• Amino acids are the monomers of proteins — a central carbon bonded to an amine group, a carboxylic acid group, a hydrogen, and a variable R group.
• Peptide bonds form between amino acids via condensation reactions (releasing water); hydrolysis breaks them back down (adding water).
• Proteins have four levels of structure: primary (sequence), secondary (α-helix / β-pleated sheet via H-bonds on the backbone), tertiary (3D folding via R-group interactions), and quaternary (multiple polypeptide chains together).
• Globular proteins (e.g. haemoglobin, enzymes) are compact, soluble, and functional. Fibrous proteins (e.g. collagen, keratin) are long, insoluble, and structural.
• Enzymes are globular proteins that act as biological catalysts, lowering activation energy via a specific active site (lock-and-key vs. induced-fit models).
• Enzyme reaction rate is affected by temperature, pH, enzyme concentration, and substrate concentration — each in a distinct, explainable way.
• Nucleotides (pentose sugar + phosphate + nitrogenous base) are the monomers of DNA and RNA, joined by phosphodiester bonds into a sugar-phosphate backbone.
• DNA is a double-stranded, antiparallel double helix held together by complementary base pairing (A-T, G-C) via hydrogen bonds; RNA is single-stranded, uses ribose and uracil instead of deoxyribose and thymine.

1.1 What is an amino acid?

Think of an amino acid like a Lego brick with four connectors sticking off a central carbon atom. Every single amino acid — all 20 of them found in living things — shares the exact same three connectors, and differs only in the fourth:

• Amine group (–NH₂) — always the same
• Carboxylic acid group (–COOH) — always the same
• A hydrogen atom — always the same
• R group — this is the ONE part that changes between amino acids, and it's what gives each amino acid its personality (acidic, basic, polar, non-polar)

Because the R group is the only thing that varies, it's the R group that ultimately decides how a protein folds and what it can do — this idea comes back again and again in this chapter, so lock it in now.

1.2 Peptide bonds — how amino acids link up

When two amino acids join, it's not magic — it's a straightforward condensation reaction: the –OH from one amino acid's carboxyl group and an –H from the next amino acid's amine group are kicked out together as a water molecule (H₂O), and the two amino acids fuse where those atoms used to be. That new bond, between the carbon of one amino acid and the nitrogen of the next, is called a peptide bond.

Run the reaction backwards — add a water molecule back in — and you break the peptide bond. That's hydrolysis, and it's how your gut breaks dietary protein back down into individual amino acids during digestion.

• Dipeptide = 2 amino acids joined (1 peptide bond)
• Polypeptide = 3 or more amino acids joined (a long chain)
• A protein might be just one polypeptide chain, or several chains working together

1.3 The Four Levels of Protein Structure

This is the single most important idea in the whole chapter, so here's the analogy that makes it click: imagine a long piece of string with beads on it (that's your primary structure). Now imagine that string curling into a coil like a phone cable (secondary structure). Now imagine that coiled cable scrunching itself into a compact ball, tucking certain parts inward (tertiary structure). And finally, imagine several of those balls clumping together to do one job as a team (quaternary structure). Each level builds directly on the one before it.

Primary structure

This is simply the sequence of amino acids in the chain, held together by covalent peptide bonds. Your DNA dictates this sequence exactly — which amino acid goes where, and how many of each. Because this sequence is so tightly controlled, even one wrong amino acid in the sequence can completely change (or destroy) how the protein folds and functions — this is the molecular basis of conditions like sickle cell anaemia (more on that later).

Secondary structure

Once you have a chain of amino acids, hydrogen bonds start to form between the –NH and C=O groups of the protein backbone (not the R groups — that's a common exam trap). These hydrogen bonds pull the chain into one of two regular, repeating shapes:

• α-helix — the chain coils into a spiral, with hydrogen bonds forming between every 4th peptide bond
• β-pleated sheet — the chain folds back on itself so that two parallel sections run alongside each other, hydrogen-bonded together

Fibrous proteins like collagen and keratin rely heavily on secondary structure for their strength.

