OxfordAQA International AS and A-level Biology: Biological molecules, enzymes, membranes and nucleic acids (9610) – Revision Notes

These notes condense sections 3.1.1 (Biological molecules), 3.1.3 (Enzymes), 3.1.4 (Transport into and out of cells), 3.1.7 (DNA, genes and chromosomes) and 3.1.8 (Protein synthesis) of the OxfordAQA International AS and A-level Biology (9610) specification, Version 5.1 (International AS from May/June 2017, International A-level from May/June 2018). All five sections sit in Unit 1, The diversity of living organisms, which is International AS content. Classification, biodiversity and genetic diversity from the same unit are in the diversity revision notes. Course pages: hub, checklist and free diagnostics.

3.1.1.1 Monomers and polymers

• Monomers are the smaller units that join to form polymers.
• Condensation: two molecules are joined by a chemical bond and a molecule of water is eliminated.
• Hydrolysis: the chemical bond between two molecules is broken in a reaction that uses a water molecule.

Polymer	Monomer	Bond formed by condensation
Starch, cellulose	Glucose (α or β)	Glycosidic
Polypeptide	Amino acid	Peptide
DNA, RNA	Nucleotide	Phosphodiester

Triglycerides are not polymers: one glycerol and three fatty acids join by ester bonds.

3.1.1.2 Carbohydrates

• Common monosaccharides: glucose and fructose.
• α-glucose and β-glucose are isomers: on carbon 1 the -OH group is below the ring in α-glucose and above it in β-glucose.
• Two monosaccharides join by condensation to form a glycosidic bond and a disaccharide.
  • Maltose = α-glucose + α-glucose.
  • Sucrose = α-glucose + fructose.
• Many monosaccharides join to form a polysaccharide.

	Starch	Cellulose
Monomer	α-glucose	β-glucose
Structure	Amylose (unbranched, coiled) and amylopectin (branched)	Straight, unbranched chains; neighbouring chains joined by many hydrogen bonds into microfibrils
Function in plants	Energy store	Strength of the cell wall
Structure suits function	Insoluble, so no effect on water potential; compact; branches give many ends for rapid hydrolysis	Hydrogen-bonded microfibrils give high tensile strength, so the wall resists bursting

Tests

Test for	Method	Positive result
Reducing sugar	Heat with Benedict’s reagent	Blue to green, yellow, orange or brick-red precipitate
Non-reducing sugar	After a negative Benedict’s test, boil a fresh sample with dilute hydrochloric acid, neutralise with sodium hydrogencarbonate, then heat with Benedict’s reagent	Coloured precipitate appears (the acid hydrolysed the sugar to reducing monosaccharides)
Starch	Add iodine/potassium iodide solution	Orange-brown to blue-black

When given unfamiliar structures, show condensation by removing H from one -OH and -OH from the other to make water, and hydrolysis by adding water back across the bond.

3.1.1.3 Lipids

• A triglyceride forms by condensation of one glycerol and three fatty acids; three water molecules are released and three ester bonds form.
• A fatty acid is RCOOH. A saturated R-group has no C=C double bonds; an unsaturated R-group has one or more.
• In a phospholipid, one fatty acid is replaced by a phosphate-containing group. The phosphate head is hydrophilic and the two fatty acid tails are hydrophobic.

Lipid	Property	Function
Saturated triglyceride	Straight chains pack closely: solid at room temperature	Energy store in animals
Unsaturated triglyceride	C=C bonds kink the chains: liquid at room temperature (oils)	Energy store in plants
Phospholipid	Hydrophilic head, hydrophobic tails	Forms the bilayer of membranes

Triglycerides are good stores because they release a lot of energy per gram and are insoluble, so they do not affect water potential.

Emulsion test. Shake the sample with ethanol, then pour into water: a milky white emulsion shows lipid.

