Large Biomolecules

In large biomolecules, such as polypeptides (proteins), multiple non-covalent interactions can occur between different parts of the same biomolecule to stabilize the structure.

Amino acids

Proteins are made of amino acids.
Amino acids consits of a carboxylic acid croup, an amine group, and a variable R group.
Neighboring amino acids are joined via peptide bonds between the amine and carboxylic acid group.
Interactions between R groups creates the complex 3D tertiary structure of a protein.
The 3D structure is usually coiled or folded.

Holding the 3D structure

There are many weak and strong interactions that determine the final 3D shape of the protein (e.g. ionic bonds and hydrogen bonds).
When the protein loses its 3D shape, it may no longer be functional.
- This 3D structure is known as the tertiary structure of the protein.

Ionic bonds

Charged amino acids have a positively or negatively charged ion in their side chain.
- Charged amino acids can form relatively strong ionic bonds with other charged amino acids.
Ionic bonds between amino acids are quite rare.

Hydrogen bonds

Hydrogen bonds also form between amino acids.
Hydrogen bonds are relatively weak but when there are many, the overall stability of the tertiary structure increases.

Hydrophobic interactions

When protein folding takes place, the hydrophobic R groups of nonpolar amino acids lie in the interior of the protein, whereas the hydrophilic R groups lie on the outside.
- These types of interactions are also known as hydrophobic interactions.

