Proteins and Enzymes: Folding, Catalysis and Inhibition

Build a protein from amino acids up to quaternary structure, classify proteins by shape and composition, name the enzyme classes, and predict how temperature, pH, substrate and inhibitors change the rate.

In the paper

Unit 1 carries 2 of the 40 botany marks; with two chapters sharing them, this one averages one (MEC publishes weights by unit, not by chapter). The MEC scope line: Structure, types and biological role of proteins; Enzymes. Three ways it is asked:

Recall: the bond joining amino acids; the class of lipase; who proposed induced fit; the vitamin behind NAD.
Understanding: why extra substrate overcomes a competitive inhibitor; why boiling stops an enzyme for good but cold does not; why one amino-acid change sickles red cells.
Application: reading Km from a rate figure; predicting what builds up when malonate is added; counting peptide bonds in a short chain.

Structure, types and biological role of proteins

Proteins are polymers of amino acids, containing C, H, O, N and usually S.

Amino acids and the peptide bond

Proteins are built from 20 common amino acids. Each has a central alpha carbon carrying an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen and a variable R group. Glycine's R group is a single hydrogen; cysteine's carries –SH.
Plants make all twenty. Humans cannot make nine — the essential amino acids — and must eat them. Cereal protein is short of lysine and pulse protein of methionine, so rice with lentils (dal-bhat) supplies a better mix than either alone.
Two amino acids join by a peptide bond (–CO–NH–) between the carboxyl of one and the amino group of the next, releasing one water molecule (condensation). A chain of n amino acids has n − 1 peptide bonds, a free N-terminal end and a free C-terminal end.

Two amino acids, each with an amino group, an alpha carbon carrying H and an R group, and a carboxyl group; the –OH of the first and an H of the second's amino group are boxed; below, the dipeptide with the –CO–NH– peptide bond boxed, a free –NH2 at the N-terminal end, a free –COOH at the C-terminal end, and a water molecule released — The –OH of one amino acid's carboxyl group and an H of the next one's amino group leave as water, and the C–N link left between them is the peptide bond. The dipeptide keeps a free –NH₂ at its N-terminal end and a free –COOH at its C-terminal end; R₁ and R₂ are the side chains. Diagram: IOM Mock.

Four levels of structure

Level	What it is	Held by	Example
Primary	Sequence of amino acids	Peptide bonds	Insulin: chain A of 21 and chain B of 30 amino acids, joined by two disulfide bridges
Secondary	Local coiling or pleating of the backbone	Hydrogen bonds between backbone C=O and N–H	Alpha-helix (3.6 residues per turn; keratin of hair); beta-pleated sheet (silk fibroin)
Tertiary	The whole chain folded into a 3-D shape	R-group interactions: hydrogen and ionic bonds, hydrophobic interactions, disulfide (S–S) bridges between cysteines	Myoglobin; most enzymes — the active site forms here
Quaternary	Two or more polypeptide subunits together	The same forces, between chains	Haemoglobin: two alpha + two beta chains

Four levels of protein structure: a primary chain of labelled amino acids (Arg, Ala, Gln, Glu and others), a secondary alpha helix and beta sheet, a tertiary folded protein of helices and sheets, and quaternary haemoglobin built of four chains — Primary structure is the sequence of amino acids; the chain coils into an alpha-helix or pleats into a beta-sheet (secondary), folds into one three-dimensional shape (tertiary), and in haemoglobin four chains fit together (quaternary). The label uses the American spelling hemoglobin. Image: LadyofHats, Public domain, via Wikimedia Commons.

Sequence dictates shape. In sickle-cell haemoglobin, valine replaces glutamic acid at position 6 of the beta chain; the altered molecules stick into fibres and bend red cells into sickles.

Denaturation. Heat, extreme pH, heavy-metal ions (Hg²⁺, Pb²⁺, Ag⁺) and organic solvents break the bonds of secondary, tertiary and quaternary structure. The protein unfolds and loses function, but its primary sequence and peptide bonds survive. Frying egg white is irreversible; mild denaturation can reverse when the agent is removed. Chaperone proteins help new chains fold correctly.

Types

	Fibrous	Globular
Shape	Long parallel chains, often cross-linked	Compact, roughly spherical
In water	Insoluble	Soluble
Job	Structure	Enzymes, transport, hormones, antibodies
Examples	Keratin, collagen, silk fibroin	Enzymes, haemoglobin, insulin, albumin

By composition:

Simple proteins give only amino acids on hydrolysis: albumins, globulins (legumin of pea), glutelins (glutenin of wheat), prolamins (zein of maize, gliadin of wheat), histones (which pack DNA).
Conjugated proteins carry a non-protein prosthetic group: nucleoproteins (chromatin, ribosomes), glycoproteins (mucin, membrane receptors), lipoproteins (membranes, blood transport), chromoproteins (haemoglobin, cytochromes, phytochrome), phosphoproteins (casein of milk), metalloproteins (ferritin with iron, plastocyanin with copper).
Derived proteins are products of partial breakdown: proteoses, peptones, peptides.