3.1.1.4 Proteins

• Amino acid general structure: a central carbon with an amine group (H₂N-), a carboxyl group (-COOH), a hydrogen and an R-group.
• There are twenty amino acids common to all organisms; they differ only in their R-groups.
• Condensation of two amino acids forms a peptide bond and a dipeptide; many amino acids form a polypeptide.

Level	Description
Primary	Sequence of amino acids in the polypeptide
Secondary	Coiling (α-helix) or folding (β-pleated sheet), held by hydrogen bonds
Tertiary	The specific 3-D folding of the whole polypeptide, held by hydrogen bonds, disulfide bridges and ionic bonds between R-groups
Quaternary	More than one polypeptide chain in the protein (for example haemoglobin)

The primary structure determines how the chain folds, so it determines the 3-D shape and therefore the function, such as the shape of an active site or an antibody’s binding site.

Biuret test. Add biuret reagent: blue to purple shows protein (peptide bonds).

3.1.3 Enzymes

• Enzymes are proteins; their properties depend on the tertiary structure of the active site.
• The enzyme combines with a complementary substrate to form an enzyme-substrate complex.
• An enzyme lowers the activation energy of the reaction it catalyses.
• Lock and key model: the active site is a fixed shape exactly complementary to the substrate.
• Induced fit model (the later model): the active site changes shape slightly as the substrate binds, putting strain on bonds in the substrate. The change from one model to the other shows how scientific models are revised by new evidence.

Factor	Effect on rate	Explanation
Temperature (up to the optimum)	Rises	More kinetic energy, more collisions between enzyme and substrate
Temperature (above the optimum)	Falls	Bonds in the tertiary structure break; the active site changes shape (denaturation), so fewer substrates can bind
pH (away from the optimum)	Falls	Ionic and hydrogen bonds are disrupted, changing the active site
Substrate concentration	Rises, then levels off	More collisions, until all active sites are occupied
Enzyme concentration	Rises (if substrate is in excess)	More active sites, more collisions
Competitive inhibitor	Falls; effect reduced by adding more substrate	Similar shape to the substrate; binds the active site and blocks it
Non-competitive inhibitor	Falls; adding substrate does not overcome it	Binds away from the active site and changes its shape

3.1.4 Transport into and out of cells

Fluid-mosaic model. A bilayer of phospholipids, with proteins scattered through it and carbohydrates attached to proteins and lipids on the outer surface. Cholesterol may be present; it restricts the movement of the other molecules in the membrane. Microvilli are folds of the cell-surface membrane that increase its surface area.

Process	Gradient	Proteins	ATP
Diffusion	Down a concentration gradient	None (through the bilayer)	No
Facilitated diffusion	Down a concentration gradient	Carrier or channel proteins	No
Osmosis	Water, from higher to lower water potential	Through a partially permeable membrane	No
Active transport	Against a concentration gradient	Carrier proteins	Yes

• Diffusion across a membrane is limited by the phospholipid bilayer: its hydrophobic core lets small, non-polar molecules through but holds back ions and large polar molecules, which need carrier or channel proteins.
• The rate of diffusion increases with a larger surface area, a greater difference in concentration and a thinner exchange surface.
• ATP is made from ADP and phosphate and is the immediate source of energy for biological processes such as active transport.

3.1.7.1 Nucleic acids

Each nucleotide = a pentose + a phosphate group + a nitrogen-containing base.

	DNA	RNA
Pentose	Deoxyribose	Ribose
Bases	Adenine, cytosine, guanine, thymine	Adenine, cytosine, guanine, uracil
Molecule	Double helix: two polynucleotide chains held by hydrogen bonds between complementary base pairs (A-T, C-G)	Relatively short single polynucleotide chain

• mRNA: a single, linear strand whose base sequence, read in triplets (codons), is copied from a gene.
• tRNA: a single strand folded into a clover-leaf shape held by hydrogen bonds between some of its bases; it has an anticodon of three bases and a site where one specific amino acid attaches.

