Biochemical Foundations: Energy, Atoms, and Chemical Bonds

Fundamentals of Biochemistry

Energy is essential for all biological processes. All atoms contain energy, and they are joined together by chemical bonds, which are crucial for life. We obtain our energy from food, converting it into chemical energy that can be stored and utilized, as opposed to other forms of energy like light and heat that cannot be retained.

Thermodynamics Principles

• First Law: Energy is neither created nor destroyed; it is only transformed from one form to another.
• Second Law: In every energy transmission, some energy is lost, typically as heat, leading to an increase in entropy.

Atomic Structure

The basic units of matter are atoms, composed of three fundamental subatomic particles: neutrons (neutral charge), protons (positive charge), and electrons (negative charge).

• If you change the number of protons, you will generate a different element.
• If you change the number of neutrons, you will produce isotopes of the same element.
• Changing the number of electrons will generate ions of the same element.
• An element is called a cation when it is positively charged (loses electrons) and an anion when it is negatively charged (gains electrons).

Chemical Bonds

Chemical bonds are the forces that hold atoms together to form molecules and compounds. They are crucial for the structure and function of all matter.

Ionic Bonds: Lower Energy Linkages

Ionic bonds are formed when atoms lose or gain a valence electron, forming ions (changing their charges). Positively charged ions (cations) are attracted to negatively charged ions (anions), and vice versa. These forces of attraction are called ionic bonds, holding oppositely charged ions together.

Many ionic compounds dissociate into positive and negative ions when dissolved in a solvent. These solutions are called electrolytes because they conduct electrical current.

An ionic bond is the force of attraction that binds oppositely charged ions.

Consider the case of sodium chloride (table salt). After sodium surrenders an electron to chlorine, they change their charges and attract each other, generating salt. All salts are electrolytes and are capable of conducting electricity.

Covalent Bonds: Highly Energetic and Stable Linkages

In covalent bonds, neither atom loses nor gains an electron. Instead, they form a molecule by sharing two or three pairs of electrons. The more pairs of valence electrons shared, the greater the energy and stability of the bond. Unlike ionic bonds, covalent bonds can form between two atoms of the same type, as well as among different elements.

There are two main types of covalent bonds:

• Non-polar covalent bonds: Electrons are shared equally between atoms.
• Polar covalent bonds: Electrons are not shared equally, as one atom attracts them more strongly than the other (e.g., water).

Hydrogen Bonds: Intermolecular Attractions

Polar covalent bonds involving hydrogen atoms can lead to the formation of hydrogen bonds, a third type of chemical bond. Hydrogen bonds are weak links, possessing only about 5% of the strength of a typical covalent bond. They cannot join atoms to form molecules, but they form crucial linkages between molecules or between different parts of a single large molecule. Hydrogen bonds offer considerable resistance and stability, and they also influence the three-dimensional configuration of molecules, especially in biological systems.

For example, hydrogen bonds are formed because the partially positive hydrogen atoms of one water molecule are attracted to the partially negative oxygen atoms in another water molecule.

Key Elements Determining Enzyme Functionality

The presence and concentration of certain elements and compounds are critical for the proper functioning of enzymes, which are biological catalysts.

Inorganic Compounds

Water, Acids, Bases, and Salts

Most chemicals in the body are compounds, which are classified into two main categories: inorganic and organic. In general, inorganic compounds do not contain carbon and have a simple structure. Examples include water, many acids, bases, and salts. They can form either ionic or covalent bonds. Conversely, all organic compounds contain carbon (with a few exceptions like carbon monoxide (CO) and carbon dioxide (CO2), which are classified as inorganic).

Chemical Composition of Living Organisms

From Atoms to Molecules to Cells

• Bioelements:
  • Primary: Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N)
  • Secondary: Sulfur (S), Phosphorus (P), Calcium (Ca), Sodium (Na), Potassium (K), Chlorine (Cl), etc.
• Biomolecules:
  • Organic: Carbohydrates, Lipids, Proteins, Nucleic Acids
  • Inorganic: Water, Minerals