3.8.5

Proteins

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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

Atoms, Molecules & Stoichiometry

1.1.1Relative Masses1.1.2The Mole1.1.3Mass Spectrometry1.1.4Empirical & Molecular Formulae1.1.5Balanced Equations1.1.6Molar Volume1.1.7End of Topic Test - Amount of Substance
1.2

Atomic Structure

1.2.1Fundamental Particles1.2.2Isotopes & Mass Number1.2.3Electron Shells, Sub-Shells & Orbitals1.2.4Electron Configuration1.2.5Ionisation Energy1.2.6Factors Affecting Ionisation Energies1.2.7Trends of Ionisation1.2.8Specific Impacts on Ionisation Energies1.2.9Electron Affinity1.2.10End of Topic Test - Atomic Structure1.2.11A-A* (AO2/3) - Atomic Structure
1.3

Chemical Bonding

1.3.1Ionic Bonding1.3.2Covalent & Dative Bonding1.3.3Shapes of Molecules1.3.4Intermolecular Forces1.3.5Intermolecular Forces 21.3.6Electronegativity1.3.7Bond Length, Bond Energy, & Bond Polarity1.3.8Metallic Bonding1.3.9Physical Properties1.3.10End of Topic Test - Bonding1.3.11A-A* (AO2/3) - Bonding
1.4

States of Matter

1.4.1Simple Covalent Molecules1.4.2The Ideal Gas Equation1.4.3States of Matter1.4.4Particle Diagrams1.4.5The Liquid State1.4.6Giant Ionic Lattices1.4.7Giant Metallic Lattices1.4.8Giant Covalent Structures1.4.9Graphene & Fullerene1.4.10Recycling
1.5

Chemical Energetics

1.5.1Calorimetry1.5.2Bond Enthalpies1.5.3Enthalpy Changes1.5.4Hess' Law1.5.5Born-Haber Cycles1.5.6Born-Haber Cycle Calculations1.5.7Entropy1.5.8Free Energy1.5.9End of Topic Test - Energetics
1.6

Electrochemistry

1.6.1Electrochemical Cells1.6.2Electrochemical Series1.6.3Commercial Application1.6.4Nernst Equation1.6.5Redox
1.7

Equilibria

1.7.1Dynamic Equilibrium & Le Chatelier1.7.2Kc1.7.3Kp1.7.4pH1.7.5The Ionic Product of Water1.7.6Weak Acids & Bases1.7.7Introduction to Solubility Equilibria1.7.8Solubility Equilibria Calculations1.7.9Free Energy of Dissolution1.7.10pH and Solubility1.7.11Common-Ion Effect1.7.12End of Topic Test - Kp & Electrochemistry1.7.13A-A* (AO2/3) - Electrochemical Cells
1.8

Partition Coefficient

1.8.1Kpc
1.9

Reaction Kinetics

1.9.1Collision Theory1.9.2Orders, Rate Constants & Equations1.9.3Rate Graphs1.9.4Rate Determining Step1.9.5Maxwell-Boltzmann Distribution1.9.6Catalysts1.9.7Homogeneous Catalysts1.9.8Heterogeneous Catalysts1.9.9End of Topic Test - Kinetics1.9.10End of Topic Test - Rate Equations1.9.11A-A* (AO2/3) - Rate Equations
2

Inorganic Chemistry

2.1

The Periodic Table

2.1.1The Periodic Table2.1.2Trends in the Periodic Table2.1.3End of Topic Test - Periodicity & Trends2.1.4Ceramics2.1.5Period 3 Elements & Oxides2.1.6Period 3 Oxides2.1.7End of Topic Test - Period 3
2.2

Group 2

2.2.1Group 2 Chemistry
2.3

Group 17

2.3.1Introduction to Halogens2.3.2Reactions of Halogens2.3.3Chlorine & Chlorate(I)2.3.4End of Topic Test - Group 172.3.5A-A* (AO2/3) - Periodicity, Group 2 & 17
2.4

