Biomolecules: common doubts, answered
The questions students ask most often about Biomolecules, each with a short answer. For the full chapter, read the Biomolecules notes.
How to analyse chemical composition
Read this section in the notes →How do we find out the chemical composition of a living tissue?
Tissue is ground in trichloroacetic acid and filtered, which gives an acid-soluble filtrate and an acid-insoluble retentate. The filtrate holds small biomicromolecules, while the retentate holds the macromolecules except lipids. Another method burns the dried tissue to ash, and the ash contains the inorganic elements such as calcium and magnesium.
Amino acids
Read this section in the notes →What is the structure of an amino acid?
An amino acid has a central carbon, the alpha carbon, to which four groups are attached: a hydrogen, a carboxyl group, an amino group and a variable R group. The R group decides the type of amino acid. Glycine has hydrogen as R, alanine has a methyl group, and serine has a hydroxy methyl group.
What is a zwitterion?
A zwitterion is an amino acid in which the amino group and the carboxyl group are both ionised, so the molecule carries a positive and a negative charge at once. The ionisation depends on the pH of the solution, which is why amino acids can behave as acids or as bases. Acidic, basic and neutral amino acids differ in their R group.
Lipids, nucleotides and sugars
Read this section in the notes →What is the difference between a nucleoside and a nucleotide?
A nucleoside is a nitrogenous base joined to a sugar, as in adenosine. A nucleotide is a nucleoside with a phosphate group esterified to the sugar, as in adenylic acid. The nucleic acids DNA and RNA are polymers of nucleotides. Students sometimes swap the two, so count whether a phosphate is present.
Which nitrogenous bases are purines and which are pyrimidines?
Adenine and guanine are purines, with a double-ring structure. Cytosine, thymine and uracil are pyrimidines, with a single ring. DNA contains thymine while RNA contains uracil in its place. Cytosine is common to both DNA and RNA, while thymine is found only in DNA.
Primary and secondary metabolites
Read this section in the notes →Are lipids macromolecules?
Not truly. Lipids have low molecular weights, never above about 800 daltons, so they are not strict macromolecules. They appear in the acid-insoluble fraction only because membrane fragments form insoluble vesicles when the tissue is ground. The real biomacromolecules are proteins, nucleic acids and polysaccharides.
What is the difference between primary and secondary metabolites?
Primary metabolites, such as amino acids and sugars, have identifiable functions in normal growth and development. Secondary metabolites, such as alkaloids, pigments, rubber, essential oils and drugs, have no obvious role in normal physiological processes of the organism, though they may serve in defence and are useful to humans.
Biomacromolecules
Read this section in the notes →What are the most abundant chemical and the most abundant protein in cells?
Water is the most abundant chemical in living organisms, making up 70 to 90 per cent of cell mass. Among organic compounds, protein is the most abundant, about 10 to 15 per cent. Collagen is the most abundant protein in the animal world, whereas RuBisCO is the most abundant in the whole biosphere.
Proteins
Read this section in the notes →What is the difference between homopolymer and heteropolymer?
A homopolymer repeats one kind of monomer, as in cellulose, which is made only of glucose. A heteropolymer has different kinds of monomers, as in a protein, which is built from many types of amino acids. Inulin is another homopolymer, made of fructose units. The chain of a protein is joined by peptide bonds.
Polysaccharides
Read this section in the notes →Why does starch give a blue colour with iodine but cellulose does not?
Starch forms helical secondary structures in which iodine molecules get held, and this complex is blue. Cellulose does not form such helices, so it gives no colour with iodine. Starch is the storage polysaccharide of plants, while cellulose is a structural homopolymer made of glucose.
What are chitin and glycogen made of?
Chitin, the hard material in the exoskeleton of arthropods, is a complex polysaccharide made of amino-sugar units. Glycogen is the storage polysaccharide of animals and is a branched glucose polymer. Both are polysaccharides, but chitin is structural and glycogen serves as a reserve of energy.
Nucleic acids
Read this section in the notes →What is the difference between DNA and RNA in terms of structure?
DNA has deoxyribose as its sugar and the base thymine, whereas RNA has ribose and uracil in place of thymine. Both are polymers of nucleotides, with adenine, guanine and cytosine common to both. Ribozymes are an unusual case where a nucleic acid, rather than a protein, acts as an enzyme.
Structure of proteins
Read this section in the notes →What are the four levels of protein structure?
The primary structure is the sequence of amino acids. The secondary structure is the regular folding of the chain, such as the right-handed helix. The tertiary structure is the three-dimensional folding of the whole chain, and the quaternary structure is the arrangement of several polypeptide subunits. Adult haemoglobin has two alpha and two beta subunits.
How enzymes speed up reactions
Read this section in the notes →How does an enzyme speed up a reaction?
An enzyme lowers the activation energy, the energy needed to reach the transition state, so the substrate converts to product more easily. It forms an enzyme-substrate complex, E + S going to ES, then EP, then releases E and P. The energy levels of substrate and product remain the same, so the enzyme does not change the overall energy released.
Can an enzyme make an endothermic reaction exothermic?
No. An enzyme only lowers the activation energy and does not alter the energy levels of the substrate and the product. Whether the reaction releases or absorbs energy overall is fixed by those levels. So enzymes make reactions faster without changing their direction or the net energy change.
Factors affecting enzyme activity
Read this section in the notes →Why does the enzyme activity stop rising with more substrate?
The velocity rises with substrate concentration only until all the enzyme molecules are occupied. After that the rate reaches its maximum, Vmax, and adding more substrate has no further effect. The curve therefore levels off into a plateau, because the enzyme, not the substrate, becomes the limiting factor.
What is the difference between the effect of high and low temperature on enzymes?
High temperature denatures an enzyme, a permanent loss of its structure and activity, since most enzymes are damaged above about 40 degrees Celsius. Low temperature only makes the enzyme temporarily inactive, and activity returns when it is warmed. Enzymes from thermophilic organisms remain active even up to 80 to 90 degrees Celsius.
What is competitive inhibition, with an example?
In competitive inhibition, an inhibitor that closely resembles the substrate competes for the enzyme's active site and so reduces the enzyme's activity. Malonate inhibits succinic dehydrogenase because it looks like the substrate succinate. Adding more substrate can overcome this kind of inhibition.
Classification of enzymes and co-factors
Read this section in the notes →What are the six classes of enzymes?
The six classes are oxidoreductases, transferases, hydrolases, lyases, isomerases and ligases. Oxidoreductases carry out oxidation and reduction, transferases move a group between substrates, hydrolases break bonds using water, lyases cleave bonds without water, isomerases rearrange a molecule, and ligases join two compounds.
What is the difference between a prosthetic group, a co-enzyme and a metal ion co-factor?
A prosthetic group is an organic co-factor bound tightly to the apoenzyme, such as haem in peroxidase and catalase. A co-enzyme is also organic but associates with the apoenzyme only briefly during catalysis, as NAD and NADP do, and both contain the vitamin niacin. A metal ion co-factor is inorganic and forms coordination bonds at the active site, as zinc does in carboxypeptidase.
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