Basic Chemistry and Biochemistry for Anatomy & Physiology

Basic Chemistry

2.1 What is Matter?

Matter is anything that occupies space and has mass. It exists in three primary states: solid, liquid, and gas.

• Definition: Matter is the substance of the universe, including all living and non-living things.

• States: Solid (fixed shape and volume), Liquid (fixed volume, variable shape), Gas (variable shape and volume).

What is Energy?

Energy is the capacity to do work or cause change. It exists in various forms and can be converted between forms, but cannot be created or destroyed (Law of Conservation of Energy).

• Kinetic Energy: Energy of motion.

• Potential Energy: Stored energy due to position or structure.

• Chemical Energy: Stored in chemical bonds.

• Electrical Energy: Movement of charged particles.

• Mechanical Energy: Direct movement of matter.

• Radiant Energy: Energy carried by electromagnetic waves.

2.2 What is Matter Composed Of?

Matter is composed of elements, which are substances that cannot be broken down by ordinary chemical means. Each element is made of atoms.

• Elements: Listed in the periodic table. Example: Oxygen (O), Carbon (C), Hydrogen (H), Nitrogen (N).

• Atoms: Smallest unit of an element, composed of:

  • Protons: Positively charged particles in the nucleus.

  • Neutrons: Neutral particles in the nucleus.

  • Electrons: Negatively charged particles orbiting the nucleus.

• Atomic Number: Number of protons in the nucleus.

• Mass Number: Number of protons plus neutrons.

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

• Radioisotopes: Unstable isotopes that emit radiation.

Models of the Atom: Planetary model vs. orbital model (modern quantum model).

2.3 How is Matter Combined into Molecules and Mixtures?

Atoms combine to form molecules and compounds, which can further mix to form mixtures.

• Molecules: Two or more atoms bonded together.

• Compounds: Molecules composed of different elements.

• Mixtures: Physical combinations of substances.

• Solutions: Homogeneous mixtures; solute dissolved in solvent.

• Colloids: Heterogeneous mixtures with larger particles that do not settle.

• Suspensions: Heterogeneous mixtures with large particles that settle out.

Concentration Units:

• Percent (%)

• mg/dL

• Molarity (M): $M = \frac{\text{moles of solute}}{\text{liters of solution}}$

2.4 What are the Three Kinds of Chemical Bonds?

Chemical bonds hold atoms together in molecules and compounds. The type of bond affects the properties of the substance.

• Ionic Bonds: Transfer of electrons between atoms, forming cations and anions.

• Covalent Bonds: Sharing of electrons between atoms; can be single, double, or triple bonds.

• Hydrogen Bonds: Weak attractions between polar molecules, important in water and biological molecules.

Role of Electrons: Electrons in the outer shell (valence electrons) determine bonding behavior.

2.5 How do Chemical Reactions Form, Rearrange, or Break Bonds?

Chemical reactions involve making or breaking chemical bonds, resulting in new substances.

• Synthesis (Anabolic) Reactions: Build larger molecules from smaller ones.

• Decomposition (Catabolic) Reactions: Break down molecules into smaller components.

• Exchange Reactions: Swap components between molecules.

• Redox (Oxidation-Reduction) Reactions: Transfer electrons between molecules.

Example: Cellular respiration: $\text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2 \rightarrow 6\text{CO}_2 + 6\text{H}_2\text{O} + \text{energy}$

• Endergonic Reactions: Absorb energy.

• Exergonic Reactions: Release energy.

• Reversible Reactions: Can proceed in both directions.

• Factors Influencing Reaction Rate: Temperature, concentration, particle size, catalysts (enzymes).

Biochemistry

2.6 What is the Importance of Inorganic Compounds in the Body?

Inorganic compounds, such as water, salts, acids, and bases, are essential for life and physiological processes.

• Water: High heat capacity, high heat of vaporization, polar solvent, reactivity, cushioning.

• Salts: Ionic compounds that dissociate in water, conduct electricity.

• Acids: Release hydrogen ions ($\text{H}^+$) in solution.

