IMAT Biology · Formula sheet
Biomolecules and Enzymes formulas
4 formulas, 18 reference tables and 27 common traps for IMAT Biology Biomolecules and Enzymes, grouped by subtopic.
Water, the Elements of Life and Condensation
Learn this subtopic in the notesCondensation and hydrolysis: building and breaking polymers
Formula of a chain of n identical units
- number of units joined in one unbranched chain
- number of bonds made, and of water molecules released
Polar water and the hydrogen bond
| 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 life
| 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 elements
| 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.
Common traps
The O-H bond inside water is not a hydrogen bond
Inside one water molecule, O and H share electrons in a covalent bond. The hydrogen bond is the weaker attraction between the H of one molecule and the O (or N) of another. An option calling the internal O-H bond a hydrogen bond is wrong.
Hydrogen bonds do not need hydrolysis to break
Hydrolysis breaks covalent bonds by adding water (a glycosidic, peptide or ester bond). Hydrogen bonds are broken simply by heat or movement, without any chemical reaction.
Heat capacity and latent heat are different properties
Specific heat capacity is the energy to warm water by one degree, and keeps temperatures steady. Latent heat of vaporisation is the energy to turn liquid into vapour, and is what makes sweating and transpiration cool. IMAT puts both among the options.
Glycerol is an alcohol, not an acid
Glycerol carries three hydroxyl groups and no carboxyl group. The carboxyl groups in a triglyceride come from the fatty acids. Options giving glycerol a carboxyl group, or no hydroxyl groups, are wrong.
One water per bond, not one per unit
A chain of units has bonds, so waters leave. Removing waters (one for each unit) is the commonest wrong option in formula questions.
Breaking a molecule into its parts releases no water
Splitting a polymer, a triglyceride or a phospholipid into its building blocks is hydrolysis: water is used up, one molecule per bond broken. The number of water molecules released is zero. It is condensation, the building direction, that releases water.
Sugars, Glycosidic Bonds and Polysaccharides
Learn this subtopic in the notesMonosaccharides: trioses, pentoses and hexoses
| Sugar | Type | Formula | Where it is found or used |
|---|---|---|---|
| Glyceraldehyde | Triose | Intermediate in respiration and photosynthesis | |
| Ribose | Pentose | RNA nucleotides, ATP, NAD | |
| Deoxyribose | Pentose | DNA nucleotides | |
| Glucose | Hexose | Main fuel for respiration; unit of starch, glycogen, cellulose | |
| Fructose and galactose | Hexoses | Fruit sugar; part of sucrose (fructose) and lactose (galactose) |
The glycosidic bond and the three common disaccharides
| 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 cellulose
| 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 |
Common traps
Glycerol and glucagon are not sugars
Glycerol is a three-carbon alcohol from lipids, and glucagon is a protein hormone that raises blood glucose. Neither is a carbohydrate, though both names sound like glucose. IMAT uses them as distractors in sugar questions.
Sucrose is not a reducing sugar
Maltose and lactose turn Benedict's reagent brick-red, but sucrose does not, because the bond between glucose and fructose ties up both reactive groups. A negative Benedict's test therefore does not prove there is no sugar: sucrose may be present.
Starch and cellulose differ in the glucose, not the sugar
Both are polymers of glucose. Starch uses α-glucose and cellulose uses β-glucose. An option saying cellulose is made of fructose, or of a different sugar from starch, is wrong.
Glycogen is the animal store, not starch
Animals and fungi store glucose as glycogen, mainly in liver and muscle. Plants store starch. Animals do not make starch.
Fatty Acids, Triglycerides, Phospholipids and Steroids
Learn this subtopic in the notesTriglycerides: ester bonds and their formula
Formula of a triglyceride
- glycerol
- one water released per ester bond
Fatty acids: saturated and unsaturated
| 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 steroids
| 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 |
Common traps
Unsaturated means fewer hydrogens, not more
Saturated means saturated with hydrogen: the most H atoms the chain can hold. Each C=C double bond removes two hydrogen atoms. So an unsaturated fatty acid always has fewer hydrogens than the saturated one of the same length.
Triglycerides are joined by ester bonds, not glycosidic or peptide bonds
Each name belongs to one class: glycosidic bonds in carbohydrates, peptide bonds in proteins, ester bonds in lipids, phosphodiester bonds in nucleic acids. Mixing them up is a favourite distractor.
Cholesterol contains no peptide bonds and no fatty acids
Cholesterol is a steroid lipid made of fused rings. It is not a protein, so it has no peptide bonds, and it is not a fat, so it has no fatty acids or ester bonds in its ring frame. It is typical of animal membranes; plant membranes use related sterols instead.
