AS Level Biology 9700

2. Biological molecules

Written by: Rhia Sakthivel
Formatted by: Pranav I

Index

2.1 Biochemistry
2.2 The building blocks of life
2.3 Monomers, polymers and macromolecules
2.4 Carbohydrates
2.5 Lipids
2.6 Proteins 
2.7 Water
2.8 Testing for biological molecules

2.1 Biochemistry

  • Biochemistry studies the chemical reactions of biological molecules
  • Molecular structure is closely linked to biological functions
  • Metabolism: total of all biochemical reactions in the body.

2.2 The building blocks of life

  • The four most common elements in living organisms are hydrogen, carbon, oxygen, and nitrogen  
  • These elements make up over 99% of the atoms in living things  
  • Carbon is crucial due to its ability to form long chains or ring structures  
  • Carbon skeletons serve as the foundation of organic molecules  
  • Before life evolved, chemical evolution led to the formation of simple carbon-based biological molecules  
  • Simple biological molecules are limited in variety and act as building blocks for larger, complex molecules 

2.3 Monomers, polymers and macromolecules

Macromolecules

  • Macromolecules are giant molecules in living organisms, categorized into:
    • Polysaccharides
    • Proteins (polypeptides)
    • Nucleic acids (polynucleotides)
  • The term “poly” means “many,” as macromolecules (polymers) consist of many repeating subunits (monomers)

Monomer

✅ Monomer (definition)

Simple molecules used as a basic building block for polymers

  • Examples: monosaccharides, amino acids, nucleotides
  • Monomers are connected by covalent bonds, which are strong bonds formed by sharing electrons:
    • Examples include glycosidic, ester, and peptide bonds

Polymer

✅ Polymer (definition)

Giant molecules consisting of many repeating subunits (monomers); joined together by covalent bonds; through a condensation reaction. 

  • Forming polymers involves condensation reactions, where two monomers join by removing a water molecule
  • Breaking down polymers requires hydrolysis, where water is added to split the bonds
  • Monomers and their corresponding polymers:
    • Monosaccharides → polysaccharides
    • Amino acids → proteins
    • Nucleotides → nucleic acids

2.4 Carbohydrates

  • Carbohydrates are composed of carbon, hydrogen, and oxygen atoms
    • Hydrogen and oxygen are present in a 2:1 ratio
  • General formula: Cx(H2O)y
  • Carbohydrates are classified into three groups:
    • Monosaccharides
    • Disaccharides
    • Polysaccharides (not sugars)

Monosaccharides

  • Monomers of polysaccharides
    • E.g. glucose, fructose, galactose
  • Joined together by glycosidic bonds during condensation
  • Monosaccharides are sugars that dissolve easily in water to form sweet solutions
    • Composed of a single sugar molecule (“mono” = one, “saccharide” = sugar)
    • General formula: (CH₂O)ₙ
  • Classified by the number of carbon atoms:
    • Trioses (3C)
    • Pentoses (5C)
      • E.g. ribose, deoxyribose
    • Hexoses (6C)
      • E.g. glucose, fructose, galactose
  • Molecular formula for hexoses: C₆H₁₂O₆
    • The structural formula shows the arrangement of atoms
  • Ring structures:
    • Pentoses and hexoses can form stable rings
    • In glucose, carbon 1 joins oxygen on carbon 5
      • α-glucose → OH on carbon 1 is below the ring
      • β-glucose→  OH on carbon 1 is above the ring
    • These are isomers (different forms of the same chemical)
Fig 2.1 The structural formula of glucose
Fig 2.2 The isomerical ring structures of glucose
  • Functions of monosaccharides
    • Energy source in respiration
      • Many carbon-hydrogen bonds release energy when broken
      • Energy helps make ATP from ADP and phosphate
      • Glucose is vital for energy metabolism
    • Building blocks for larger molecules:
      • Glucose forms polysaccharides like starch, glycogen, and cellulose
      • Ribose forms RNA and ATP
      • Deoxyribose forms DNA

Disaccharides

✅ Disaccharide (definition)

A simple sugar molecule consisting of two monosaccharides joined together by glycosidic bonds through a condensation reaction

  • Disaccharides are sugars formed by joining two monosaccharides (“di” = two)
  • Common disaccharides
    • Maltose: glucose + glucose
    • Sucrose: glucose + fructose (transport sugar in plants; table sugar)
    • Lactose: glucose + galactose (milk sugar, essential for young mammals)
  • Formation
    • Condensation reaction
      • Two –OH groups align
      • One –OH combines with hydrogen from another to form water
      • An oxygen bridge forms, creating a glycosidic bond between the monosaccharides
  • Breaking down
    • Hydrolysis reaction
      • Water is added to break the glycosidic bond
      • It occurs during digestion to convert disaccharides into monosaccharides
  • Many possible disaccharides exist due to multiple –OH groups in monosaccharides
    • Enzymes control which –OH groups align, so only a few disaccharides are common in nature
Fig 2.3 Condensation reaction to form a disaccharide

