Exam 1: Foundational Biology Concepts in
Properties of Life
Criteria that distinguish living from non-living systems:
Order and organization at multiple levels (molecular to organismal)
Reproduction and heredity
Growth and development governed by genetic information
Energy processing and metabolism (acquisition, transformation, use of energy)
Regulation and homeostasis to maintain stable internal conditions
Response to environmental stimuli and adaptation over time through evolution
Living systems are complex, organized, and capable of dynamic interactions with their environment.
Significance:
Serves as a framework for understanding biology from molecules to ecosystems
Guides experimental design and interpretation of biological phenomena
Atomic Structure
Atoms are the fundamental units of matter composed of three main types of subatomic particles:
Protons (positive charge) in the nucleus
Neutrons (neutral) in the nucleus
Electrons (negative charge) orbiting the nucleus in electron shells or orbitals
Key terms:
Atomic number, Z: number of protons in the nucleus
Mass number, A: total number of protons and neutrons
Isotopes: atoms with same Z but different A due to varying neutrons
Electrons determine bonding and reactivity:
Valence electrons reside in outermost shell and drive chemical bonding
Electron configuration influences bond type and molecular shape
Basic consequences for biology:
Atom identity and bonding capabilities dictate molecular structure and function
Elements combine to form compounds essential for life (C, H, O, N, P, S, etc.)
Chemical Bonding and Interactions
Covalent bonds:
Atoms share one or more pairs of electrons
Can be nonpolar (equal sharing) or polar (unequal sharing due to electronegativity differences)
Strong, directional bonds that form the backbone of organic molecules
Ionic bonds:
Transfer of electrons from one atom to another, forming cations and anions
Electrostatic attraction holds ions together; typically form salts in aqueous environments
Hydrogen bonds and van der Waals forces:
Hydrogen bonds: attractive interactions between a hydrogen atom and an electronegative atom (e.g., O, N)
Van der Waals forces: weak, transient interactions important for molecular packing and protein folding
Polar vs nonpolar covalent bonds:
Polar covalent bonds: partial charges on atoms due to electronegativity differences
Nonpolar covalent bonds: electrons shared more evenly
Significance:
Bonding determines molecular shape, stability, reactivity, and interactions with water and other biomolecules
Water: Structure, Properties, and Interactions
Water is a polar molecule with a bent geometry, leading to strong hydrogen bonding network
Properties arising from hydrogen bonding:
Cohesion and surface tension: molecules stick together, enabling capillary action
High specific heat and high heat of vaporization: stabilizes temperatures in organisms and environments
Density anomaly: ice is less dense than liquid water, allowing ice to float
Excellent solvent for many solutes, facilitating biochemical reactions
Water’s role in chemistry and biology:
Medium for biochemical reactions and transport
Participates in acid–base reactions and hydrolysis/condensation processes
Acids, Bases, and the pH Scale
Definitions:
Arrhenius model:
Acid: substance that increases H⁺ in solution
Base: substance that increases OH⁻ in solution
Bronsted–Lowry model:
Acid: proton (H⁺) donor
Base: proton (H⁺) acceptor
Lewis model (brief): acids accept electron pairs; bases donate electron pairs (broader concept)
pH scale:
\mathrm{pH} = -\log_{10}[\mathrm{H^+}]
pOH can be defined similarly for OH⁻; relationship: \mathrm{pH} + \mathrm{pOH} = 14.0 at 25°C
Water autoionization (Kw):
K_w = [\mathrm{H^+}][\mathrm{OH^-}] \approx 1.0 \times 10^{-14} at 25°C
Acid-base reactions in biological systems:
Buffers stabilize pH by neutralizing added acids or bases
Important in blood and cellular environments
Significance:
pH affects enzyme activity, protein structure, and metabolic pathways
Carbon and Macromolecules
Carbon's unique versatility:
Tetravalence allows formation of diverse, stable, complex structures
Can form single, double, or triple bonds, rings, and long chains
Basis for organic chemistry and all macromolecules in biology
Polymers and polymerization:
Monomers link to form polymers via dehydration (condensation) reactions, releasing water
