BIOL 202 Exam 1 Comprehensive Study Notes
Introduction to Cell and Molecular Biology
Cells exhibit extraordinary diversity in their visual appearance, physical dimensions, structural shapes, and specialized functions. Despite these widespread differences, all living cells share a fundamental underlying chemical architecture. The universal central dogma of molecular biology dictates that genetic information stored within double-stranded DNA is transcribed into RNA molecules, which are subsequently translated into functional proteins.
The historical development of microscopy led to the establishment of cell theory, which posits that all living organisms are composed of one or more cells, and that all single cells arise exclusively through the division of pre-existing cells.
Organisms are broadly categorized into two primary structural types: prokaryotes and eukaryotes. Prokaryotic cells lack a distinct membrane-bound nucleus and specialized internal compartments. In contrast, eukaryotic cells are characterized by a prominent membrane-bound nucleus and a complex network of internal organelles.
The eukaryotic cell relies on compartmentalized organelles to perform specialized biochemical functions. The nucleus houses the genetic material of the cell. Surrounding the organelles is the cytosol, the liquid portion of the cytoplasm where many metabolic pathways occur. Mitochondria act as the powerhouses of the cell, carrying out cellular respiration to yield chemical energy. Chloroplasts perform photosynthesis in plant cells and algae to convert light energy into chemical energy. The rough endoplasmic reticulum is studded with ribosomes and functions in protein synthesis and processing. The smooth endoplasmic reticulum lacks ribosomes and is dedicated to lipid synthesis and metabolic detoxification. The Golgi apparatus receives lipids and proteins from the endoplasmic reticulum to modify, sort, and package them for delivery. Lysosomes contain hydrolytic enzymes responsible for breaking down cellular waste and macromolecular debris. Intracellular transport is mediated by membrane-bound vesicles through endocytosis, which imports extracellular materials into the cell, and exocytosis, which secretes intracellular molecules into the extracellular environment. The structural framework, internal movement, and overall shape of the eukaryotic cell are maintained by the cytoskeleton, an intricate network of protein filaments.
Basics of Biological Chemistry
The vast majority of biological molecules are constructed from four primary chemical elements: hydrogen, carbon, nitrogen, and oxygen. The physical structure of an atom consists of a central nucleus containing positively charged protons and uncharged neutrons, surrounded by a cloud of negatively charged electrons residing in atomic orbitals.
Chemical bonds hold atoms together to form molecules. Covalent bonds form when atoms share pairs of valence electrons. When electrons are shared unequally between atoms with differing electronegativities, polar molecules are created. Ionic bonds form through strong electrostatic interactions between oppositely charged ions resulting from complete electron transfer. Hydrogen bonds represent weak, non-covalent electrostatic attractions between a hydrogen atom covalently bound to an electronegative atom and another nearby electronegative atom. Chemical substances interact differently with water depending on their bonding; hydrophilic molecules are polar or charged and dissolve readily in aqueous environments, whereas hydrophobic molecules are non-polar and resist interacting with water.
Cells contain four major classes of small organic molecules: sugars, fatty acids, amino acids, and nucleotides.
Sugars serve as essential energy sources and structural components. Monosaccharides represent single sugar units that can link together to form disaccharides, short oligosaccharides, or long polymeric polysaccharides. The covalent glycosidic bonds holding sugar monomers together are formed via condensation reactions, which yield a molecule of water. Conversely, these glycosidic bonds are broken down through hydrolysis reactions, which consume a water molecule.
Fatty acids consist of non-polar hydrocarbon chains attached to a polar carboxyl group. Saturated fatty acids contain no double bonds between carbon atoms in their tail, maximizing hydrogen saturation. Unsaturated fatty acids contain one or more double bonds that introduce kinks into the hydrocarbon chain. Fatty acid chains attach to glycerol or other backbones through condensation reactions to build lipids.
Amino acids are the fundamental building blocks of proteins. Each amino acid possesses a central alpha carbon bonded to an amino group, a carboxylic acid group, a single hydrogen atom, and a variable side chain known as an R group. There are 20 standard amino acids that differ based on the chemical properties of their side chains. Side chains are classified as charged (which may be acidic or basic), polar, or non-polar. Polypeptide chains are synthesized through condensation reactions that link the amino group of one amino acid to the carboxylic acid group of another.
Nucleotides consist of three basic components: a nitrogenous base, a five-carbon sugar, and one or more phosphate groups. The five-carbon sugar is either ribose, found in RNA, or deoxyribose, found in DNA. Nucleotides polymerize to form the nucleic acids DNA and RNA via phosphodiester bonds that link adjacent nucleotide units.
