Biomolecules — Carbohydrates, Proteins and Nucleic Acids

Biomolecules is the one organic chapter where the paper asks mostly for recall, and that makes it unusually efficient to prepare: the questions repeat, and a compact set of facts covers almost all of them. But it is worth noticing that the chemistry underneath is entirely familiar. A carbohydrate is a polyhydroxy aldehyde or ketone, so it does aldehyde reactions. A protein is a polyamide. A nucleic acid is a phosphate ester. Nothing new is being introduced — you are watching the functional groups from the last five chapters assembled into larger molecules, which is why the reactions behave exactly as you would predict.

Carbohydrates

Classification, with the examples the paper names
ClassDefinitionExamples
MonosaccharideCannot be hydrolysed furtherGlucose, fructose, ribose
DisaccharideGives two monosaccharidesSucrose, maltose, lactose
PolysaccharideMany units; not sweet, not reducingStarch, cellulose, glycogen
Reducing sugarHas a free aldehyde or ketone groupGlucose, fructose, maltose, lactose
Non-reducing sugarBoth anomeric carbons are tied up in the linkageSucrose — the standard exception
🎯 Why fructose reduces Tollens' reagent even though it is a ketone
A ketone should not reduce Tollens' reagent, so fructose looks like a contradiction. The resolution is that Tollens' reagent is alkaline, and in alkali fructose undergoes keto–enol tautomerism and rearranges into glucose and mannose, both of which are aldehydes. So the aldehyde that does the reducing was not there to begin with; the base created it. This is why fructose counts as a reducing sugar despite being a ketose, and it is also a reminder that a test tells you what a compound becomes under the test conditions, not only what it was.

Glucose's structure is settled by a short list of reactions. It forms a pentaacetate, so it has five OH groups; it reduces Tollens' and Fehling's reagents and gives an oxime, so it has an aldehyde; mild oxidation with bromine water gives gluconic acid, and stronger oxidation with nitric acid gives the dicarboxylic saccharic acid, which shows a primary alcohol at the far end. Reduction with HI gives n-hexane, proving a straight chain. In the cyclic pyranose form the C-1 hydroxyl can point either way, giving the alpha and beta anomers, and their interconversion in solution is what causes mutarotation.

Amino Acids and Proteins

An amino acid carries both a basic amino group and an acidic carboxyl group, so in solution it exists as a zwitterion — internally ionised, dipolar and overall neutral. That explains its high melting point and its solubility in water but not in organic solvents, and it explains amphoteric behaviour: the same molecule reacts with acid and with base. The pH at which the zwitterion has no net charge is the isoelectric point, and at that pH the amino acid does not migrate in an electric field, which is how mixtures are separated.

The four levels of protein structure
LevelWhat it describesHeld together by
PrimaryThe sequence of amino acidsPeptide (covalent) bonds
SecondaryLocal shape — alpha helix or beta sheetHydrogen bonds
TertiaryThe overall three-dimensional foldDisulphide bridges, hydrophobic and ionic forces
QuaternaryHow several folded chains assembleThe same weak forces between subunits
📖 Boiling an egg is denaturation, and it explains the whole hierarchy
Egg white is soluble albumin; heat it and it turns into an opaque solid that will never dissolve again. What has happened is that the hydrogen bonds and hydrophobic contacts holding the secondary and tertiary structure have been broken, so the chains unfold and tangle irreversibly. But the peptide bonds are untouched — the primary sequence is exactly what it was, which is why cooked protein is still nutritious. That single observation fixes the hierarchy in mind: heat, acid and alcohol destroy the higher levels while leaving the primary structure intact, and only hydrolysis breaks peptide bonds. A question asking what denaturation destroys wants "secondary and tertiary structure, not primary".

Enzymes are proteins that catalyse with extraordinary specificity, work best near 310 K and a narrow pH, and are denatured outside those limits — which is why a fever is dangerous and why enzyme catalysis has no industrial equivalent at high temperature. Vitamins divide into water-soluble (B group and C, excreted and so needed regularly) and fat-soluble (A, D, E, K, stored in the liver and toxic in excess). The deficiency diseases most often asked are scurvy for C, beriberi for B₁, pernicious anaemia for B₁₂, night blindness for A, rickets for D and impaired clotting for K.

Nucleic Acids

DNA compared with RNA
FeatureDNARNA
Sugar2-deoxy-D-riboseD-ribose
BasesA, G, C and thymineA, G, C and uracil
StrandsDouble helixUsually single
FunctionStores and transmits genetic informationCarries out protein synthesis
Base pairingA–T by two H bonds, G–C by threeA–U where pairing occurs
🎯 Why G–C rich DNA is harder to melt
Adenine and thymine are held together by two hydrogen bonds, but guanine and cytosine by three. So a stretch of DNA rich in G–C pairs takes more energy to pull apart, and its melting temperature is measurably higher — an effect real enough that organisms living in hot springs have G–C rich genomes. The same pairing rule explains why the two strands are complementary, so that knowing one sequence gives you the other for free, and why replication can be accurate at all. For the exam the two facts to hold are the pairing partners and the bond counts, because most questions reduce to one or the other.

A nucleoside is a base joined to a sugar; add a phosphate and it becomes a nucleotide, which is the repeating unit of the chain. The backbone is a sugar–phosphate chain and the bases point inwards. Note the naming trap: adenosine is the nucleoside, adenosine monophosphate the nucleotide, and only the phosphate-containing form appears in the polymer — a distinction questions test by asking which of four listed species is a nucleotide.

