6.7.2

Proteins (A2 Only)

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Proteins

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

Synthesis

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

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

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

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

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

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

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

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

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.
Jump to other topics
1

Physical Chemistry

1.1

Atomic Structure

1.1.1Fundamental Particles1.1.2Isotopes & Mass Number1.1.3Mass Spectrometry1.1.4Electron Shells, Sub-Shells & Orbitals1.1.5Electron Configuration1.1.6Ionisation Energy1.1.7Factors Affecting Ionisation Energies1.1.8Trends of Ionisation1.1.9Specific Impacts on Ionisation Energies1.1.10End of Topic Test - Atomic Structure1.1.11A-A* (AO3/4) - Atomic Structure
1.2

Amount of Substance

1.2.1Relative Masses1.2.2The Mole1.2.3The Ideal Gas Equation1.2.4Empirical & Molecular Formulae1.2.5Balanced Equations1.2.6Percentage Yield1.2.7A-A* (AO3/4) - Percentage Yield1.2.8Atom Economy1.2.9End of Topic Test - Amount of Substance1.2.10A-A* (AO3/4) - Substances & Yield1.2.11Diagnostic Misconceptions - Moles
1.3

Bonding

1.3.1Ionic Bonding1.3.2Covalent & Dative Bonding1.3.3Carbon Structures1.3.4Metallic Bonding1.3.5Physical Properties1.3.6Shapes of Molecules1.3.7Polarity1.3.8Intermolecular Forces1.3.9Intermolecular Forces 21.3.10End of Topic Test - Bonding1.3.11Exam-Style Question - Shape of Molecules1.3.12A-A* (AO3/4) - Bonding1.3.13Diagnostic Misconceptions - Ions1.3.14Diagnostic Misconceptions - Ionic & Covalent1.3.15Diagnostic Misconceptions - Phase Change1.3.16Diagnostic Misconceptions - Boiling1.3.17Diagnostic Misconceptions - Polar Bonds
1.4

Energetics

1.4.1Enthalpy Changes1.4.2Bond Breaking and Making1.4.3Enthalpy Changes: Standard Conditions1.4.4Calorimetry1.4.5Hess' Law1.4.6Bond Enthalpies1.4.7End of Topic Test - Energetics1.4.8Diagnostic Misconceptions - Calorimetry
1.5

Kinetics

1.5.1Collision Theory1.5.2Maxwell-Boltzmann Distribution1.5.3Increasing Rates1.5.4End of Topic Test - Kinetics
1.6

Equilibria

1.6.1Le Chatelier1.6.2Equilibrium Constants1.6.3A-A* (AO3/4) - Energetics, Kinetics, Equilibria1.6.4End of Topic Test - Equilibria1.6.5Diagnostic Misconceptions - Solids
1.7

Redox

1.7.1Redox1.7.2End of Topic Test - Redox
2

Physical Chemistry 2 (A2 Only)

2.1

Thermodynamics (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 - Thermodynamics2.1.6A-A* (AO3/4) - Thermodynamics
2.2

Rate 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 Equations2.2.6Exam-Style Question - Rates2.2.7A-A* (AO3/4) - Rate Equations
2.3

The Equilibrium Constant Kp (A2 Only)

2.3.1Properties of Kp (A2 Only)
2.4

Electrochemical 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 & Electrochemistry2.4.5A-A* (AO3/4) - Electrochemical Cells2.4.6Diagnostic Misconceptions - Salt Bridges2.4.7Diagnostic Misconceptions - Electrode, Electrolyte
2.5

Acids & 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 & Bases2.5.9Exam-Style Question - Weak Acids2.5.10A-A* (AO3/4) - Acids & Bases2.5.11Diagnostic Misconceptions - Ammonia is an Alkali2.5.12Diagnostic Misconceptions - Water's Neutrality2.5.13Diagnostic Misconceptions - Concentrate & Strength
3

