Biology (9700) | Biological molecules

AS Level Biology 9700: Comprehensive Study Notes (Topic 2)

Biological Molecules: The Foundation of Life

Hey there, future biologists! Welcome to one of the most fundamental chapters in AS Biology:
Biological Molecules.
These are the large, complex organic molecules that build cells, store energy, and control all the chemical reactions that keep you alive. Think of them as the vital construction materials and tools of the body.
Don't worry if the names sound complicated; we will break down their structures and relate them directly to their amazing jobs!

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2.1 Testing for Biological Molecules (Practical Skills)

Before diving into structures, we need to know how to identify these molecules in a lab setting. These tests are essential for practical papers!

Test 1: Reducing Sugars (e.g., Glucose, Fructose, Maltose)

Test Name: The Benedict’s Test.

Principle: Reducing sugars donate electrons to the blue copper(II) ions in Benedict’s reagent, reducing them to brick-red copper(I) oxide precipitate.

Procedure:

• Add Benedict’s reagent to the sample solution.
• Heat the mixture in a water bath (usually 95°C or boiling) for 5 minutes.

Result:

• Positive: Colour change from blue $\to$ green $\to$ yellow $\to$ orange $\to$ brick-red precipitate.
• Negative: Remains blue.

Semi-Quantitative Benedict’s Test (Estimating Concentration)

The intensity of the final colour and the amount of precipitate formed are proportional to the concentration of the reducing sugar. For semi-quantitative results, we can:

• Compare the final colour change to known colour standards.
• Measure the time to first colour change (the faster the change, the higher the concentration).

Test 2: Non-Reducing Sugars (e.g., Sucrose)

Procedure: Non-reducing sugars must first be broken down into reducing sugars before the Benedict’s test works.

1. Heat the sample solution with a few drops of dilute hydrochloric acid (HCl). (This hydrolyses the non-reducing sugar bond).
2. Neutralise the solution by adding sodium hydrogencarbonate (checking with pH paper).
3. Carry out the standard Benedict’s test (add Benedict’s reagent and heat).

Result:

• Positive: Brick-red precipitate formed.
• Negative: Remains blue.

Test 3: Starch (A Polysaccharide)

Test Name: The Iodine Test.

Reagent: Iodine dissolved in potassium iodide solution (Iodine solution).

Procedure: Add a few drops of iodine solution directly to the sample.

Result:

• Positive: Colour changes from brown/orange to blue-black.
• Negative: Remains brown/orange.

Test 4: Lipids (Fats and Oils)

Test Name: The Emulsion Test.

Principle: Lipids dissolve readily in organic solvents like ethanol, but not in water. When the lipid-ethanol mix is poured into water, the lipid forms tiny dispersed droplets (an emulsion).

Procedure:

1. Add ethanol (or absolute alcohol) to the sample and shake vigorously to dissolve any lipid present.
2. Pour the resulting alcohol solution into a test tube containing cold water.

Result:

• Positive: A milky-white emulsion is formed (the solution turns cloudy).
• Negative: The solution remains clear.

Test 5: Proteins

Test Name: The Biuret Test.

Principle: Detects the presence of peptide bonds (found in proteins) using an alkaline copper sulfate solution.

Reagent: Biuret reagent (Sodium hydroxide solution + copper(II) sulfate solution).

Procedure: Add sodium hydroxide solution to the sample, then add copper(II) sulfate solution and mix gently.

Result:

• Positive: Colour changes from blue to purple/lilac.
• Negative: Remains blue.

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2.2 Carbohydrates and Lipids

The Building Blocks (Monomers and Polymers)

Most biological molecules are huge, complex structures called macromolecules. They are built up from smaller, repeating units.

• Monomer: A small molecule that can be joined to other similar molecules (e.g., glucose, amino acid).
• Polymer: A large molecule made up of many repeating monomers joined together (e.g., starch, protein).

The process of joining monomers uses covalent bonds and is called Condensation (or dehydration synthesis). A molecule of water is removed (produced) for every bond formed.
The reverse process is Hydrolysis, where a water molecule is added to break the bond, separating the polymer into monomers.

Carbohydrates (Saccharides)

Carbohydrates are composed of C, H, and O, often in the ratio \(C_x(H_2O)_y\). Their main roles are energy storage and structural support.

Monosaccharides (Single Sugar Units)

These are the monomers (simple sugars).

• Examples: Glucose, Fructose, Galactose.
• They are generally soluble and sweet.
• They are reducing sugars (they can reduce other chemicals, like copper ions in Benedict’s test).

We must know the ring forms of glucose:

1. Alpha (\(\alpha\))-Glucose: The hydroxyl (-OH) group on Carbon 1 points down.
2. Beta (\(\beta\))-Glucose: The hydroxyl (-OH) group on Carbon 1 points up.