Tertiary structure

Now the R groups get involved. As the secondary structure folds further into a compact 3D shape, the R groups (side chains) that stick outward interact with each other to lock the shape in place. There are four types of bond/interaction possible here:

This tertiary structure is what gives 3D globular proteins (like enzymes) their highly specific shape — including the exact shape of an enzyme's active site.

Quaternary structure

Some proteins are made of more than one polypeptide chain working together — each chain is called a subunit. The same bonds that hold tertiary structure together (hydrogen, ionic, disulphide, hydrophobic) also hold the subunits together. Haemoglobin is the classic example: four subunits (2 α-globin + 2 β-globin) working as one functional molecule.

1.4 Globular vs. Fibrous Proteins

Here's an intuitive way to think about it: globular proteins are built to do things (soluble, active, mobile — think enzymes and hormones), while fibrous proteins are built to hold things (insoluble, strong, structural — think tendons and hair).

Globular proteins

• Compact, roughly spherical shape
• Non-polar (hydrophobic) R groups fold inward, away from water
• Polar (hydrophilic) R groups face outward, toward water
• This arrangement makes them generally soluble in water — essential for being transported around the body and taking part in metabolic reactions
• Examples: enzymes, haemoglobin, immunoglobulins, insulin

Fibrous proteins

• Long strands with cross-linkages via hydrogen bonds
• Little or no tertiary structure
• Highly repetitive amino acid sequence — creates very organised, regular structures
• Large numbers of hydrophobic R groups make them insoluble in water — perfect for structural roles that need to resist dissolving
• Examples: collagen, keratin, elastin

1.5 Case Study: Haemoglobin (globular)

Haemoglobin is the textbook globular protein, and it's worth knowing in detail because it shows up constantly in exam questions.

• Quaternary structure: 4 polypeptide chains (2 α-globin + 2 β-globin subunits), held together by disulphide bonds
• Each subunit carries a prosthetic haem group containing an Fe²⁺ ion — this is what actually binds oxygen (reversibly), forming oxyhaemoglobin
• 4 haem groups = 4 oxygen molecules (8 oxygen atoms) can be carried per haemoglobin molecule
• Hydrophobic R groups face inward (preserving the spherical shape); hydrophilic R groups face outward (maintaining solubility)
• When one oxygen molecule binds, it slightly alters the quaternary structure, making it easier for the next oxygen molecules to bind — this is called cooperative binding

1.6 Case Study: Collagen (fibrous)

Collagen is the most abundant structural protein in vertebrates — found in tendons, cartilage, ligaments, bone, teeth, skin, blood vessel walls, and the cornea.

• Formed from 3 polypeptide chains wound tightly together into a triple helix (called tropocollagen)
• Held together mainly by hydrogen bonds, plus some covalent bonds
• Almost every third amino acid is glycine — the smallest amino acid (R group = single H atom), which fits neatly on the inside of the tight triple helix
• Covalent cross-links form between neighbouring triple helices, bundling them into fibrils, which bundle further into fibres
• Fibrils have staggered ends — this gives collagen its striped (striated) appearance under an electron microscope, and adds strength
• High proline and hydroxyproline content adds stability (their R groups repel each other, resisting unwinding)
• Insoluble in water — the molecule is simply too long to dissolve

2.1 Enzymes are globular proteins

Because enzymes are globular proteins, everything you just learned about tertiary structure applies directly to them. The complex 3D folding creates a uniquely-shaped pocket called the active site, where a specific substrate binds to form an enzyme-substrate complex. Because the active site's shape comes from a highly specific tertiary structure, each enzyme is generally restricted to working with only one substrate (or a very small group of similar ones) — this is called enzyme specificity.

2.2 Lock-and-Key vs. Induced-Fit

Two models have been proposed over time to explain exactly how enzymes and substrates interact:

Lock-and-key hypothesis (Emil Fischer, 1890s)

The original idea: both the enzyme's active site and the substrate are rigid, fixed shapes that fit together perfectly — like a key sliding into a specific lock. No flexibility involved.