Proteins: Structure and Function
The biological capability of a protein molecule is determined by its specific three-dimensional spatial conformation. Amino acids are linked sequentially by covalent peptide bonds to form a continuous polypeptide backbone. This structural chain possesses directional polarity, featuring a free amino terminus at one end and a free carboxyl terminus at the opposing end. Projecting outward from this polypeptide backbone are the variable amino acid side chains. The specific chemical charge and polarity of these 20 distinct side chains directly influence how the overall protein chain folds into space.
Four non-covalent interactions stabilize the three-dimensional structure of folded proteins: electrostatic interactions, hydrophobic interactions, hydrogen bonds, and van der Waals forces. Electrostatic interactions occur between fully or partially charged groups. Hydrophobic interactions force non-polar side chains to aggregate internally away from aqueous surroundings. Hydrogen bonds form along the backbone and between polar side chains. Van der Waals forces consist of weak attractive forces between non-polar atoms in close proximity. Two additional factors impact proper protein folding: specialized chaperone proteins, which assist nascent polypeptide chains in reaching their correct native conformations, and covalent disulfide bonds, which form between the reactive sulfur-containing side chains of neighboring cysteine residues to reinforce protein stability.
Protein structure is categorized into four distinct hierarchical levels. The primary structure is the linear sequence of amino acids joined together by peptide bonds. The secondary structure refers to localized spatial folding patterns along the polypeptide backbone, stabilized by hydrogen bonds to form ̑\alpha-helices and ̑\beta-sheets. The tertiary structure is the complete three-dimensional conformation of a single folded polypeptide chain. The quaternary structure describes the multi-subunit complex formed by the association of more than one individual polypeptide chain.
Extracellular or intracellular environmental changes can alter protein structure. Denaturation occurs when a protein loses its functional three-dimensional shape due to disruptions in non-covalent interactions. Unfavorable shifts in pH or temperature serve as major factors that denature proteins. Structural misfolding of proteins can lead to cellular malfunction and severe medical conditions. Misfolded proteins can aggregate into insoluble, highly ordered amyloid structures. These aggregations are associated with neurodegenerative diseases and prion pathologies, where infectious misfolded prions induce normally folded proteins to adopt diseased conformations.
Proteins accomplish their biological functions by binding selectively to target molecules. Any molecule that is bound by a protein is termed a ligand, and the region of the protein that physically interacts with the ligand is designated as the binding site. When a protein functions as an enzyme, its specific chemical ligand is called a substrate, which binds directly to a catalytic domain known as the active site.
Proteins: Regulation and Methods of Study
Cells strictly regulate protein activity through multiple control mechanisms. In feedback inhibition, an end product of a metabolic pathway acts as an inhibitor of an upstream enzyme within that same pathway to prevent overproduction. Allosteric enzymes possess regulatory sites separate from their active sites; binding of a regulatory ligand at the allosteric site induces a conformational change that alters enzyme activity. Proteins are also regulated by covalent modifications, most notably phosphorylation, where the reversible addition of a phosphate group shifts protein activity or interaction affinity. Energy-driven structural movements occur through ATP hydrolysis, which supplies energy to drive directed directional shifts in protein complexes. In addition, scaffold proteins assemble interacting groups of enzymes and signaling proteins into physical proximity to streamline signaling cascades.
To study proteins, researchers first disrupt cells to extract a crude cellular homogenate. This homogenate is fractionated into sub-cellular compartments using physical separation techniques. Centrifugation separates cellular components based on size, shape, and density under high rotational speeds. Liquid chromatography techniques isolate proteins based on specific chemical properties: affinity chromatography separates proteins using specific binding interactions with immobilized ligands; ion-exchange chromatography separates proteins based on surface net charge; and gel-filtration chromatography separates proteins based on their molecular size as they pass through porous beads. Proteins can also be separated by mass and charge using gel electrophoresis. The precise amino acid composition and molecular weight of isolated proteins are determined using mass spectrometry. High-resolution three-dimensional structures of proteins are solved using X-ray crystallography, allowing scientists to extrapolate detailed mechanisms of catalytic function and molecular regulation.
Membrane Structure
Biological membranes are organized around a phospholipid bilayer. Phospholipids are amphipathic molecules possessing hydrophilic heads and hydrophobic hydrocarbon tails. When exposed to aqueous environments, phospholipids spontaneously self-assemble into closed bilayer structures to isolate their hydrophobic tails from water. Individual phospholipid molecules move rapidly within the two-dimensional plane of their monolayer, but they rarely cross or flip-flop spontaneously from one leaflet of the bilayer to the other.
