The Chemistry and Energy of Life: Atomic Structure, Chemical Bonds, and Water

Chapter 2: The Chemistry and Energy of Life

Key Concepts

• 2.1 Atomic Structure is the Basis for Life's Chemistry

• 2.2 Atoms Interact and Form Molecules

• 2.3 Carbohydrates Consist of Sugar Molecules

• 2.4 Lipids Are Hydrophobic Molecules

• 2.5 Biochemical Changes Involve Energy

2.1 Atomic Structure is the Basis for Life's Chemistry

Atoms and Elements

All matter, living and nonliving, is composed of atoms. Atoms are the smallest units of elements, which are pure substances containing only one kind of atom.

• Element: A pure substance that contains only one kind of atom.

• Six elements make up most living things: Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen (O), Phosphorus (P), Sulfur (S).

Atomic Structure

• Atoms consist of a nucleus (protons and neutrons) and electrons in orbitals (electron shells).

• Proton: Positively charged particle in the nucleus.

• Neutron: Neutral particle in the nucleus.

• Electron: Negatively charged particle in orbitals around the nucleus.

• Like charges repel; different charges attract.

• Most atoms are neutral: number of protons = number of electrons.

Atomic Number and Mass Number

• Atomic number: Number of protons in the nucleus; identifies the element.

• Mass number: Number of protons plus neutrons.

• Dalton: Unit of mass for protons and neutrons ($1.7 \times 10^{-24}$ grams).

Bohr Model and Electron Shells

• The Bohr model describes atoms as having a nucleus surrounded by electrons in orbits or electron shells.

• Electron shells represent energy levels; electrons fill lower shells first.

• The behavior of electrons determines chemical bonding and molecular shape.

Octet Rule

• Atoms tend to gain, lose, or share electrons to achieve a stable configuration of 8 electrons in their outermost shell (octet rule).

• When atoms share electrons, they form stable associations called molecules.

2.2 Atoms Interact and Form Molecules

Chemical Bonds

A chemical bond is an attractive force that links atoms together in molecules. There are several types of chemical bonds:

• Covalent bonds: Atoms share pairs of electrons to achieve full outer shells. Each atom contributes one member of the electron pair.

• Polar covalent bonds: Electrons are shared unequally due to differences in electronegativity.

• Nonpolar covalent bonds: Electrons are shared equally between atoms with similar electronegativities.

• Hydrogen bonds: Weak attractions between the δ- end of one molecule and the δ+ hydrogen end of another molecule.

Table: Chemical Bonds and Interactions

Bond/Interaction	Relative Strength	Bond Energy (kcal/mol)
Covalent bond	Strong	50–110
Ionic attraction	Moderate	3–7
Hydrogen bond	Weak	3–7
Hydrophobic interaction	Very weak	1–2
van der Waals interaction	Very weak	1

Covalent Bonding Capacities

Each element has a characteristic number of covalent bonds it can form, based on the number of electrons needed to fill its outer shell.

Element	Usual Number of Covalent Bonds
Hydrogen (H)	1
Oxygen (O)	2
Sulfur (S)	2
Nitrogen (N)	3
Carbon (C)	4
Phosphorus (P)	5

Bond Strength and Types

• Single bond: Sharing 1 pair of electrons (e.g., C–H).

• Double bond: Sharing 2 pairs of electrons (e.g., C=C).

• Triple bond: Sharing 3 pairs of electrons (e.g., N≡N).

• Covalent bonds are very strong; it takes a lot of energy to break them.

Electronegativity and Polarity

• Electronegativity: The attractive force that an atomic nucleus exerts on electrons in a bond.

• Depends on the number of protons and the distance between the nucleus and electrons.

• If two atoms have similar electronegativities, they share electrons equally (nonpolar covalent bond).

• If two atoms have different electronegativities, electrons tend to be near the more attractive atom, forming a polar covalent bond.

Table: Some Electronegativity Values

Element	Electronegativity
Fluorine (F)	4.0
Oxygen (O)	3.5
Chlorine (Cl)	3.2
Nitrogen (N)	3.0
Carbon (C)	2.5
Phosphorus (P)	2.2
Hydrogen (H)	2.1
Potassium (K)	0.8

Polarity and Hydrogen Bonds

• Partial charges from polar covalent bonds produce polar molecules or polar regions of large molecules.

• Polarity influences interactions with other molecules and determines many of water's unique properties.

• Hydrogen bonds: Attraction between the δ- end of one molecule and the δ+ hydrogen end of another molecule. Important in the structure of DNA and proteins.

Properties of Water

• Water is a solvent in living systems—a liquid in which other molecules dissolve.

• Water molecules form multiple hydrogen bonds with each other, contributing to high heat capacity.

• High heat of vaporization: A lot of energy is required to change water from liquid to gas (break hydrogen bonds).

• Evaporation of water has a cooling effect (e.g., sweating cools the body).

• Cohesion: Hydrogen bonds give water cohesive strength, allowing water molecules to resist coming apart.

• Adhesion: Hydrogen bonding between water molecules and solid surfaces allows for adhesion between water and other materials.

Summary Table: Water's Unique Properties

Property	Biological Significance
High heat capacity	Buffers organisms from temperature fluctuations
High heat of vaporization	Evaporation cools organisms
Solvent properties	Facilitates chemical reactions in cells
Cohesion and adhesion	Supports transport in plants and surface tension

Example: Methane (CH4)

• Methane always forms a tetrahedral shape due to the orientation of its covalent bonds.

Additional info:

• Understanding atomic structure and chemical bonding is foundational for studying the structure and function of biological molecules such as carbohydrates, lipids, proteins, and nucleic acids.