Memory Aid: Alpha starts low (like A) - OH is down. Beta starts high (like B) - OH is up.

Disaccharides (Two Sugar Units)

Formed when two monosaccharides join via a condensation reaction, forming a glycosidic bond.

• Maltose: Glucose + Glucose (Reducing sugar)
• Sucrose: Glucose + Fructose (Non-reducing sugar - must be hydrolysed first)
• Lactose: Glucose + Galactose (Reducing sugar)

Polysaccharides (Many Sugar Units)

Formed from many monosaccharides (usually glucose) joined by glycosidic bonds.

1. Starch (Energy Storage in Plants)

• Structure: Made of $\alpha$-glucose monomers. It is a mixture of two molecules:
  • Amylose: Straight, unbranched chain, coils into a spiral/helix.
  • Amylopectin: Branched chain, also spirals but less tightly.
• Function Relation:
  • Being large and insoluble means it doesn't affect the water potential of the cell (no osmotic effect).
  • Coiled structure makes it compact, storing a lot of energy in a small space.
  • Branched nature (amylopectin) provides many end points for enzymes to hydrolyse, allowing rapid release of glucose when needed.

2. Glycogen (Energy Storage in Animals/Fungi)

• Structure: Made of $\alpha$-glucose. Highly branched (even more so than amylopectin).
• Function Relation: High branching means rapid hydrolysis and glucose release, crucial for active animals (e.g., muscle cells).

3. Cellulose (Structural Support in Plants)

• Structure: Made of \(\beta\)-glucose monomers. The \(\beta\)-linkage causes the chain to be straight, and every alternate glucose molecule is rotated 180°.
• Arrangement: Long, straight chains are held together by hydrogen bonds between adjacent chains, forming strong structures called microfibrils. Many microfibrils combine to form fibres.
• Function Relation: The strong, rigid arrangement of fibres provides high tensile strength, making it perfect for the plant cell wall structure.

Lipids (Fats, Oils, and Waxes)

Lipids are large, non-polar molecules, meaning they are hydrophobic (water-fearing) and insoluble in water, but soluble in organic solvents.

Triglycerides (Fats and Oils)

Structure: Formed by the condensation reaction between one molecule of Glycerol and three molecules of Fatty Acids. The bonds formed are called Ester Bonds.

• Fatty acids can be saturated (no C=C double bonds, solid at room temperature, straight chain) or unsaturated (at least one C=C double bond, liquid at room temperature, bent chain).
• Triglycerides are entirely non-polar and hydrophobic.

Function Relation:

• Excellent long-term energy storage (they have twice the energy content per gram compared to carbohydrates).
• Act as insulation (thermal and electrical).
• Provide buoyancy and protection for organs.

Did you know? Because they are hydrophobic, they can be stored without water, making them efficient storage molecules.

Phospholipids (Key Component of Membranes)

Structure: Similar to a triglyceride, but one fatty acid is replaced by a phosphate group.

• The phosphate group forms a hydrophilic (polar) head.
• The two fatty acid tails form hydrophobic (non-polar) tails.

Function Relation: Because they have both polar and non-polar parts (amphipathic), when placed in water, they naturally form a phospholipid bilayer, which is the basic structure of the cell surface membrane (Topic 4).

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2.3 Proteins

Proteins are the most diverse group of biological molecules, performing roles from catalysis (enzymes) to transport (haemoglobin) to structure (collagen).

Amino Acids (The Monomers)

The monomers of proteins are amino acids. There are about 20 different types used in living organisms.

General Structure of an Amino Acid:

Each amino acid has a central carbon atom bonded to four different groups:

1. An amino group (\(NH_2\))
2. A carboxyl group (\(COOH\))
3. A hydrogen atom (H)
4. A variable R group (or side chain) - this is what makes each amino acid unique.

Peptide Bonds and Polypeptides

Amino acids join together via a condensation reaction between the carboxyl group of one amino acid and the amino group of another. This forms a peptide bond.

A chain of many amino acids linked by peptide bonds is called a polypeptide.

Protein Structure Hierarchy

The sequence and three-dimensional shape of a polypeptide determine the protein’s final function. This shape is described in four levels:

1. Primary Structure (\(1^\circ\))

• This is the sequence of amino acids in the polypeptide chain.
• Determined by the DNA base sequence (gene).
• Held together only by peptide bonds.
• Analogy: It is like spelling a word correctly—if the letters (amino acids) are wrong, the whole word (protein) is altered.

2. Secondary Structure (\(2^\circ\))

• This is the local folding of the polypeptide chain, usually into regular repeating structures.
• Common structures include the $\alpha$-helix (coil) and the $\beta$-pleated sheet (folded structure).
• Held together by hydrogen bonds forming between the C=O and N-H groups of the polypeptide backbone.

