The Chemical Context of Life: Foundations for General Biology

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Chemical Connection to Biology

Introduction to Chemistry in Biology

All living organisms and their environments are governed by the fundamental laws of physics and chemistry. Understanding these principles is essential for studying biological processes, as life is deeply rooted in chemical interactions.

Key Point: Biological systems operate within the constraints of chemical and physical laws.
Example: Cellular respiration and photosynthesis are chemical processes vital to life.

Matter, Elements, and Compounds

Definition and Properties of Matter

Organisms are composed of matter, which is anything that occupies space and has mass. Matter is the physical substance of the universe, including all living and nonliving things.

Key Point: Matter consists of chemical elements in pure form and in combinations called compounds.
Definition: Element – A substance that cannot be broken down to other substances by chemical reactions.
Definition: Compound – A substance consisting of two or more elements in a fixed ratio.
Key Point: Compounds have characteristics different from those of their constituent elements.
Example: Sodium (Na) and chlorine (Cl) are both hazardous in pure form, but together they form sodium chloride (NaCl), or table salt, which is safe to consume.

Elements and Compounds in Biology

Of the 92 naturally occurring elements, about 20-25% are essential for life. Four elements—carbon, hydrogen, oxygen, and nitrogen—make up about 96% of living matter. The remaining 4% consists mainly of calcium, phosphorus, potassium, and sulfur, with trace elements required in minute quantities.

Key Point: Essential elements are required for an organism to survive and reproduce.
Key Point: Trace elements are needed in very small amounts but are still vital for health.

Table: Elements in the Human Body

The following table summarizes the major elements found in the human body and their approximate percentage of body mass (including water):

Element	Symbol	Percentage of Body Mass
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%

Additional info: Trace elements include boron, chromium, cobalt, copper, fluorine, iodine, iron, manganese, molybdenum, selenium, silicon, tin, vanadium, and zinc.

Elements, Atoms, and Compounds

Atomic Structure and Properties

The properties of an element depend on the structure of its atoms. Each element consists of unique atoms, which are the smallest units of matter that retain the properties of the element.

Key Point: Atoms are composed of subatomic particles: protons (positive charge), neutrons (no charge), and electrons (negative charge).
Key Point: Protons and neutrons form the atomic nucleus, while electrons form a cloud around the nucleus.
Key Point: The mass of protons and neutrons is nearly identical and measured in daltons.

Atomic Number and Atomic Mass

Atoms of different elements differ in the number of subatomic particles.

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, approximately equal to the mass number.

Isotopes and Radioactivity

Atoms of the same element may have different numbers of neutrons, resulting in isotopes. Some isotopes are unstable and decay spontaneously, emitting particles and energy (radioactive isotopes).

Key Point: Radioactive isotopes are used as diagnostic tools in medicine and for radiometric dating.
Example: Carbon-14 is used to date ancient biological materials.

Chemical Bonds and Molecules

Types of Chemical Bonds

Chemical bonds are the forces that hold atoms together in molecules and compounds. The main types of chemical bonds in biology are covalent bonds, ionic bonds, hydrogen bonds, and van der Waals interactions.

Covalent bond: Sharing of a pair of valence electrons between two atoms.
Ionic bond: Attraction between oppositely charged ions (cation and anion).
Hydrogen bond: Weak attraction between a hydrogen atom covalently bonded to an electronegative atom and another electronegative atom.
Van der Waals interactions: Weak attractions due to transient local partial charges.

Covalent Bonds and Molecules

Covalent bonds can be single (one pair of electrons shared) or double (two pairs shared). Molecules are formed when two or more atoms are held together by covalent bonds.

Structural formula: Representation of atoms and bonds (e.g., H—H for hydrogen gas).
Molecular formula: Abbreviated representation (e.g., H2).

Electronegativity and Bond Polarity

Electronegativity is an atom's ability to attract electrons in a covalent bond. If atoms share electrons equally, the bond is nonpolar; if not, the bond is polar, resulting in partial charges.

Nonpolar covalent bond: Equal sharing of electrons.
Polar covalent bond: Unequal sharing, leading to partial positive and negative charges.

Ionic Bonds and Salts

Ionic bonds form when one atom transfers an electron to another, creating ions. Compounds formed by ionic bonds are called salts and often exist as crystals.

Cation: Positively charged ion.
Anion: Negatively charged ion.
Example: Sodium chloride (NaCl) is formed from sodium (Na+) and chloride (Cl-) ions.

Weak Chemical Bonds and Molecular Interactions

Importance of Weak Bonds

Weak chemical bonds, such as hydrogen bonds and van der Waals interactions, are crucial for the structure and function of large biological molecules. Their reversibility allows for dynamic biological processes.

Example: Hydrogen bonds stabilize the structure of DNA and proteins.

Molecular Shape and Biological Function

Shape Determines Function

The shape of a molecule is determined by the arrangement of its atoms and the orbitals involved in bonding. Molecular shape is critical in biology because it determines how molecules interact and recognize each other.

Key Point: Similar shapes allow molecules to bind to the same receptors (e.g., morphine and endorphins).

Chemical Reactions in Biology

Making and Breaking Bonds

Chemical reactions involve the making and breaking of chemical bonds. The starting substances are called reactants, and the resulting substances are products.

Example: Photosynthesis is a chemical reaction powered by sunlight:

Key Point: Chemical reactions are reversible, and equilibrium is reached when the forward and reverse reactions occur at the same rate.

Additional info: Chemical equilibrium does not mean equal concentrations of reactants and products, but rather that their concentrations remain constant over time.