General Biology Study Notes: Atoms, Chemical Bonds, Water, Macromolecules, and Biological Molecules

Atoms and Atomic Structure

Definition and Properties of Atoms

Atoms are the fundamental units of matter, retaining the properties of elements. They are composed of subatomic particles and are electrically neutral when the number of protons equals the number of electrons.

• Subatomic particles can be defined by their location, charge, and mass:

  • Proton: Mass of 1, positive charge (+1)

  • Neutron: Mass of 1, no charge (neutral)

  • Electron: Negligible mass, negative charge (-1)

• Atoms are organized in the periodic table by their properties.

• Six elements (C, H, O, N, P, S) are the fundamental molecular components of all organisms.

Isotopes

Isotopes are atoms of the same element with the same number of protons but different numbers of neutrons. Some isotopes are stable, while others are radioactive.

• Most elements have several isotopes; most are stable.

• Some isotopes have special names (e.g., 1H, 2H, 3H for hydrogen).

• Example: Carbon isotopes: 12C (6 neutrons), 13C (7 neutrons), 14C (8 neutrons).

Electrons and Chemical Behavior

Electrons occupy energy levels (shells) around the nucleus. The arrangement of electrons determines how atoms interact and bond.

• Outermost electron shell (valence shell) determines chemical reactivity.

• Atoms are stable when their outermost shell is full (octet rule: 8 electrons).

• Atoms with unfilled valence shells are reactive.

• The energy level of each shell increases with distance from the nucleus.

Elements, Molecules, and Compounds

Definitions

• Element: Pure substance containing only one kind of atom.

• Molecule: Electrically neutral group of two or more atoms held together by chemical bonds (e.g., O2).

• Compound: Molecule made up of two or more different elements in a fixed ratio (e.g., H2O, NaCl).

• Molecular weight: Sum of atomic weights of all atoms in a molecule.

Chemical Bonds

Types of Chemical Bonds

Chemical bonds are attractive forces that link two atoms together, forming molecules.

• Covalent Bonds: Shared pairs of electrons between atoms.

  • Polar covalent: Unequal sharing of electrons (atoms differ in electronegativity).

  • Nonpolar covalent: Equal sharing of electrons (atoms have similar electronegativity).

• Ionic Bonds: Attraction between oppositely charged ions (cations and anions).

• Hydrogen Bonds: Weak bonds between polar molecules, especially involving hydrogen and electronegative atoms (e.g., O, N).

Electronegativity

• Electronegativity is the ability of an atom to attract electrons in a bond.

• The more electronegative an atom, the more strongly it pulls shared electrons toward itself.

Ions

• Cation: Positively charged ion.

• Anion: Negatively charged ion.

• Ionic compounds are formed by the electrical attraction of positive and negative ions.

• Ions can interact with polar molecules (e.g., salts dissolve in water).

Chemical Reactions

Nature of Chemical Reactions

• Chemical reactions involve the making and breaking of chemical bonds.

• Reactants are the starting substances; products are the final substances.

• Law of Conservation of Matter: Chemical reactions cannot create or destroy matter (1st law of thermodynamics).

Water and Its Properties

Importance of Water

• Water is a polar molecule, making it a universal solvent for life.

• Water is essential for most biochemical reactions.

• Water's covalent bonds are polar.

Hydrogen Bonding in Water

• Polar molecules form hydrogen bonds with water (hydrophilic).

• Nonpolar molecules (hydrophobic) do not interact well with water.

• Hydrogen bonds give water unique properties (cohesion, adhesion, high specific heat).

Special Properties of Water

• Cohesion: Water molecules stick together.

• Surface tension: Water molecules at the surface are hydrogen-bonded to those below.

• High specific heat: Water resists changes in temperature.

• High heat of vaporization: Large amount of energy required to change water from liquid to gas.

• Ice floats: Solid water is less dense than liquid water due to hydrogen bonding.

Water as Acid and Base

• Water can act as both a weak acid and a weak base:

• $H_2O \rightleftharpoons H^+ + OH^-$

• $pH = -\log[H^+]$

• Ionization of water is important for biological reactions.

Acids, Bases, and pH

Definitions

• Acids: Release hydrogen ions (H+) in solution.