Induced-fit hypothesis (1959, current model)

The modern, more accurate model: the active site (and sometimes the substrate) can slightly change shape as the substrate approaches and binds — these are called conformational changes. This flexibility creates an ideal binding arrangement, maximising the enzyme's ability to catalyse the reaction.

2.3 Enzymes lower activation energy

Enzymes are biological catalysts — "biological" because they work inside living systems, "catalysts" because they speed up reactions without being used up or permanently changed themselves.

Every chemical reaction needs a minimum amount of energy to get going — the activation energy — enough to destabilise the bonds in the reactants so a reaction can occur. Enzymes work by providing an alternative reaction pathway with a lower activation energy. They don't change the overall energy released or absorbed by the reaction — they just make it easier to get started.

Without enzymes, biological reactions would need extreme heat or pressure to occur at a usable rate — conditions that would kill living cells. Enzymes let these reactions happen fast at normal body temperatures.

2.4 Intracellular vs. Extracellular Enzymes

All enzymes are made inside cells (via protein synthesis), but not all of them stay there.

Extracellular enzymes are needed for digestion specifically because the food molecules being broken down (like starch) are far too large to fit inside a cell — digestion has to happen outside first.

2.5 Factors Affecting Enzyme Reaction Rate

Temperature

Two competing effects are happening at once, and you need to explain both to get full marks:

• Below the optimum: molecules move more slowly → fewer successful collisions between substrate and active site → slower reaction. As temperature rises toward the optimum, kinetic energy increases, collisions become more frequent and more energetic, so the rate increases.
• Above the optimum: the rate drops sharply because the enzyme starts to denature — hydrogen bonds holding the tertiary structure break, the active site's shape permanently changes, and the substrate can no longer bind.

Most human enzymes work best around 37°C (body temperature) and denature above around 40-50°C.

pH

Every enzyme has an optimum pH — the pH at which its ionic and hydrogen bonds are most stable, keeping the active site in its correct shape. Move away from that optimum (in either direction) and excess H⁺ ions (acidic) or OH⁻ ions (alkaline) start to break those bonds, distorting the active site until the substrate no longer fits. Different enzymes are adapted to work in wildly different pH environments:

• Pepsin (stomach) — optimum pH ≈ 2 (matches the stomach's hydrochloric acid environment)
• Urease — optimum pH ≈ 7 (neutral)
• Trypsin (small intestine) — optimum pH ≈ 8 (slightly alkaline)

Enzyme concentration

More enzyme molecules = more active sites available = more enzyme-substrate complexes can form at once, so the rate increases linearly with enzyme concentration — as long as there's plenty of substrate available. If substrate becomes limited, adding more enzyme stops making a difference (substrate becomes the limiting factor).

Substrate concentration

More substrate = more collisions with active sites = faster rate — but only up to a point. Once every active site is constantly occupied (a saturation point), adding more substrate has no further effect, because enzyme concentration has become the limiting factor.

2.6 Core Practical 4: Investigating Enzyme Reaction Rate

A classic version of this practical uses catalase breaking down hydrogen peroxide into water and oxygen — the volume of oxygen gas produced is used as a measure of reaction rate.

Method outline

1. Add a set volume of hydrogen peroxide + buffer solution to a boiling tube (buffer keeps pH constant)
2. Set up an inverted, water-filled measuring cylinder in a trough of water, with a delivery tube leading into it
3. Add a set volume of catalase solution (a specific concentration), and immediately seal the boiling tube with the bung
4. Record the volume of oxygen gas collected (via water displacement) every 10 seconds for 60 seconds
5. Repeat twice more and average the results at each time point
6. Repeat the whole experiment at different catalase concentrations
7. Plot volume of oxygen against time for each concentration, and compare initial rates

Calculating initial rate of reaction

The initial rate (the fastest, most reliable point of the reaction, before substrate starts running out) is found by:

1. Drawing a tangent to the graph at time = 0 (through the origin, along the steepest initial part of the curve)
2. Calculating the gradient of that tangent — this gradient IS the initial rate of reaction

Alternative version: the breakdown of starch by amylase can be tracked using iodine solution (which turns blue-black with starch) and a colorimeter, measuring how absorbance decreases over time as starch is broken down into maltose.

