Proteins (A2 Only)

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

1.1Atomic Structure

1.1.1Fundamental Particles

1.1.2Isotopes & Mass Number

1.1.3Mass Spectrometry

1.1.4Electron Shells, Sub-Shells & Orbitals

1.1.5Electron Configuration

1.1.6Ionisation Energy

1.1.7Factors Affecting Ionisation Energies

1.1.8Trends of Ionisation

1.1.9Specific Impacts on Ionisation Energies

1.1.10End of Topic Test - Atomic Structure

1.1.11A-A* (AO3/4) - Atomic Structure

1.2Amount of Substance

1.2.1Relative Masses

1.2.2The Mole

1.2.3The Ideal Gas Equation

1.2.4Empirical & Molecular Formulae

1.2.5Balanced Equations

1.2.6Percentage Yield

1.2.7A-A* (AO3/4) - Percentage Yield

1.2.8Atom Economy

1.2.9End of Topic Test - Amount of Substance

1.2.10A-A* (AO3/4) - Substances & Yield

1.3Bonding

1.3.1Ionic Bonding

1.3.2Covalent & Dative Bonding

1.3.3Carbon Structures

1.3.4Metallic Bonding

1.3.5Physical Properties

1.3.6Shapes of Molecules

1.3.7Polarity

1.3.8Intermolecular Forces

1.3.9Intermolecular Forces 2

1.3.10End of Topic Test - Bonding

1.3.11Exam-Style Question - Shape of Molecules

1.3.12A-A* (AO3/4) - Bonding

1.4Energetics

1.4.1Enthalpy Changes

1.4.2Calorimetry

1.4.3Hess' Law

1.4.4Bond Enthalpies

1.4.5End of Topic Test - Energetics

1.5Kinetics

1.5.1Collision Theory

1.5.2Maxwell-Boltzmann Distribution

1.5.3Increasing Rates

1.5.4End of Topic Test - Kinetics

1.6Equilibria

1.6.1Le Chatelier

1.6.2Equilibrium Constants

1.6.3A-A* (AO3/4) - Energetics, Kinetics, Equilibria

1.6.4End of Topic Test - Equilibria

1.7Redox

1.7.1Redox

1.7.2End of Topic Test - Redox

2Physical Chemistry 2 (A2 Only)

2.1Thermodynamics (A2 Only)

2.1.1Born-Haber Cycles (A2 Only)

2.1.2Born-Haber Cycle Calculations (A2 Only)

2.1.3Entropy (A2 Only)

2.1.4Free Energy (A2 Only)

2.1.5End of Topic Test - Thermodynamics

2.1.6A-A* (AO3/4) - Thermodynamics

2.2Rate Equations (A2 Only)

2.2.1Rate Equations (A2 Only)

2.2.2Rate Equations 2 (A2 Only)

2.2.3The Arrhenius Equation (A2 Only)

2.2.4Experimental Methods for Rates (A2 Only)

2.2.5End of Topic Test - Rate Equations

2.2.6Exam-Style Question - Rates

2.2.7A-A* (AO3/4) - Rate Equations

2.3The Equilibrium Constant Kp (A2 Only)

2.3.1Properties of Kp (A2 Only)

2.4Electrochemical Cells (A2 Only)

2.4.1Electrochemical Cells (A2 Only)

2.4.2Electrochemical Series (A2 Only)

2.4.3Commercial Application (A2 Only)

2.4.4End of Topic Test - Kp & Electrochemistry

2.4.5A-A* (AO3/4) - Electrochemical Cells

2.5Acids & Bases (A2 Only)

2.5.1Brønsted-Lowry Acids & Bases (A2 Only)

2.5.2pH (A2 Only)

2.5.3The Ionic Product of Water (A2 Only)

2.5.4Weak Acids & Bases (A2 Only)

2.5.5pH Curves & Titrations (A2 Only)

2.5.6pH Curves & Titrations 2 (A2 Only)

2.5.7Buffer Solutions (A2 Only)

2.5.8End of Topic Test - Acids & Bases

2.5.9Exam-Style Question - Weak Acids

2.5.10A-A* (AO3/4) - Acids & Bases

3Inorganic Chemistry

3.1Periodicity & Trends

3.1.1The Periodic Table

3.1.2Trends in the Periodic Table

3.1.3End of Topic Test - Periodicity & Trends

3.2Group 2

3.2.1Group 2 Chemistry

3.2.2End of Topic Test - Group 2

3.3Group 7

3.3.1Introduction to Halogens

3.3.2Reactions of Halogens

3.3.3Chlorine & Chlorate(I)

3.3.4End of Topic Test - Group 7

3.3.5Exam-Style Question - Group 7

3.3.6A-A* (AO3/4) - Periodicity, Group 2 & 7

4Inorganic Chemistry 2 (A2 Only)

4.1Period 3 (A2 Only)

