The Chemistry of Life: Organization, Atomic Structure, and Biological Molecules

Organization of Matter

• Matter: Defined as anything that occupies space and possesses mass.

• Mass: Refers to the specific amount of matter contained within a substance.

• Weight: Defined as the force exerted by gravity acting upon a given mass.

• Element: A substance that cannot be decomposed or split into smaller substances through ordinary chemical means.

• Distribution of Elements on Earth: There are $112$ identified elements.

  • $92$ elements occur naturally.

  • $20$ elements are synthetic (man-made).

• Composition of the Human Body:

  • Main Elements: Approximately $96\%$ of the body's mass is composed of four primary elements: Oxygen ($O$), Carbon ($C$), Nitrogen ($N$), and Hydrogen ($H$).

  • Minor Elements: Approximately $3.6\%$ of the body's mass is derived from $8$ specific elements.

  • Trace Elements: The remaining $0.4\%$ of the body's mass consists of $14$ trace elements.

Atomic Structure

• Atom: The smallest constituent unit of an element that retains the properties of that element.

• Nucleus: The centrally located core of the atom.

  • Protons: Positively charged particles ($+$) located in the nucleus.

  • Neutrons: Particles with no electrical charge (neutral) located in the nucleus.

• Electrons: Negatively charged particles ($-$) that revolve around the nucleus within specific regions known as energy shells.

• Neutral Elements: In a neutral state, the number of protons equals the number of electrons ( $\text{\# of protons} = \text{\# of electrons}$ ).

Atomic Number and Mass Number

• Atomic Number: This value represents the total $\text{\# of protons in nucleus}$.

• Mass Number: The sum of the protons and neutrons in the nucleus ( $\text{protons} + \text{neutrons}$ ).

• Isotope: Refers to different atoms of the same element that share the same atomic number but have a different mass number. In an isotope, the $\text{\# of protons}$ is NOT equal to the $\text{\# of neutrons}$.

Matter Combined: Ions, Molecules, and Compounds

• Ion: An atom that has acquired a positive or negative charge by either gaining or losing electrons.

• Molecule: Formed when $2$ or more atoms are chemically bonded together.

• Compound: A substance formed when $2$ or more atoms of DIFFERENT ELEMENTS are chemically bonded together.

• Free Radicals: Chemical species characterized by having unpaired electrons in their outermost electron shell.

Matter Combined: Mixtures

• Mixture: A blend of elements or compounds that are physically intermingled but not chemically bonded together in a solution.

• Suspension: A mixture containing $2$ or more components with large particles that will eventually settle out over time.

• Colloid: A mixture containing $2$ or more components with small particles that remain dispersed and will not settle out.

• Solution: A clear mixture where a solute (such as salt) is completely dissolved within a solvent (such as water).

• Concentration: The measure of the amount of solute that has been dissolved in a given volume of solution.

Matter Combined: Chemical Bonds

• Chemical Bonds: The attractive forces that hold atoms together.

• Bond Formation: The formation of bonds is primarily dependent on the $\text{\# of electrons in outer shell}$.

• Ionic Bonds: These are formed through the electrostatic attraction between cations (positively charged ions) and anions (negatively charged ions).

  • Ionic Compounds: These typically exist as solids and have the property of dissociating easily when placed in water.

• Covalent Bonds: These are the most common and the strongest chemical bonds found within the human body.

  • Mechanism: They are formed when atoms share $1$, $2$, or $3$ pairs of electrons.

  • Nonpolar Covalent Bond: Characterized by the equal sharing of electrons between atoms.

  • Polar Covalent Bond: Characterized by the unequal sharing of electrons. The most common example of this is water ($H_2O$).

• Hydrogen Bonds: These are weak attractions useful for linking different molecules to one another rather than forming new molecules.

Types of Chemical Reactions

• Chemical reactions occur whenever chemical bonds are either formed or broken.

• Synthesis (Anabolism): A reaction where two or more substances combine to form a new, larger molecule.

  • Formula: $A + B \rightarrow AB$

• Decomposition (Catabolism): A reaction where a larger molecule is broken down into smaller constituent parts.

  • Formula: $AB \rightarrow A + B$

• Reversible Reactions: Biological reactions that can proceed in either direction depending on the conditions.

  • Formula: $A + B \rightleftharpoons AB$

• Exchange Reactions: Reactions involving the replacement of one atom or group of atoms by another.

  • Formula: $A + BC \rightarrow AB + C$

Energy and Chemical Reactions

• Energy: Defined as the capacity to perform work.

• Exergonic Reactions: Chemical reactions that result in the release of energy.

• Endergonic Reactions: Chemical reactions that require an input of energy to proceed.

• Activation Energy: The minimum amount of energy required for a specific chemical reaction to occur.

Catalysts and Enzymes

• Catalysts: Substances that speed up the rate of chemical reactions by lowering the required activation energy.

• Enzymes: Biological catalysts that accelerate the rate of reactions within the body.