3.1.7.2 DNA, genes and chromosomes

	Eukaryotic nucleus	Mitochondria, chloroplasts, prokaryotes
Shape	Linear	Circular
Length	Long	Shorter
Proteins	Associated with proteins, including histones, which package it into chromosomes	Not associated with proteins

• Most genes occupy a fixed position, a locus, on a particular DNA molecule.
• A gene is a section of DNA that codes for polypeptides that determine the nature and development of an organism.
• Much eukaryotic nuclear DNA does not code for polypeptides: there are non-coding multiple repeats between genes, and within a gene the coding exons are separated by non-coding introns.
• The genome is the complete set of genes in a cell.

3.1.7.3 DNA replication

1. DNA helicase unwinds the double helix and breaks the hydrogen bonds between complementary base pairs.
2. Each separated strand acts as a template.
3. Free DNA nucleotides are attracted to the exposed bases and pair with them by complementary base pairing.
4. DNA polymerase joins the new nucleotides together.
5. Each new molecule has one original and one new strand: semi-conservative replication.

3.1.8 Protein synthesis

The genetic code

• A base triplet codes for a specific amino acid.
• Universal: the same triplets code for the same amino acids in all organisms.
• Non-overlapping: each base belongs to only one triplet.
• Degenerate: most amino acids are coded for by more than one triplet.

You will be given the code table when it is needed; you do not have to recall which codon codes for which amino acid.

Transcription is the production of mRNA from DNA. RNA polymerase joins the mRNA nucleotides that have paired with the template strand.

• In prokaryotes, transcription produces mRNA directly.
• In eukaryotes, transcription produces pre-mRNA, which is spliced (the introns are removed) to form mRNA.

Translation is the production of a polypeptide from the sequence of codons on mRNA.

1. The mRNA attaches to a ribosome.
2. A tRNA with a complementary anticodon brings its specific amino acid to each codon.
3. Adjacent amino acids are joined by peptide bonds; ATP provides the energy.
4. The ribosome moves along the mRNA until the whole sequence has been read.

Protein folding. The polypeptide folds into its characteristic 3-D structure. The folding is determined by the amino acid sequence, and specialised proteins called chaperones assist the folding of other proteins.

Worked reminder. A DNA template strand reads TAC GGT CAA. The mRNA is AUG CCA GUU; the tRNA anticodons are UAC, GGU and CAA. Three codons give three amino acids.

Model answer shapes

Explain how the structure of cellulose relates to its function. Cellulose is made of β-glucose, so it forms long, straight, unbranched chains. Many hydrogen bonds form between neighbouring chains, making microfibrils. These give high tensile strength, so the cell wall resists the pressure of water entering the cell.

Explain why a high temperature reduces the rate of an enzyme reaction. The bonds holding the tertiary structure break. The active site changes shape, so it is no longer complementary to the substrate. Fewer enzyme-substrate complexes form.

Explain how a competitive inhibitor reduces the rate. It has a similar shape to the substrate, so it binds to the active site. Fewer substrate molecules can bind and fewer enzyme-substrate complexes form.

Must-know distinctions

• Condensation or hydrolysis: water released or water used.
• α-glucose or β-glucose: starch or cellulose.
• Saturated or unsaturated: no C=C bonds or at least one.
• Competitive or non-competitive inhibitor: binds the active site or elsewhere.
• Facilitated diffusion or active transport: down a gradient with no ATP, or against it with ATP.
• Exon or intron: coding or non-coding.
• Pre-mRNA or mRNA: before or after splicing (eukaryotes only).
• DNA polymerase or RNA polymerase: replication or transcription.

Quick self-test

1. Define hydrolysis.
2. Which two monosaccharides form sucrose?
3. Describe the test for a non-reducing sugar.
4. Name the bonds formed when a triglyceride is made.
5. How does a phospholipid differ from a triglyceride?
6. Name two bonds that hold the tertiary structure of a protein.
7. Why does adding more substrate reduce the effect of a competitive inhibitor but not a non-competitive one?
8. What is the role of cholesterol in a membrane?
9. State two ways active transport differs from facilitated diffusion.
10. Give two differences between nuclear DNA in a eukaryote and DNA in a prokaryote.
11. State the roles of DNA helicase and DNA polymerase.
12. What happens to pre-mRNA in a eukaryotic cell?
13. A DNA template strand reads TAC AAG. Give the mRNA sequence.

