Basic Chemistry for Biology: Study Notes

Basic Chemistry for Biology

Introduction

Chemistry forms the foundation for understanding biological processes. This section introduces the essential chemical principles that underpin the study of biology, focusing on matter, elements, atoms, chemical bonds, and the properties of water.

2.1 Matter and Elements

Definition of Matter

• Matter is anything that takes up space and has mass.

• solid, liquid, & gas.

• all matter is made up of elements.

Elements

• An element is a substance that cannot be broken down.

• Each element is made up of only one kind of atom.

• Atom: The smallest unit of matter that still has the properties of an element.

Elemental Composition of the Human Body

• Four elements—oxygen, carbon, hydrogen, and nitrogen

• Make up about 96% of the human body’s mass.

• Other elements are present in small amounts and are called trace elements (e.g., iodine, calcium, phosphorus).

• Trace elements are essential for health; for example, iodine deficiency can cause thyroid gland enlargement (goiter).

Molecules and Compounds

Definitions

• A molecule is a combination of two or more atoms held together by chemical bonds.

• A compound is a molecule composed of atoms of two or more different elements.

Examples

• Oxygen gas: $O_2$ (molecule of two oxygen atoms)

• Carbon dioxide: $CO_2$ (compound of one carbon atom and two oxygen atoms)

• Water: $H_2O$ (compound of two hydrogen atoms and one oxygen atom)

2.2 Atoms

Structure of Atoms

• Atoms are made up of 3 types of subatomic particles:

  • Protons: Positively charged, located in the nucleus

  • Neutrons: Neutral (no charge), located in the nucleus

  • Electrons: Negatively charged, orbit the nucleus in energy levels (shells)

• The nucleus is the central part of the atom, containing protons and neutrons.

• Electrons are so small they don't contribute any mass.

• Atomic number is always the same as the number of protons.

  Example: 1 - atomic number

  H - element

  1.00 - atomic mass (# of protons + neutrons)

2.3 Electron Shells and Chemical Bonds

Electron Arrangement

• Electrons are arranged in energy levels (shells) around the nucleus.

  • farther away = more energy

• Each shell can hold a specific number of electrons

  • (first 4 shells: 2e-, 8e-, 8e-, 32e-)

• Atoms tend to fill their outermost shell by interacting with other atoms, leading to chemical bonding. (Electrons are the only particle interacting when atoms form bonds or undergo reactions.)

• Full outer shell = chemically unreactive

Chemical Bonds

• Ionic Bonds: Formed when one atom gives electrons to another.

  • 2 results: both has now full outer shells; atoms now have electrical charges that are not neutral = "ions"

  • Held together by the attraction between + and - charge (opposites attract) = polarity

  • Example: Formation of Sodium Chloride (Table Salt)

    • Sodium ($Na$) transfers an electron to chlorine ($Cl$), forming $Na^+$ and $Cl^-$ ions.

    • These ions attract each other to form sodium chloride ($NaCl$).

• Covalent Bonds: Formed when two atoms share one or more pairs of electrons.

  • strongest bonds (held together).

  • The number of covalent bonds an atom can form is limited by the number of electrons needed to complete its outer shell.

  • Electrons are not always shared equally sometimes one atom will pull harder than the other atom.

• Polar Covalent Bonds: Occur when electrons are shared unequally, causing uneven charges within the molecule (e.g., water).

Chemical Reactions

Overview

• In chemical reactions, matter is neither created nor destroyed just rearranged (Law of Conservation of Mass).

• Chemical bonds are broken and new ones are formed.

• Reactants: Starting molecules.

  Products: Molecules formed as a result of the reaction.

Example: Combustion of Methane

• $CH_4 + 2O_2 \rightarrow CO_2 + 2H_2O$

• Methane and oxygen react to form carbon dioxide and water.

2.4 The Importance of the Water Molecule

Properties of Water

• All life on Earth is dependent by water.

• Water is essential for life and supports biological processes.

• Water molecules are polar, with an uneven distribution of charge (oxygen is slightly negative, hydrogen is slightly positive).

• Hydrogen bonds form between water molecules.

1. Cohesion and Adhesion

• Cohesion: Water molecules stick to each other due to hydrogen bonding.

• Adhesion: Water molecules stick to other surfaces, aiding in transport within living organisms.

2. Temperature Regulation

• Hydrogen bonds help water resist changes in temperature.

  • more heat = faster molecule movement.

• Temperature: measures how fast molecules are moving, not the total amount of heart energy.

3. Water as a Solvent and the pH Scale

Water as a Solvent

• A solvent is a substance that dissolves other substances (solutes).

• A solution is a mixture of two or more substances.

• When water is the solvent, the solution is called an aqueous solution.

The pH Scale

• The pH scale measures the concentration of hydrogen ions ($H^+$) in a solution.

• The scale ranges from 0 (most acidic) to 14 (most basic), with 7 being neutral.

• Each pH unit represents a tenfold change in $H^+$ concentration.

• Acids: Compounds that release $H^+$ ions in solution.

• Bases: Compounds that release $OH^-$ ions in solution.

pH Value	Type	Example
1-6	Acidic	Lemon juice, stomach acid
7	Neutral	Pure water
8-14	Basic (Alkaline)	Baking soda, seawater

Additional info: Some explanations and examples have been expanded for clarity and completeness, including the Law of Conservation of Mass and the full chemical equation for methane combustion.