Protein interactions

1Structure - Models of the Particulate of Matter

1.1Introduction to the Particulate Model of Matter

1.1.1States of Matter

1.1.2Kinetic Molecular Theory

1.1.3Simple Sphere

1.1.4Changing State

1.1.5Forces Between Particles

1.1.6Changes of State

1.1.7Predicting States

1.1.8Changing State HyperLearning

1.1.9Ionization Energy

1.2The Nuclear Atom

1.2.1Fundamental Particles

1.2.2Isotopes & Mass Number

1.2.3Mass Spectrometry

1.2.4Mass Spectrometry

1.2.5Mass Spectroscopy - Analysis

1.2.6Extended Response - Mass Spectrometry

1.2.7Radioactivity

1.3Electron Configuration

1.3.1Electron Shells, Sub-Shells & Orbitals

1.3.2Electron Configuration

1.3.3Absorption & Emission Spectra

1.3.4IB Multiple Choice - Atomic Structure

1.3.5Extended Response - The Atom & Electrons

1.4Counting Particles by Mass: The Mole

1.4.1Relative Masses

1.4.2The Mole

1.4.3IB Multiple Choice - Moles

1.5Ideal Gases

1.5.1Ideal Gas Equation

1.5.2Gas Laws

1.5.3IB Multiple Choice - Gases & Kinetics

1.6Elements, Compounds & Mixtures

1.6.1Fundamental Particles

1.6.2Pure Substances

1.6.3Purity & The Law of Definite Proportion

1.6.4Mixtures

1.6.5Separating Mixtures

1.6.6IB Multiple Choice - Pure Substances

1.6.7Extended Response - Moles & Pure Substances

1.7States of Matter & Changes of State

1.7.1States of Matter

1.7.2Particle Diagrams

1.7.3IB Multiple Choice - Solids, Liquids, & Gases

1.7.4Balancing Equations & Ionic Equations

1.7.5Empirical & Molecular Formulas

1.8Reacting Masses &. Volumes

1.8.1Balancing Equations & Ionic Equations

1.8.2Percentage Yield

1.9Solutions

1.9.1Molarity

1.9.2Particulate Model of Solutions

2Structure - Models of Bonding & Structure

2.1The Ionic Model

2.1.1Ionic Bonding

2.2The Covalent Model

2.2.1Covalent Bonds

2.2.2Complex Ions

2.2.3Factors Affecting Covalent Bond Strength

2.2.4Polarity

2.3Covalent Structures

2.3.1Ionic Lewis Structures

2.3.2Covalent Lewis Structures

2.3.3VSEPR Theory

2.3.4Resonance Structures

2.3.5Allotropes of Carbon

2.3.6Formal Charge

2.3.7End of Topic Quiz - Bonding

2.3.8IB Multiple Choice - Bonding & Lewis Structures

2.3.9IB Multiple Choice - Resonance & Formal Charge

2.4The Metallic Model

2.4.1Metallic Bonding

2.5From Models to Materials

2.5.1Alloys

2.5.2Properties of Polymers

2.5.3Polymerisation Reactions

2.5.4Introduction to Alkenes

2.5.5Reactions of Alkenes

2.5.6End of Topic Quiz - Alkenes

2.6Valence Electrons & Ionic Compounds

2.6.1Valence Electrons & Forming Ions

2.6.2Ionic Compounds

2.6.3End of Topic Quiz - Atoms & Ions

2.6.4IB Multiple Choice - Valence & Ions

2.7Molecular Shape

2.7.1VSEPR

2.7.2Molecular Shapes

2.7.3Bond Hybridization

2.7.4IB Multiple Choice - VSEPR & Bond Hybridization

2.7.5Extended Response - Bonding & Molecular Shape

2.8Intermolecular Forces

2.8.1Introduction to Intermolecular Forces

2.8.2London Dispersion Forces

2.8.3Dipole-Dipole Interactions

2.8.4Ion-Dipole Interactions

2.8.5Hydrogen Bonding

2.8.6Large Biomolecules

2.8.7IB Multiple Choice - Intermolecular Forces

2.8.8Extended Response - Hydrogen Bonding

3Structure - Classification of Matter

3.1The Periodic Table: Classification of Elements

3.1.1The Periodic Table

3.1.2Trends in the Periodic Table

3.1.3End of Topic Quiz - Periodicity & Trends

3.1.4Periodic Trends - Electronegativity & Affinity

3.1.5End of Topic Quiz - Periodic Trends

3.1.6IB Multiple Choice - Periodic Trends

3.1.7Extended Response - Periodic Table

3.2Periodic Trends

3.2.1Atomic & Ionic Radii

3.2.2Ionisation & Electronegativity

3.2.3Metallic Behaviour & Oxides

3.2.4Period 3 Elements & Oxides

3.2.5Period 3 Oxides

3.2.6End of Topic Quiz - Period 3

3.2.7Periodic Trends: Blocks

3.2.8Redox Chemistry

3.3Group 1 Alkali Metals

3.3.1Alkali Metals

3.4Halogens

3.4.1Introduction to Halogens

3.4.2Reactions of Halogens

3.4.3Chlorine & Chlorate(I)

3.4.4End of Topic Quiz - Group 7

3.4.5Exam-Style Question - Group 7

3.4.6End of Topic Quiz - Periodicity, Group 2 & 7

3.5Noble gases, group 18

3.5.1Noble Gases

3.6Functional Groups: Classification of Organic

3.6.1Nomenclature

3.6.2Trends in Physical Properties

3.6.3Saturated & Unsaturated Hydrocarbons

3.6.4Nomenclature contd.

3.6.5Types of Formulas

3.6.6Isomerism

3.6.7Formulae

3.6.8Homologous Series

3.6.9Structural Isomers

3.7Functional Group Chemistry

3.7.1Degrees of Substitution

3.7.2Arenes

3.8Alkanes

3.8.1Alkanes

3.8.2Fractional Distillation

3.8.3Cracking

3.8.4Combustion

3.8.5Chlorination

3.8.6End of Topic Quiz - Alkanes

3.9Alcohols

3.9.1Production of Alcohols

3.9.2Oxidation of Alcohols

3.9.3Oxidation of Alcohols - 2

3.9.4Elimination Reactions

3.9.5End of Topic Quiz - Alcohols

3.9.6Exam-Style Question - Alcohols

3.10Halogenoalkanes

3.10.1Substitution Reactions

3.10.2Elimination Reactions

3.10.3Ozone Depletion

3.10.4End of Topic Quiz - Halogenoalkanes

4Reactivity - What Drives Chemical Reaction?

4.1Endothermic & Exothermic Reactions

4.1.1Endothermic & Exothermic Reactions

4.1.2Energy Diagrams

4.1.3Heat Transfer & Thermal Equilibrium

4.1.4IB Multiple Choice - Enthalpy & Energy

4.2Enthalpy of Reaction, Formation, & Hess' Law

4.2.1Enthalpy of Reaction

4.2.2Bond Enthalpies

4.2.3Enthalpy of Formation

4.2.4Hess’ Law

4.2.5Thermodynamics & Kinetic Control

4.2.6End of Topic Quiz - Thermodynamics

4.2.7IB Multiple Choice - Enthalpy

4.2.8Extended Response - Enthalpy Change

4.3Entropy

4.3.1Introduction to Entropy

4.3.2Absolute Entropy & Entropy Change

4.3.3Free Energy

4.3.4Thermodynamically Favorable Reactions

4.3.5IB Multiple Choice - Entropy & Free Energy

4.3.6Extended Response - Free Energy

5Reactivity - How Much, How Fast & How Far?

