Biochemistry Fundamentals: Atoms, Bonds, Water, and Biological Molecules

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Biochemistry (Ch. 2 and 3)

Introduction to Biochemistry

Biochemistry is the study of the chemical processes and substances that occur within living organisms. It focuses on the structure and function of biomolecules, the chemical bonds that hold them together, and the interactions that enable life.

Atoms, Elements, and Compounds

Basic Atomic Structure

Atom: The smallest unit of matter that retains the properties of an element. Examples: carbon (C), hydrogen (H), sodium (Na).
Element: A pure substance consisting of only one type of atom. Examples: C, H, O, N.
Compound: A substance formed when two or more atoms are bonded together. Compounds can be ionic or molecular (covalent).
Ion: An atom or molecule that has gained or lost one or more electrons, acquiring a charge. Examples: Na+, Cl-, Ca2+.
Ionic Compound: A compound formed from ions, e.g., NaCl.
Molecular Compound (Molecule): A compound formed by covalent bonds, e.g., H2O.
Atomic #: Number of protons in the nucleus (defines the element).
Mass #: Number of protons plus neutrons in the nucleus.
Isotopes: Atoms of the same element with different numbers of neutrons. Example: Carbon-12 (6 protons, 6 neutrons), Carbon-14 (6 protons, 8 neutrons).

Chemical Bonds

Ionic and Covalent Bonds

Ionic Bond: Formed when one or more electrons are transferred from one atom to another, resulting in oppositely charged ions that attract each other. Example: NaCl.
Covalent Bond: Formed when one or more electrons are shared between two atoms. Covalent bonds are strong and form molecules. Example: H2O.
Valence Electrons: Electrons in the outermost shell of an atom, involved in bonding.

Polarity of Covalent Bonds

Polar Covalent Bond: Electrons are shared unequally due to differences in electronegativity, resulting in partial charges. Example: In water, oxygen is more electronegative and pulls electrons closer, making it slightly negative and hydrogen slightly positive.
Non-polar Covalent Bond: Electrons are shared equally between atoms with similar electronegativity.

Intermolecular and Intramolecular Forces

Types of Molecular Interactions

INTRAmolecular: Forces within the same molecule (covalent bonds, ionic bonds).
INTERmolecular: Forces between different molecules (hydrogen bonds, van der Waals interactions).
Hydrogen Bond: A weak bond between a hydrogen atom (attached to a highly electronegative atom like O or N) and another electronegative atom. Important in water and biological molecules.

Properties of Water

Polarity and Hydrogen Bonding

Water is a polar molecule due to the unequal sharing of electrons between oxygen and hydrogen.
Hydrogen bonds form between water molecules, leading to unique properties such as high cohesion, adhesion, and surface tension.
Hydrophilic: "Water-loving"; polar and ionic compounds dissolve easily in water.
Hydrophobic: "Water-fearing"; non-polar molecules do not dissolve well in water.
Water is known as the universal solvent because it dissolves many substances, especially polar and ionic compounds.

Solubility

Soluble: Polar and ionic compounds.
Not soluble: Non-polar molecules.

Acids, Bases, and pH

pH Scale and Buffers

pH is measured on a scale of 1–14.
Low pH (below 7): Acidic, higher concentration of H+ ions.
High pH (above 7): Basic, lower concentration of H+ ions.
pH 7 is neutral.
Most mammalian cells maintain an internal pH of 6.5–7.5.
Buffers: Substances that help maintain a stable pH in biological systems, crucial for homeostasis and proper enzyme function.

Carbon Chemistry

Properties of Carbon

Carbon has 4 valence electrons and can form up to 4 covalent bonds.
Can form single, double, or triple bonds with other atoms, including other carbon atoms.
Carbon chains can be straight, branched, or form rings, allowing for a diversity of organic molecules.
Bonds are covalent and very strong.

Macromolecules: Monomers and Polymers

Monomers and Polymers

Monomer: A small molecule that can join with others to form a polymer. Example: glucose.
Polymer: A large molecule (macromolecule) made by bonding many monomers together. Example: starch, proteins.
Four major classes of biological molecules: carbohydrates, lipids, proteins, nucleic acids. Each (except lipids) has characteristic monomers.

Dehydration Synthesis and Hydrolysis

Dehydration Synthesis: A reaction that joins two monomers by removing a water molecule, forming a covalent bond.
Hydrolysis: A reaction that splits a polymer into monomers by adding a water molecule.

Lipids

Structure and Function of Lipids

Composed mainly of carbon and hydrogen, with some oxygen.
Glycerol and fatty acids are the building blocks of triglycerides (a common type of lipid).
Saturated fatty acids: All single C–C bonds in the fatty acid chain; solid at room temperature.
Unsaturated fatty acids: At least one double C=C bond in the fatty acid chain; liquid at room temperature due to "kinks" in the chain.
Phospholipids: Major component of cell membranes.
Oils/fats: Energy storage, insulation.

Key Tables

Comparison of Bond Types

Bond Type	How Formed	Strength	Example
Ionic	Transfer of electrons	Moderate	NaCl
Covalent	Sharing of electrons	Strong	H2O, O2
Hydrogen	Attraction between polar molecules	Weak	Between water molecules

pH Scale Reference

pH Value	Type	H+ Concentration
1–6	Acidic	High
7	Neutral	Equal
8–14	Basic	Low

Key Equations

Atomic mass number:
pH calculation:

Summary

Atoms combine to form molecules and compounds through ionic and covalent bonds.
Water's polarity and hydrogen bonding give it unique properties essential for life.
pH and buffers are critical for maintaining homeostasis in biological systems.
Carbon's bonding versatility allows for the diversity of organic molecules.
Monomers and polymers form the basis of biological macromolecules, with dehydration synthesis and hydrolysis controlling their assembly and breakdown.
Lipids are hydrophobic molecules important for energy storage, insulation, and membrane structure.