Polysaccharides

✅ Polysaccharide (definition)

Polymers of many repeating units of monosaccharides are joined together by many glycosidic bonds

  • Composition: can be several thousand monosaccharide units long, forming macromolecules
  • Examples: starch, glycogen, and cellulose
  • Polysaccharides are not sugars

Starch and glycogen

  • Purpose: store glucose in a compact, inert, insoluble form
    • To maintain osmotic balance
    • To avoid glucose reactivity interfering with cell chemistry
  • In plants → starch
  • In animals → glycogen
  • Starch
    • A mixture of two substances → amylose and amylopectin
      • Amylose: long, unbranched chains of α-glucose (1,4 linkages), forming a helical, compact structure
      • Amylopectin: branched chains with 1,4 and 1,6 linkages
    • Starch forms grains found in plant storage organs like potato tubers and cereal seeds
  • Glycogen:
    • Similar to amylopectin but more branched
    • Found in liver and muscle cells as an energy reserve
Fig 2.4 The formation of a 1, 6 link, and the overall structure of amylopectin or glycogen

Cellulose

  • Most abundant organic molecule due to presence in plant cell walls
  • Function: structural role due to high mechanical strength
  • Composition: polymer of β-glucose
    • Formation
      • Glycosidic bonds between carbon 1 of one β-glucose and carbon 4 of another, with alternating glucose molecules rotated 180°
      • Hydrogen bonds between –OH groups within and between molecules provide strength
    • Structure
      • Molecules form microfibrils (bundles of 60–70 molecules), which further bundle into fibers
      • Fibers arranged in layers for tensile strength and flexibility
  • Properties
    • High tensile strength (withstands osmotic pressure)
    • Freely permeable, allowing water and solutes to pass
Fig 2.5 The structure of cellulose fibers

Dipoles and hydrogen bonds

  • Dipole formation: unequal electron sharing creates partial charges (δ+ on hydrogen, δ− on oxygen)
  • Hydrogen bonds
    • Weak but significant forces between molecules with dipoles (e.g., –OH, –CO, –NH groups)
    • Affect structure and properties of carbohydrates and proteins
  • Polarity and solubility
    • Polar molecules (e.g. sugars) are hydrophilic (water-soluble)
    • Non-polar molecules are hydrophobic (insoluble in water)

2.5 Lipids

  • A diverse group of organic molecules that are insoluble in water
  • Formation: most lipids result from fatty acids combining with an alcohol
  • Types
    • Fats: solid at room temperature
    • Oils: liquid at room temperature
  • Similarity: fats and oils are chemically very similar despite physical differences

Fatty acids

  • Structure: consist of a carboxyl group (–COOH) at one end and a hydrocarbon tail (usually 15 or 17 carbon atoms long)
  • Saturation
    • Unsaturated → fatty acids with double bonds between carbon atoms (e.g. oils like olive oil)
    • Monounsaturated → one double bond
    • Polyunsaturated → multiple double bonds
    • Saturated → fatty acids without double bonds, typically found in animal fats

Alcohols and esters

  • Alcohols: organic molecules containing a hydroxyl group (–OH)
  • Glycerol: a three-hydroxyl alcohol
  • Ester formation: when fatty acids react with glycerol, they form ester bonds and produce esters, like triglycerides, through condensation (water is released)

Triglycerides

  • Structure: made from glycerol and three fatty acids, each connected via ester bonds
  • The –COOH group on the acid reacts with the –OH group on the alcohol to form the ester bond, –COO– 
  • Properties
    • Insoluble in water, soluble in organic solvents
    • Hydrophobic (due to non-polar hydrocarbon tails)
  • Functions
    • Energy storage: rich in carbon-hydrogen bonds, yielding more energy than carbohydrates
    • Insulation: stored beneath the skin and around organs for heat retention
    • Metabolic water: provides water when oxidized in respiration (important for animals in dry habitats)
Fig 2.6 Formation of a triglyceride

Phospholipids

  • Structure: similar to triglycerides, but one fatty acid is replaced by a phosphate group, making one end hydrophilic (water-attracting) and the other hydrophobic (water-repelling)
  • Function
    • Form biological membranes, where hydrophilic heads face aqueous environments and hydrophobic tails form an impermeable barrier
    • Important for cell membrane structure

