Edexcel (B) Biology A-level - Topic 1: Biological Molecules Study Guide

Carbohydrates Overview

Definition: Carbohydrates are biological molecules consisting exclusively of carbon, hydrogen, and oxygen.
Basic Structure: They are characterized as long chains of sugar units referred to as saccharides.
Classification of Saccharides: * Monosaccharide: A single sugar monomer. * Disaccharide: A molecule composed of two monosaccharides. * Polysaccharide: A complex molecule composed of many monosaccharides.
Bonding and Formation: Monosaccharides join to form disaccharides and polysaccharides through the formation of glycosidic bonds, which occur during condensation reactions.

Monosaccharides: Structure and Examples

Glucose: * Contains six carbon atoms in each molecule ( $C_6H_{12}O_6$ ). * Function: It serves as the primary substrate for respiration. * Isomers: Glucose exists as two isomers, alpha- ( $\alpha$ ) and beta- ( $\beta$ ) glucose, which differ in their structural arrangements.
Ribose: * A pentose sugar containing five carbon atoms ( $C_5H_{10}O_5$ ). * Function: It is a vital component of RNA.
Deoxyribose: * An isomer of ribose found in DNA. * Distinction: It lacks the hydroxyl ( $OH$ ) group on the second carbon of the sugar ring.

Disaccharides and Formation

Disaccharides are formed by the condensation of two monosaccharides: * Maltose: Formed by the condensation of two glucose molecules. * Sucrose: Formed by the condensation of one glucose molecule and one fructose molecule. * Lactose: Formed by the condensation of one glucose molecule and one galactose molecule.

Polysaccharides: Storage and Structure

Polysaccharides are formed from many glucose units joined together. Major types include:

Glycogen: * Main energy storage molecule in animals. * Composition: Many $\alpha$ -glucose molecules joined by $1,4$ and $1,6$ glycosidic bonds. * Structure: Highly branched with a large number of side branches. * Properties: The branching allows it to be hydrolysed rapidly for quick energy release. It is a large yet compact molecule, maximizing energy storage density.
Starch: * Primary energy storage in plants, consisting of a mixture of two polysaccharides: * Amylose: An unbranched chain of glucose molecules joined by $1,4$ glycosidic bonds. Its structure is coiled and very compact, enabling high-density energy storage. * Amylopectin: Composed of glucose molecules joined by $1,4$ and $1,6$ glycosidic bonds. It is a branched molecule. The numerous side branches allow it to be digested rapidly by enzymes for quick energy release. While compact, it is less so than amylose.
Cellulose: * A structural component of plant cell walls. * Composition: Long, unbranched chains of $\beta$ -glucose monomers joined by $1,4$ glycosidic bonds. * Structural Organization: Multiple cellulose chains are held together by hydrogen bonds to form strong threads called microfibres and microfibrils, which provide high tensile strength and structural support.

Lipids: Types and Physical Properties

Solubility: Lipids are biological molecules only soluble in organic solvents, such as alcohols.
Saturated Lipids: * Found typically in animal fats. * Chemical Structure: Contain only carbon-carbon single bonds ( $C-C$ ). * Physical State: Solid at room temperature because the straight chains (without kinks) allow molecules to pack close together.
Unsaturated Lipids: * Commonly found in plants. * Chemical Structure: Contain carbon-carbon double bonds ( $C=C$ ). * Physical State: Liquid at room temperature (oils) because the double bonds create "kinks" in the chain, preventing close packing and resulting in weaker intermolecular forces and a lower melting point.

Functional Properties of Lipids

Waterproofing: Fatty tails are hydrophobic, making lipids effective waterproof barriers.
Energy Density: Lipids are very compact and offer better gram-for-gram energy release than carbohydrates or proteins. This is because more $C-O$ bonds are hydrolysed during metabolism.
Storage: Being non-polar and insoluble in water, lipids do not interfere with water-based reactions in the cytoplasm, making them ideal for long-term storage.
Thermal Insulation: Lipids conduct heat slowly, providing an effective insulation layer for organisms.

