General Biology: Core Concepts, Chemistry of Life, and Biological Molecules

Five Unifying Themes of Biology

Emergent Properties: Result from the Arrangement and Interactions of Parts as Complexity Increases

Emergent properties are new characteristics that arise at each level of biological organization due to the arrangement and interactions of components.

• Example: Hydrogen and oxygen combine to make water; parts of a bicycle form a functioning whole.

• Reductionist Approach: Studies simpler components of living systems, but systems biology examines interactions among parts.

• Selective Permeability: An example of an emergent property in cell membranes.

Within Cells, Structures Called Chromosomes Contain Genetic Material in the Form of DNA

Genetic information is stored in DNA, which is organized into chromosomes. Each chromosome contains one long DNA molecule consisting of thousands of genes.

• Genes: Units of inheritance transmitted from parent to offspring.

• Gene Expression: The central dogma of biology; DNA is transcribed to RNA, which is translated to protein.

Life Requires the Transfer and Transformation of Energy

All living organisms require energy to perform work. Energy transfer and transformation are fundamental to biological processes.

• Photosynthesis: Plants convert solar energy into chemical energy.

• Feedback Regulation: Mechanisms that regulate biological systems, such as negative feedback in blood glucose regulation.

From Molecules to Ecosystems, Interactions Are Important in Biological Systems

• Molecules: Interactions within organisms (e.g., between proteins, DNA, and other molecules).

• Cells: Interactions between organelles and molecules.

• Organisms: Interactions with other organisms and the environment.

• Ecosystems: Interactions among organisms and with physical factors (soil, air, water).

• Example: High blood glucose stimulates the pancreas to secrete insulin, which lowers blood glucose by promoting uptake in body cells and storage in the liver.

Levels of Biological Organization

Hierarchy of Life

• Biosphere: All life on Earth and all places where life exists.

• Ecosystems: All living things in a particular area, plus nonliving components (soil, water, atmosphere).

• Communities: Array of organisms inhabiting an ecosystem.

• Populations: All individuals of a species in a specific area.

• Organisms: Individual living things.

• Organs and Organ Systems: Body parts with specific functions.

• Tissues: Groups of cells working together.

• Cells: Fundamental unit of structure and function.

• Organelles: Functional components within cells (e.g., chloroplasts).

• Molecules: Chemical structures consisting of two or more atoms.

Gene Expression

Genetic Information and Its Use

• Cells use information encoded in genes to synthesize functional proteins.

• Differences between organisms reflect differences in nucleotide sequences, not genetic codes.

• The complete set of genetic instructions in an organism is called its genome.

Matter, Elements, and Compounds

Basic Chemical Concepts

• Matter: Anything that takes up space and has mass (e.g., rocks, metals, water, gases).

• Element: A substance that cannot be broken down by chemical reactions.

• Compound: A substance consisting of two or more different elements combined in a fixed ratio (e.g., NaCl).

Subatomic Particles

• Proton: Positive charge.

• Electron: Negative charge.

• Neutron: No charge.

• Atomic Number: Number of protons in an atom.

• Mass Number: Number of protons plus neutrons.

• Number of Neutrons: $\text{Mass number} - \text{Atomic number}$

Valence Electrons

• The chemical behavior of an atom depends mostly on the number of electrons in its outermost shell (valence electrons).

Chemical Bonds

Types of Chemical Bonds

• Covalent Bond: Sharing of a pair of valence electrons by two atoms.

• Single Bond: One pair of shared electrons ($\text{H}—\text{H}$).

• Double Bond: Two pairs of shared electrons ($\text{O}=\text{O}$).

• Electronegativity: Attraction of an atom for electrons in a covalent bond.

• Nonpolar Covalent Bond: Electrons shared equally (e.g., $\text{O}_2$).

• Polar Covalent Bond: Electrons shared unequally due to differences in electronegativity (e.g., $\text{H}_2\text{O}$).

• Ionic Bond: Attraction between oppositely charged ions (cation and anion).

• Hydrogen Bond: Weak bond between a hydrogen atom covalently bonded to an electronegative atom and another electronegative atom.

• Van der Waals Interactions: Weak attractions between molecules or parts of molecules that result from transient local partial charges.

Properties of Water

Cohesive and Adhesive Behavior

• Cohesion: Water molecules stick together via hydrogen bonds, contributing to surface tension.

• Adhesion: Water molecules stick to other substances, aiding movement of water against gravity in plants.

Ability to Moderate Temperature

• Kinetic Energy: Energy of motion; atoms and molecules are always moving.

• Thermal Energy: Total kinetic energy due to molecular motion.

• Specific Heat: Amount of heat required to raise 1g of a substance by 1°C.

• Water's High Specific Heat: Helps moderate Earth's climate and organismal temperature.

Expansion Upon Freezing

• Water expands as it freezes due to hydrogen bonding, making ice less dense than liquid water.

• Importance: Ice floats, insulating bodies of water and protecting aquatic life.

Versatility as a Solvent

• Solution: Liquid that is a homogeneous mixture of two or more substances.

• Solvent: The dissolving agent (e.g., water).

• Solute: The substance dissolved.

Acids, Bases, and pH

Definitions

• Acid: Substance that increases H+ concentration in a solution (e.g., HCl).

• Base: Substance that reduces H+ concentration (e.g., NH3).

• pH Scale: Numeric scale expressing H+ concentration; $\text{pH} = -\log[\text{H}^+]$.

• Acidic Solutions: pH < 7 (e.g., lemon juice, urine).

• Basic Solutions: pH > 7 (e.g., seawater, household bleach).

• Neutral Solutions: pH = 7 (e.g., pure water, human blood).

Organic Molecules and Carbon Chemistry

Stanley Miller Experiment

• Demonstrated that organic molecules could form under prebiotic conditions, supporting the idea of abiotic synthesis of life's building blocks.

Carbon Skeletons and Functional Groups

• Carbon skeletons can be straight, branched, or arranged in rings.

• Functional groups confer specific chemical properties to organic molecules.

Functional Group	Structure	Properties/Examples
Hydroxyl (–OH)	Alcohols	Increases solubility in water (e.g., ethanol)
Carbonyl (C=O)	Ketones/Aldehydes	Found in sugars
Amino (–NH2)	Amines	Acts as a base (e.g., amino acids)
Phosphate (–OPO32–)	Organic phosphates	Involved in energy transfer (e.g., ATP)
Methyl (–CH3)	Methylated compounds	Affects gene expression

Isomers

• Structural Isomers: Differ in covalent arrangements of atoms.

• Cis-Trans Isomers: Differ in arrangement around a double bond.

• Enantiomers: Mirror-image isomers; important in pharmaceuticals.

Classes of Biological Molecules

Carbohydrates

• Polymers of sugar monomers (e.g., glucose).

• Serve as energy sources and structural support.

• Carbohydrates often depicted as chains of hexagonal rings.

Proteins

• Composed of amino acid monomers.

• Diverse structures and functions, including catalysis (enzymes), transport, and support.

Nucleic Acids

• DNA and RNA; polymers of nucleotide monomers.

• Store and transmit genetic information.

• Double helix structure for DNA.

Lipids

• Not true polymers; hydrophobic molecules used for energy storage, cell membranes, and hormones.

• Include fats, phospholipids, and steroids.

Dehydration Synthesis and Hydrolysis

• Dehydration Synthesis: Joins monomers by removing water; forms polymers.

• Hydrolysis: Breaks polymers into monomers by adding water.

Additional info: Some explanations and examples were expanded for clarity and completeness based on standard biology curriculum.