IMAT Biology · Free notes

Biomolecules and Enzymes: Water, Sugars, Lipids, Proteins and Catalysis

Biomolecules and Enzymes has 29 past questions since 2011, and the ministry papers from 2023 on have asked 9 of them. The ministry papers ask short recall questions: a definition, the name of a sugar, the type of a digestive enzyme, what a competitive inhibitor does. The older papers went further, asking for the formula of a molecule after water is removed, or for the levels of structure in a named protein. The difficulty sits in the details that sound alike: glucagon and glycogen, cofactor and coenzyme, a hydrogen bond and a covalent bond, so learn the exact words.

The handout has every subtopic, worked example, formula and trap with answers shown. The formula sheet is the chapter’s formulas and traps alone, on one page.

IMAT home All formulas on one page

Subtopic notes

Formula & revision sheet

4 formulas · 18 reference tables · 27 gotchas across all subtopics — the exam-eve cheat-sheet

Water, the Elements of Life and Condensation

Formulas (1)

Condensation and hydrolysis: building and breaking polymers · Formula of a chain of n identical units $\text{chain} = n \times (\text{unit}) - (n-1)\,\mathrm{H_2O}$

Reference tables (3)

Polar water and the hydrogen bond4 rows

Bond or attraction	Between	Strength	Example in biology
Covalent bond	Atoms sharing electrons inside one molecule	Strong	O-H inside a water molecule; C-C in a sugar
Ionic bond	Oppositely charged ions or charged R groups	Strong when dry, weaker in water	Between charged R groups in a folded protein
Hydrogen bond	H on O or N, and an O or N of another molecule	Weak, temporary	Between water molecules; DNA base pairs
Hydrophobic interaction	Non-polar groups clustering away from water	Weak	Fatty acid tails inside a membrane

Only the covalent bond lies inside a water molecule. The hydrogen bond lies between molecules.

Properties of water that matter for life5 rows

Property	Cause	Why it matters to living things
Good solvent for polar and ionic substances	Polar molecule surrounds ions	Transport in blood and sap; reactions in cytoplasm
High specific heat capacity	Energy goes into breaking hydrogen bonds	Stable body and habitat temperature
High latent heat of vaporisation	Many hydrogen bonds break on evaporation	Cooling by sweating and transpiration
Cohesion and surface tension	Hydrogen bonds between water molecules	Water columns in xylem; insects walk on ponds
Ice less dense than liquid water	Hydrogen bonds hold ice in an open lattice	Ice floats and insulates; lakes do not freeze solid

The four classes of biological molecules and their elements4 rows

Class	Elements	Building block	Bond joining blocks
Carbohydrates	C, H, O	Monosaccharide (for example glucose)	Glycosidic bond
Lipids (triglycerides)	C, H, O (phospholipids also P)	Glycerol and fatty acids	Ester bond
Proteins	C, H, O, N, often S	Amino acid	Peptide bond
Nucleic acids	C, H, O, N, P	Nucleotide	Phosphodiester bond

Lipids are not true polymers: a triglyceride is one glycerol with three fatty acids, not a long chain of repeating units.

Watch out for (6)

The O-H bond inside water is not a hydrogen bond
→ Polar water and the hydrogen bond
Hydrogen bonds do not need hydrolysis to break
→ Polar water and the hydrogen bond
Heat capacity and latent heat are different properties
→ Properties of water that matter for life
Glycerol is an alcohol, not an acid
→ The four classes of biological molecules and their elements
One water per bond, not one per unit
→ Condensation and hydrolysis: building and breaking polymers
Breaking a molecule into its parts releases no water
→ Condensation and hydrolysis: building and breaking polymers

Sugars, Glycosidic Bonds and Polysaccharides

Reference tables (3)

Monosaccharides: trioses, pentoses and hexoses5 rows

Sugar	Type	Formula	Where it is found or used
Glyceraldehyde	Triose	$\mathrm{C_3H_6O_3}$	Intermediate in respiration and photosynthesis
Ribose	Pentose	$\mathrm{C_5H_{10}O_5}$	RNA nucleotides, ATP, NAD
Deoxyribose	Pentose	$\mathrm{C_5H_{10}O_4}$	DNA nucleotides
Glucose	Hexose	$\mathrm{C_6H_{12}O_6}$	Main fuel for respiration; unit of starch, glycogen, cellulose
Fructose and galactose	Hexoses	$\mathrm{C_6H_{12}O_6}$	Fruit sugar; part of sucrose (fructose) and lactose (galactose)

