General Biology Core Concepts and Learning Objectives Study Guide

Chemical Bonds and Water

Types of Chemical Bonds and Interactions

Chemical bonds are forces that hold atoms together in molecules and compounds. The type of bond formed depends on the atoms' electronegativity and electron configuration.

• Nonpolar Covalent Bonds: Electrons are shared equally between atoms (e.g., O2, H2).

• Polar Covalent Bonds: Electrons are shared unequally, resulting in partial charges (e.g., H2O).

• Ionic Bonds: Electrons are transferred from one atom to another, creating ions (e.g., NaCl).

• Hydrogen Bonds: Weak attractions between a hydrogen atom covalently bonded to an electronegative atom (like O or N) and another electronegative atom.

Bond strength and mechanisms depend on the atoms' structure and electronegativity differences. Basic atomic structure, such as the number of valence electrons, influences bond formation and strength.

Bonds in Water Molecules

Within a single water molecule, the bonds are polar covalent due to the difference in electronegativity between hydrogen and oxygen. Between water molecules, hydrogen bonds form due to the attraction between the partial positive charge on hydrogen and the partial negative charge on oxygen.

Properties of Water and Hydrogen Bonding

Hydrogen bonding and other properties of water (including hydrophobic interactions) contribute to:

• Sweating: Evaporation of water cools the body due to high heat of vaporization.

• Cohesion/Adhesion/Surface Tension: Water molecules stick to each other and to other surfaces, allowing capillary action.

• Moderation of Coastal Climate: Water's high specific heat stabilizes temperatures.

• Oceans' Response to Global Warming: Water absorbs heat, buffering climate changes.

Acids, Bases, and pH

Acids donate protons (H+), while bases accept protons. The pH scale measures the concentration of H+ ions in a solution:

• pH < 7: Acidic (e.g., gastric juice)

• pH = 7: Neutral (pure water)

• pH > 7: Basic (e.g., bleach)

The pH is calculated as:

$\text{pH} = -\log_{10}[\text{H}^+]$

Chemical Properties of Carbon

Carbon's tetravalency allows it to form four covalent bonds, enabling the creation of diverse and complex molecules essential for life.

Chemical Functional Groups

Functional groups are specific groups of atoms within molecules that confer characteristic chemical properties. Examples include:

• Hydroxyl (-OH): Polar, forms hydrogen bonds.

• Carboxyl (-COOH): Acts as an acid.

• Amino (-NH2): Acts as a base.

• Phosphate (-PO4): Involved in energy transfer.

These groups affect molecule polarity, reactivity, and interactions.

Polymers and Monomers

Polymers are large molecules made by joining monomers through dehydration (condensation) reactions, which remove water to form covalent bonds. Hydrolysis breaks polymers into monomers by adding water.

• Dehydration: Monomer + Monomer → Polymer + H2O

• Hydrolysis: Polymer + H2O → Monomer + Monomer

Proteins

Protein Monomers and Polymerization

Amino acids are the monomers of proteins. They polymerize via peptide bonds (a type of covalent bond) formed between the amino group of one amino acid and the carboxyl group of another.

Core Structural Components of Amino Acids

• A central carbon (α-carbon)

• Amino group (-NH2)

• Carboxyl group (-COOH)

• Hydrogen atom

• R group (side chain, variable)

Chemical Properties of Amino Acid R Groups

The R group determines the amino acid's properties:

• Nonpolar (hydrophobic)

• Polar (hydrophilic)

• Acidic (negatively charged)

• Basic (positively charged)

Levels of Protein Structure

• Primary: Sequence of amino acids (peptide bonds)

• Secondary: Local folding (α-helix, β-sheet) stabilized by hydrogen bonds

• Tertiary: 3D shape stabilized by interactions among R groups (hydrophobic, ionic, disulfide bridges)

• Quaternary: Association of multiple polypeptide chains

Protein Folding and Function

Proper folding is essential for protein function (e.g., enzymes, transport, signaling). Misfolding can lead to loss of function or disease. Molecular chaperones assist in correct folding.