• Bases: Accept hydrogen ions or release hydroxide ions ($\text{OH}^-$).

pH Scale: Measures hydrogen ion concentration.

• Neutral: $\text{pH} = 7$

• Acidic: $\text{pH} < 7$

• Basic (alkaline): $\text{pH} > 7$

• $\text{pH} = -\log[\text{H}^+]$

Buffers: Resist changes in pH by binding or releasing $\text{H}^+$.

2.7 How are the Four Types of Large Organic Compounds Made and Broken Down?

Organic compounds are carbon-based molecules essential for life. They are synthesized by dehydration synthesis and broken down by hydrolysis.

• Dehydration Synthesis: Removal of water to join molecules.

• Hydrolysis: Addition of water to break molecules apart.

2.8 What are the Roles of the Four Classes of Organic Compounds in Living Systems?

The four major classes of organic compounds are carbohydrates, lipids, proteins, and nucleic acids.

• Carbohydrates: Provide energy and structural support.

  • Monosaccharides: Simple sugars (glucose, fructose).

  • Disaccharides: Two sugars joined (sucrose, lactose).

  • Polysaccharides: Long chains (starch, glycogen).

• Lipids: Store energy, insulate, cushion organs.

  • Triglycerides: Fats and oils.

  • Phospholipids: Major component of cell membranes.

  • Steroids: Hormones, cholesterol.

• Proteins: Perform a wide variety of functions.

  • Amino Acids: Building blocks of proteins.

  • Peptide Bonds: Link amino acids.

  • Levels of Structure: Primary, secondary, tertiary, quaternary.

  • Fibrous Proteins: Structural (collagen, myosin).

  • Globular Proteins: Functional (enzymes, antibodies).

• Nucleic Acids: Store and transmit genetic information.

  • DNA: Double helix, stores genetic code.

  • RNA: Single strand, involved in protein synthesis.

  • Nucleotides: Building blocks (adenine, guanine, cytosine, thymine, uracil).

2.9 Proteins: Structure and Function

Proteins are polymers of amino acids, essential for structure and function in cells.

• Primary Structure: Sequence of amino acids.

• Secondary Structure: Alpha helix, beta pleated sheet.

• Tertiary Structure: 3D folding due to side chain interactions.

• Quaternary Structure: Multiple polypeptide chains.

• Denaturation: Loss of structure and function due to environmental changes.

• Fibrous Proteins: Collagen, myosin (structural).

• Globular Proteins: Enzymes, antibodies (functional).

• Enzymes: Biological catalysts that speed up chemical reactions by lowering activation energy.

2.10 Nucleic Acids

Nucleic acids are polymers of nucleotides, responsible for genetic information and protein synthesis.

• DNA: Double-stranded, contains deoxyribose sugar, bases: adenine, guanine, cytosine, thymine.

• RNA: Single-stranded, contains ribose sugar, bases: adenine, guanine, cytosine, uracil.

• ATP (Adenosine Triphosphate): Main energy carrier in cells.

• ATP Hydrolysis: $\text{ATP} \rightarrow \text{ADP} + \text{P}_i + \text{energy}$

Summary Table: Types of Chemical Bonds

Bond Type	Description	Example
Ionic	Transfer of electrons; forms ions	NaCl (sodium chloride)
Covalent	Sharing of electrons; forms molecules	H2O (water)
Hydrogen	Weak attraction between polar molecules	Between water molecules

Summary Table: Classes of Organic Compounds

Class	Monomer	Main Function	Example
Carbohydrates	Monosaccharide	Energy, structure	Glucose, starch
Lipids	Fatty acid, glycerol	Energy storage, insulation	Triglyceride, phospholipid
Proteins	Amino acid	Structure, function	Collagen, enzyme
Nucleic Acids	Nucleotide	Genetic information	DNA, RNA

Additional info:

• Enzymes are specific to substrates and are regulated by factors such as temperature and pH.

• ATP is regenerated from ADP and phosphate during cellular respiration.

• Proteins can be denatured by heat, pH changes, or chemicals, losing their function.