Answers

1. Breaking the chemical bond between two molecules in a reaction that uses a water molecule.
2. α-glucose and fructose.
3. After a negative Benedict’s test, boil a fresh sample with dilute hydrochloric acid, neutralise with sodium hydrogencarbonate, then heat with Benedict’s reagent; a coloured precipitate shows a non-reducing sugar.
4. Ester bonds (three).
5. One fatty acid is replaced by a phosphate-containing group, giving a hydrophilic head.
6. Any two: hydrogen bonds, disulfide bridges, ionic bonds.
7. A competitive inhibitor competes for the active site, so more substrate wins more of the sites; a non-competitive inhibitor changes the active site shape, so extra substrate cannot bind.
8. It restricts the movement of the other molecules in the membrane.
9. Active transport moves substances against a concentration gradient and uses ATP; facilitated diffusion moves them down a gradient with no ATP.
10. Eukaryotic nuclear DNA is linear, longer and associated with histones; prokaryotic DNA is circular, shorter and not associated with proteins.
11. Helicase unwinds the helix and breaks the hydrogen bonds; DNA polymerase joins the new nucleotides.
12. It is spliced: the introns are removed to form mRNA.
13. AUG UUC.

Where marks are usually lost

• Writing that hydrolysis releases water, or condensation uses it.
• Saying cellulose is made of α-glucose.
• Leaving out the neutralising step in the non-reducing sugar test.
• Calling a triglyceride a polymer.
• Writing “the active site is the same shape as the substrate” instead of complementary.
• Saying an enzyme is “killed” instead of denatured.
• Forgetting that splicing happens only in eukaryotes.
• Using thymine (T) in an mRNA sequence.

What these notes do not cover

Other Unit 1 sections are revised elsewhere or not yet condensed here: cell structure and microscopy (3.1.2), gas exchange and haemoglobin (3.1.5), variation (3.1.6), meiosis (3.1.9), and species, taxonomy and biodiversity (3.1.10-3.1.11, in the diversity revision notes).

Frequently asked questions

What is the difference between condensation and hydrolysis? Condensation joins two molecules with a chemical bond and eliminates a molecule of water. Hydrolysis breaks the chemical bond between two molecules in a reaction that uses a water molecule.

How do you test for a non-reducing sugar? After a negative Benedict’s test, boil a fresh sample with dilute hydrochloric acid, neutralise with sodium hydrogencarbonate, then heat with Benedict’s reagent. A coloured precipitate shows a non-reducing sugar, because the acid hydrolysed it to reducing monosaccharides.

What is the difference between the lock and key and induced fit models of enzyme action? In the lock and key model the active site is a fixed shape exactly complementary to the substrate. In the induced fit model the active site changes shape slightly as the substrate binds, putting strain on bonds in the substrate.

What is the difference between a competitive and a non-competitive inhibitor? A competitive inhibitor has a similar shape to the substrate and binds the active site, so adding more substrate reduces its effect. A non-competitive inhibitor binds away from the active site and changes its shape, so adding substrate does not overcome it.

Is this content on the International AS in OxfordAQA Biology (9610)? Yes. Sections 3.1.1, 3.1.3, 3.1.4, 3.1.7 and 3.1.8 sit in Unit 1, The diversity of living organisms, which is International AS content.

Official syllabus

Source: OxfordAQA, International AS and A-level Biology (9610), Version 5.1, International AS exams May/June 2017 onwards and International A-level exams May/June 2018 onwards, sections 3.1.1, 3.1.3, 3.1.4, 3.1.7 and 3.1.8.