BIOL 251 Exam 1 Study Guide: Organization of Life, Chemical Context, and Cells

Chapter 1 – Basic Introduction to the Organization of Life

Cells: The Basic Unit of Life

Cells are the fundamental structural and functional units of all living organisms. Understanding their properties is essential for studying microbiology and biology in general.

• Cell Theory: All living things are composed of cells; cells are the basic unit of life; all cells arise from pre-existing cells.

• DNA: Cells contain DNA, which encodes information for synthesizing cellular products such as proteins.

• Structure-Function Relationship: The structure of biological molecules and cells is closely related to their function.

The Three Domains of Life

Life is classified into three domains based on cellular characteristics and genetic differences.

• Bacteria: Prokaryotic cells lacking a nucleus; diverse metabolic capabilities.

• Archaea: Prokaryotic cells; often found in extreme environments; distinct molecular characteristics.

• Eukarya: Eukaryotic cells with a nucleus and membrane-bound organelles; includes plants, animals, fungi, and protists.

Chapter 2 – The Chemical Context of Life

The Nature of Atoms

Atoms are the smallest units of matter, composed of protons, neutrons, and electrons. Their arrangement determines the properties of elements and molecules.

• Element: Defined by the number of protons in its nucleus.

• Atomic Number: Number of protons in an atom.

• Mass Number: Sum of protons and neutrons.

• Atomic Mass: Average mass of an atom, accounting for isotopes.

• Ions: Atoms with a net charge due to loss or gain of electrons.

• Isotopes: Atoms of the same element with different numbers of neutrons.

• Electron Distribution: Electrons occupy energy levels; valence electrons determine chemical reactivity.

Chemical Bonds, Molecular Shape, and Chemical Reactions

Chemical bonds hold atoms together in molecules, and the shape of molecules is crucial for their biological function.

• Non-polar Covalent Bonds: Electrons are shared equally.

• Polar Covalent Bonds: Electrons are shared unequally, creating partial charges.

• Single vs. Double Covalent Bonds: Single bonds share one pair of electrons; double bonds share two pairs.

• Ionic Bonds: Formed by transfer of electrons, resulting in charged ions.

• Hydrogen Bonds: Weak attractions between partial charges, important in water and biological molecules.

• Molecular Shape: 3-D shape determines function (e.g., enzyme specificity).

• Chemical Reactions: Involve breaking and forming bonds; reactants are transformed into products.

Characteristics and Properties of Water

Water is essential for life due to its unique chemical properties.

• Polar Molecule: Water has partial positive and negative charges due to electronegativity differences.

• Hydrogen Bonding: Water molecules form hydrogen bonds, leading to cohesion, adhesion, and high specific heat.

• Hydration Shell: Water surrounds ions, stabilizing them in solution.

• Solubility: Ability of a substance to dissolve in water; hydrophilic substances dissolve easily, hydrophobic substances do not.

• Aqueous Solution: Solution where water is the solvent.

Acids and Bases

Acids and bases affect the pH of solutions, which is critical for biological processes.

• Acid: Substance that increases hydrogen ion concentration (H+).

• Base: Substance that decreases hydrogen ion concentration.

• Buffer: Substance that minimizes changes in pH.

• pH Scale: Measures hydrogen ion concentration; $\text{pH} = -\log_{10}[H^+]$

• Hydrogen Ions (H+): Determine acidity.

• Hydroxide Ions (OH-): Determine basicity.

Carbon: The Framework of Biological Macromolecules

Carbon atoms form the backbone of biological molecules due to their ability to form multiple covalent bonds.

• Covalent Bonds: Carbon can form up to four simultaneous covalent bonds.

• Isomers: Molecules with the same formula but different structures; includes structural isomers and enantiomers.

• Functional Groups: Specific groups of atoms that confer properties; hydroxyl, carboxyl, amino, and phosphate groups are hydrophilic.

• Hydrophilic vs. Hydrophobic: Functional groups affect solubility and reactivity.

• Biological Macromolecules: Four major types: carbohydrates, proteins, lipids, nucleic acids.

• Monomers and Polymers: Monomers are building blocks; polymers are chains of monomers.

• Dehydration Synthesis: Formation of polymers by removing water.

• Hydrolysis: Breakdown of polymers by adding water.

Carbohydrates: Energy Storage, Fuel, and Structural Molecules

Carbohydrates serve as energy sources and structural components in cells.

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

• Polysaccharides: Long chains; starch (plants), glycogen (animals), cellulose (plant cell walls).