• Bases: Accept hydrogen ions or release hydroxide ions (OH-).

• pH scale: Measures the concentration of H+ ions; lower pH = more acidic, higher pH = more basic.

• Most biological fluids have pH values in the range of 6 to 8.

Biological Importance of pH

• pH influences the rates of biological reactions.

• pH can change the 3-D structure of biological molecules.

• Buffers help maintain constant pH by absorbing or releasing H+ or OH-.

Macromolecules

Introduction to Macromolecules

Macromolecules are large, complex molecules essential for life, including proteins, carbohydrates, nucleic acids, and lipids. They are typically polymers made from repeating monomer units.

Carbon Chemistry

• Carbon can form four covalent bonds, allowing for diverse and complex molecules.

• Carbon chains form the skeletons of most organic molecules.

• Carbon chains vary in length and shape.

Isomers

• Structural isomers: Same chemical formula, different bonding arrangement.

• Optical isomers: Mirror images of each other.

Functional Groups

• Groups of atoms that confer specific chemical properties to molecules.

• Determine the shape and reactivity of molecules.

Monomers and Polymers

• Monomers are joined by condensation reactions (dehydration synthesis), releasing water.

• Polymers are broken down by hydrolysis reactions, which consume water.

Carbohydrates

Types and Functions

• Monosaccharides: Simple sugars (3-7 carbons), general formula: (C1H2O1)n

• Disaccharides: Two monosaccharides linked by glycosidic bonds (e.g., maltose, sucrose, lactose).

• Oligosaccharides: 3-20 monosaccharide units, often involved in cell recognition.

• Polysaccharides: Long chains of monosaccharides (e.g., starch, glycogen, cellulose, chitin).

• Polysaccharides serve as energy storage (starch in plants, glycogen in animals) and structural components (cellulose in plants, chitin in fungi and arthropods).

Nucleic Acids

Structure and Function

• DNA and RNA: Store, transmit, and use genetic information.

• Monomer: Nucleotide; Polymer: Nucleic acid.

• Nucleotides are linked by phosphodiester bonds (phosphate group links 3' carbon of one sugar to 5' carbon of the next).

• DNA is double-stranded, RNA is usually single-stranded.

• Bases: A, G, C, T (DNA); A, G, C, U (RNA).

• DNA stores hereditary information; RNA is involved in protein synthesis.

DNA Structure

• Double helix: Sides are sugar-phosphate backbone; rungs are nitrogenous base pairs held by hydrogen bonds.

• Chargaff's rules: A pairs with T, G pairs with C.

Lipids

Types and Functions

• Fatty acids: Nonpolar hydrocarbon chains with a polar carboxyl group.

• Saturated fatty acids: No double bonds, solid at room temperature.

• Unsaturated fatty acids: One or more double bonds, liquid at room temperature.

• Lipids are hydrophobic and not polymers.

• Major types:

  • Fats and oils (triglycerides): Glycerol + 3 fatty acids (ester linkage).

  • Phospholipids: Major components of cell membranes; amphipathic (hydrophilic head, hydrophobic tails).

  • Steroids: Four fused carbon rings (e.g., cholesterol, hormones).

  • Vitamins: Some are lipid-soluble and must be acquired from diet.

Proteins

Structure and Function

• Proteins are polymers of amino acids joined by peptide bonds.

• Most abundant macromolecule type in cells.

• Functions include:

  • Enzymatic proteins: Catalyze chemical reactions (e.g., digestive enzymes).

  • Defensive proteins: Protect against disease (e.g., antibodies).

  • Storage proteins: Store amino acids (e.g., casein in milk, plant seed proteins).

  • Transport proteins: Transport substances (e.g., hemoglobin transports oxygen).

  • Signal proteins: Coordination of organism's activities (e.g., hormones).

Summary Table: Types of Biological Macromolecules

Macromolecule	Monomer	Bond Type	Main Functions
Carbohydrates	Monosaccharide	Glycosidic linkage	Energy storage, structure
Nucleic Acids	Nucleotide	Phosphodiester bond	Genetic information storage and transfer
Proteins	Amino acid	Peptide bond	Catalysis, structure, transport, defense
Lipids	Fatty acid, glycerol (not true polymers)	Ester linkage	Energy storage, membranes, signaling