Transition Metals

2.4.1General Properties2.4.2Titrations2.4.3Shapes of Complex Ions2.4.4Variable Oxidation States2.4.5Ligands2.4.6Colours of Ions2.4.7Stereoisomerism of Complex Ions2.4.8Cisplatin2.4.9Ligand Substitutions & Kstab2.4.10End of Topic Test - Transition Metals2.4.11A-A* (AO2/3) - Transition Metals
2.5

Nitrogen & Sulfur

2.5.1Nitrogen & Ammonia2.5.2Formulated vs Manure Fertilisers2.5.3Nitrogen Containing Fertilisers2.5.4Fertilizers & Eutrophication2.5.5Common Atmospheric Pollutants & Their Properties2.5.6Catalytic Converters2.5.7Atmospheric Oxides
3

Organic Chemistry & Analysis

3.1

Introduction to Organic Chemistry

3.1.1Naming Conventions3.1.2Mechanism3.1.3Isomerism3.1.4End of Topic Test - Introduction to Organic Chem
3.2

Hydrocarbons

3.2.1Fractional Distillation3.2.2Cracking3.2.3Combustion3.2.4Chlorination3.2.5End of Topic Test - Alkanes3.2.6Introduction to Alkenes3.2.7Reactions of Alkenes3.2.8Polymerisation Reactions3.2.9End of Topic Test - Alkenes3.2.10Arenes3.2.11Evidence for Structure of Arenes3.2.12Reactions of Benzene3.2.13End of Topic Test -Arenes
3.3

Halogen Derivatives

3.3.1Properties of Haloalkanes3.3.2Substitution Reactions of Haloalkanes3.3.3Environmental Impacts of Haloalkanes3.3.4End of Topic Test - Halogenoalkanes
3.4

Hydroxy Compounds

3.4.1Types of Alcohol3.4.2Oxidation 13.4.3Oxidation 23.4.4Elimination3.4.5Acids & Esters3.4.6Acyl Chlorides & Acylation3.4.7Phenols & Their Reactions3.4.8End of Topic Test - Alcohols
3.5

Carbonyl Compounds

3.5.1Carbonyls3.5.2Hydrogen Bonding & Carbonyls3.5.3Aldehydes & Ketones3.5.4Tri-Iodomethane Reaction3.5.5End of Topic Test -Carbonyls
3.6

Carboxylic Acids & Derivatives

3.6.1Properties of Carboxylic Acids3.6.2Esters3.6.3Acyl Chlorides3.6.4End of Topic Test - Carboxylic Acids
3.7

Nitrogen Compounds

3.7.1Nature & Preparation of Amines3.7.2Basicity & Nucleophilicity3.7.3Amides3.7.4Reactions of Amino Acids3.7.5Amino Acids
3.8

Polymerisation

3.8.1Properties of Addition Polymers3.8.2Condensation Polymerisation3.8.3Effects of Side-Chains on Polymers3.8.4Hydrolysis of Ester & Amide Groups3.8.5Proteins3.8.6DNA3.8.7Adhesive & Conducting Polymers3.8.8End of Topic Test - Amines & Proteins
3.9

Analytical Techniques

3.9.1Chromatography3.9.2High-Performance Liquid Chromatography3.9.3Gas Chromatography3.9.4IR Spectroscopy3.9.5Uses of IR Spectroscopy3.9.6Mass Spectrometry3.9.7Mass Spectrometry Analysis3.9.8Nuclear Magnetic Resonance3.9.9Carbon-13 NMR3.9.10Proton NMR I3.9.11Proton NMR II3.9.12End of Topic Test - Analytical Techniques3.9.13A-A* (AO2/3) - Analytical Techniques
3.10

Organic Synthesis

3.10.1Chirality & Drug Synthesis3.10.2Organic Synthesis3.10.3Examples of Synthetic Routes3.10.4End of Topic Test - Organic Synthesis

Practice questions on Proteins

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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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Hydrolysis of Ester & Amide Groups

DNA