3.1 What is a nucleotide?

Just like amino acids are the building blocks of proteins, nucleotides are the building blocks (monomers) of DNA and RNA. Each nucleotide is made of three parts joined together:

• A pentose sugar (a 5-carbon sugar)
• A phosphate group
• A nitrogen-containing organic base

3.2 Purines vs. Pyrimidines

The 5 possible nitrogenous bases split into two structural families based on how many rings their molecular structure contains — this matters because it explains why base pairing always happens the way it does (see 3.4).

A useful memory trick: "Pyrimidines are sh-Y" — Cytosine, Thymine, Uracil all end in a "Y-sound" pattern... or simply remember pyrimidines have the shorter names and the smaller (single) ring.

3.3 Building a Polynucleotide: The Sugar-Phosphate Backbone

Individual nucleotides link together via condensation reactions — just like amino acids did for proteins. This time, the bond forms between the phosphate group of one nucleotide and the pentose sugar of the next, creating a phosphodiester bond (named because it contains a phosphate group flanked by two ester bonds).

Specifically, the phosphodiester bond links the 5-carbon of one sugar (via its phosphate) to the 3-carbon of the next sugar. This directional linking is why every polynucleotide strand has a distinct 5' end and 3' end.

3.4 DNA Structure & Complementary Base Pairing

DNA is made of two polynucleotide strands, running in opposite directions to each other (antiparallel — one strand runs 5'→3', the other runs 3'→5'). The two strands are held together not by strong covalent bonds, but by hydrogen bonds between specific pairs of bases that always pair the same way:

This is called complementary base pairing — always a purine paired with a pyrimidine, which keeps the width of the DNA molecule constant all the way along (two rings + one ring = always the same combined width). A purine can never pair with another purine (too wide) and a pyrimidine can never pair with another pyrimidine (too narrow) — the geometry simply wouldn't fit.

The full 3D shape formed by these two antiparallel strands twisting around each other is called the double helix — described as "double" (two strands) and "helix" (a 3D spiral, not flat like the simplified 2D diagrams usually show).

3.5 RNA Structure — What's Different from DNA

RNA shares the same basic building blocks as DNA (nucleotides, phosphodiester bonds, a sugar-phosphate backbone) but differs in several important ways:

There are three main types of RNA you should know: mRNA (messenger RNA — a transcript copy of a gene that codes for a specific polypeptide), tRNA (transfer RNA), and rRNA (ribosomal RNA).

Secondary structure H-bonds only form between the backbone's amino (–NH) and carboxyl (C=O) groups. Tertiary structure H-bonds form between R groups. Examiners specifically test this distinction — always specify which groups are bonding.

For temperature questions, you MUST explain both halves of the curve separately: the increase (kinetic energy → collision frequency) AND the decrease (denaturation → active site shape change). Missing either half loses marks. For pH, don't mention collision frequency at all — pH only affects bond stability in the active site, not molecular movement.

Be precise: enzymes reduce the activation energy by providing an alternative reaction pathway — they do NOT change the overall energy change (ΔG) of the reaction. Don't say they "make the reaction release less energy."

Phosphodiester bonds are covalent and hold nucleotides together within ONE strand (the backbone). Hydrogen bonds are weaker and hold the TWO strands together via base pairing. If asked "what breaks first when DNA is heated," the answer is hydrogen bonds — they're weaker.

Whenever asked to explain why a protein can do its job, always link back to structure: sequence → bonding → 3D shape → function. Examiners give marks for this chain of reasoning, not just naming the function.

Remember %A = %T and %G = %C always (in double-stranded DNA only — this rule does NOT apply to single-stranded RNA). Double-check your subtraction from 100% before halving to find the individual G and C percentages.