Inorganic Chemistry

3.1

Periodicity & Trends

3.1.1The Periodic Table3.1.2Trends in the Periodic Table3.1.3End of Topic Test - Periodicity & Trends3.1.4Diagnostic Misconceptions - Atomic Radius
3.2

Group 2

3.2.1Group 2 Chemistry3.2.2End of Topic Test - Group 2
3.3

Group 7

3.3.1Introduction to Halogens3.3.2Reactions of Halogens3.3.3Chlorine & Chlorate(I)3.3.4End of Topic Test - Group 73.3.5Exam-Style Question - Group 73.3.6A-A* (AO3/4) - Periodicity, Group 2 & 7
4

Inorganic Chemistry 2 (A2 Only)

4.1

Period 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
4.2

Transition 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 Metals4.2.10A-A* (AO3/4) - Transition Metals
4.3

Reactions 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
5

Organic Chemistry 1

5.1

Introduction

5.1.1Naming Conventions5.1.2Mechanism5.1.3Isomerism5.1.4End of Topic Test - Introduction to Organic Chem
5.2

Alkanes

5.2.1Fractional Distillation5.2.2Cracking5.2.3Combustion5.2.4Chlorination5.2.5End of Topic Test - Alkanes
5.3

Halogenoalkanes

5.3.1Substitution Reactions5.3.2Elimination Reactions5.3.3Ozone Depletion5.3.4End of Topic Test - Halogenoalkanes
5.4

Alkenes

5.4.1Introduction to Alkenes5.4.2Reactions of Alkenes5.4.3Polymerisation Reactions5.4.4Properties of Polymers5.4.5End of Topic Test - Alkenes
5.5

Alcohols

5.5.1Production of Alcohols5.5.2Oxidation of Alcohols5.5.3Oxidation of Alcohols - 25.5.4Elimination Reactions5.5.5End of Topic Test - Alcohols5.5.6Exam-Style Question - Alcohols
5.6

Organic Analysis

5.6.1Reactions5.6.2Reactions 25.6.3Mass Spectrometry5.6.4Infrared Spectroscopy5.6.5End of Topic Test - Organic Analysis
5.7

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

5.7.1A-A* (AO3/4) - Organic 1
6

Organic Chemistry 2 (A2 Only)

6.1

Optical Isomerism (A2 Only)

6.1.1Optical Isomerism (A2 Only)6.1.2End of Topic Test - Optical Isomerism
6.2

Aldehydes & Ketones (A2 Only)

6.2.1Aldehydes & Ketones (A2 Only)6.2.2End of Topic Test - Aldehydes & Ketones
6.3

Carboxylic Acids & Esters (A2 Only)

6.3.1Acids & Esters (A2 Only)6.3.2Acylation (A2 Only)6.3.3End of Topic Test - Carboxylic Acids & Esters
6.4

Aromatic Chemistry (A2 Only)

6.4.1Structure & Reactivity (A2 Only)6.4.2Reactions of Benzene (A2 Only)6.4.3End of Topic Test - Aromatic Chemistry
6.5

Amines (A2 Only)

6.5.1Nature & Preparation of Amines (A2 Only)6.5.2Basicity & Nucleophilicity (A2 Only)6.5.3End of Topic Test - Amines
6.6

Polymers (A2 Only)

6.6.1Condensation Polymers (A2 Only)6.6.2Biodegradability (A2 Only)
6.7

Biological 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
6.8

Organic 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
6.9

NMR 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
6.10

Chromatography (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
6.11

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

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

Practice questions on Proteins (A2 Only)

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  1. 1
    Secondary structure of a protein:Fill in the list
  2. 2
    The tertiary structure of a protein is held together by:Fill in the list
  3. 3
    What makes enzymes so selective?Multiple choice
  4. 4
    The level of inhibition on enzymes is dependant on:Fill in the list
  5. 5
    Computers can model drugs. What two features must drugs have to "fit" into an active site?Multiple choice
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Amino Acids (A2 Only)

DNA (A2 Only)