Finding out what cells are made of
To analyse the chemicals in living tissue, it is ground in trichloroacetic acid, giving a thick slurry that is filtered:
the filtrate (acid-soluble pool) contains small molecules with molecular mass below about 1000 Da: sugars, amino acids, nucleotides;
the retentate (acid-insoluble fraction) contains large molecules, the macromolecules: proteins, polysaccharides and nucleic acids. Lipids also appear here, because they form membranes that break into vesicles, although they are small molecules.
Living tissue is about 70–90% water. Of the rest, proteins form the largest share.
Small molecules
Amino acids have an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen and a variable R group attached to the same carbon (the α-carbon). There are 20 types in proteins, differing in their R group: glycine (R = H), alanine (R = CH₃), serine (R = CH₂OH).
Lipids are generally insoluble in water. A fatty acid has a carboxyl group attached to a hydrocarbon chain, which may be saturated (no double bonds) or unsaturated. Fats and oils are esters of glycerol with three fatty acids: triglycerides. Oils have lower melting points and are liquid in winter. Phospholipids, which contain phosphorus, form cell membranes.
Nucleotides consist of a nitrogenous base, a pentose sugar and a phosphate.
Bases: purines (adenine, guanine) and pyrimidines (cytosine, uracil, thymine).
A base + sugar is a nucleoside; adding a phosphate makes a nucleotide.
Polysaccharides
Long chains of sugar units (monosaccharides) joined by glycosidic bonds.
Polysaccharide | Monomer | Role |
|---|---|---|
Cellulose | glucose | structural; plant cell walls; does not give a blue colour with iodine |
Starch | glucose | stored food in plants; forms a blue-black complex with iodine |
Glycogen | glucose | stored food in animals (liver and muscles) |
Inulin | fructose | a fructose polymer |
Chitin | amino sugars | exoskeletons of insects and other arthropods; fungal cell walls |
A polysaccharide chain has a reducing end on one side and a non-reducing end on the other. Starch forms helices that can trap iodine, giving the blue colour.
Proteins
Proteins are polypeptides: chains of amino acids joined by peptide bonds, formed between the carboxyl group of one amino acid and the amino group of the next with the loss of water.
Proteins do many jobs: transport (haemoglobin carries oxygen), enzymes (trypsin), hormones (insulin), defence (antibodies), structure (collagen, the most abundant protein in animals), and receptors. RuBisCO is the most abundant protein in the whole biosphere.
Levels of protein structure:
Level | Description |
|---|---|
Primary | the sequence of amino acids, from the N-terminal to the C-terminal end |
Secondary | local folding into an α-helix (right-handed) or β-pleated sheet, held by hydrogen bonds |
Tertiary | the whole chain folds into a 3D shape, essential for biological activity |
Quaternary | several polypeptide chains combine; adult haemoglobin has 2 α and 2 β chains |
Some amino acids are essential: our bodies can't make them, so they must come from food.
Nucleic acids
Nucleic acids (DNA and RNA) are polymers of nucleotides, joined by phosphodiester bonds between the sugar of one nucleotide and the phosphate of the next.
DNA exists as a double helix (Watson and Crick). The two strands are antiparallel and held by hydrogen bonds between bases: A pairs with T (two hydrogen bonds) and G pairs with C (three). The helix makes one full turn every 10 base pairs, a pitch of 3.4 nm.
Metabolism
Biomolecules are constantly being made and broken down. These reactions, always catalysed by enzymes, form metabolic pathways.
Anabolic pathways build complex molecules and consume energy (e.g. making protein from amino acids).
Catabolic pathways break molecules down and release energy (e.g. glycolysis, glucose → lactic acid in muscle).
The energy currency of the cell is ATP. Living systems exist in a steady state that is not at equilibrium; reaching equilibrium would mean death.
Enzymes
Almost all enzymes are proteins (a few nucleic acids, called ribozymes, also act as catalysts). An enzyme has an active site, a pocket into which the substrate fits.
Enzymes speed up reactions by lowering the activation energy. The enzyme and substrate form an enzyme-substrate complex (ES), which changes into the enzyme-product complex and releases the product, leaving the enzyme unchanged:
E + S ⇌ ES → EP → E + P
Example. Carbonic anhydrase speeds the reaction of CO₂ with water about 10 million times.
Factors affecting enzyme activity:
Temperature and pH: each enzyme has an optimum. Activity falls on either side. High temperatures denature the protein; low temperatures only make it temporarily inactive.
Substrate concentration: the rate rises with substrate concentration until it reaches a maximum velocity (Vmax), when all active sites are occupied.
Inhibitors: a competitive inhibitor closely resembles the substrate and competes for the active site. Malonate inhibits succinic dehydrogenase because it resembles succinate. Such inhibition is used in some drugs to control bacterial pathogens.
Six classes of enzymes:
Class | Catalyses |
|---|---|
Oxidoreductases / dehydrogenases | oxidation-reduction |
Transferases | transfer of a group between substrates |
Hydrolases | breaking bonds by adding water |
Lyases | removing groups without hydrolysis, leaving double bonds |
Isomerases | interconversion of isomers |
Ligases | joining two compounds together |
Cofactors are non-protein parts some enzymes need. The protein part alone is the apoenzyme. Cofactors include prosthetic groups (tightly bound, like haem in peroxidase), coenzymes (loosely bound, like NAD and NADP, which contain the vitamin niacin) and metal ions (zinc in carboxypeptidase).
Summary
The acid-insoluble fraction holds the macromolecules: proteins, polysaccharides and nucleic acids (plus lipids).
Proteins have primary, secondary, tertiary and quaternary structure; collagen is the most abundant animal protein.
DNA is a double helix with A–T and G–C pairing.
Enzymes lower activation energy, have optimum temperature and pH, and can be competitively inhibited.