Evolution, the Themes of Biology, and Scientific Inquiry Part 2

Estradiol and testosterone: steroids/sex hormones with a common carbon skeleton in the form of 4 fused rings; differ only in chemical groups attached to the rings of the carbon skeleton (variation at molecular level lies at foundation of all biological diversity) Functional groups: components of organic molecules that are most commonly involved in chemical reactions; # and arrangement give each molecule its unique properties 6 most important functional groups in chemistry of life: 1. Hydroxyl group: some of these on the monomers of cellulose can hydrogen bond with hydroxyls of parallel cellulose molecules 2. Carbonyl group 3. Carboxyl group 4. Amino group 5. Sulfhydryl group 6. Phosphate group Adenosine triphosphate (ATP): important organic phosphate/source of energy for cellular processes; consists of an organic molecule called adenosine attached to a string of 3 phosphate group (stores the potential to react with water, a reaction that releases energy to be used by the cell) Chapter 5: The Structure and Function of Large Biological Molecules - All living things are made up of 4 classes of large biological molecules: 1. Carbohydrates: include sugars and polymers of sugars; simplest ones are monosaccharides (simple sugars). Carbohydrate macromolecules are polysaccharides (polymers composed of many sugar building blocks) 2. Lipids: unifying feature is that they mix poorly, if at all, with water (hydrophobic because they consist mostly of hydrocarbons, which form nonpolar covalent bonds). The most biologically important ones are fats, phospholipids, and steroids 3. Proteins: biologically functional molecule that consists of 1 or more polypeptides; constructed from same set of 20 amino acids 4. Nucleic acids Macromolecule: large, complex molecules (polymers); large biological molecules have unique properties that arise from the orderly arrangement of their atoms. Each cell has thousands of different ones. They vary among cells of an organism, vary more within species, and vary the most between species (proteins and amino acids, lipids and fatty acids, DNA and RNA and nucleotides, carbohydrates and monosaccharides) Polymers: long molecules consisting of many similar building blocks (carbohydrates, proteins, nucleic acids); huge variety of polymers can be built from a small set of monomers Enzyme: specialized macromolecules that speed up chemical reactions like those that make or break down polymers; enzymes that digest starch by hydrolyzing linkages cannot hydrolyze linkages in cellulose, but some microbes use enzymes to digest cellulose, and many herbivores have symbiotic relationships with these microbes - Proteins that act as catalysts to speed up chemical reactions Can perform their functions repeatedly, functioning as workhorses that carry out the processes of life Dehydration reaction: happens when 2 monomers bond together through the loss of a water molecule Hydrolysis: how polymers and disassembled to monomers; reverse of dehydration reaction because a water molecule is added, breaking the bond Monomers: repeating units that serve as building blocks (lipids) Monosaccharides: have molecular formulas that are usually multiples of CH2O (glucose is the most common); classified by location of carbonyl group as aldose or ketose, and the # of carbons in the carbon skeleton - Form rings in aqueous solutions but are often drawn as linear skeletons - Serve as major fuel for cells and raw material for building molecules Disaccharide: formed when dehydration reaction joins 2 monosaccharides (covalent bond called glycosidic linkage) Polysaccharide: polymers of sugar; architecture and function determined by its sugar monomers and positions of its glycosidic linkages (have storage and structural roles) Starch: a configuration. Largely helical. Storage polysaccharide of plants; consists entirely of glucose monomers (simplest form is amylose). Plants store surplus starch as granules within chloroplasts and other plastids Glycogen: storage polysaccharide in animals; hydrolysis of glycogen in these cells releases glucose when sugar demand increases (stored mainly in liver and muscle cells) Cellulose: Polysaccharide in b configuration. Straight, unbranched; the cellulose in human food passes through the digestive tract as insoluble fiber. Major component of touch wall of plant cells (polymer of glucose, but glycosidic linkages differ due to 2 ring forms for glucose, alpha and beta) Chitin: structural polysaccharide; found in exoskeleton of arthropods (provides structural support for the cell walls of many fungi). Used to make a strong and flexible surgical thread Fats: constructed from 2 types of smaller molecules, glycerol and fatty acids; separate from water because water molecules hydrogen-bond