Proteins

Amino acids are the monomers that form proteins. Proteins are important biological molecules with complex 3D structures.

Synthesis

Amino acids undergo condensation reactions to form proteins.
- The carboxylic acid and amine groups can react to form a peptide linkage (biological word for amide linkage).
- Two amino acid groups will react to form a dipeptide. Three amino acid groups will form a tripeptide and so on.

Primary structure

The primary structure is given by the sequence of amino acids.
The primary structure is held together by strong covalent bonds with peptide linkages happening between amino acid units.
In biology notation, each amino acid is represented by a three letter code. For example, alanine is Ala.

Secondary structure

The secondary structure is a result of the arrangement of polypeptide chains which causes specific hydrogen bonding interactions and lead to a specific secondary structure.
- There are two types of secondary structure.
The first is the α-helix:
- α-Helix is a regular coiled configuration held together by hydrogen bonding. The chain twists into a coiled helix shape.

Secondary structure

The second secondary structure is β-pleated sheets:
- β-pleated sheets cause amino acid sequences to run parallel to one another and extend to give a structure with pleated sheets.

Tertiary structure

The helices and sheets in the secondary structure can fold and interact to order the polypeptide strands into the final shape of the protein.
The complex 3-D shape is stabilised by the following interactions of the amino acid side chains:
- Disulfide bridges (covalent S-S bonds).
- Weak van der Waals’ forces.
- Hydrogen bonding.
- Ionic bonds.

Enzymes

One of the most important functions of proteins is their use as enzymes. Enzymes are biological catalysts, which are highly specific.

Specificity

Enzymes are made specific by their selective active sites.
They are so specific that they can even select between stereoisomers such that they will only bind to one enantiomer of a substrate.
- An example is L-amino oxidase, which only works on the L-amino acid and not the other enantiomer, the D-amino acid.

Enzyme action

A simple representation of enzyme action is the lock-and-key mechanism.
- This shows a simple representation of the importance of the shape of the active site.
- Because enzymes are proteins, this shape is determined by the 3D structure of the protein.

Drugs as inhibitors

Enzymes can be deactivated using drugs.
- The drug molecule can also bind to the active site.
The level of inhibition is dependant on:
- The relative concentration of substrate and drugs.
- The relative binding strength of the drug and the substrate.

Using computers to design drugs

If we know the structure of the enzyme and its active site, chemists can use computer modelling to find new drugs that would fit into the active site.
The modelling calculates whether or not molecules have the correct polarity and stereochemistry to fit into the active site.
The proposed models are then synthesised and their structure is optimised by experimental work.