The glycosidic bond and the three common disaccharides3 rows

Disaccharide	Made from	Bond	Source
Maltose	α-glucose + α-glucose	α(1→4)	Digestion of starch by amylase; germinating seeds
Sucrose	α-glucose + β-fructose	α(1→2)	Transport sugar in plant phloem; table sugar
Lactose	β-galactose + glucose	β(1→4)	Milk sugar of mammals

Maltose and lactose are reducing sugars; sucrose is not.

Polysaccharides: starch, glycogen and cellulose5 rows

Polysaccharide	Monomer and bonds	Shape	Role
Amylose	α-glucose, α(1→4)	Unbranched helix	Compact plant store (part of starch)
Amylopectin	α-glucose, α(1→4) with α(1→6) branches	Branched	Plant store (part of starch)
Glycogen	α-glucose, α(1→4) with many α(1→6) branches	Highly branched	Animal store in liver and muscle
Cellulose	β-glucose, β(1→4)	Straight chains in microfibrils	Strength of plant cell walls
Chitin	Glucose with an N-containing group, β(1→4)	Straight chains	Insect exoskeleton, fungal walls

Watch out for (4)

Glycerol and glucagon are not sugars
→ Monosaccharides: trioses, pentoses and hexoses
Sucrose is not a reducing sugar
→ The glycosidic bond and the three common disaccharides
Starch and cellulose differ in the glucose, not the sugar
→ Polysaccharides: starch, glycogen and cellulose
Glycogen is the animal store, not starch
→ Polysaccharides: starch, glycogen and cellulose

Fatty Acids, Triglycerides, Phospholipids and Steroids

Formulas (1)

Triglycerides: ester bonds and their formula · Formula of a triglyceride $\mathrm{C_3H_8O_3} + 3\,(\text{fatty acid}) - 3\,\mathrm{H_2O}$

Reference tables (2)

Fatty acids: saturated and unsaturated4 rows

Feature	Saturated fatty acid	Unsaturated fatty acid
C=C double bonds	None	One or more
Shape of chain	Straight	Kinked at each cis double bond
State of the fat at room temperature	Usually solid (butter, lard)	Usually liquid (olive oil)
Hydrogen atoms for the same chain length	The maximum possible	Two fewer for each double bond

Phospholipids and steroids4 rows

Lipid	Built from	Key property	Main role
Triglyceride	Glycerol + 3 fatty acids	Non-polar, insoluble	Energy store, insulation
Phospholipid	Glycerol + 2 fatty acids + phosphate	Amphipathic (polar head, non-polar tails)	Membrane bilayer
Cholesterol (steroid)	Four fused carbon rings	Mostly non-polar, one OH group	Membrane fluidity; makes steroid hormones
Wax	Fatty acid + long-chain alcohol	Very water-repellent	Waterproofing of leaves and cuticles

Watch out for (3)

Unsaturated means fewer hydrogens, not more
→ Fatty acids: saturated and unsaturated
Triglycerides are joined by ester bonds, not glycosidic or peptide bonds
→ Triglycerides: ester bonds and their formula
Cholesterol contains no peptide bonds and no fatty acids
→ Phospholipids and steroids

Amino Acids, Protein Structure and Nucleotides

Formulas (1)

The peptide bond and the mass of a polypeptide · Mass of a single polypeptide chain $M = n\,\bar{m} - 18\,(n-1)$

Reference tables (4)

The structure of an amino acid4 rows

Part	Formula	Property
Amino group	$\mathrm{-NH_2}$	Basic; same in all amino acids
Carboxyl group	$\mathrm{-COOH}$	Acidic; same in all amino acids
Hydrogen on the α-carbon	$\mathrm{-H}$	Same in all amino acids
R group (side chain)	Varies (H in glycine, $\mathrm{CH_3}$ in alanine)	Decides polarity, charge and size; the only part that differs