to each other and exclude fats - Major function is energy storage; mammals store long-term food reserves in adipose cells (adipose tissue cushions vital organs and insulates body) - In a fat, 3 fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol or triglyceride - Fatty acids in a fat can be all the same or 2 or 3 different kinds Triacylglycerol (triglyceride): made when an ester linkage joins 3 fatty acids to glycerol Glycerol: 3-carbon alcohol with a hydroxyl group attached to each carbon Fatty acid: consists of carboxyl group attached to a long carbon skeleton; vary in length (number of carbons) and # of locations of double bonds Saturated fatty acid: have maximum # of hydrogen atoms; no double bonds Unsaturated fatty acids: have 1 or more double bonds; certain ones are not synthesized in the human body and must be supplied in the diet (essential fatty acid omega-3, which is required for normal growth and thought to provide protection against cardiovascular diseases) Saturated fats: fats made from saturated fatty acids; solid at room temperature (most animal fats). Too much can cause cardiovascular disease through plaque deposits Unsaturated fats/oils: fats made from unsaturated fatty acids; liquid at room temperature (plant and fish fats) Hydrogenation: process of converting unsaturated fats to saturated fats by adding hydrogen; hydrogenating vegetable oils creates unsaturated fats with trans double bonds Trans fats: may contribute more than saturated fats to cardiovascular disease; trans double bonds Phospholipid: 2 fatty acids and a phosphate group attached to glycerol; the 2 fatty acids are hydrophobic, but the phosphate group and its attachments form a hydrophilic head (when added to water, they self-assemble into double-layered structures called bilayers) - Arranged in a bilayer with the hydrophobic tails pointing toward the interior at the surface of a cell - Structure results in a bilayer arrangement found in cell membranes - Existence of cells depends on these Steroid: lipids characterized by a carbon skeleton consisting of 4 fused rings Cholesterol: type of steroid; component in animal cell membranes and a precursor from which other steroids are synthesized (high level in the blood may contribute to cardiovascular disease) Protein: include diversity of structures resulting in a wide range of functions; account for more than 50% of the dry mass of most cells (some speed up chemical reactions) - Other protein functions include defense, storage, transport, cellular communication, movement, structural support - Activities result from their 3D architecture; functional protein has 1 or more polypeptides twisted, folded, and coiled into a unique shape - 3D structure determined by sequence of amino acids; function depends on ability to recognize and bind to some other molecule 8 Kinds of Proteins: 1. Enzymatic proteins: selective acceleration of chemical reactions 2. Defensive proteins: protection against disease 3. Storage proteins: storage of amino acids 4. Transport proteins: transport of substances 5. Hormonal Proteins: coordination of organism’s activities 6. Structural proteins: support 7. Receptor proteins: response of cell to chemical stimuli 8. Contractile and motor proteins: movement Polypeptide (amino acid polymer): unbranched polymer built from the 20 amino acids that construct proteins; range in length from a few to more than 1,000 monomers (each polypeptide has a unique linear sequence of amino acids, with a carboxyl end, C-terminus, and an amino end, N-terminus Amino acid: organic molecules with amino and carboxyl groups; differ in their properties due to differing side chains (R groups) Peptide bonds: amino acids linked to covalent bonds Short Answer Questions: 1. What are the properties of water and why are they necessary for life? Explain. - The properties of water are cohesion, the ability to moderate temperature, expansion upon freezing, and versatility as a solvent. They are necessary for life because, for instance, water’s cohesive behavior aids plants in obtaining water through the roots. Also, if temperatures reach levels that are incompatible with life, species would die off and if water did not expand upon freezing, ice would sink and animals that depend on that ice would be unable to survive, as they would freeze. Its versatility as a solvent means it can dissolve a vast myriad of molecules and helps plants’ in their movement and usage of nutrients and other important substances; without this feature, life could not be sustained. 2. Compare and contrast the formation, properties, and characteristics of covalent and ionic bonds. Covalent bonds share a pair of valence electrons by 2 atoms and they can form between atoms of the same or different elements. The shared electrons count as part of each atoms’ valence shell. They have lower melting points than ionic bonds. Ionic bonds are attractions between a cation and an anion and they are generally soluble in polar substances. They have higher melting points than covalent bonds and lower electrical conductivity. 