Nucleic Acids

Nucleotide Monomers and Polymerization

Nucleotides are the monomers of nucleic acids (DNA and RNA). They polymerize via phosphodiester bonds between the phosphate group of one nucleotide and the sugar of another.

Base Pairing and Double Helix Structure

DNA's secondary structure is a double helix stabilized by hydrogen bonds between complementary bases:

• Adenine (A) pairs with Thymine (T)

• Guanine (G) pairs with Cytosine (C)

Base pairing ensures accurate DNA replication and function.

Lipids and Membranes

Types of Lipids

• Fats (triglycerides): Glycerol + 3 fatty acids; energy storage

• Phospholipids: Glycerol + 2 fatty acids + phosphate group; major component of cell membranes

• Steroids: Four fused carbon rings; hormones and membrane structure (e.g., cholesterol)

Saturated vs. Unsaturated Fatty Acids

• Saturated: No double bonds; straight chains; solid at room temperature

• Unsaturated: One or more double bonds; kinked chains; liquid at room temperature

Phospholipid Bilayers

Phospholipids have hydrophilic heads and hydrophobic tails. In water, they spontaneously form bilayers, creating the basic structure of cell membranes.

Membrane Fluidity and Permeability

Membrane fluidity is influenced by fatty acid saturation and cholesterol content. More unsaturated fatty acids and cholesterol increase fluidity and permeability.

Membrane Transport

Diffusion, Osmosis, and Facilitated Diffusion

• Diffusion: Movement of molecules from high to low concentration

• Osmosis: Diffusion of water across a selectively permeable membrane

• Facilitated Diffusion: Movement of molecules via transport proteins

Passive vs. Active Transport

• Passive Transport: No energy required; moves down concentration gradient

• Active Transport: Requires energy (ATP); moves against concentration gradient

Membrane Proteins and Transport

• Integral Proteins: Span the membrane; involved in transport

• Peripheral Proteins: Attached to membrane surface

Carbohydrates and lipids are also present, contributing to cell recognition and signaling.

Permeability of Ions and Molecules

Nonpolar molecules cross membranes easily; ions and polar molecules require transport proteins. The rate of crossing depends on size, polarity, and charge.

Carbohydrates

Monosaccharides and Polymerization

Monosaccharides (simple sugars) are the monomers of carbohydrates. They polymerize via glycosidic bonds to form polysaccharides (e.g., starch, cellulose).

Roles of Carbohydrates

• Energy storage (e.g., glycogen, starch)

• Structural support (e.g., cellulose in plants, chitin in fungi)

• Cell recognition and signaling

Comparison of Biological Macromolecules

Macromolecule	Monomer	Bond Type	Main Functions
Proteins	Amino acids	Peptide bond	Enzymes, structure, transport, signaling
Nucleic acids	Nucleotides	Phosphodiester bond	Genetic information storage and transfer
Carbohydrates	Monosaccharides	Glycosidic bond	Energy storage, structure, recognition
Lipids	Fatty acids, glycerol	Ester bond	Membranes, energy storage, signaling

Cell Structure and Function

Prokaryotic vs. Eukaryotic Cells

• Prokaryotes: No nucleus, no membrane-bound organelles (e.g., bacteria, archaea)

• Eukaryotes: Nucleus and membrane-bound organelles (e.g., plants, animals, fungi, protists)

Significance of Organelles

Organelles compartmentalize cellular functions, increasing efficiency. They are more common in eukaryotes due to larger cell size and complexity.

Plant vs. Animal Cells

• Plant cells: Have cell walls, chloroplasts, and large central vacuoles

• Animal cells: Lack cell walls and chloroplasts, have small vacuoles

Endomembrane System

Includes the endoplasmic reticulum, Golgi apparatus, lysosomes, and vesicles. Responsible for synthesis, sorting, and transport of proteins and lipids.

Cytoskeleton

Component	Structure	Function
Microtubules	Hollow tubes	Cell shape, transport, chromosome movement
Actin filaments (microfilaments)	Thin, solid rods	Cell movement, muscle contraction
Intermediate filaments	Fibrous proteins	Structural support, cell stability

Example: Microtubules form the mitotic spindle during cell division; actin filaments are involved in muscle contraction; intermediate filaments provide mechanical strength to cells.