General Biology: Chemistry Fundamentals for Life

Topic 2: Chemistry

Elements and Atoms

Chemistry is fundamental to understanding biological processes. All living things are composed of matter, which is made up of elements and atoms. This section introduces the basic building blocks of matter and their relevance to life.

• Matter: Anything that occupies space and has mass.

• Element: A pure substance that cannot be broken down into simpler substances by chemical means. Each element is defined by its number of protons.

• Atom: The smallest unit of an element that retains its chemical properties. Atoms consist of a nucleus (containing protons and neutrons) and electrons in surrounding clouds.

Major elements in living organisms:

• Oxygen (O)

• Carbon (C)

• Hydrogen (H)

• Nitrogen (N)

• Phosphorus (P)

• Calcium (Ca)

These elements make up the majority of living cells, with oxygen, carbon, hydrogen, and nitrogen being the most abundant.

Element	Approximate % in Human Body
Oxygen	65.0%
Carbon	18.5%
Hydrogen	9.5%
Nitrogen	3.2%
Phosphorus	1.0%
Calcium	1.5%

Atomic Structure:

• Protons: Positively charged particles in the nucleus; 1 atomic mass unit (amu).

• Neutrons: Neutral particles in the nucleus; 1 amu.

• Electrons: Negatively charged particles in electron clouds; negligible mass (0 amu).

• Atomic number: Number of protons; defines the element.

• Atomic mass: Sum of protons and neutrons.

• Isotopes: Atoms of the same element with different numbers of neutrons, resulting in different atomic masses.

Example: Carbon-12 has 6 protons and 6 neutrons; Carbon-14 has 6 protons and 8 neutrons.

Radioactivity

Some isotopes are unstable and emit energy as radiation. These radioactive isotopes have important applications in biology and medicine.

• Radioactive decay: The process by which unstable isotopes lose energy by emitting radiation, transforming into different elements.

• Applications:

  • Radiocarbon dating: Uses the ratio of 14C to 12C to estimate the age of formerly living materials (up to ~60,000 years).

  • Medical imaging: Techniques like PET scans use radioactive tracers to visualize processes in the body.

  • Research: Radioisotopes are used to trace biochemical pathways.

Example: The use of radiocarbon dating to determine the age of archaeological samples, such as the remains of Ötzi the Iceman.

Molecules and Chemical Bonds

Atoms combine to form molecules through chemical bonds, which are essential for the structure and function of biological molecules.

• Molecule: Two or more atoms held together by chemical bonds.

• Ionic bonds: Formed when electrons are transferred from one atom to another, resulting in oppositely charged ions that attract each other (e.g., NaCl).

• Covalent bonds: Formed when atoms share electrons to fill their outer shells. Can be single, double, or triple bonds.

• Polar covalent bonds: Electrons are shared unequally due to differences in electronegativity, resulting in partial charges (e.g., water).

• Nonpolar covalent bonds: Electrons are shared equally (e.g., O2).

• Hydrogen bonds: Weak attractions between a hydrogen atom (covalently bonded to an electronegative atom like O or N) and another electronegative atom. Critical for the structure of DNA, proteins, and water's properties.

Example: Hydrogen bonds hold together the two strands of DNA and give water its unique properties.

Chemical Reactions

Chemical reactions involve the making and breaking of bonds, transforming reactants into products. These reactions are fundamental to metabolism and energy flow in living systems.

• Reactants: Substances that start a chemical reaction.

• Products: Substances formed as a result of a chemical reaction.

• Balanced equations: The number of atoms of each element is the same on both sides of the equation.

• Reversible reactions: Many biological reactions can proceed in both directions and reach equilibrium.

• Energy: Some reactions require energy input (endergonic), while others release energy (exergonic).

Example: Aerobic respiration and photosynthesis are key biological reactions:

• Aerobic respiration: $6O_2 + C_6H_{12}O_6 \rightarrow 6CO_2 + 6H_2O$

• Photosynthesis (reverse reaction): $6CO_2 + 6H_2O \xrightarrow{sunlight} C_6H_{12}O_6 + 6O_2$

Water and Its Properties

Water is essential for life due to its unique chemical and physical properties, many of which arise from its ability to form hydrogen bonds.

• Polarity: Water is a polar molecule, with partial positive (H) and partial negative (O) charges.

• Hydrogen bonding: Each water molecule can form up to four hydrogen bonds, leading to high cohesion and surface tension.

• High specific heat: Water can absorb or release large amounts of heat with little temperature change, helping regulate temperature in organisms and environments.

• Universal solvent: Water dissolves many substances, especially ionic and polar compounds, facilitating chemical reactions in cells.

• Cohesion and adhesion: Water molecules stick to each other (cohesion) and to other surfaces (adhesion), enabling processes like capillary action in plants.

• Density: Ice is less dense than liquid water, allowing it to float and insulate aquatic environments.

Example: Water's high specific heat stabilizes climate and body temperature; its solvent properties enable nutrient transport in blood.

Acids, Bases, and pH

The concentration of hydrogen ions (H+) in a solution determines its acidity or alkalinity, measured by the pH scale. Biological systems tightly regulate pH to maintain homeostasis.

• Acid: Substance that increases H+ concentration in solution (pH < 7).

• Base: Substance that decreases H+ concentration, often by increasing OH- (pH > 7).

• Neutral: Equal concentrations of H+ and OH- (pH = 7).

• Buffer: Solution that resists changes in pH by absorbing or releasing H+ ions. Buffers are critical in maintaining the pH of blood and tissues.

pH Value	Type	Example
0-6	Acidic	Stomach acid, lemon juice
7	Neutral	Pure water
8-14	Basic (alkaline)	Bleach, baking soda

Example: Human blood is maintained at a pH of about 7.4; deviations can disrupt biological functions.

Additional info: The notes above expand on brief points from the original slides, providing definitions, examples, and context for each concept to ensure a self-contained study guide suitable for exam preparation.