• Structure-Function: The arrangement of sugar units determines their function (energy storage vs. structure).

Lipids: Diverse Group of Hydrophobic Molecules

Lipids are hydrophobic molecules important for energy storage, membrane structure, and signaling.

• Triglycerols: Composed of glycerol and three fatty acids; main energy-storage molecules.

• Saturated vs. Unsaturated Fatty Acids: Saturated have no double bonds; unsaturated have one or more double bonds, affecting fluidity.

• Phospholipids: Form cell membranes; hydrophilic head and hydrophobic tails.

• Steroids: Include cholesterol; important for membrane structure and signaling.

• Waxes: Protective coatings; hydrophobic.

Proteins: Molecules with Diverse Structures and Functions

Proteins are polymers of amino acids with diverse roles in cells.

• Amino Acids: Building blocks; classified as non-polar, polar, or charged.

• Levels of Protein Structure:

  • Primary (1°): Amino acid sequence

  • Secondary (2°): Alpha helices and beta sheets

  • Tertiary (3°): 3D folding

  • Quaternary (4°): Multiple polypeptides

• Structure-Function Relationship: Protein function depends on its structure.

• Major Functions: Enzymes, structural support, transport, signaling, defense; not primarily used for energy storage.

Nucleic Acids: Information Molecules

Nucleic acids store and transmit genetic information and participate in energy conversions.

• Nucleotides: Composed of a sugar (ribose or deoxyribose), phosphate group, and nitrogenous base.

• Polynucleotides: Nucleotides linked by phosphodiester bonds.

• DNA vs. RNA: DNA is double-stranded, contains deoxyribose and thymine; RNA is single-stranded, contains ribose and uracil.

• Other Nucleotides: ATP, NAD+, FAD involved in energy metabolism.

• Key Terms: Deoxyribose, ribose, phosphate group, cytosine (C), thymine (T), uracil (U), adenine (A), guanine (G), sugar-phosphate backbone, double helix, complementary, 5′ end, 3′ end, antiparallel.

Chapter 3 – Cells: The Fundamental Units of Life

Cell Structure and Function

All cells share basic structural features, but there are important differences between prokaryotic and eukaryotic cells.

• Common Features: Plasma membrane, DNA, ribosomes, cytosol.

• Prokaryotic Cells: Lack a nucleus; include Bacteria and Archaea.

• Eukaryotic Cells: Have a nucleus and membrane-bound organelles; include Eukarya.

• Comparison: Bacteria and Archaea are prokaryotes; Eukarya are eukaryotes.

Eukaryotic Cells: Genetic Instructions in the Nucleus

The nucleus is the control center of eukaryotic cells, containing genetic material and regulating gene expression.

• Nucleus: Large, membrane-bound organelle with nuclear pores; contains chromosomes (DNA-protein complexes called chromatin).

• DNA: Remains in the nucleus; RNA (mRNA, rRNA) is transcribed from DNA and can exit the nucleus.

• Ribosomes: Sites of protein synthesis; can be free in cytosol or bound to endoplasmic reticulum.

The Endomembrane System

The endomembrane system includes organelles involved in synthesis, transport, and breakdown of cellular materials.

• Smooth ER: Lipid synthesis, detoxification.

• Rough ER: Protein synthesis (ribosomes attached).

• Golgi Apparatus: Modifies, sorts, and packages proteins and lipids.

• Lysosomes: Contain hydrolytic enzymes for digestion.

• Vacuoles: Storage and transport.

• Transport Vesicles: Move materials between organelles.

• Phagocytosis: Cellular ingestion of particles.

• Hydrolytic Enzymes: Break down macromolecules in lysosomes.

Mitochondria and Chloroplasts: Cellular Generators

Mitochondria and chloroplasts are energy-converting organelles with unique origins.

• Mitochondria: Convert food energy into ATP via cellular respiration.

• Chloroplasts: Capture light energy to fix carbon into sugars (photosynthesis).

• Endosymbiotic Theory: Mitochondria and chloroplasts originated from prokaryotes engulfed by ancestral eukaryotes.

Cytoskeleton: Extracellular Structures, Cell Movement, and Cell-to-Cell Interactions

The cytoskeleton provides structural support, enables movement, and facilitates cell interactions.

• Cytoskeletal Elements: Microfilaments, intermediate filaments, microtubules.

• Functions: Maintain cell shape, enable movement, organize organelles, facilitate cell division.

Additional info: Refer to BIOL 251 textbook Ch. 3 for more detailed coverage of cell structures.