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.
What counts as a carbohydrate
Read this section in the notes →Why isn't every compound with formula Cₓ(H₂O)ᵧ a carbohydrate?
The old idea of carbohydrates as hydrates of carbon fails in both directions. Acetic acid, C₂H₄O₂, fits the formula but is not a carbohydrate, while rhamnose, C₆H₁₂O₅, does not fit and is one. So carbohydrates are defined chemically instead, as optically active polyhydroxy aldehydes or ketones, or compounds that give these on hydrolysis.
What is the difference between reducing and non-reducing sugars?
A reducing sugar has a free aldehyde or ketone group, or a ring that can open to give one, so it reduces Fehling's solution and Tollens' reagent. All monosaccharides, maltose and lactose are reducing. In sucrose the two units are joined through both their reducing carbons, C1 of glucose and C2 of fructose, so no free group remains and it is non-reducing.
Glucose: how it is made and the open-chain evidence
Read this section in the notes →What evidence shows glucose has a straight chain of six carbons and an aldehyde group?
Prolonged heating with HI gives n-hexane, so the six carbons form an unbranched chain. Glucose forms an oxime with hydroxylamine and adds HCN, which shows a carbonyl group. Mild oxidation with bromine water gives gluconic acid with the same six carbons, so the carbonyl must be an aldehyde. Acetylation to a pentaacetate shows five –OH groups.
D and L: relative configuration
Read this section in the notes →Do D and L in sugar names tell us the direction of optical rotation?
No. D and L give the relative configuration: in a D sugar the –OH on the lowest chiral carbon points right in the Fischer projection, matching D-glyceraldehyde. The sign of rotation, written (+) or (−), has to be measured. D-glucose is dextrorotatory but D-fructose is laevorotatory, so the two labels are independent.
Ring forms of glucose and fructose
Read this section in the notes →What evidence shows glucose exists mainly in a ring form?
Several observations do not fit the open chain. Glucose gives no Schiff's test and no addition product with sodium hydrogensulphite, and its pentaacetate does not react with hydroxylamine, so no free –CHO is present. Glucose also exists as two crystalline forms with different properties. All of this is explained by the –OH on C5 joining the aldehyde to make a six-membered ring.
What are anomers?
Anomers are the two ring forms of a sugar that differ only at the carbon that was the carbonyl carbon, C1 in glucose, called the anomeric carbon. In α-D-glucose the –OH on C1 is on the opposite side to the CH₂OH group, and in β-D-glucose it is on the same side. They have different melting points, 419 K and 423 K.
Why does glucose form a pyranose ring but fructose a furanose ring?
Glucose is an aldose; its C5 –OH attacks the C1 aldehyde, forming a six-membered ring of five carbons and an oxygen, like pyran. Fructose is a ketose with its carbonyl at C2; its C5 –OH attacks C2, forming a five-membered ring of four carbons and an oxygen, like furan. Both rings exist in α and β forms.
Disaccharides and the glycosidic link
Read this section in the notes →Why is the hydrolysis product of sucrose called invert sugar?
Sucrose is dextrorotatory. Hydrolysis splits it into equal amounts of D-(+)-glucose and D-(−)-fructose, and fructose rotates light to the left more strongly than glucose rotates it to the right. So the mixture as a whole is laevorotatory, and the sign of rotation has flipped, or inverted. The mixture is called invert sugar.
What are maltose and lactose made of?
Maltose is two α-D-glucose units joined from C1 of one to C4 of the other. Lactose, milk sugar, is β-D-galactose joined from C1 to C4 of β-D-glucose. In both, one unit keeps a free anomeric carbon that can open to a carbonyl, so both are reducing sugars, unlike sucrose. The bond joining sugar units is called a glycosidic linkage.
Polysaccharides and why carbohydrates matter
Read this section in the notes →What is the difference between starch and cellulose?
Both are polymers of D-glucose, but starch is made of α-glucose and cellulose of β-glucose. In cellulose, β-1,4 links produce straight chains that pack side by side into strong fibres, making it the main material of plant cell walls. Starch is a food store in plants. Humans can digest starch but lack the enzymes to break the β links of cellulose.
What is the difference between amylose and amylopectin?