1Physical Chemistry

1.1Atoms, Molecules & Stoichiometry

1.1.1Relative Masses

1.1.2The Mole

1.1.3Mass Spectrometry

1.1.4Empirical & Molecular Formulae

1.1.5Balanced Equations

1.1.6Molar Volume

1.1.7End of Topic Test - Amount of Substance

1.2Atomic Structure

1.2.1Fundamental Particles

1.2.2Isotopes & Mass Number

1.2.3Electron Shells, Sub-Shells & Orbitals

1.2.4Electron Configuration

1.2.5Ionisation Energy

1.2.6Factors Affecting Ionisation Energies

1.2.7Trends of Ionisation

1.2.8Specific Impacts on Ionisation Energies

1.2.9Electron Affinity

1.2.10End of Topic Test - Atomic Structure

1.2.11A-A* (AO2/3) - Atomic Structure

1.3Chemical Bonding

1.3.1Ionic Bonding

1.3.2Covalent & Dative Bonding

1.3.3Shapes of Molecules

1.3.4Intermolecular Forces

1.3.5Intermolecular Forces 2

1.3.6Electronegativity

1.3.7Bond Length, Bond Energy, & Bond Polarity

1.3.8Metallic Bonding

1.3.9Physical Properties

1.3.10End of Topic Test - Bonding

1.3.11A-A* (AO2/3) - Bonding

1.4States of Matter

1.4.1Simple Covalent Molecules

1.4.2The Ideal Gas Equation

1.4.3States of Matter

1.4.4Particle Diagrams

1.4.5The Liquid State

1.4.6Giant Ionic Lattices

1.4.7Giant Metallic Lattices

1.4.8Giant Covalent Structures

1.4.9Graphene & Fullerene

1.4.10Recycling

1.5Chemical Energetics

1.5.1Calorimetry

1.5.2Bond Enthalpies

1.5.3Enthalpy Changes

1.5.4Hess' Law

1.5.5Born-Haber Cycles

1.5.6Born-Haber Cycle Calculations

1.5.7Entropy

1.5.8Free Energy

1.5.9End of Topic Test - Energetics

1.6Electrochemistry

1.6.1Electrochemical Cells

1.6.2Electrochemical Series

1.6.3Commercial Application

1.6.4Nernst Equation

1.6.5Redox

1.7Equilibria

1.7.1Dynamic Equilibrium & Le Chatelier

1.7.2Kc

1.7.3Kp

1.7.4pH

1.7.5The Ionic Product of Water

1.7.6Weak Acids & Bases

1.7.7Introduction to Solubility Equilibria

1.7.8Solubility Equilibria Calculations

1.7.9Free Energy of Dissolution

1.7.10pH and Solubility

1.7.11Common-Ion Effect

1.7.12End of Topic Test - Kp & Electrochemistry

1.7.13A-A* (AO2/3) - Electrochemical Cells

1.8Partition Coefficient

1.8.1Kpc

1.9Reaction Kinetics

1.9.1Collision Theory

1.9.2Orders, Rate Constants & Equations

1.9.3Rate Graphs

1.9.4Rate Determining Step

1.9.5Maxwell-Boltzmann Distribution

1.9.6Catalysts

1.9.7Homogeneous Catalysts

1.9.8Heterogeneous Catalysts

1.9.9End of Topic Test - Kinetics

1.9.10End of Topic Test - Rate Equations

1.9.11A-A* (AO2/3) - Rate Equations

2Inorganic Chemistry

2.1The Periodic Table

2.1.1The Periodic Table

2.1.2Trends in the Periodic Table

2.1.3End of Topic Test - Periodicity & Trends

2.1.4Ceramics

2.1.5Period 3 Elements & Oxides

2.1.6Period 3 Oxides

2.1.7End of Topic Test - Period 3

2.2Group 2

2.2.1Group 2 Chemistry

2.3Group 17

2.3.1Introduction to Halogens

2.3.2Reactions of Halogens

2.3.3Chlorine & Chlorate(I)

2.3.4End of Topic Test - Group 17

2.3.5A-A* (AO2/3) - Periodicity, Group 2 & 17

2.4Transition Metals

2.4.1General Properties

2.4.2Titrations

2.4.3Shapes of Complex Ions

2.4.4Variable Oxidation States

2.4.5Ligands

2.4.6Colours of Ions

2.4.7Stereoisomerism of Complex Ions

2.4.8Cisplatin

2.4.9Ligand Substitutions & Kstab

2.4.10End of Topic Test - Transition Metals

2.4.11A-A* (AO2/3) - Transition Metals

2.5Nitrogen & Sulfur

2.5.1Nitrogen & Ammonia

2.5.2Formulated vs Manure Fertilisers

2.5.3Nitrogen Containing Fertilisers

2.5.4Fertilizers & Eutrophication

2.5.5Common Atmospheric Pollutants & Their Properties

2.5.6Catalytic Converters

2.5.7Atmospheric Oxides

3Organic Chemistry & Analysis

3.1Introduction to Organic Chemistry

3.1.1Naming Conventions

3.1.2Mechanism

3.1.3Isomerism

3.1.4End of Topic Test - Introduction to Organic Chem

3.2Hydrocarbons

3.2.1Fractional Distillation

3.2.2Cracking

3.2.3Combustion

3.2.4Chlorination

3.2.5End of Topic Test - Alkanes

3.2.6Introduction to Alkenes

3.2.7Reactions of Alkenes

3.2.8Polymerisation Reactions

3.2.9End of Topic Test - Alkenes

3.2.10Arenes

3.2.11Evidence for Structure of Arenes

3.2.12Reactions of Benzene

3.2.13End of Topic Test -Arenes

3.3Halogen Derivatives

3.3.1Properties of Haloalkanes

3.3.2Substitution Reactions of Haloalkanes

3.3.3Environmental Impacts of Haloalkanes

3.3.4End of Topic Test - Halogenoalkanes

3.4Hydroxy Compounds

3.4.1Types of Alcohol

3.4.2Oxidation 1

3.4.3Oxidation 2

3.4.4Elimination

3.4.5Acids & Esters

3.4.6Acyl Chlorides & Acylation

3.4.7Phenols & Their Reactions

3.4.8End of Topic Test - Alcohols

3.5Carbonyl Compounds

3.5.1Carbonyls

3.5.2Hydrogen Bonding & Carbonyls

3.5.3Aldehydes & Ketones

3.5.4Tri-Iodomethane Reaction

3.5.5End of Topic Test -Carbonyls

3.6Carboxylic Acids & Derivatives

3.6.1Properties of Carboxylic Acids

3.6.2Esters

3.6.3Acyl Chlorides

3.6.4End of Topic Test - Carboxylic Acids

3.7Nitrogen Compounds

3.7.1Nature & Preparation of Amines

3.7.2Basicity & Nucleophilicity

3.7.3Amides

3.7.4Reactions of Amino Acids

3.7.5Amino Acids

3.8Polymerisation

3.8.1Properties of Addition Polymers

3.8.2Condensation Polymerisation

3.8.3Effects of Side-Chains on Polymers

3.8.4Hydrolysis of Ester & Amide Groups

3.8.5Proteins

3.8.6DNA

3.8.7Adhesive & Conducting Polymers

3.8.8End of Topic Test - Amines & Proteins

3.9Analytical Techniques

3.9.1Chromatography

3.9.2High-Performance Liquid Chromatography

3.9.3Gas Chromatography

3.9.4IR Spectroscopy

3.9.5Uses of IR Spectroscopy

3.9.6Mass Spectrometry

3.9.7Mass Spectrometry Analysis

3.9.8Nuclear Magnetic Resonance

3.9.9Carbon-13 NMR

3.9.10Proton NMR I

3.9.11Proton NMR II

3.9.12End of Topic Test - Analytical Techniques

3.9.13A-A* (AO2/3) - Analytical Techniques

3.10Organic Synthesis

3.10.1Chirality & Drug Synthesis

3.10.2Organic Synthesis

3.10.3Examples of Synthetic Routes

3.10.4End of Topic Test - Organic Synthesis

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