The four levels of protein structure4 rows

Level	What it is	Held by	Example
Primary	Sequence of amino acids	Peptide bonds	Any protein; one change can alter the whole fold (sickle cell haemoglobin)
Secondary	α-helix or β-pleated sheet	Hydrogen bonds in the backbone	α-helices of keratin; β-sheets of silk
Tertiary	3D fold of a single chain	R-group bonds: hydrogen, ionic, disulfide, hydrophobic	Myoglobin (one chain); many enzymes
Quaternary	Several chains together	The same R-group bonds, between chains	Haemoglobin (four chains, each with a haem group); collagen (three chains)

Fibrous and globular proteins, where they act, and denaturation5 rows

Protein	Type	Where it acts	Function
Collagen	Fibrous	Outside cells (extracellular matrix)	Tensile strength of skin, tendon, bone
Keratin	Fibrous	Inside cells of skin, hair and nails	Toughness, waterproofing
Haemoglobin	Globular	Inside red blood cells	Carries oxygen
Antibodies	Globular	Blood plasma and body fluids	Bind antigens
Myosin and actin	Fibrous filaments	Inside muscle cells	Contraction (myosin thick filaments, actin thin filaments)

Nucleotides and nucleic acids in outline5 rows

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose
Bases	A, T, G, C	A, U, G, C
Strands	Two, in a double helix	Usually one
Bond within a strand	Phosphodiester	Phosphodiester
Main location in a eukaryotic cell	Nucleus (also mitochondria and chloroplasts)	Nucleus, cytoplasm and ribosomes

Watch out for (6)

The R group can contain N, O or even its own COOH
→ The structure of an amino acid
Hydrolysis breaks the C-N peptide bond, not a bond inside an R group
→ The peptide bond and the mass of a polypeptide
A protein with a quaternary level still has all the lower levels
→ The four levels of protein structure
Denaturation does not break peptide bonds
→ Fibrous and globular proteins, where they act, and denaturation
Collagen is not a muscle filament
→ Fibrous and globular proteins, where they act, and denaturation
Hydrogen bonds join the strands; phosphodiester bonds join the nucleotides
→ Nucleotides and nucleic acids in outline

Enzymes: Catalysis, the Active Site and Cofactors

Reference tables (4)

Enzymes as catalysts that lower the activation energy5 rows

Quantity	Changed by an enzyme?	Comment
Activation energy	Yes, lowered	This is how the enzyme speeds the reaction
Rate of reaction	Yes, increased	Often by millions of times
Overall energy released or taken in	No	Products and reactants are the same as without the enzyme
Position of equilibrium	No	Equilibrium is reached faster, not shifted
The enzyme itself	No	Unchanged at the end and used again

The active site: lock-and-key and induced fit2 rows

Model	Active site before binding	On binding	What it explains
Lock-and-key	Rigid, exactly complementary to the substrate	No change of shape	Specificity
Induced fit	Roughly complementary	Moulds around the substrate, straining its bonds	Specificity, the lowering of activation energy, broad specificity of some enzymes

Cofactors, coenzymes and prosthetic groups3 rows

Kind of helper	How it is bound	Example	Dietary source
Inorganic cofactor (ion)	Bound in or near the active site	$\mathrm{Zn^{2+}}$ in carbonic anhydrase	Minerals
Coenzyme	Loosely; moves between enzymes	$\mathrm{NAD^+}$ carrying electrons in respiration	Vitamins (niacin for NAD)
Prosthetic group	Tightly and permanently	Haem in catalase	Iron from the diet for the haem

Where enzymes work, and the main enzyme classes5 rows

Enzyme	Substrate	Products	Where it works
Amylase	Starch	Maltose	Mouth (saliva) and small intestine (from pancreas)
Pepsin	Proteins	Shorter polypeptides	Stomach, at about pH 2
Trypsin and other peptidases	Polypeptides	Short peptides and amino acids	Small intestine
Lipase	Triglycerides	Fatty acids and glycerol (or monoglycerides)	Small intestine, helped by bile
Catalase	Hydrogen peroxide	Water and oxygen	Inside cells, especially liver

Watch out for (4)