Hydrolysis reactions break polymers into monomers by adding water
General concept: polymer formation increases molecular complexity and functionality
Examples of macromolecular categories (to be studied in detail below):
Carbohydrates, proteins, nucleic acids, lipids (not all discussed in this transcript, but foundational)
Carbohydrates: Structure and Function
Structural hierarchy:
Monosaccharides (e.g., glucose, galactose)
Disaccharides (e.g., sucrose, lactose) formed by glycosidic bonds
Polysaccharides (e.g., starch, glycogen, cellulose) formed by polymerization of monosaccharides
Glycosidic bonds:
Link monosaccharides via covalent bonds; can be alpha (α) or beta (β) linkages, affecting digestibility and structure
Functions:
Energy storage (starch in plants, glycogen in animals)
Structural roles (cellulose in plants, chitin in some organisms)
Communication and recognition (glycoproteins and glycolipids on cell surfaces)
Amino Acids and Proteins
Amino acid structure:
Central (alpha) carbon attached to:
Amino group (–NH₂)
Carboxyl group (–COOH)
Hydrogen atom
Variable side chain (R group) that determines chemical nature
Peptide bonds:
Formed by dehydration synthesis between the carboxyl of one amino acid and the amino group of the next
General representation of a dipeptide: \text{Amino}{1}-\text{COOH} + \text{Amino}{2}-\text{NH}{2} \rightarrow \text{Amino}{1}-\text{CO}-\text{NH}-\text{Amino}{2} + \mathrm{H2O}
Protein structure levels (overview):
Primary: amino acid sequence
Secondary: local folding patterns (α-helix, β-pleated sheet) stabilized by hydrogen bonds
Tertiary: overall 3D conformation driven by hydrophobic interactions, disulfide bonds, ionic interactions, hydrogen bonds
Quaternary (in some proteins): multiple polypeptide subunits assemble into functional complexes
Side chain properties (R-group categories):
Nonpolar (hydrophobic)
Polar (uncharged)
Acidic (negatively charged)
Basic (positively charged)
Importance of folding for function:
Correct folding is essential for catalytic activity, binding, and regulation
Misfolding can lead to loss of function or disease; chaperones assist folding
Major protein types and functions:
Enzymes (catalysts)
Structural proteins (e.g., collagen, keratin)
Transport proteins (membrane channels and carriers)
Storage proteins
Regulatory and signaling proteins (receptors, transcription factors)
Defense proteins (antibodies, complement)
Motor proteins (myosin, actin systems)
Connection to biology:
Proteins are the workhorses of cells; their structure dictates function
Lipids and Membranes
Major lipid types in cells:
Triglycerides: glycerol backbone with three fatty acid tails; primary energy storage molecules
Phospholipids: glycerol, two fatty acids, and a phosphate-containing head group; amphipathic; major component of membranes
Steroids: four fused carbon rings (e.g., cholesterol, hormones)
Fatty acids and saturation:
Saturated: no double bonds, typically straight chains
Unsaturated: one or more double bonds, introduces kinks; cis vs trans configurations
Phospholipid bilayer structure:
Hydrophilic (polar) heads face outward toward water
Hydrophobic (nonpolar) tails face inward, away from water
Bilayer forms the basic structure of cell membranes and provides a semi-permeable barrier
Membrane functions and fluidity:
Regulate passage of ions and molecules
Contain membrane proteins for transport, signaling, and adhesion
Cholesterol modulates membrane stiffness and permeability
Membrane Components and Selective Permeability
Components:
Phospholipid bilayer as a hydrophobic core and hydrophilic surfaces
Integral and peripheral membrane proteins
Carbohydrates on extracellular face (glycoproteins and glycolipids) involved in recognition
Selective permeability:
Small nonpolar molecules diffuse easily across the bilayer
Ions and polar molecules require channels, carriers, or pumps
Membrane transport can be passive (no energy) or active (requires energy)
Transport processes:
Diffusion: movement down a concentration gradient
Osmosis: diffusion of water across a selectively permeable membrane
Facilitated diffusion: diffusion via membrane proteins (channels or carriers) without energy input
Active transport: movement against gradients using energy (e.g., Na⁺/K⁺-ATPase)
Bulk transport: endocytosis and exocytosis for large cargo
Representations of diffusion (example formula):
