General Biology: Chemical Foundations, Macromolecules, and Nucleic Acids Study Guide

Chemical Bonds and Properties of Water

Types of Chemical Bonds

Chemical bonds are the forces that hold atoms together in molecules and compounds. The main types are:

• Covalent Bonds: Atoms share electrons. Can be polar (unequal sharing) or nonpolar (equal sharing).

• Ionic Bonds: Atoms transfer electrons, resulting in oppositely charged ions that attract each other.

Hydrogen Bonds

Hydrogen bonds are weak attractions between a hydrogen atom covalently bonded to an electronegative atom (like oxygen or nitrogen) and another electronegative atom. They are crucial in stabilizing biological molecules.

• Example: Hydrogen bonds between water molecules.

Polarity of Water

Water is a polar covalent molecule because oxygen is more electronegative than hydrogen, causing an unequal sharing of electrons.

• Polarity leads to partial positive (H) and partial negative (O) charges.

Properties of Water Due to Hydrogen Bonds

Water's unique properties arise from its polarity and hydrogen bonding:

• Cohesion and Adhesion: Cohesion is water molecules sticking to each other; adhesion is sticking to other surfaces.

• Surface Tension: Water's surface resists external force due to cohesive hydrogen bonds.

• High Specific Heat: Water absorbs heat without a large temperature increase.

• High Heat of Vaporization: Requires significant energy to convert water from liquid to gas.

• Density of Water: Ice is less dense than liquid water due to hydrogen bond arrangement.

pH, Buffers, and Functional Groups

pH and Buffers

pH measures the concentration of hydrogen ions in a solution. Buffers are substances that help maintain a stable pH in biological systems.

• Importance: Enzyme activity and cellular processes require specific pH ranges.

• Physiological Buffer Example: Bicarbonate buffer system in blood.

Functional Groups

Functional groups are specific groups of atoms within molecules that determine their chemical properties and reactivity.

• Examples: Hydroxyl (-OH), carboxyl (-COOH), amino (-NH2), phosphate (-PO4).

• Polarity of functional groups affects solubility and interactions.

Atoms, Elements, and Macromolecules

Atoms and Elements

Atoms are the basic units of matter, composed of protons, neutrons, and electrons. Elements are pure substances consisting of one type of atom.

• Valence Electrons: Electrons in the outer shell that determine chemical reactivity.

• Major Biological Elements: Carbon, hydrogen, oxygen, nitrogen, phosphorus, sulfur.

Dehydration and Hydrolysis Reactions

Macromolecules are formed and broken down by specific chemical reactions:

• Dehydration (Condensation) Reaction: Joins monomers by removing water.

• Hydrolysis Reaction: Breaks polymers into monomers by adding water.

Carbohydrates

Structure and Function

Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen. They serve as energy sources and structural components.

• Monosaccharides: Simple sugars (e.g., glucose).

• Disaccharides: Two monosaccharides joined (e.g., sucrose).

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

Types of Linkages

• Alpha and Beta Linkages: Refer to the orientation of the glycosidic bond between monosaccharides.

Starch vs. Cellulose

• Starch: Storage polysaccharide in plants; contains alpha linkages.

• Cellulose: Structural polysaccharide in plants; contains beta linkages.

• Glycogen: Storage polysaccharide in animals.

Comparison Table: Starch vs. Cellulose

Property	Starch	Cellulose
Type of Bond	Alpha (1→4) glycosidic	Beta (1→4) glycosidic
Function	Energy storage in plants	Structural support in plants
Digestibility	Digestible by humans	Not digestible by humans

Lipids

Structure and Function

Lipids are hydrophobic molecules including fats, oils, and steroids. They are important for energy storage, membrane structure, and signaling.

• Linkages: Ester bonds between glycerol and fatty acids.

• Types: Triglycerides, phospholipids, steroids.

Proteins

Structure and Levels of Folding

Proteins are polymers of amino acids. Their function depends on their structure, which is organized into four levels:

Level of Folding	Description	Types of Bonds
Primary	Sequence of amino acids	Peptide bonds
Secondary	Local folding (alpha helix, beta sheet)	Hydrogen bonds
Tertiary	Overall 3D shape	Hydrogen, ionic, disulfide, hydrophobic interactions
Quaternary	Multiple polypeptides	Same as tertiary

• Peptide Bond: Covalent bond between amino acids ($\text{Peptide bond:} \ \text{CO-NH}$).

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

Nucleic Acids

Structure and Function

Nucleic acids (DNA and RNA) store and transmit genetic information. They are polymers of nucleotides.

• Monomers: Nucleotides (composed of a pentose sugar, phosphate group, and nitrogenous base).

• DNA: Double-stranded, contains deoxyribose, bases A, T, C, G.

• RNA: Single-stranded, contains ribose, bases A, U, C, G.

Comparison Table: DNA vs. RNA

Property	DNA	RNA
Pentose Sugar	Deoxyribose	Ribose
Nitrogenous Base	A, T, C, G	A, U, C, G
Strandedness	Double-stranded	Single-stranded
Traditionally	Genetic storage	Protein synthesis, regulation
Directionality	5' to 3'	5' to 3'

• Chargaff's Rule: In DNA, the amount of adenine equals thymine, and cytosine equals guanine ($[A] = [T], [C] = [G]$).

• Hydrogen Bonds: Hold base pairs together (A-T: 2 bonds, C-G: 3 bonds).

• Denaturation: DNA strands separate at high temperature.

Experiments: Key experiments (e.g., Hershey-Chase, Watson-Crick) elucidated DNA structure.

Additional info: The notes infer some context about the importance of macromolecules and their chemical properties in biological systems.