2.6 Proteins

  • Proteins make up more than 50% of the dry mass in most cells
  • Functions of proteins include:
    • All enzymes are proteins
    • Essential components of cell membranes
    • Some hormones are proteins (e.g. insulin, glucagon)
    • Oxygen-carrying pigments like haemoglobin and myoglobin
    • Antibodies that attack microorganisms
    • Collagen provides strength to tissues (e.g. bones, arteries)
    • Keratin found in hair, nails, and skin
    • Actin and myosin are responsible for muscle contraction
    • Storage proteins like casein in milk and ovalbumin in egg white
    • All proteins are made from amino acids

Amino acids

  • Amino acids have a central carbon atom bonded to:
    • Amino group → –NH2
    • Carboxylic acid group → –COOH
    • Hydrogen atom
    • R group (fourth group) varies between amino acids, giving them unique properties
  • There are 20 amino acids in proteins of living organisms, each with a different R group
  • Amino acids have three-letter abbreviations
  • Other amino acids have been synthetically created in laboratories
Fig 2.7 The general structure of an amino acid

The peptide bond

  • Peptide bond forms when:
    • One amino acid loses a hydroxyl group (–OH) from its carboxylic acid group
    • The other amino acid loses a hydrogen atom from its amino group
    • The remaining carbon atom bonds with the nitrogen atom of the second amino acid
    • Water (H2O) is released in the process (condensation reaction)
  • Dipeptide: a molecule made of two linked amino acids
  • Polypeptide: a chain of many amino acids linked by peptide bonds; can be one or more chains in a protein
  • Protein synthesis occurs at ribosomes in living cells
  • Protein breakdown involves hydrolysis (adding water) to break peptide bonds, releasing amino acids, which are absorbed into the blood

The primary structure

  • Primary structure refers to the sequence of amino acids in a polypeptide chain
  • This sequence determines the specific properties and function of the protein
  • A change in just one amino acid can significantly alter the protein’s properties and function
  • Polypeptides can have hundreds of amino acids linked in a specific sequence

The secondary structure

  • Secondary structure refers to the folding or coiling of a polypeptide chain due to interactions between amino acids
  • An α-helix is a corkscrew shape stabilized by hydrogen bonds between the oxygen of one amino acid’s C=O group and the hydrogen of the –NH group of an amino acid four places ahead
  • A β-pleated sheet is a straighter shape formed by hydrogen bonding between amino acids in parallel sheets, holding the structure in place
  • Hydrogen bonds are strong but can be easily broken by high temperatures or pH changes
  • Some proteins lack regular structures, depending on the interactions between R groups of amino acids
Fig 2.8 The α-helix and ß-pleated sheet structures

The tertiary structure

  • Tertiary structure is the further folding of the secondary structure, forming a complex 3D shape
  • The shape is held by bonds between amino acids in different parts of the chain
  • Four types of bonds contribute to the stability of the tertiary structure
    • Hydrogen bonds form between a variety of R groups; weak individually but strong in numbers
    • Disulfide bonds form between 2 cysteine molecules (which contain sulfur atoms); the sulfur atoms create strong covalent bonds
    • Ionic bonds form between R groups containing amino and carboxyl groups
    • Hydrophobic interactions occur between non-polar R groups, 
      • Non-polar R groups are hydrophobic and avoid water
      • In watery environments, the hydrophobic R groups come together (hydrophilic R groups outwards), forming the shape

The quarternary structure

  • Quaternary structure refers to the overall structure formed by multiple polypeptide chains
  • Example: haemoglobin (which has four polypeptide chains)
  • The polypeptide chains in quaternary structures are held together by the same 4 bonds as in the tertiary structure

Globular and fibrous proteins

  • Globular proteins
    • Curl into a ball shape (e.g. myoglobin, haemoglobin)
    • Non-polar, hydrophobic R groups face the center; polar, hydrophilic R groups face the outside
    • Typically soluble in water due to hydrophilic R groups
    • Key role in metabolic reactions (e.g. enzymes)
  • Fibrous proteins
    • Form long strands
    • Not usually soluble in water
    • Primarily structural (e.g. keratin in hair, nails, and skin, collagen for structural support)

Haemoglobin - a globular protein

  • Haemoglobin
    • Oxygen-carrying pigment in red blood cells
    • Globular protein with quaternary structure (four polypeptide chains)
    • Composed of two α-globin (alpha-globin) and two β-globin (beta-globin) chains
    • Nearly spherical shape, with hydrophobic R groups inside and hydrophilic R groups on the outside
    • Interactions between hydrophobic R groups hold the structure; hydrophilic groups maintain solubility
    • In sickle cell anaemia, a mutation replaces glutamic acid (polar) with valine (non-polar), reducing solubility and causing symptoms
  • Haem group
    • Each polypeptide chain of haemoglobin contains a haem group (prosthetic group)
    • Haem group contains an iron atom that binds to one oxygen molecule (O2)
    • One haemoglobin molecule can carry four oxygen molecules (eight oxygen atoms)
    • Responsible for haemoglobin’s color
      • Bright red when oxygenated (oxyhaemoglobin)
      • Darker red when deoxygenated