Lipid Varieties: Triglycerides and Phospholipids

Triglycerides: * Composition: One molecule of glycerol joined to three fatty acids. * Bonding: Formed via ester bonds during condensation reactions. * Variability: Fatty acid chains vary in length and the presence of single or double carbon bonds. * Function: Used as energy reserves in both plant and animal cells.
Phospholipids: * Structure: Similar to a triglyceride, but one fatty acid is substituted by a phosphate-containing group. * Amphipathic Nature: The phosphate head is hydrophilic (attracts water), and the fatty acid tails are hydrophobic (repels water). * Arrangement: They form a bilayer in cell membranes; heads point outward toward the aqueous environment, and tails point inward, away from the water.

Protein Structure and Amino Acids

Amino Acids: The monomers of proteins. * General Structure: Consist of an amino group ( $NH_2$ ), a carboxyl group ( $COOH$ ), and a variable $R$ group. * Diversity: There are $20$ different amino acids, each distinguished by its unique $R$ group, which determines its chemical properties.
Bonding: Amino acids join via peptide bonds formed in condensation reactions. * Dipeptide: Two amino acids joined. * Polypeptide: Three or more amino acids joined.
Levels of Protein Structure: * Primary Structure: The specific linear sequence of amino acids in the polypeptide chain, maintained by peptide bonds. * Secondary Structure: The folding of the chain into an $\alpha$ -helix or $\beta$ -pleated sheet, stabilized exclusively by hydrogen bonds (electrostatic attraction between oxygen/nitrogen/fluorine and electron-deficient hydrogen). * Tertiary Structure: The complex 3D folding of the secondary structure. It is maintained by hydrogen bonds, ionic bonds (salt bridges between oppositely charged $R$ groups), and disulphide bridges (covalent bonds between sulphur atoms in cysteine). * Quaternary Structure: The 3D arrangement and interaction of more than one polypeptide chain.

Classification of Proteins: Fibrous vs. Globular

Fibrous Proteins: * Consist of long parallel polypeptides with very little tertiary or quaternary structure (mainly secondary). * Feature occasional cross-linkages to form microfibres for high tensile strength. * Property: Insoluble in water. * Function: Used for structural purposes. * Example (Collagen): High tensile strength due to numerous hydrogen bonds. Composed of three distinct $\alpha$ -chains forming a triple gamma helix. These link into fibrils and fibres to form bones, cartilage, connective tissue, and tendons.
Globular Proteins: * Possess complex tertiary and quaternary structures. * Property: Form colloids in water (soluble). * Function: Diverse roles including hormones and antibodies. * Example (Haemoglobin): A water-soluble protein made of four polypeptide chains (two $\alpha$ and two $\beta$ ). Each subunit has a prosthetic haem group containing an $Fe^{2+}$ ion. Its function is to bind oxygen and transport it to tissues for respiration.

Nucleic Acids: DNA and RNA

Nucleic acids are polymers of nucleotides.
Nucleotide Structure: Composed of a pentose (5-carbon sugar), a nitrogen-containing organic base, and a phosphate group.
DNA Nucleotides: * Sugar: Deoxyribose. * Bases: Adenine ( $A$ ), Cytosine ( $C$ ), Guanine ( $G$ ), or Thymine ( $T$ ).
RNA Nucleotides: * Sugar: Ribose. * Bases: Adenine ( $A$ ), Cytosine ( $C$ ), Guanine ( $G$ ), or Uracil ( $U$ ).
Base Classification: * Purines: Adenine and Guanine; these have two nitrogen-containing rings. * Pyrimidines: Cytosine, Thymine, and Uracil; these are smaller and have a single nitrogen-containing ring.
Bonding: Nucleotides are linked by phosphodiester bonds formed in condensation reactions.
Double Helix Structure: DNA consists of two polynucleotide strands joined by hydrogen bonds between complementary bases: * Adenine pairs with Thymine (2 hydrogen bonds). * Cytosine pairs with Guanine (3 hydrogen bonds).
RNA Characteristics: Usually single-stranded and exists in forms such as $mRNA$ (messenger), $tRNA$ (transfer), and $rRNA$ (ribosomal).

Semi-Conservative DNA Replication

This process ensures genetic continuity between generations of cells. Steps include:

Unwinding: The DNA double helix unwinds as hydrogen bonds between bases are broken, catalysed by DNA helicase.
Templating: One strand acts as a template. Free nucleotides align via complementary base pairing.
Joining: Adjacent nucleotides are joined by phosphodiester bonds through condensation reactions, catalysed by DNA polymerase.
Re-folding: New molecules fold into double helices as hydrogen bonds form. The resulting DNA contains one original (parental) strand and one newly-synthesised strand.

