Biology 1306: Study Guide for Chapters 1–3 (The Study of Life, Chemical Basis of Life, Protein Structure and Function)

Biology: The Study of Life

Five Fundamental Characteristics of Living Organisms

• Cells: All living things are composed of one or more cells, which are the basic units of life.

• Replication: Living organisms are capable of reproduction, passing genetic information to offspring.

• Information: Organisms process hereditary information encoded in genes as well as information from the environment.

• Energy: All organisms acquire and use energy to maintain internal order and support life processes.

• Evolution: Populations of organisms evolve over time through changes in genetic makeup.

The Cell and Cell Theory

• Cell: The smallest unit of life that can perform all life processes.

• Cell Theory: States that all living things are composed of cells and all cells come from pre-existing cells.

• Prokaryotic Cells: Cells lacking a nucleus and membrane-bound organelles (e.g., Bacteria and Archaea).

• Eukaryotic Cells: Cells with a nucleus and membrane-bound organelles (e.g., Plants, Animals, Fungi, Protists).

Louis Pasteur’s Experiment and Spontaneous Generation

• Spontaneous Generation: The (disproven) idea that living organisms can arise from nonliving matter.

• Pasteur’s Experiment: Used swan-necked flasks to show that cells arise from pre-existing cells, not spontaneously.

• Conclusion: Supported the cell theory and refuted spontaneous generation.

Theory vs. Scientific Hypothesis

• Theory: A broad explanation for a wide range of phenomena, supported by a large body of evidence.

• Hypothesis: A testable, specific prediction about the outcome of an experiment or observation.

Food Competition Hypothesis (Giraffe Experiment)

• Proposes that giraffes evolved long necks to compete for food in tall trees.

• Tested by observing feeding behavior and food availability.

Phylogenetic Trees

• Definition: Diagrams showing evolutionary relationships among species.

• Reading Trees: Branch points represent common ancestors; closer branches indicate closer relationships.

Three Domains of Life

• Bacteria

• Archaea

• Eukarya

Evolutionary Fitness

• Definition: The ability of an organism to survive and reproduce, passing its genes to the next generation.

Natural vs. Artificial Selection

• Natural Selection: Process by which traits that improve survival and reproduction become more common in a population.

• Artificial Selection: Humans select for desirable traits in organisms (e.g., dog breeding).

Good Experimental Design

• Includes controls, replicates, and minimizes bias.

• Variables are clearly defined and only one variable is changed at a time.

Water and Carbon: The Chemical Basis of Life

Types of Chemical Bonds

• Polar Covalent Bonds: Electrons are shared unequally; one atom is more electronegative (e.g., O-H in water).

• Nonpolar Covalent Bonds: Electrons are shared equally (e.g., C-H bonds).

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

• Hydrogen Bonds: Weak attractions between a hydrogen atom (partially positive) and an electronegative atom (e.g., O or N).

• Single Covalent Bond: Involves two electrons (one pair) shared between two atoms.

Atoms, Ions, and Molecules

• Atom: Smallest unit of an element, composed of protons, neutrons, and electrons.

• Ion: Atom or molecule with a net electric charge due to loss or gain of electrons.

• Molecule: Two or more atoms held together by covalent bonds.

Characteristics of Nonpolar Molecules

• Hydrophobic (do not mix with water).

• Even distribution of electrical charge.

Valence Shell and Chemical Reactivity

• Valence Shell: The outermost electron shell of an atom.

• Atoms with incomplete valence shells tend to form bonds to achieve stability.

Atomic Mass and Atomic Number

• Atomic Number: Number of protons in an atom’s nucleus.

• Atomic Mass: Sum of protons and neutrons in the nucleus.

Water: Specific Heat and Heat of Vaporization

• Specific Heat: Amount of energy required to raise the temperature of 1 gram of a substance by 1°C.

• Heat of Vaporization: Energy required to convert 1 gram of a liquid into a gas at boiling point.

• Example: Water has a high specific heat and heat of vaporization, helping organisms maintain stable temperatures.

Representing Molecules

• Molecular Formulas: Show the types and numbers of atoms (e.g., H2O).

• Structural Formulas: Show how atoms are bonded (e.g., H–O–H).

• Ball-and-Stick Models: Show 3D arrangement of atoms.

• Space-Filling Models: Show relative sizes and spatial relationships of atoms.

Electronegativity

• Definition: The tendency of an atom to attract electrons in a bond.

• Determines bond type (polar, nonpolar, ionic).

Chemical Evolution Hypothesis

• Proposes that simple molecules present on early Earth reacted to form more complex molecules, leading to life.

Condensation and Hydrolysis Reactions

• Condensation (Dehydration) Reaction: Two molecules join, releasing water.

• Hydrolysis Reaction: A molecule is split into two by adding water.

Spontaneous vs. Nonspontaneous Reactions

• Spontaneous Reaction: Occurs without external energy input; increases entropy or releases energy.

• Nonspontaneous Reaction: Requires energy input to proceed.

Protein Structure and Function

Functions of Proteins

• Catalysis: Enzymes speed up chemical reactions.

• Defense: Antibodies protect against disease.

• Transport: Move substances across membranes.

• Signaling: Coordinate cellular activities.

• Structure: Provide support (e.g., collagen, keratin).

• Movement: Enable cell and organism movement (e.g., actin, myosin).

Structure of Amino Acids

• Central carbon atom (alpha carbon) bonded to:

  • Amino group (–NH2)

  • Carboxyl group (–COOH)

  • Hydrogen atom

  • R group (side chain, varies among amino acids)

Ionized vs. Non-Ionized Amino Acids

• Non-Ionized: Amino and carboxyl groups are uncharged; occurs in gas phase or non-aqueous environments.

• Ionized: In aqueous solution, amino group gains a proton (+ charge), carboxyl group loses a proton (– charge).

• Conditions: Ionization occurs at physiological pH (around 7).

• Charges: Amino group is positive; carboxyl group is negative.

Levels of Protein Structure

• Primary Structure: Sequence of amino acids in a polypeptide; held by peptide bonds.

• Secondary Structure: Local folding (alpha helices, beta sheets); stabilized by hydrogen bonds.

• Tertiary Structure: 3D shape of a single polypeptide; stabilized by interactions among R groups (hydrogen bonds, ionic bonds, hydrophobic interactions, disulfide bridges).

• Quaternary Structure: Association of multiple polypeptide chains.

• Hierarchy: Each level builds on the previous one.

Peptide Bond

• Definition: Covalent bond formed between the carboxyl group of one amino acid and the amino group of another, releasing water (condensation reaction).

Table: Comparison of Prokaryotic and Eukaryotic Cells

Feature	Prokaryotic Cells	Eukaryotic Cells
Nucleus	Absent	Present
Membrane-bound Organelles	Absent	Present
Size	Generally smaller	Generally larger
Examples	Bacteria, Archaea	Plants, Animals, Fungi, Protists

Key Equations

• Atomic Mass: $\text{Atomic Mass} = \text{Number of Protons} + \text{Number of Neutrons}$

• Spontaneity (Gibbs Free Energy): $\Delta G = \Delta H - T\Delta S$ Where $\Delta G$ is change in free energy, $\Delta H$ is change in enthalpy, $T$ is temperature in Kelvin, and $\Delta S$ is change in entropy.

Summary

• Understanding the characteristics of life, cell theory, and experimental design is foundational for biology.

• Chemical principles such as bonding, molecular structure, and water’s properties are essential for understanding biological molecules.

• Proteins are vital macromolecules with diverse functions, and their structure is hierarchical and determines their function.