Enzymes do not raise the temperature or supply energy
→ Enzymes as catalysts that lower the activation energy
The active site is not built only from neighbouring amino acids
→ The active site: lock-and-key and induced fit
Every coenzyme is a cofactor, but not every cofactor is a coenzyme
→ Cofactors, coenzymes and prosthetic groups
Amylase digests starch, peptidases digest proteins, lipase digests fats
→ Where enzymes work, and the main enzyme classes

Temperature, pH, Substrate and Inhibitors

Formulas (1)

Substrate concentration, Vmax and Km · Michaelis-Menten equation $v = \frac{V_{\max}\,[S]}{K_m + [S]}$

Reference tables (2)

Effect of temperature and pH on enzyme activity5 rows

Condition	Effect on rate	Reason
Temperature rising below the optimum	Increases	More frequent and more energetic collisions
Temperature above the optimum	Falls steeply	Bonds holding the shape break; the enzyme denatures
Low temperature	Very slow, but recovers on warming	Few collisions; the enzyme is not denatured
pH away from the optimum	Falls on both sides	Charges on R groups change; the active site changes shape
More enzyme, with plenty of substrate	Increases in proportion	More active sites available

Competitive, non-competitive and irreversible inhibition4 rows

Type	Where it binds	Effect of adding more substrate	Effect on Vmax and Km
Competitive	Active site	Overcomes the inhibition	Vmax same; Km higher
Non-competitive	Another site (allosteric)	Does not help	Vmax lower; Km same
Irreversible	Usually the active site, permanently	Does not help	Enzyme molecules lost for good
End-product (feedback)	Allosteric site of an early enzyme	Depends on the product level	Pathway slows when product builds up

Watch out for (4)

Low temperature inactivates; high temperature denatures
→ Effect of temperature and pH on enzyme activity
Km is a substrate concentration, not a rate
→ Substrate concentration, Vmax and Km
A competitive inhibitor binds the enzyme, not the substrate
→ Competitive, non-competitive and irreversible inhibition
The one property all inhibitors share is a lower rate
→ Competitive, non-competitive and irreversible inhibition

PYQ weightage by concept

22 concepts · 0 PYQs — where the marks actually sit, so you know what to drill first

Water, the Elements of Life and Condensation0 PYQs · 0%

Concept	PYQs	Share
Polar water and the hydrogen bondfoundation	—	—
Properties of water that matter for lifefoundation	—	—
The four classes of biological molecules and their elementsfoundation	—	—
Condensation and hydrolysis: building and breaking polymersfoundation	—	—

Sugars, Glycosidic Bonds and Polysaccharides0 PYQs · 0%

Concept	PYQs	Share
Monosaccharides: trioses, pentoses and hexosesfoundation	—	—
The glycosidic bond and the three common disaccharidesfoundation	—	—
Polysaccharides: starch, glycogen and cellulosefoundation	—	—

Fatty Acids, Triglycerides, Phospholipids and Steroids0 PYQs · 0%

Concept	PYQs	Share
Fatty acids: saturated and unsaturatedfoundation	—	—
Triglycerides: ester bonds and their formulafoundation	—	—
Phospholipids and steroidsfoundation	—	—

Amino Acids, Protein Structure and Nucleotides0 PYQs · 0%

Concept	PYQs	Share
The structure of an amino acidfoundation	—	—
The peptide bond and the mass of a polypeptidefoundation	—	—
The four levels of protein structurefoundation	—	—
Fibrous and globular proteins, where they act, and denaturationfoundation	—	—
Nucleotides and nucleic acids in outlinefoundation	—	—

Enzymes: Catalysis, the Active Site and Cofactors0 PYQs · 0%

Concept	PYQs	Share
Enzymes as catalysts that lower the activation energyfoundation	—	—
The active site: lock-and-key and induced fitfoundation	—	—
Cofactors, coenzymes and prosthetic groupsfoundation	—	—
Where enzymes work, and the main enzyme classesfoundation	—	—

Temperature, pH, Substrate and Inhibitors0 PYQs · 0%

Concept	PYQs	Share
Effect of temperature and pH on enzyme activityfoundation	—	—
Substrate concentration, Vmax and Kmfoundation	—	—
Competitive, non-competitive and irreversible inhibitionfoundation	—	—