3. Tertiary Structure (\(3^\circ\))

• This is the overall, specific three-dimensional shape of a single polypeptide chain.
• It is crucial for function (especially in enzymes, where the active site shape is determined here).
• Held together by interactions between the variable R groups (side chains), including:
  • Hydrophobic interactions: Non-polar R groups cluster in the centre (away from water).
  • Hydrogen bonding: Weak bonds between polar R groups.
  • Ionic bonding: Stronger bonds between oppositely charged R groups.
  • Covalent bonding (Disulfide bonds): Very strong covalent link formed between two cysteine amino acids.

4. Quaternary Structure (\(4^\circ\))

• Applies only if the final functional protein consists of two or more polypeptide chains (subunits) linked together.
• Example: Haemoglobin has four subunits.
• Held together by the same R-group interactions as the tertiary structure.

Protein Shape and Function: Globular vs. Fibrous

Proteins are classified based on their overall 3D structure and solubility.

Globular Proteins

• Shape: Compact, spherical, complex tertiary/quaternary structure.
• Solubility: Generally soluble in water (due to hydrophilic R groups facing outwards).
• Role: Have physiological roles (carrying out reactions or transport).
• Example: Enzymes, Haemoglobin, Antibodies, Insulin.

Fibrous Proteins

• Shape: Long, narrow, parallel chains, often organized into long fibres.
• Solubility: Generally insoluble in water.
• Role: Have structural roles (providing strength and support).
• Example: Collagen, Keratin, Elastin.

Case Study 1: Haemoglobin (A Globular Protein)

Function: Transporting oxygen in the blood of mammals.

Structure: A complex quaternary structure composed of four polypeptide chains:

• Two alpha ($\alpha$) chains (or $\alpha$-globin).
• Two beta ($\beta$) chains (or $\beta$-globin).
• Each chain is associated with a prosthetic group called a haem group.

Structure-Function Relationship:

• Each haem group contains one central Iron ion (\(Fe^{2+}\)).
• Crucially, one oxygen molecule (\(O_2\)) binds specifically and reversibly to each iron ion. Therefore, one haemoglobin molecule can transport four oxygen molecules.
• Its compact, soluble globular structure allows it to move easily within the red blood cells.

Case Study 2: Collagen (A Fibrous Protein)

Function: Providing high tensile strength to tissues (e.g., skin, tendons, cartilage, artery walls).

Structure:

• Consists of three polypeptide chains (a quaternary structure), each being an $\alpha$-helix.
• These three helices are wound around each other to form a characteristic triple helix structure (a collagen molecule).

Arrangement into Fibres:

• Collagen molecules are cross-linked to each other end-to-end and side-by-side.
• They are staggered (not exactly parallel) to maximize strength, similar to overlapping bricks in a wall.
• This staggered arrangement forms strong, tough collagen fibres.

Structure-Function Relationship: The strong, insoluble, rope-like structure provides immense strength without stretching, which is essential for structural tissues.

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2.4 Water

Water is often overlooked because it is so common, but life as we know it depends entirely on its unique properties. These properties all stem from one concept: Hydrogen Bonding.

Hydrogen Bonding in Water

A water molecule (\(H_2O\)) is formed by two hydrogen atoms covalently bonded to one oxygen atom.

• Oxygen is highly electronegative, meaning it pulls the shared electrons towards itself.
• This makes the oxygen atom slightly negative ($\delta^-$) and the hydrogen atoms slightly positive ($\delta^+$).
• Therefore, water is a polar molecule.

The slight positive charge on one water molecule (H) is attracted to the slight negative charge on an adjacent water molecule (O). This weak electrical attraction is a hydrogen bond.

Relating Water Properties to Biological Roles

1. Solvent Action

Property: Water is an excellent solvent for other polar molecules (like sugars, salts, and ions).

Biological Role:

• Aids in transport (e.g., dissolving mineral ions in plants, dissolving glucose and plasma proteins in mammalian blood).
• Allows biochemical reactions to occur easily, as reactants are dissolved and can move freely.

2. High Specific Heat Capacity

Property: Water requires a large amount of energy to change its temperature.

Mechanism: The extensive network of hydrogen bonds absorbs a lot of heat energy before the temperature increases.

Biological Role:

• Allows for temperature regulation (thermoregulation) in organisms. Because water absorbs/releases heat slowly, body temperature remains relatively stable, even when external temperatures fluctuate widely. This protects enzymes from denaturation.

3. Latent Heat of Vaporisation (High)

Property: Water requires a large amount of energy to change from a liquid to a gas (evaporate).

Mechanism: All the hydrogen bonds must be broken for water molecules to escape as a gas.

Biological Role:

• Effective as a cooling mechanism (evaporative cooling or sweating in mammals, transpiration in plants). When water evaporates, it carries a large amount of heat energy away from the surface, cooling the organism efficiently.