Key takeaways

  • Sucrose is the standard non-reducing sugar, because both anomeric carbons are used in the linkage.
  • Fructose reduces Tollens because alkali tautomerises it into glucose and mannose first.
  • Glucose has five OH groups, an aldehyde and a straight chain — each established by a specific reaction.
  • Amino acids exist as zwitterions, which is why they melt high and are amphoteric.
  • Primary structure is peptide bonds; secondary is hydrogen bonds; tertiary adds disulphide bridges.
  • Denaturation destroys secondary and tertiary structure but leaves the primary sequence intact.
  • DNA has thymine and deoxyribose; RNA has uracil and ribose. A–T uses two H bonds, G–C three.
  • A nucleoside is base plus sugar; adding phosphate makes it a nucleotide, the unit of the chain.

Practice questions (8)

Attempt each one before opening the answer. Every explanation names the tempting wrong option as well as the right one, because that is where marks are lost.

  1. Which of the following is a non-reducing sugar?

    1. Glucose
    2. Maltose
    3. Sucrose
    4. Lactose
    Show answer

    Answer: C — Sucrose

    In sucrose the glycosidic linkage uses the anomeric carbon of both glucose and fructose, so no free aldehyde or ketone group is left and the sugar cannot reduce Tollens' or Fehling's reagent. Maltose and lactose each keep one anomeric carbon free and so are reducing, and glucose has an open aldehyde group in equilibrium with its ring form.
  2. Fructose gives a positive Tollens test although it is a ketose. This is because:

    1. Ketones normally reduce Tollens' reagent
    2. In alkaline medium it tautomerises into glucose and mannose, which are aldehydes
    3. It contains a carboxylic acid group
    4. Fructose is actually an aldose
    Show answer

    Answer: B — In alkaline medium it tautomerises into glucose and mannose, which are aldehydes

    Tollens' reagent is alkaline, and base promotes keto–enol tautomerism that converts fructose into the aldoses glucose and mannose; those aldehydes then reduce the silver ion. So the aldehyde group is created by the test conditions rather than being present at the outset — which is why an isolated ketone in a neutral medium gives no reaction at all.
  3. Denaturation of a protein destroys:

    1. The primary structure only
    2. Secondary and tertiary structure, leaving the primary intact
    3. All four levels of structure
    4. Nothing — it is a reversible physical change
    Show answer

    Answer: B — Secondary and tertiary structure, leaving the primary intact

    Heat, acid or alcohol break the hydrogen bonds and hydrophobic contacts that hold the folded shape, so the chain unravels and loses its biological activity, but the covalent peptide bonds of the primary sequence survive. That is why a boiled egg is still nutritious even though the albumin will never redissolve, and why only hydrolysis, not denaturation, breaks a protein down into amino acids.
  4. The base present in RNA but not in DNA is:

    1. Thymine
    2. Uracil
    3. Cytosine
    4. Guanine
    Show answer

    Answer: B — Uracil

    Adenine, guanine and cytosine occur in both nucleic acids; the fourth base differs, being thymine in DNA and uracil in RNA. The sugar differs too — deoxyribose in DNA and ribose in RNA — and those two substitutions together are what most questions on this comparison are testing.
  5. Amino acids have unusually high melting points because they exist as:

    1. Neutral covalent molecules
    2. Zwitterions with internal charge separation
    3. Dimers held by hydrogen bonds
    4. Free radicals
    Show answer

    Answer: B — Zwitterions with internal charge separation

    The carboxyl group protonates the amino group internally, so the molecule carries both a positive and a negative site and behaves like a salt: strong electrostatic attractions between neighbours push the melting point far above what a molecule of that size would otherwise have. The same zwitterionic structure explains solubility in water but not in organic solvents, and amphoteric reactivity with both acid and base.
  6. Glucose forms a pentaacetate on treatment with acetic anhydride. This shows that glucose has:

    1. Five hydroxyl groups
    2. An aldehyde group
    3. A straight chain of six carbons
    4. A primary alcohol at one end
    Show answer

    Answer: A — Five hydroxyl groups

    Acetylation converts each free hydroxyl into an acetate ester, so counting five acetate groups counts five OH groups. Each of the other three facts is established by a different reaction: Tollens' or oxime formation for the aldehyde, reduction with HI to n-hexane for the straight chain, and nitric acid oxidation to a dicarboxylic acid for the terminal primary alcohol.
  7. Which vitamin deficiency causes scurvy?

    1. Vitamin A
    2. Vitamin B₁
    3. Vitamin C
    4. Vitamin D
    Show answer

    Answer: C — Vitamin C

    Scurvy comes from a deficiency of ascorbic acid, vitamin C, which is water-soluble and therefore excreted rather than stored — so it must be supplied regularly. Vitamin A deficiency gives night blindness, B₁ gives beriberi and D gives rickets; the fat-soluble vitamins A, D, E and K are stored in the liver and can be toxic in excess, which the water-soluble ones generally are not.
  8. DNA rich in G–C pairs has a higher melting temperature than A–T rich DNA because:

    1. G–C pairs are held by three hydrogen bonds against two for A–T
    2. G and C are larger bases
    3. G–C pairs are covalently bonded
    4. A–T pairs do not form hydrogen bonds
    Show answer

    Answer: A — G–C pairs are held by three hydrogen bonds against two for A–T

    Guanine pairs with cytosine through three hydrogen bonds while adenine pairs with thymine through only two, so more energy is needed to separate a G–C rich duplex. The base pairs are held by hydrogen bonds, not covalent ones — the covalent bonds run along each backbone — which is precisely why the strands can be separated and rejoined during replication.