Biology - Simple Chemical Reactions and Bonds Study Notes

Module 1.1.1: Biology - Simple Chemical Reactions and Bonds

Overview of Matter and Elements

• Definition of Matter: Matter is defined as anything that takes up space and has mass. Examples of matter include:
    - Rocks
    - Gases
    - Living organisms (e.g., kittens, humans)
    - Everyday objects (e.g., shoes)

• Elements: Elements are pure substances that cannot be broken down into simpler substances by chemical means. Examples of elements include:
    - Carbon (C)
    - Oxygen (O)
    - Hydrogen (H)

• Atoms: An atom is the smallest unit of matter that retains the properties of an element. Key points include:
    - Atoms are extremely small, beyond microscopic in size.
    - Each element has unique atoms composed of three types of subatomic particles:
      - Neutrons: Neutrally charged particles found in the nucleus.
      - Protons: Positively charged particles also found in the nucleus.
      - Electrons: Negatively charged particles that orbit the nucleus.

Atomic Structure and Binding

• Formation of Compounds and Molecules:
    - Compound: A compound consists of two or more different elements combined in a fixed ratio. Example: Table salt (sodium chloride, $NaCl$) is formed from sodium (Na) and chlorine (Cl).
    - Molecule: A molecule can consist of two or more of the same or different elements combined in a fixed ratio. Example: Oxygen gas ($O_2$) consists of two oxygen atoms.
    - Distinction: Every compound qualifies as a molecule, but not every molecule qualifies as a compound.

• Electron Configuration:
    - Electrons are arranged in shells around the nucleus. The outermost shell is referred to as the valence shell.
    - Valence Electrons: Electrons in the valence shell that can interact with other atoms. Interaction is less likely with inner-shell electrons.
    - Atom Reactivity: Atoms are most reactive when their valence shell is incomplete; such atoms are more inclined to interact with other atoms to achieve stability.

Chemical Bonds

• Chemical Bonds Overview: Bonds are attractions that hold atoms together. The fundamental forces at work include the attraction between protons and electrons.

Types of Chemical Bonds:

1. Covalent Bonds:
      - Definition: A covalent bond occurs when atoms share one or more pairs of electrons.
      - Characteristics:
        - Considered strong bonds.
        - Example: In methane ($CH_4$), carbon shares electrons with hydrogen, leading to satisfaction of valence shells.
      - Types of Covalent Bonds:
        - Nonpolar Covalent Bond: Electrons are shared equally between atoms (example: $H_2$ - hydrogen gas).
        - Polar Covalent Bond: Electrons are shared unequally, resulting in partial charges. Example: In water ($H_2O$), oxygen attracts electrons more than hydrogen, creating partial negative and positive charges, respectively.

2. Ionic Bonds:
      - Definition: An ionic bond is formed when one atom donates an electron to another atom, resulting in the formation of charged ions.
      - Terminology:
        - The atom that gains an electron is called an anion.
        - The atom that loses an electron is called a cation.
      - Characteristics:
        - Considered strong bonds due to the electrostatic attraction between oppositely charged ions.

3. Hydrogen Bonds:
      - Definition: A hydrogen bond is a weak attraction between a hydrogen atom covalently bonded to a highly electronegative atom and another electronegative atom.
      - Characteristics:
        - Illustrates weak attractions in water molecules where the partially positive hydrogen attracts the partially negative oxygen of another water molecule.
        - Contribute to significant phenomena such as cohesion and surface tension in water.

Chemical Reactions

• Definition: A chemical reaction involves the making and breaking of chemical bonds, where substances known as reactants interact to form new substances called products.

• Chemical Reaction Representation:
     - General formula: $A + B <br>ightarrow C$
     - Indicates that reactants (A and B) interact to yield products (C).
     - Reactions can also be reversible, signified by a double arrow indicating that products can revert to reactants.

• Example Reaction:
     - Reactants: $NH_3 + H_2O$
     - Products: $NH_4^+ (cation) + OH^- (anion)$.

Energy and Thermodynamics

• Energy: Energy is discussed within the context of chemical reactions, where it is relevant to physical sciences, including biology.

• First Law of Thermodynamics: Energy cannot be created or destroyed, only transformed or transferred.

• Second Law of Thermodynamics: Reactions tend to increase disorder (entropy), rendering energy less available for biological processes.

Types of Reactions Based on Energy Changes:

• Endothermic Reaction: Absorbs energy from the environment.

• Exothermic Reaction: Releases energy into the environment (e.g., combustion of explosives).