The Genetic Code

Definition: A sequence of bases on DNA that codes for a sequence of amino acids in a polypeptide.
Codons: Triplets of bases that each code for a specific amino acid.
Genomic Regions: * Exons: Coding regions of DNA. * Introns: Non-coding regions.
Key Features of the Code: * Non-overlapping: Each triplet is read once; bases are not shared between adjacent triplets. * Degenerate: More than one triplet can code for the same amino acid, reducing the impact of mutations like substitutions. * Universal: The code is identical in all species and organisms. * Start and Stop: Contains specific codons to initiate or terminate protein synthesis.
Mutations: * Changes in the base sequence (deletions, insertions, substitutions). * Sickle Cell Anaemia: A mutation that distorts haemoglobin and red blood cell shape. * Frameshift: Caused by deletions or insertions, where all subsequent codons downstream are misread.

Protein Synthesis: Transcription and Translation

Transcription (Nucleus): 1. DNA helicase uncoils DNA and breaks hydrogen bonds. 2. The antisense strand acts as a template; the sense strand is the coding strand. 3. Free nucleotides align and RNA polymerase joins them with phosphodiester bonds to form $mRNA$ . 4. $mRNA$ exits through a nuclear pore to reach a ribosome.
Translation (Ribosomes on Rough ER): 1. $mRNA$ attaches to a ribosome. A $tRNA$ molecule with a specific amino acid binds to the $mRNA$ via its anticodon. 2. Hydrogen bonds form between the $tRNA$ anticodon and the $mRNA$ codon. 3. A second $tRNA$ binds to the next codon; the two amino acids form a peptide bond. 4. The process repeats, creating a polypeptide chain until a stop codon is reached.

Enzymes and Kinetics

Definition: Biological catalysts that lower the activation energy of reactions (anabolic, catabolic, intracellular, or extracellular).
Active Site: The specific area where a substrate binds.
Induced Fit Model: The enzyme's structure is distorted as the substrate binds, molding the active site around the substrate to form an enzyme-substrate complex.
Measurement: Initial rate of reaction is found by calculating the gradient of a concentration-time graph at $t=0$ .
Factors Affecting Rate: * Enzyme Concentration: Rate increases as more active sites become available until substrate concentration becomes the limiting factor. * Substrate Concentration: Rate increases as more complexes form until enzyme concentration becomes the limiting factor (all active sites saturated). * Temperature: Rate increases up to an optimum temperature. Beyond this, enzymes denature as hydrogen bonds are broken.

Enzyme Inhibition

Competitive Inhibition: Inhibitor molecules compete with the substrate for the active site. This can be reversed by increasing substrate concentration.
Non-competitive Inhibition: Inhibitor binds to an allosteric site (different from the active site), changing the enzyme's shape and preventing substrate binding. This cannot be reversed by increasing substrate concentration.
Feedback Inhibition: Also known as end-product inhibition, where the final product of a pathway inhibits the enzyme responsible for the initial stage.

Inorganic Ions in Plants

Nitrate Ions: Required for synthesis of DNA and amino acids.
Calcium Ions: Needed for calcium pectate in the middle lamellae of plant cell walls.
Phosphate Ions: Essential for ADP, ATP, DNA, and RNA.
Magnesium Ions: Necessary for the production of chlorophyll.

Properties of Water

Polarity: Uneven charge distribution (electronegative oxygen vs. electropositive hydrogen). This allows ionic substances like $NaCl$ to dissolve.
Polar Solvent: Acts as a medium for metabolic reactions.
High Specific Heat Capacity: Requires significant energy to change temperature, minimizing fluctuations and protecting aquatic environments.
Latent Heat of Vaporisation: High energy requirement for evaporation provides cooling (e.g., sweating) with minimal water loss.
Cohesion and Adhesion: Cohesion (sticking together via hydrogen bonds) allows transport through xylem and high surface tension. Adhesion allows water to stick to cell walls.
Density: Maximum density occurs at $4\,^{\circ}\text{C}$ . Ice is less dense and floats, creating an insulating layer on bodies of water that prevents freezing of the entire habitat.
Incompressibility: Provides physical support and is useful in hydraulic mechanisms in organisms.