3. Distinguish among the three types of isomers: structural, geometric, and enantiomer - Structural isomers possess the same molecular formula, but different arrangements of atoms. Geometric isomers have the same number and type of atoms, but differ in their geometric structures. Enantiomer isomers are types of geometric isomers that are mirror images of each other, but differ in terms of shape because of an asymmetric carbon. 4. Identify the levels of organization for protein molecules-primary, secondary, tertiary and quaternary. - The primary structure is the sequence of amino acids forming a polypeptide chain. The secondary structure is the regular local patterns of polypeptide chain coils. The tertiary structure is the 3D shape of a polypeptide resulting from amino acid R groups’ interactions forming the chain. The quaternary structure is the shape caused by the association of 2 or more polypeptide units. 5. Describe the differences between DNA and RNA. - DNA contains the sugar deoxyribose and thymine, while RNA contains the sugar ribose and uracil. Exam 2: Chapter 6: A Tour of the Cell - Most cells synthesize and secrete materials that are external to the plasma membrane; these extracellular structures are involved in many cellular functions Basic features of all cells: plasma membrane, cytosol, chromosomes, ribosomes Cytosol: semifluid substance Ribosomes: complexes made of ribosomal RNA and protein; carry out protein synthesis in the cytosol (free ribosomes)and on the outside of the endoplasmic reticulum or nuclear envelope (bound ribosomes) Microscope: used to visualize cells Light microscope: visible light is passed through a specimen and then through glass lenses; lenses refract or bend the light so that the image is magnified (can magnify effectively to about 1,000 times the size of the actual specimen) - Various techniques enhance contrast and enable cell components to be stained or labeled - Recent advances give new techniques for labeling cells that improve resolution and confocal microscopy and deconvolution microscopy provide sharper images of 3D tissues and cells 3 important parameters of microscopy: 1. Magnification: the ratio of an object’s image size to its real size 2. Resolution: the 3. Contrast Organelle: membrane-enclosed structures in eukaryotic cells; standard light microscopy resolution is too low to study them (plant and animal cells have most of the same organelles) Basic electron microscopes: used to study subcellular structures 1. Scanning electron microscope (SEM): focuses a beam of electrons onto the surface of a specimen, providing images that look 3D 2. Transmission electron microscope (TEM): focuses a beam of electrons through a specimen; used mainly to study the internal structure of cells Cell fractionation: takes cells apart and separates the major organelles from 1 another; enables scientists to determine the functions of organelles (centrifuges fractionate cells into their component parts) - Biochemistry and cytology help correlate cell function and structure Nucleoid: unbound region Nucleus: contains most of the cell’s genes; usually the most conspicuous organelle (DNA is organized into chromosomes which are discrete units) Nuclear envelope: encloses nucleus and separates it from the cytoplasm Nuclear membrane: double membrane where each membrane consists of a lipid bilayer Pore: regulates entry and exit of molecules from the nucleus Nuclear lamina: lines the nuclear size of the nuclear envelope; composed of proteins and maintains the shape of the nucleus Nucleolus: site of ribosomal RNA synthesis; located within the nucleus Chromatin: DNA and proteins of chromosomes together; condense to form discrete chromosomes as a cell prepares to divide Endomembrane system: compartmental organization, regulates protein traffic and performs metabolic functions in the cell; consists of nuclear envelope, endoplasmic reticulum, golgi apparatus, lysosomes, vacuoles, plasma membrane (these components are either continuous or connected via transfer of vesicles) Endoplasmic reticulum: accounts for more than ½ of the total membrane in many eukaryotic cells; continuous with the nuclear envelope - 2 distinct regions of the ER: 1. Smooth: lacks ribosomes, synthesizes lipids, metabolizes carbohydrates, detoxifies drugs and poisons, stores calcium ions 2. Rough: surface is studded with ribosomes which secret glycoproteins, distributes transport vesicles, membrane factory for the cell Glycoproteins: proteins covalently bonded to carbohydrates Transport vesicles: secretory proteins surrounded by membranes Vacuole: large vesicle derived from the ER and golgi apparatus; perform a variety of functions in different kinds of cells - Food vacuole: formed by phagocytosis - Contractile vacuole: found in many freshwater protists; pumps excess water out of cells - Central vacuole: found in many mature plant cells; holds organic compounds and water Golgi apparatus: shipping and receiving center; consists of cisternae (modifies products of the ER, manufactures certain macromolecules, sorts and packages material into transport vesicles) Cisternae: flattened membranous sacs Lysosome: membranous sac of hydrolytic enzymes that can digest macromolecules; lysosomal enzymes work best in the acidic environment inside the lysosome (hydrolytic enzymes and lysosomal membranes are made by the rough ER and then transferred to the golgi apparatus for further processing) Autophagy: process used by lysosomes where enzymes are used to recycle the cell’s own organelles and macromolecules Phagocytosis: how some types of cells can engulf another cell; forms a food vacuole (lysosome fuses with the food vacuole and digests the molecules) Mitochondria: sites of cellular respiration (has similarities with bacteria); are in nearly all eukaryotic cells and have a smooth outer membrane and an inner membrane folded into cristae - Inner membrane creates 2 compartments: intermembrane space and mitochondrial matrix Cristae: present a large surface area for enzymes that synthesize ATP Chloroplast (plastid): sites of photosynthesis; found in plants, algae, leaves, other green organs (has similarities with bacteria) - Contain the green pigment chlorophyll, enzymes, and other molecules that function in photosynthesis - Structure includes thylakoids and stroma Thylakoid: membranous sacs stacked to form a granum Stroma: internal fluid Similarities with bacteria: enveloped by a double membrane, contain free ribosomes and circular DNA molecules, grow and reproduce somewhat independently in cells; lead to endosymbiont theory Endosymbiont theory: an early ancestor of eukaryotes engulfed an oxygen-using non-photosynthetic prokaryotic cell, forming a relationship with the host cell, becoming endosymbiont; endosymbionts evolved into mitochondria (at least one of these cells may have taken up a photosynthetic prokaryote, which evolved into a chloroplast) Cellular respiration: metabolic process that uses oxygen to generate ATP; some of its metabolic steps are catalyzed in the mitochondrial matrix Cytoskeleton: network of fibers extending throughout the cytoplasm that organizes the cell’s structures and activities, anchoring many organelles; helps support the cell and maintain its shape (interacts with motor proteins to produce motility) - Composed of 3 types of molecular structures: 1. Microtubules: thickest; hollow rods about 25 nm and 200 nm to 25 microns long (shape the cell, guide movement of organelles, separate chromosomes during cell division) 2. Microfilaments (actin filaments): thinnest; solid rods about 7nm built as twisted double chain of actin subunits (thicker filaments composed of myosin interdigitate with the thinner actin fibers) - Those that function in cellular motility contain the protein myosin and actin - In muscle cells, thousands of actin filaments are arranged parallel to one another - Localized contraction brought about by actin and myosin drives amoeboid movement - Cells crawl along a surface extending pseudopodia and moving toward them 3. Intermediate filaments: fibers with diameters in a middle range of 8-12 nm; support cell shape and fix organelles in place (most permanent cytoskeleton fixtures) - Inside the cell, vesicles can travel along tracks provided by the cytoskeleton Pseudopodia: cellular extensions Cell junctions: neighboring cells in tissues, organs, or organ systems that often adhere, interact, and communicate through direct contact; 3 types are common in epithelial tissues: 1. Tight junctions: membranes of neighboring cells are pressed together, preventing leakage of extracellular fluid 2. Desmosomes: anchoring junctions fasten cells together in strong sheets 3. Gap junctions: provide cytoplasmic channels between adjacent cells; communicating junctions Plasmodesmata: channels that perforate plant cell walls; water, small solutes, and sometimes proteins and RNA can pass from cell to cell Chapter 7: Membrane Structure and Function Plasma membrane: selective barrier or boundary that separates the living cell from its surroundings; exhibits selective permeability and allows sufficient passage of oxygen, nutrients, and waste to service the volume of every cell (collage of different proteins, often grouped together, embedded in fluid matrix of the lipid bilayer) - The basic feature of biological membranes is a double layer