5.1Kinetics

5.1.1Collision Theory & Rates of Reaction

5.1.2Maxwell-Boltzmann Distribution

5.1.3Increasing Rates

5.1.4End of Topic Quiz - Kinetics

5.2Rates of Reaction

5.2.1Rate Equations

5.2.2Rate Equations 2

5.2.3The Effect of a Catalyst

5.3Stoichometry

5.3.1Stoichiometry

5.4Le Châtelier’s Principle

5.4.1Introduction to Le Châtelier’s Principle

5.4.2Reaction Quotient & Le Châtelier’s Principle

5.4.3Temperature & Le Châtelier’s Principle

5.4.4IB Multiple Choice -Le Châtelier’s Principle

5.4.5Extended Response - Le Châtelier

5.5Introduction to Equilibrium

5.5.1Equilibrium & Equilibrium Graphs

5.5.2Dynamic Equilibria

5.5.3Reversible Reactions & Directions

5.6Equilibrium Constant

5.6.1Calculating the Equilibrium Constant

5.6.2Magnitude of the Equilibrium Constant

5.6.3Properties of the Equilibrium Constant

5.6.4Calculating Equilibrium Concentrations

5.6.5Representations of Equilibrium

5.6.6IB Multiple Choice - Equilibrium Constants

5.6.7Extended Response - Calculating Kc

5.7Reaction Quotient & Equilibrium Constant

5.7.1Reaction Quotient

5.7.2Equilibrium Constants

5.7.3Partial Pressures

5.7.4Kp

5.7.5IB Multiple Choice - Reaction Quotient & Kp

5.7.6Extended Response - Kp & Bond Enthalpy

6Reactivity - The Mechanisms of Chemical Change

6.1Proton Transfer Reactions

6.1.1Brønsted-Lowry Theory

6.2The pH Scale

6.2.1pH & pOH

6.2.2Ionic Product of Water

6.2.3Using Kw

6.2.4IB Multiple Choice - pH & Kw

6.2.5Extended Response - Kw

6.3Strong & Weak Acids and Bases

6.3.1Strong Acids & Bases

6.3.2Weak Acids & Ka

6.3.3Weak Bases & Kb

6.3.4Weak Acids & Bases Calculation Walkthrough

6.4Acid Deposition

6.4.1Acid Deposition

6.5Types of Organic Reactions

6.5.1Electrophilic Substitution

6.6Oxidation & Reduction

6.6.1Oxidation Number Method

6.6.2Winkler Method

6.6.3Redox Reactions

6.6.4Oxidation States & Equations

6.6.5End of Topic Quiz - Redox

6.6.6Extended Response - Redox Reactions

6.7Electrochemical Cells

6.7.1Introduction to Electrochemical Cells

6.7.2Galvanic Cells

6.7.3Cell Notation

6.7.4Electrolytic Cells

6.7.5Extended Response - Voltaic Cells & Redox

6.8Titration

6.8.1Redox Titrations

6.8.2Titration Calculations

6.8.3Atom Economy

6.9Acid-Base Titrations

6.9.1Titration Calculation Weak Acid & Strong Base

6.9.2Titration Experimental Detail

6.9.3Extended Response - Titration

6.9.4Titration Calculations

6.9.5Titration Curves

6.9.6Titration Calculation Strong Acid & Weak Base

6.9.7IB Multiple Choice - Titrations

6.9.8Polyprotic Acids

6.9.9Titration Calculations Strong Acid & Strong Base

6.9.10Titrations Curves 2

7Measurement, Data Processing & Analysis

7.1Uncertainties & Errors in Measurements & Results

7.1.1Qualitative & Quantitative data

7.2Graphical Techniques

7.2.1Drawing & Interpreting Graphs

7.2.2Linear Interpolation

7.3Spectroscopic Identification of Organic Compounds

7.3.1Understanding NMR

7.3.2Carbon-13 NMR

7.3.3Hydrogen-1 NMR

7.3.4Hydrogen-1 NMR 2

7.3.5End of Topic Quiz - NMR

7.4Infrared Spectroscpy

7.4.1Infrared Spectroscopy

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