30% adenine. Find the percentage of guanine.
A = T, so T = 30%. A + T = 60%, so G + C = 40%. G = C, so G = 20%.
4. Name the level of protein structure: (a) the order of amino acids, (b) 4 chains in haemoglobin, (c) the helix.
(a) Primary, (b) quaternary, (c) secondary.
5. An enzyme joins two DNA pieces by forming a P–O bond. To which class does it belong?
It joins two molecules by a new bond → ligase (DNA ligase).
6. An enzyme shows Vmax = 100 units. At what rate is the substrate concentration equal to Km?
Km is the substrate concentration at which the rate is half of Vmax: 100 ÷ 2 = 50 units.
Common mistakes
- Calling lipids macromolecules. They are under 800 Da; they land in the acid-insoluble pool only because membranes form vesicles.
- Thinking low temperature denatures enzymes. Cold only makes them inactive for a while; high temperature destroys the shape.
- Mixing nucleoside and nucleotide: nucleoside has no phosphate; nucleotide = nucleoside + phosphate.
- Saying cellulose turns blue with iodine. Only starch does, because its helices trap iodine; cellulose has no helices.