Amylose is the water-soluble part of starch, about 15–20%, and is an unbranched chain of α-glucose joined C1 to C4. Amylopectin is the insoluble part, about 80–85%, and is branched: its chains are linked C1 to C4, with branches attached by C1 to C6 links. Glycogen, the animal store found in the liver, muscles and brain, resembles amylopectin but branches even more.
Amino acids
Read this section in the notes →What is the difference between essential and non-essential amino acids?
Non-essential amino acids can be made by the body, while essential ones cannot and must come from the diet. Both are needed to build proteins, so the word refers only to where they come from, not to their importance. Valine, leucine, isoleucine, lysine and phenylalanine are among the essential ones.
Why do amino acids have high melting points and dissolve in water?
In water and in the solid, an amino acid's acidic –COOH gives its proton to its own basic –NH₂ group, forming a zwitterion that carries both a positive and a negative charge. Amino acids therefore behave like salts, with strong attractions between the dipolar ions. That explains their high melting points and good solubility in water, unlike typical organic molecules.
Why is glycine not optically active?
Glycine, NH₂CH₂COOH, has two hydrogens on its α-carbon, so that carbon is not bonded to four different groups and is not a chiral centre. Every other amino acid found in proteins has a chiral α-carbon and is optically active, and the natural ones mostly have the L configuration.
Peptides and the four levels of protein structure
Read this section in the notes →What is the difference between the primary, secondary, tertiary and quaternary structures of proteins?
Primary structure is the sequence of amino acids, held by peptide bonds. Secondary structure is the local folding into an α-helix or β-pleated sheet, held by hydrogen bonds between peptide groups. Tertiary structure is the overall folding of a chain into a fibrous or globular shape. Quaternary structure is how several chains, or subunits, are arranged together.
Denaturation and enzymes
Read this section in the notes →What happens to a protein when it is denatured?
Heat or a change in pH disrupts the hydrogen bonds and other attractions that hold the protein in shape, so its secondary and tertiary structure unfold. The protein loses its biological activity. But the peptide bonds are untouched, so the primary structure, the amino acid sequence, stays the same. Boiling an egg, which hardens its white, and curdling milk are examples.
What are enzymes and why are they so specific?
Enzymes are biological catalysts, almost all of them proteins, that speed up reactions in living cells by lowering activation energy. Each has an active site shaped to fit particular substrate molecules, so it catalyses only one reaction or one kind of reaction. Their names usually end in -ase, such as maltase, which hydrolyses maltose into glucose.
Vitamins
Read this section in the notes →Why must water-soluble vitamins be taken regularly in the diet?
Vitamins B and C dissolve in water, so any excess is lost in urine and the body cannot store them. They must be supplied steadily through food. Vitamin B₁₂ is an exception and can be stored. Fat-soluble vitamins A, D, E and K are stored in fat tissue and the liver, so a large excess of them can build up.
Nucleic acids
Read this section in the notes →How is a nucleotide different from a nucleoside?
A nucleoside is a nitrogenous base joined to a pentose sugar at its 1′ carbon. A nucleotide is a nucleoside with a phosphate group attached to the sugar at its 5′ carbon. Nucleotides are joined into nucleic acid chains through phosphodiester links between the 5′ and 3′ carbons of neighbouring sugars.
What is the difference between DNA and RNA?
DNA contains the sugar 2-deoxyribose and the bases adenine, guanine, cytosine and thymine, and forms a double helix. RNA contains ribose and has uracil instead of thymine, and it is usually single-stranded. DNA stores genetic information and copies itself. RNA, in its messenger, ribosomal and transfer forms, helps turn that information into proteins.
How do the two strands of DNA pair up?
The strands are held together by hydrogen bonds between bases, and pairing is specific. Adenine pairs with thymine, and guanine pairs with cytosine, so the strands are complementary, and knowing one gives the sequence of the other. This specific pairing is what allows DNA to be copied accurately during replication.
Hormones
Read this section in the notes →How are hormones classified chemically?
Hormones are grouped by chemical type. Some are steroids, such as the sex hormones estrogens and androgens. Others are polypeptides, such as insulin and glucagon, which control blood glucose. Still others are derived from amino acids, such as thyroxine, which comes from tyrosine, and epinephrine. Their job is to carry messages between cells.
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