Collagen - a fibrous protein

  • Collagen
    • The most common protein in animals, making up 25% of total protein in mammals
    • Insoluble fibrous protein found in skin, tendons, cartilage, bones, teeth, and blood vessel walls
    • Important structural protein in nearly all animals
  • Collagen structure
    • Composed of three polypeptide chains in a helical shape (not α-helix)
    • Three helices form a triple helix or “rope” structure, held together by hydrogen and covalent bonds
    • Every third amino acid is glycine, allowing the chains to lie close together and form a tight coil
    • Collagen molecules interact with each other to form fibrils through covalent bonds between adjacent amino acid R groups
    • Collagen fibrils form strong bundles called collagen fibres
  • Function and properties
    • Flexible but with tremendous tensile strength (can withstand large pulling forces without stretching or breaking)
    • Collagen fibre alignment varies depending on the forces it must endure
      • In tendons, fibres align in parallel along the length of the tendon
      • In skin, fibres may form layers with different directions to resist pulling forces from multiple directions

2.7 Water

  • Major component of cells, typically making up 70-95% of cell mass; humans are about 60% water
    • Provides an environment for organisms living in water, covering three-quarters of the planet
  • Properties of water
    • Water molecules are held together by hydrogen bonds, which gives water unique properties
      • Water exists as a liquid at Earth temperatures due to hydrogen bonding
    • Provides a medium for molecules and ions to mix, enabling life processes to occur
  • Effects of hydrogen bonding
    • Makes it harder to separate water molecules, which influences physical properties
    • More energy required to break hydrogen bonds makes it difficult to convert water from liquid to gas

Water as a solvent

  • Water is an excellent solvent for ions and polar molecules due to the attraction between water molecules
  • Dissolves chemicals by separating and surrounding them
    • This allows molecules or ions in solution to move freely and react with other chemicals
  • Many biological processes occur in solution, making water ideal for transporting substances (e.g. in blood, lymphatic systems, xylem, phloem)
  • Water and non-polar molecules
    • Non-polar molecules (like lipids) are insoluble in water
    • Water molecules are attracted to each other, causing non-polar molecules to cluster together
    • This hydrophobic interaction is crucial in protein structure, membrane structure, and the stability of proteins and membranes

High specific heat capacity

  • The heat capacity of a substance is the heat required to raise its temperature by a given amount
  • The specific heat capacity of water is the heat required to raise the temperature of 1 kg of water by 1°C.
    • It’s high because hydrogen bonds between water molecules resist movement, requiring more energy
    • Also allows water to store more energy per temperature rise hydrogen bonding
  • Biological implications
    • Maintains constant cellular and body temperature for optimal reactions
    • Large water bodies provide stable habitats for aquatic ecosystems (despite air temperature changes)

High latent heat of vaporization

  • High latent heat of vaporization
    • Latent heat of vaporization measures the heat energy required to change a liquid to a gas, such as when water evaporates.
    • Water has a high latent heat of vaporization due to its strong hydrogen bonds, which require significant energy to break before the molecules can escape as gas
    • This energy loss during vaporization causes cooling in the surroundings
  • Cooling mechanism
    • Evaporation acts as a cooling mechanism in organisms, such as sweating or panting in mammals, which helps regulate body temperature and prevent overheating
    • A large amount of heat can be lost with minimal water loss, helping reduce the risk of dehydration
    • In plants, evaporation during transpiration helps cool the leaves.
  • Freezing resistance
    • Must release a lot of energy → lower chances of freezing
    • This protects aquatic habitats by reducing freezing in water bodies
    • Prevent freezing in organisms with high water content

2.8 Testing for biological molecules

Reducing sugars

  • Add Benedict’s reagent to the sample solution you are testing and heat it in a water bath
  • Positive result: turns green/yellow/orange/red-brown

Starch

  • Add iodine solution to the sample solution
  • Positive result: turns blue black

Lipids

  • Add absolute ethanol to a sample solution
  • Shake vigorously (allows lipids to dissolve in ethanol)
  • Pour solution into water
  • Positive result: forms a cloudy white suspension

Proteins

  • Add Biuret’s reagant to the sample solution
  • Positive result: turns purple

Non-reducing sugars

  • Carry out Benedict’s test on the sample solution
    • If you get a negative result, start again with a fresh sample of the solution
  • Heat the sample solution with hydrochloric acid
    • If a non-reducing sugar is present, it will break down to monosaccharides
  • Add sodium hydroxide to neutralize the solution (to ensure Benedict’s reagent works)
  • Add Benedict’s reagent and heat as before and look for a positive result
Prev
Next
error: Content is protected.