4.1.1Period 3 Elements & Oxides (A2 Only)

4.1.2Period 3 Oxides (A2 Only)

4.1.3End of Topic Test - Period 3

4.2Transition Metals (A2 Only)

4.2.1General Properties (A2 Only)

4.2.2Substitution Reactions (A2 Only)

4.2.3Shapes of Complex Ions (A2 Only)

4.2.4Colours of Ions (A2 Only)

4.2.5Variable Oxidation States (A2 Only)

4.2.6Titrations (A2 Only)

4.2.7Homogeneous Catalysts (A2 Only)

4.2.8Heterogeneous Catalysts (A2 Only)

4.2.9End of Topic Test - Transition Metals

4.2.10A-A* (AO3/4) - Transition Metals

4.3Reactions of Ions in Aqueous Solutions (A2 Only)

4.3.1Acidity (A2 Only)

4.3.2Identification (A2 Only)

4.3.3End of Topic Test - Reactions of Ions in Solution

5Organic Chemistry 1

5.1Introduction

5.1.1Naming Conventions

5.1.2Mechanism

5.1.3Isomerism

5.1.4End of Topic Test - Introduction to Organic Chem

5.2Alkanes

5.2.1Fractional Distillation

5.2.2Cracking

5.2.3Combustion

5.2.4Chlorination

5.2.5End of Topic Test - Alkanes

5.3Halogenoalkanes

5.3.1Substitution Reactions

5.3.2Elimination Reactions

5.3.3Ozone Depletion

5.3.4End of Topic Test - Halogenoalkanes

5.4Alkenes

5.4.1Introduction to Alkenes

5.4.2Reactions of Alkenes

5.4.3Polymerisation Reactions

5.4.4Properties of Polymers

5.4.5End of Topic Test - Alkenes

5.5Alcohols

5.5.1Production of Alcohols

5.5.2Oxidation of Alcohols

5.5.3Oxidation of Alcohols - 2

5.5.4Elimination Reactions

5.5.5End of Topic Test - Alcohols

5.5.6Exam-Style Question - Alcohols

5.6Organic Analysis

5.6.1Reactions

5.6.2Reactions 2

5.6.3Mass Spectrometry

5.6.4Infrared Spectroscopy

5.6.5End of Topic Test - Organic Analysis

5.7A-A* (AO3/4) - Organic 1

5.7.1A-A* (AO3/4) - Organic 1

6Organic Chemistry 2 (A2 Only)

6.1Optical Isomerism (A2 Only)

6.1.1Optical Isomerism (A2 Only)

6.1.2End of Topic Test - Optical Isomerism

6.2Aldehydes & Ketones (A2 Only)

6.2.1Aldehydes & Ketones (A2 Only)

6.2.2End of Topic Test - Aldehydes & Ketones

6.3Carboxylic Acids & Esters (A2 Only)

6.3.1Acids & Esters (A2 Only)

6.3.2Acylation (A2 Only)

6.3.3End of Topic Test - Carboxylic Acids & Esters

6.4Aromatic Chemistry (A2 Only)

6.4.1Structure & Reactivity (A2 Only)

6.4.2Reactions of Benzene (A2 Only)

6.4.3End of Topic Test - Aromatic Chemistry

6.5Amines (A2 Only)

6.5.1Nature & Preparation of Amines (A2 Only)

6.5.2Basicity & Nucleophilicity (A2 Only)

6.5.3End of Topic Test - Amines

6.6Polymers (A2 Only)

6.6.1Condensation Polymers (A2 Only)

6.6.2Biodegradability (A2 Only)

6.7Biological Organic (A2 Only)

6.7.1Amino Acids (A2 Only)

6.7.2Proteins (A2 Only)

6.7.3DNA (A2 Only)

6.7.4Anti-Cancer Drugs (A2 Only)

6.7.5End of Topic Test - Biological Organic

6.8Organic Synthesis (A2 Only)

6.8.1Organic Synthesis (A2 Only)

6.8.2Examples of Synthetic Routes (A2 Only)

6.8.3End of Topic Test - Polymers & Organic Synthesis

6.9NMR Spectroscopy (A2 Only)

6.9.1Understanding NMR (A2 Only)

6.9.2Carbon-13 NMR (A2 Only)

6.9.3Hydrogen-1 NMR (A2 Only)

6.9.4Hydrogen-1 NMR 2 (A2 Only)

6.9.5End of Topic Test - NMR

6.10Chromatography (A2 Only)

6.10.1Overview of Chromatography (A2 Only)

6.10.2Thin-Layer Chromatography (A2 Only)

6.10.3Column Chromatography (A2 Only)

6.10.4Gas Chromatography (A2 Only)

6.10.5End of Topic Test - Chromatography

6.11A-A* (AO3/4) - Organic 2

6.11.1A-A* (AO3/4) - Organic 2

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