Biological roles

Role	Examples
Catalysis	Enzymes — amylase, RuBisCO
Structure	Collagen, keratin, tubulin
Transport	Haemoglobin (oxygen), membrane carriers and channels
Storage	Seed proteins in aleurone grains (zein, gluten), casein, ferritin (iron)
Hormones	Insulin, glucagon
Defence	Antibodies, fibrinogen, plant lectins
Movement	Actin, myosin; tubulin in the spindle
Sensing	Phytochrome (red and far-red light), hormone receptors

Enzymes

Enzymes are biological catalysts. Holding substrates in the right orientation at the active site, they lower the activation energy, so the reaction reaches equilibrium sooner — but the equilibrium point itself does not move, and the enzyme comes out unchanged. Almost all are proteins; the exceptions are ribozymes (catalytic RNA, such as the peptidyl transferase of the ribosome).

Year	Who	What
1877	Wilhelm Kühne	Coined the word "enzyme" ("in yeast")
1894	Emil Fischer	Lock-and-key model
1897	Eduard Buchner	Yeast extract ferments sugar with no living cells (zymase); Nobel 1907
1913	Michaelis and Menten	Rate equation and Km
1926	James Sumner	Crystallised urease, proving an enzyme is a protein
1958	Daniel Koshland	Induced-fit model

Parts of an enzyme

The protein part is the apoenzyme; the non-protein helper is the cofactor; together they make the active holoenzyme. Cofactors come in three kinds:

Prosthetic group — organic, tightly bound: haem in catalase and peroxidase.
Coenzyme — organic, loosely bound, shuttling hydrogen or groups between enzymes and regenerated after each cycle; most are built from B vitamins.
Metal-ion activator — Zn²⁺ (carbonic anhydrase, DNA polymerase), Mg²⁺ (hexokinase and other kinases, RuBisCO), Mo (nitrogenase), Cu (cytochrome oxidase).

Coenzyme	Vitamin	Carries
NAD⁺, NADP⁺	Niacin (B3)	Hydrogen — dehydrogenases
FAD, FMN	Riboflavin (B2)	Hydrogen
Coenzyme A	Pantothenic acid (B5)	Acetyl groups
Thiamine pyrophosphate	Thiamine (B1)	Removal of CO₂ from pyruvate
Pyridoxal phosphate	Pyridoxine (B6)	Amino groups (transaminases)

Naming and classification

Most names add -ase to the substrate (maltase, lipase, urease) or the reaction (dehydrogenase, polymerase); a few old names survive (pepsin, trypsin, ptyalin). The IUB (now IUBMB) Enzyme Commission gives each enzyme a four-part EC number. The Grade 11 text teaches six classes; a seventh, translocases, was added in August 2018.

EC	Class	Reaction	Examples
1	Oxidoreductases	Oxidation–reduction (hydrogen or electron transfer)	Alcohol and succinate dehydrogenase, catalase, cytochrome oxidase
2	Transferases	Move a group other than hydrogen	Hexokinase (phosphate), transaminases (amino group)
3	Hydrolases	Break bonds by adding water	Amylase, lipase, pepsin, sucrase, urease
4	Lyases	Remove groups without water, leaving a double bond (or add to one)	Aldolase, carbonic anhydrase, pyruvate decarboxylase
5	Isomerases	Rearrange atoms within one molecule	Phosphoglucoisomerase, triose phosphate isomerase
6	Ligases	Join two molecules using ATP	DNA ligase, pyruvate carboxylase
7	Translocases	Move ions or molecules across membranes	ATP synthase, Na⁺/K⁺ pump

How enzymes work

E + S ⇌ ES → E + P. In Fischer's lock-and-key model a rigid active site fits one substrate exactly, explaining specificity (urease acts on urea alone). In Koshland's induced fit, the active site is flexible and closes round the substrate as it binds, straining the bonds to be broken — hexokinase clamps shut on glucose.

Two rows of enzyme cartoons. Lock and key: a key-shaped substrate fits a rigid notch in the enzyme, forms an enzyme-substrate complex, and leaves as two products with the enzyme unchanged. Induced fit: a round substrate enters an open active site that closes around it, then the site reopens as two products leave — A: in Fischer's model the rigid active site already has the substrate's shape. B: in Koshland's induced fit the site changes shape as the substrate binds, closing round it and straining the bonds to be broken. In both, the products leave and the enzyme comes out unchanged. Diagram: IOM Mock.