The physical fluidity of the lipid bilayer depends heavily on its molecular composition. Membrane fluidity is increased by shorter hydrocarbon tail lengths, which reduce internal molecular interactions. Fluidity is also enhanced by unsaturated hydrocarbon chains containing double bonds, which introduce kinks that prevent tight packing of adjacent lipids. Additionally, the presence of cholesterol intercalates between membrane lipids to modulate bilayer fluidity depending on temperature and lipid composition.
Membrane proteins carry out vital functions across the lipid bilayer. These functions include acting as transport channels to import or export specific solutes, serving as structural anchors to bind extracellular or intracellular matrix components, functioning as receptors to detect external chemical signals and relay messages inward, and acting as enzymes to catalyze localized chemical reactions. Membrane proteins are classified as integral if they are embedded directly within the hydrophobic core of the bilayer, or peripheral if they associate non-covalently with the surface of integral membrane proteins or lipid head groups.
Cells can restrict the lateral movement of specific membrane proteins to create localized functional domains. Protein mobility constraints were demonstrated through classical cell fusion experiments involving mouse and human cells, which tracked the lateral mixing of membrane proteins over time. The rate of protein lateral diffusion within living membranes is quantitatively measured using Fluorescence Recovery After Photobleaching (FRAP), where fluorescently labeled membrane proteins are photobleached in a targeted area and the recovery of fluorescence is monitored as unbleached proteins diffuse back into the region.
Membrane Transport
Cellular membranes function as selectively permeable barriers that regulate the movement of substances into and out of the cell. The diffusion rate of a molecule across the membrane depends on its molecular size, charge, and lipophilicity. Charged ions cannot freely diffuse through the hydrophobic lipid core and are unequally distributed across the cell membrane. The concentrations of sodium (), chloride (), and calcium () ions are maintained at significantly higher levels in the extracellular space than in the cytosol. Conversely, potassium () ions are maintained at a much higher concentration inside the cell than outside.
Solute transport across membranes occurs via passive or active mechanisms. Passive transport moves molecules down their electrochemical gradient without requiring metabolic energy expenditure. The electrochemical gradient combines two distinct driving forces: the concentration gradient across the membrane and the membrane potential, which is the electrical voltage difference across the lipid bilayer. Active transport moves solutes against their electrochemical gradient and requires an input of metabolic energy.
The relative solute concentration of extracellular solutions dictates water movement across cell membranes. In a hypertonic solution, high extracellular solute concentration causes water to leave the cell, shrinking it. In a hypotonic solution, low extracellular solute concentration causes water to rush into the cell, causing it to swell. In an isotonic solution, solute concentrations are balanced inside and outside, maintaining cell volume. The movement of water across membranes down its concentration gradient is termed osmosis, a process facilitated by specialized water-channel proteins called aquaporins.
Membrane transporters mediate the selective passage of solutes. Transporters operating via passive transport facilitate downhill movement along electrochemical gradients. Active transport is executed by specialized protein pumps, such as the ATPase pump, which utilizes energy from ATP hydrolysis to transport out of the cell and into the cell against their respective concentration gradients. Active transport can also occur via coupled transport, where the unfavorable movement of one solute against its gradient is driven by the favorable movement of a co-transported solute down its gradient. Coupled transport operates as symport, moving both solutes in the same direction, or antiport, moving solutes in opposite directions. An example of symport occurs in intestinal epithelial cells, where an influx of down its steep electrochemical gradient drives the active co-transport of glucose into the cell against its concentration gradient.
Ion channels facilitate rapid passive transport of ions and are heavily involved in controlling membrane potential. Many ion channels operate as gated channels that open or close in response to specific stimuli. Ligand-gated channels open upon binding a specific chemical ligand, whereas voltage-gated channels open in response to alterations in the electrical membrane potential.
Ion channel gating is central to neuronal signaling. Neurons possess specialized anatomical structures, including an elongated axon that conducts electrical signals and terminal nerve endings that transmit signals to target cells. Signal transmission down a neuron occurs via an action potential, which is a localized wave of electrical depolarization that travels down the axon length. Depolarization opens voltage-gated channels, allowing influx. To preserve signal directionality and prevent backward propagation, these channels become temporarily inactivated immediately following depolarization. Following an action potential, the ATPase pump actively restores and ions to their original sides of the membrane.
Communication between a neuron and its target cell occurs at a junction called a synapse, across which signals pass from the presynaptic cell to the postsynaptic cell. When an action potential reaches the nerve terminal of the presynaptic cell, local membrane depolarization triggers the opening of voltage-gated channels. The resulting influx of triggers the exocytosis of chemical neurotransmitters into the synaptic cleft. These neurotransmitters diffuse across the synapse and bind to neurotransmitter receptors on the postsynaptic membrane. These receptors operate as ligand-gated channels; binding of the neurotransmitter opens the channel, causing an influx of into the postsynaptic cell that initiates a new action potential.