of phospholipids and other lipids - As temperatures cool, membranes switch from a fluid state to a solid state; the temperature at which a membrane solidifies depends on the types of lipids (membranes must be fluid to work properly) - Membranes rich in unsaturated fatty acids are more fluid than those rich in saturated fatty acids (they are usually as fluid as salad oil) - The steroid cholesterol has different effects on membrane fluidity at different temperatures; at warm temperatures, cholesterol restrains movement of phospholipids and at cool temperatures, it maintains fluidity by preventing tight packing - Variations in lipid composition of cell membranes in many species appear to be adaptations to specific environmental conditions - Ability to change the lipid compositions in response to temperature changes has evolved in organisms that live where temperatures vary - Proteins determine most of the membrane’s specific functions - HIV must bind to the immune cell surface protein CD4 and a “co-receptor” CCR5 in order to infect a cell; HIC cannot enter the cells of resistant individuals that lack CCR5 - Controls the process of the cell exchanging materials with its surroundings - Nonpolar hydrophobic molecules like hydrocarbons can dissolve in the lipid bilayer and pass through the membrane rapidly; hydrophilic molecules like ions and polar molecules do not cross the membrane easily Selective permeability: allows some substances to cross the plasma membrane more easily than others - Cellular membranes are fluid mosaics of lipids and proteins Cholesterol: steroid that reduces membrane fluidity at moderate temperatures and hinders solidification at low temperatures Phospholipids: most abundant lipid in the plasma membrane that can move within the bilayer; amphipathic molecules containing hydrophobic and hydrophilic regions (phospholipid bilayer can exist as a stable boundary between 2 aqueous compartments) - Most lipids and some proteins drift laterally; rarely, a lipid may flip-flop traversely across the membrane Fluid mosaic model: a membrane is a fluid structure with a “mosaic” of various proteins embedded in it; proteins are not randomly distributed in the membrane Peripheral proteins: bound to the surface of the membrane Integral proteins: penetrate the hydrophobic core; the hydrophobic regions of an integral protein have 1 or more stretches of nonpolar acids often coiled into alpha helix Transmembrane proteins: integral proteins that span the membrane 6 Major functions of membrane proteins 1. Transport 2. Enzymatic activity 3. Signal transduction 4. Cell-cell recognition 5. Intercellular joining 6. Attachment to the cytoskeleton and extracellular matrix (ECM) Role of membrane carbohydrates in cell-cell recognition: cells recognize each other by binding to molecules, often containing carbohydrates, on the extracellular surface of the plasma membrane; membrane carbohydrates may be covalently bonded to lipids forming glycolipids or more commonly to proteins forming glycoproteins (carbohydrates on the external side of the plasma membrane vary among species, individuals, and cell types in an individual Synthesis and sidedness of membranes: membranes have distinct inside and outside faces; the asymmetrical distribution of proteins, lipids, and associated carbohydrates in the plasma membrane is determined when the membrane built by the ER and golgi apparatus Transport proteins: specific for substance it moves and allows passage of hydrophobic substances across the membrane; channel proteins, have a hydrophilic channel that certain molecules or ions can use as a tunnel (channel proteins called aquaporins facilitate the passage of water) - Some can move solutes against their concentration gradients - Channel proteins provide corridors that allow a specific molecule or ion to cross the membrane - Carrier proteins bind to molecules and change shape to shuttle them across the membrane Ion channel: facilitates the diffusion of ions; gated channels open or close in response to a stimulus Diffusion: tendency for molecules to spread out evenly into the available space; each molecule moves randomly but diffusion of a population of molecules may be directional (at dynamic equilibrium, as many molecules cross the membrane in 1 direction as in the other) Concentration gradient: region along which the density of a chemical substance increases or decreases; substances diffuse down it (no work must be done to move substances down it) Passive transport: diffusion of a substance across a biological membrane; no energy is expended by the cell Active transport: moves substances against their concentration gradients; requires energy, usually as ATP (performed by specific proteins embedded in the membranes) - Allows cells to maintain concentration gradients that