Chapter 2: The Chemical Context of Life – General Biology Study Notes

Chapter 2: The Chemical Context of Life

Introduction

Biology is deeply rooted in chemistry, as all living organisms are composed of matter and governed by chemical laws. Understanding the chemical basis of life is essential for studying biological processes.

Concept 2.1: Matter Consists of Chemical Elements in Pure Form and in Combinations Called Compounds

Definition of Matter

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

• All living organisms are composed of matter.

Elements and Compounds

• Element: A substance that cannot be broken down to other substances by chemical reactions.

• Compound: A substance consisting of two or more elements in a fixed ratio.

• Compounds have characteristics different from those of their constituent elements.

• Example: Sodium (Na) and chlorine (Cl) are both elements; when combined, they form sodium chloride (NaCl), a compound with properties distinct from either element.

Elements of Life

• About 20-25% of the 92 natural elements are essential for life.

• Major elements: Carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) make up about 96% of living matter.

• Other important elements: Calcium (Ca), phosphorus (P), potassium (K), and sulfur (S) constitute most of the remaining 4%.

• Trace elements: Required by organisms in minute quantities (e.g., iron, iodine, zinc).

Table: Elements in the Human Body

Element	Symbol	Percentage of Body Mass (including water)
Oxygen	O	65.0%
Carbon	C	18.5%
Hydrogen	H	9.5%
Nitrogen	N	3.3%
Calcium	Ca	1.5%
Phosphorus	P	1.0%
Potassium	K	0.4%
Sulfur	S	0.3%
Sodium	Na	0.2%
Chlorine	Cl	0.2%
Magnesium	Mg	0.1%
Trace elements	-	<0.01%

Concept 2.2: An Element’s Properties Depend on the Structure of Its Atoms

Atomic Structure

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

• Atoms are composed of subatomic particles:

  • Neutrons: No electrical charge

  • Protons: Positive charge

  • Electrons: Negative charge

• Protons and neutrons form the atomic nucleus; electrons form a cloud around the nucleus.

• Proton and neutron mass are nearly identical and measured in daltons.

Atomic Number and Atomic Mass

• Atomic number: Number of protons in the nucleus.

• Mass number: Sum of protons and neutrons in the nucleus.

• Atomic mass: Total mass of the atom, approximated by the mass number.

• Number of neutrons: $\text{Mass number} - \text{Atomic number}$

• In a neutral atom, number of protons equals number of electrons.

Isotopes and Radioactivity

• Isotopes: Atoms of the same element with different numbers of neutrons.

• Radioactive isotopes: Decay spontaneously, giving off particles and energy.

• Applications: Radioactive tracers are used in medicine to track atoms through metabolism and to monitor cancer growth.

Concept 2.3: The Formation and Function of Molecules and Ionic Compounds Depend on Chemical Bonding Between Atoms

Chemical Bonds

• Atoms with incomplete valence shells can share or transfer valence electrons, resulting in chemical bonds.

• Covalent bond: Sharing of a pair of valence electrons between two atoms.

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

• Single bond: Sharing of one pair of electrons ($\text{H-H}$).

• Double bond: Sharing of two pairs of electrons ($\text{O=O}$).

• Valence: Bonding capacity of an atom.

Electronegativity and Bond Types

• Electronegativity: An atom’s attraction for electrons in a covalent bond.

• Nonpolar covalent bond: Electrons are shared equally (e.g., $\text{H}_2$, $\text{O}_2$).

• Polar covalent bond: Electrons are shared unequally, causing partial charges (e.g., $\text{H}_2\text{O}$).

Ionic Bonds

• Atoms sometimes strip electrons from their bonding partners, forming ions.

• Cation: Positively charged ion.

• Anion: Negatively charged ion.

• Ionic bond: Attraction between cations and anions (e.g., $\text{Na}^+$ and $\text{Cl}^-$ form $\text{NaCl}$).

• Ionic compounds (salts): Compounds formed by ionic bonds, often found as crystals.

Hydrogen Bonds and Van der Waals Interactions

• Hydrogen bond: Forms when a hydrogen atom covalently bonded to one electronegative atom is attracted to another electronegative atom (commonly oxygen or nitrogen).

• Van der Waals interactions: Weak attractions between molecules due to transient local partial charges.

Concept 2.4: Chemical Reactions Make and Break Chemical Bonds

Chemical Reactions

• Chemical reaction: The making and breaking of chemical bonds.

• Reactants: Starting molecules in a chemical reaction.

• Products: Resulting molecules from a chemical reaction.

• Example: Formation of water: $2\text{H}_2 + \text{O}_2 \rightarrow 2\text{H}_2\text{O}$

• Photosynthesis: $6\text{CO}_2 + 6\text{H}_2\text{O} \xrightarrow{\text{sunlight}} \text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2$

• Chemical equilibrium: Reached when forward and reverse reactions occur at the same rate; concentrations of reactants and products remain constant.

• Reversible reactions: Indicated by two opposite-headed arrows ($\rightleftharpoons$).

Additional info:

• Atomic orbitals and electron shells determine the chemical behavior and bonding of atoms.

• Molecular shape is crucial for biological function, as it determines how molecules interact (e.g., morphine and endorphins binding to brain receptors).