  • Specificity: Enzymes are highly specific to the type of substrate involved in a reaction; this specificity is determined by the unique shape of the enzyme.

  • Persistence: Enzymes are not consumed or changed by the chemical reactions they catalyze.

Inorganic vs. Organic Compounds

• Inorganic Compounds:

  • Characterized by having no chains of carbon-hydrogen ($C-H$) bonds.

  • Contain either ionic or covalent bonds.

  • Examples include water, salts, acids, and bases.

• Organic Compounds:

  • Always contain chains of $C-H$ bonds.

  • Usually contain Oxygen ($O$).

  • Are characterized by covalent bonding.

Inorganic Compounds: Water

• Polar Bonds: Water features polar covalent bonds, which is the key to its biological importance.

• Solvent Properties: It acts as a solvent that easily dissolves hydrophilic (water-loving) substances.

• Metabolism: Most metabolic reactions in the body utilize water molecules.

• Thermal Properties: Water possesses a high heat capacity and a high heat of vaporization, helping to regulate body temperature.

• Physical Protection: Water provides essential lubrication and cushioning for various body parts.

Acids, Bases, and Salts

• Dissociation: The process by which a compound separates into its constituent ions when in a solution.

• Acid: A substance that dissociates into Hydrogen ions ($H^+$) and one or more anions.

• Bases: Substances that dissociate into Hydroxide ions ($OH^-$) and one or more cations.

• Salts: Substances that dissociate into cations and anions, but importantly, do not form $H^+$ or $OH^-$ ions.

pH and Buffer Systems

• pH: A measure of the concentration of $H^+$ ions in a solution.

• Impact: pH levels significantly affect the speed and rate of chemical reactions.

• Homeostasis: The maintenance of internal stability depends heavily on a balanced pH.

• Buffers: Chemical systems that maintain pH stability by converting strong acids or strong bases into weak acids or weak bases.

Organic Compounds: Characteristics and Reactions

• Carbon: The backbone of organic chemistry, carbon can form up to $4$ covalent bonds. It is not readily soluble in water.

• Dehydration Reactions: Anabolic processes that link monomers together to form polymers by removing a water molecule.

• Hydrolysis Reactions: Catabolic processes that break polymers apart into monomers by adding a water molecule.

Organic Compounds: Carbohydrates

• Elemental Composition: Contain Carbon ($C$), Hydrogen ($H$), and Oxygen ($O$) in a specific ratio of $1:2:1$.

• Body Mass: Comprise $2-3\%$ of total body mass.

• Function: Provide the vast majority of energy required for life processes.

• Monosaccharides: Single-molecule sugars, which can exist in pentose (5-carbon) and hexose (6-carbon) forms.

• Disaccharides: Formed when two monosaccharide molecules are bonded together.

• Polysaccharides: Complex molecules that may contain hundreds of monosaccharides.

  • Characterized by an increased amount of stored energy.

  • Glycogen: The primary storage form of glucose in animals.

  • Starch: The primary storage form of glucose in plants.

  • Fiber (Cellulose): The structural form of carbohydrates found in plants.

Organic Compounds: Lipids

• Elemental Composition: Contain $C$, $H$, and $O$, but crucially do NOT follow the $1:2:1$ ratio.

• Body Mass: Comprise $18-25\%$ of total body mass.

• Polarity: Possess very few polar covalent bonds, making them hydrophobic (insoluble in water).

• Triglyceride: Consists of three fatty acid chains attached to a glycerol backbone; can be saturated or unsaturated.

• Phospholipids: Consist of two fatty acid chains and a phosphate group; they form the lipid bilayer of cell membranes.

• Cholesterol: Composed of four rings of carbon atoms; vital for cell membranes and the production of certain hormones.

Organic Compounds: Proteins

• Elemental Composition: Contain Carbon ($C$), Hydrogen ($H$), Oxygen ($O$), and Nitrogen ($N$).

• Body Mass: Comprise $12-18\%$ of total body mass.

• Functions: Involved in regulation, protection, contraction, and transport.

• Building Blocks: Constructed from a set of $20$ different amino acids.

  • Dipeptide: Two amino acids joined by a peptide bond.

  • Polypeptide: Chains consisting of up to thousands of amino acids.

Organic Compounds: Nucleic Acids

• Elemental Composition: Contain $C$, $H$, $O$, $N$, and Phosphorus ($P$).

• Nucleotide: The basic structural unit of a nucleic acid which contains:

  1. A nitrogenous base.

  2. A pentose sugar.

  3. A phosphate group.

• Types:

  • Deoxyribonucleic acid (DNA).

  • Ribonucleic acid (RNA).

Organic Compounds: Adenosine Triphosphate (ATP)

• Structure: Composed of $3$ phosphate groups, a $5$-carbon sugar, and Adenosine (a nitrogenous base).

• Function: Acts as the primary chemical currency of the cell, providing the necessary energy for cellular work.