Amino Acids, Protein Structure and Nucleotides
Learn this subtopic in the notesThe peptide bond and the mass of a polypeptide
Mass of a single polypeptide chain
- number of amino acids in the chain
- average relative mass of the free amino acids
- relative mass of one water molecule lost per peptide bond
The structure of an amino acid
| Part | Formula | Property |
|---|---|---|
| Amino group | Basic; same in all amino acids | |
| Carboxyl group | Acidic; same in all amino acids | |
| Hydrogen on the α-carbon | Same in all amino acids | |
| R group (side chain) | Varies (H in glycine, in alanine) | Decides polarity, charge and size; the only part that differs |
The four levels of protein structure
| 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 denaturation
| 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 outline
| 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 |
Common traps
The R group can contain N, O or even its own COOH
Some R groups carry extra amino, amide or carboxyl groups. When asked for the part common to all amino acids, choose the α-carbon with one amino group, one carboxyl group and one H, and treat everything else on that carbon as the R group.
Hydrolysis breaks the C-N peptide bond, not a bond inside an R group
To split a dipeptide back into its two amino acids, the bond between the carbonyl carbon and the nitrogen of the next unit is broken by adding water. The C=O and N-H bonds next to it, and bonds in the R groups, stay as they are.
A protein with a quaternary level still has all the lower levels
Levels build on each other. A protein made of several chains has primary, secondary, tertiary and quaternary structure, never a quaternary structure with a level missing. A single-chain protein stops at tertiary.
Denaturation does not break peptide bonds
A denatured protein has lost its shape, not its sequence. Breaking peptide bonds is hydrolysis, done by proteases or by boiling in strong acid for a long time, not by ordinary heating.
Collagen is not a muscle filament
Collagen is a fibrous protein outside cells, in connective tissue. The thick filaments in muscle are myosin and the thin ones actin.
Hydrogen bonds join the strands; phosphodiester bonds join the nucleotides
The covalent phosphodiester bonds make the backbone of each strand. The weak hydrogen bonds between bases hold the two strands of DNA together and let them separate for copying.
Enzymes: Catalysis, the Active Site and Cofactors
Learn this subtopic in the notesEnzymes as catalysts that lower the activation energy
| 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 fit
| 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 groups
| Kind of helper | How it is bound | Example | Dietary source |
|---|---|---|---|
| Inorganic cofactor (ion) | Bound in or near the active site | in carbonic anhydrase | Minerals |
| Coenzyme | Loosely; moves between enzymes | 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 classes
| 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 |
Common traps
Enzymes do not raise the temperature or supply energy
An enzyme speeds up a reaction at the same temperature by providing a route with a lower activation energy. It gives no energy to the reaction and is not used up. Options saying it heats the mixture, supplies energy, or turns into product are wrong.
The active site is not built only from neighbouring amino acids
The amino acids that line an active site can be far apart in the primary sequence, or even on different chains. They meet only because the chain folds. That is why the higher levels of structure decide the shape of the active site.
Every coenzyme is a cofactor, but not every cofactor is a coenzyme
Cofactor is the general word for any non-protein helper. Coenzymes are the organic ones. A metal ion such as is a cofactor but never a coenzyme.
Amylase digests starch, peptidases digest proteins, lipase digests fats
The name tells you the substrate. A protein is broken down by proteases and peptidases, not by amylase or lipase. Isomerases and transaminases are not digestive enzymes at all: they rearrange molecules or move amino groups inside cells.
Temperature, pH, Substrate and Inhibitors
Learn this subtopic in the notesSubstrate concentration, Vmax and Km
Michaelis-Menten equation
- initial rate of reaction
- maximum rate, when all active sites are occupied
- substrate concentration
- substrate concentration giving half of
Effect of temperature and pH on enzyme activity
| 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 inhibition
| 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 |
Common traps
Low temperature inactivates; high temperature denatures
Cooling slows an enzyme but leaves its shape intact, so activity returns on warming. Heating above the optimum breaks the bonds holding the shape, and this is usually permanent. Do not say an enzyme is denatured by cold.
Km is a substrate concentration, not a rate
is the substrate concentration at half the maximum rate, so its unit is a concentration. A smaller means higher affinity, not a slower enzyme.
A competitive inhibitor binds the enzyme, not the substrate
The inhibitor and the substrate compete for the same active site. The inhibitor does not attach to the substrate, and it does not block the release of products. Options describing either are wrong.
The one property all inhibitors share is a lower rate
Competitive inhibitors do not change the active site's shape; no inhibitor denatures the enzyme; none raise the activation energy of the catalysed reaction. The only statement true of every inhibitor is that it reduces the rate of the reaction.