J = -D \frac{dC}{dx} where J is flux, D is diffusion coefficient, and dC/dx is the concentration gradient
Cells: Prokaryotic and Eukaryotic
General distinction:
Prokaryotic cells: no nucleus, no membrane-bound organelles; generally smaller; bacteria and archaea
Eukaryotic cells: nucleus and membrane-bound organelles; plants, animals, fungi, protists
Prokaryotic cell structures and roles:
Nucleoid region containing circular DNA
Ribosomes (smaller 70S) for protein synthesis
Cell wall (peptidoglycan in bacteria) and plasma membrane
External structures: capsules, pili, flagella for adhesion, movement, and genetic exchange
Eukaryotic cell organelles and functions:
Nucleus: stores genetic material; transcription occurs here; houses chromatin
Endoplasmic reticulum (ER): rough ER with ribosomes for protein synthesis; smooth ER for lipid synthesis and detoxification
Golgi apparatus: protein processing, sorting, and shipping
Mitochondria: powerhouse; ATP production via cellular respiration
Chloroplasts (plants/algae): photosynthesis and energy capture
Lysosomes and peroxisomes: digestion and metabolism; waste processing
Vacuoles: storage and maintenance of turgor (plants)
Vesicles and cytoskeleton: transport pathways and structural support
Integration and coordination:
The endomembrane system coordinates protein synthesis, processing, and trafficking
Mitochondria and chloroplasts provide energy and metabolic intermediates
Nucleus and ribosomes coordinate gene expression and protein production
Organelles and Functional Integration in Eukaryotic Cells
Distinct organelle roles and their coordination in cellular activities:
Nucleus: genome storage, transcription; RNA processing
ER: synthesis of proteins and lipids; ribosome association (rough ER)
Golgi: post-translational modification, sorting, and trafficking of proteins to appropriate destinations
Mitochondria: ATP generation; regulation of metabolic pathways; contains own DNA and ribosomes
Chloroplasts (plants/algae): light capture and sugar production via photosynthesis; chloroplasts contain their own DNA and ribosomes
Lysosomes: hydrolysis of macromolecules; waste disposal
Peroxisomes: breakdown of fatty acids; detoxification reactions
Vesicles: transport cargo between organelles and to the plasma membrane
Cellular activities that depend on organelle cooperation:
Gene expression and protein synthesis -> trafficking to destinations via vesicles
Energy production and utilization aligning with biosynthetic needs
Membrane synthesis, remodeling, and signaling coordinated across ER, Golgi, and plasma membrane
Connections, Implications, and Relevance
Foundational principles:
Structure determines function: molecular composition and 3D structure drive behavior of molecules and organelles
Emergent properties: complex systems exhibit properties not evident from individual components
Energy flow and metabolism underpin all cellular activities
Real-world relevance:
Understanding how membranes regulate transport informs drug delivery and pathology (e.g., antibiotic targets, metabolic disorders)
Protein folding and misfolding relate to diseases; chaperones are critica for proteostasis
Carbon versatility underlies all biomolecules and life’s diversity
Ethical and practical implications:
Biotechnological advancements rely on manipulating cellular processes; responsible use and biosafety are essential
Medical interventions target cellular pathways (e.g., transport defects, organelle function) with ethical considerations for risks and benefits
Quick Reference: Key Formulas and Concepts
pH and acid-base chemistry:
\mathrm{pH} = -\log_{10}[\mathrm{H^+}]
K_w = [\mathrm{H^+}][\mathrm{OH^-}] \approx 1.0 \times 10^{-14} at 25\degree C
Diffusion and transport:
J = -D \frac{dC}{dx}
Polymerization (dehydration synthesis) and hydrolysis (conceptual):
Dehydration: monomers join, releasing water
Hydrolysis: polymers broken into monomers by water addition
Peptide bond formation (example):
\text{Amino}{1}-\text{COOH} + \text{Amino}{2}-\text{NH}{2} \rightarrow \text{Amino}{1}-\text{CO}-\text{NH}-\text{Amino}{2} + \mathrm{H2O}
Notes
This set of notes follows the provided learning objectives to give a comprehensive overview of foundational biology topics that are essential for Exam 1.
Use these as a structured study guide to link basic chemical principles to biological structures and processes.