Factors affecting activity

Temperature: the rate roughly doubles or trebles for each 10 °C rise (Q10 about 2–3) up to an optimum (about 35–40 °C for most plant and animal enzymes); above it the protein denatures and activity collapses. Cold only inactivates, reversibly.
pH: each enzyme has an optimum — pepsin about 2, salivary amylase about 6.8, trypsin about 8. Away from it the charges on active-site R groups change.
Substrate concentration: rate rises with substrate, then levels at Vmax when every active site is busy (saturation). Km, the Michaelis constant, is the substrate concentration giving half Vmax; a low Km means high affinity.
Enzyme concentration: with substrate in excess, rate is proportional to the amount of enzyme.

Inhibition

	Competitive	Non-competitive
Resembles substrate?	Yes — a structural analogue	No
Binds	The active site	Elsewhere (an allosteric site)
Overcome by more substrate?	Yes	No
Vmax	Unchanged	Lowered
Apparent Km	Raised	Unchanged
Example	Malonate blocks succinate dehydrogenase (which turns succinate into fumarate); sulpha drugs mimic PABA in bacteria	Cyanide on cytochrome oxidase; Hg²⁺ and Ag⁺ binding –SH groups

Four rate graphs: rate against temperature rising to an optimum at about 35 to 40 degrees C then falling to zero; rate against pH with separate peaks for pepsin at about 2, salivary amylase at about 6.8 and trypsin at about 8; rate against substrate concentration levelling at Vmax with Km marked at half Vmax; and curves with no inhibitor, a competitive inhibitor reaching the same Vmax more slowly, and a non-competitive inhibitor levelling lower — A: the rate rises to an optimum near 35–40 °C, then falls as the enzyme denatures. B: each enzyme has its own optimum pH. C: the rate levels off at Vmax, and Km is the substrate concentration giving half Vmax. D: with a competitive inhibitor the same Vmax is reached only at higher substrate (Km raised); a non-competitive inhibitor lowers Vmax and leaves Km unchanged. Curves are schematic. Diagram: IOM Mock.

Feedback (allosteric) inhibition: the end product of a pathway binds an allosteric site on the pathway's first enzyme and switches it off — isoleucine inhibits threonine deaminase. Allosteric activators do the reverse: ADP stimulates some glycolytic enzymes that ATP inhibits.

Numbers and names to memorise

Item	Value
Amino acids in proteins	20; nine essential for humans
Peptide bonds in a chain of n residues	n − 1
Alpha-helix	3.6 residues per turn; hydrogen bonds
Insulin	A chain 21, B chain 30 amino acids
Haemoglobin	Two alpha + two beta chains; sickle cell: Glu → Val at beta 6
"Enzyme" / cell-free fermentation	Kühne 1877 / Buchner 1897
First enzyme crystallised	Urease, Sumner 1926
Lock and key / induced fit	Fischer 1894 / Koshland 1958
Km	Substrate concentration at half Vmax
EC classes	Six in the Grade 11 text; translocases (EC 7) added 2018
Optimum pH	Pepsin about 2, salivary amylase about 6.8, trypsin about 8

Traps

Denaturation keeps the peptide bonds; hydrolysis breaks them.
All coenzymes are cofactors, not all cofactors are coenzymes — a metal ion is a cofactor but not a coenzyme; a prosthetic group is bound tightly.
Competitive raises Km and leaves Vmax; non-competitive lowers Vmax and leaves Km. Do not swap them.
Low Km = high affinity, not low.
Enzymes change the rate, not the equilibrium or the energy released.
Cold inactivates, heat denatures.
Class slips: carbonic anhydrase is a lyase, hexokinase a transferase, DNA ligase a ligase; hydrolases are EC 3.
Not every enzyme is a protein: ribozymes are RNA.

Quick check

0 of 5 answered

Pick an answer to see whether you are right, and why.

1
The alpha-helix of a protein is held in shape mainly by:
2
Adding a large excess of substrate restores an inhibited enzyme to its normal maximum rate. The inhibitor is most likely:
3
Hexokinase moves a phosphate group from ATP to glucose. It belongs to the class:
4
Enzyme P has a Km of 0.5 mM and enzyme Q a Km of 5 mM for the same substrate. At 0.5 mM substrate:
5
A protein solution heated to 90 °C loses its activity. Which feature remains unchanged?

Sources

OpenStax, Biology 2e, 3.4 Proteins and 6.5 Enzymes (consulted), read 2026-09-15.
Wikipedia: Enzyme (Kühne 1877, Buchner, Sumner, Fischer 1894, Koshland), Enzyme Commission number, Translocase (EC 7, August 2018), Michaelis–Menten kinetics (Km, 1913), read 2026-09-15.
NCERT Biology Class 11, ch. 9 Biomolecules; Nepal CDC Grade 11 Biology — consulted for the classification scheme, inhibition framing and terminology.
Figures: credited in each caption (Wikimedia Commons and original diagrams).