differ from their surroundings Sodium-potassium pump: 1 type of active transport system; major electrogenic pump of animal cells Proton pump: main electrogenic pump of plants, fungi, and bacteria Osmosis: diffusion of water across a selectively permeable membrane; water diffuses across a membrane from the region of lower solute concentration to the region of higher solute concentration until the solute concentration is = on both sides Tonicity: ability of a surrounding solution to cause a cell to gain or lose water Isotonic: solute concentration is the same as that inside the cell; no net water movement across the plasma membrane (if a plant cell and its surroundings are isotonic, the cell becomes flaccid) Hypertonic: solute concentration is greater than that inside the cell; cell loses water (create osmotic problems for organisms) Hypotonic: solute concentration is less than that inside the cell; cell gains water (create osmotic problems for organisms) - A plant cell in a hypotonic solution swells until the wall opposes uptake, making the cell turgid - The membrane pulls away from the cell wall causing it to wilt Turgid: firm Plasmolysis: lethal effect of a plant wilting when the membrane pulls away from the cell wall Osmoregulation: control of solute concentrations and water balance; necessary adaptation for life in such environments Paramecium: protist; hypertonic to its pond water environment and has a contractile vacuole that acts as a pump Cell wall: helps maintain water balance Facilitated diffusion: transport proteins speed the passive movement of molecules across the plasma membrane; passive transport because the solute moves down its concentration gradient (the transport requires no energy) Membrane potential: voltage difference across a membrane; voltage is created by differences in the distribution of positive and negative ions across a membrane Electrochemical gradient: drives the diffusion of ions across a membrane; made up of 2 combined forces: 1. Chemical force: ion’s concentration gradient 2. Electrical force: effect of membrane potential on the ion’s movement Electrogenic pump: transport protein that generates voltage across a membrane; helps store energy that can be used for cellular work Cotransport: occurs when active transport of a solute indirectly drives transport of other substances - Plants commonly use the gradient of hydrogen ions generated by proton pumps to drive active transport of nutrients into the cell Exocytosis: transport vesicles migrate to the membrane, fuse with it, and release their contents outside the cell; many secretory cells use it to export their products Endocytosis: cell takes in macromolecules by forming vesicles from the plasma membrane (a reversal of exocytosis, involving different proteins); 3 types of endocytosis: 1. Phagocytosis: “cellular eating” 2. Pinocytosis: molecules dissolved in droplets are taken up when extracellular fluid is “gulped” into tiny vesicles; cellular drinking 3. Receptor-mediated endocytosis: binding of ligands to receptors triggers vesicle formation Bulk transport: large molecules, such as polysaccharides and proteins, cross the membrane in bulk via vesicles; requires energy Ligand: any molecule that binds specifically to a receptor site of another molecule Chapter 8: Introduction to Metabolism - Living cell is a mini chemical factory where thousands of reactions occur; it extracts energy stored in sugars and other fuels and applies energy to perform work (some organisms even convert energy to light as bioluminescence Metabolism: totality of an organism’s chemical reactions; emergent property of life that arises from orderly interactions between molecules Metabolic pathway: begins with a specific molecule and ends with a product; each step is catalyzed by a specific enzyme Catabolic pathways: release energy by breaking down complex molecules into simpler compounds (example: the breakdown of glucose in the presence of oxygen) Anabolic pathways: consume energy to build complex molecules from simpler ones (example: synthesis of protein from amino acids) Bioenergetics: study of how energy flows through living organisms Energy: capacity to cause change; exists in various forms and can be converted from one form to another (some of which can do work) Kinetic energy: energy associated with motion Heat (thermal energy): kinetic energy associated with random movement of atoms or molecules Potential energy: energy that matter possesses because of its location or structure Chemical energy: potential energy available for release in a chemical reaction Thermodynamics: study of energy transformations 1st law of thermodynamics (principle of conservation of energy): energy of the universe is constant; energy can be transferred and transformed, but cannot be created or destroyed