Review Notes.docx

Chapter 1: Themes in the Study of Life 1.1 Biology  Emergent properties: properties that are not present at the preceding level o Complexity increases: tissue→ cell→ organ→ organ system  Reductionism: reducing complex systems o simpler components for study  Systems biology: approach that attempts to model the dynamic behavior of whole biological systems based on the study of the interactions of the system’s parts o Predict how change in one variable affects other components Ecosystem Organization 1. Biosphere: all life on earth and where life exists 2. Ecosystem: forest, grassland, desert,; all living/nonliving things in a particular area 3. Communities: entire array of organisms in a particular area; trees, plants, fungi 4. Populations: all individuals of a species within a specific area 5. Organisms: individual living things 6. Organs and organ systems: stems, roots, brain, heart 7. Tissues: skin (epidermis) 8. Cells: single and multi-celled organisms; specialized cells (muscle, nerve) 9. Organelles: various functional components present in cells; chloroplasts 10. Molecules: chemical structure consisting of 2+ atoms; chlorophyll  Eukaryotic: multi-celled organism  Prokaryotic: lack membrane enclosure and nucleus  DNA (deoxyribonucleic acid): stored in chromosomes; is the substance of genes  Enzymes: catalysts for specific chemical reactions  Gene expression: info in a gene that directs production of a cellular product o Differences b/w organisms are changes in nucleotide sequence, not genetic code  RNA: translated into proteins; some manufactures protein  Genome: entire “library” of genetic instructions that is inherited  Negative feedback: accumulation of and end process slows that process  Positive feedback: end product speeds up own production  Cell’s breakdown of sugar produces ATP 1.2 Evolution 1. Species: ursus americanus 2. Genus: ursus 3. Family: ursidae 4. Order: carnivore 5. Class: mammalia 6. Phylum: chordata 7. Kingdom: animalia 8. Domain: a. Bacteria: rod-shaped b. Archaea: round and live in extreme environments c. Eukarya: plantae, fungi, protists, animalia  Natural selection: Charles Darwin 1. Individuals in a population vary in traits which seems to be heritable 2. Populations produce more offspring than can survive; competition 3. Species generally suit their environments; adaptation 1.3 Observations and Hypothesis  Inductive reasoning: collecting and analyzing observations to lead to important conclusions  Deductive reasoning: used after hypothesis developed o General to specific  Theory: encompass multiple hypotheses  Scientific fact: well-tested and confirmed but may be rejected in the future  Discovery science: descriptive or observational science 1.4 Cooperative Approach and Diverse Viewpoints  Model organism: a species that is easy to grow in a lab and lends itself particularly well to questioning Chapter 2: The Chemical Context of Life 2.1 Elements and Compounds  Essential elements: 20-25% of 92 elements needed to support life o 25 for humans, 17 for plants  Oxygen, carbon, hydrogen, nitrogen make up 96% of living matter o Phosphorus, potassium, and sulfur account for remaining 4%  Trace elements: required by an organism in minute quantities 2.2 Element Properties Depend on the Structure of Atoms  Dalton: unit of measure for atoms and subatomic particles; amu  Atomic number of protons (bottom number)  Mass number: sum of protons and neutrons (top number)  Isotope: same number of protons but different number of protons o Radioactive isotope: ones in which the nucleus decays spontaneously  Energy: capacity to cause change  Potential energy: energy matter possesses based on location or structure 2.3 Formation and Function of Molecules  Valence: bonding capacity  Substrates: reactants  Ionic compounds: salts  Biological molecules: can bond temporarily if shapes are complementary o Opiates, pain relievers 2.4 Making and Breaking Chemical Bonds  Chemical equilibrium: point at which reactants offset one another because of stabilized ratios o Reaction still occurs but with no net change in concentrations Chapter 3: Water and Life 3.1 Polar Covalent Bonds in H O2Result in Hydrogen Bonding  Each hydrogen in H O has partial positive charge b/c oxygen more electronegative 2 3.2 Four Emergent Properties of H O2Contribute to Earth’s Suitability for Life  Cohesion: linking together of like molecules often by H-bonding o Allows transport of H2O and dissolved nutrients against gravity  Adhesion: clinging of one substance to another o Adhesion of H 2 to cell walls by H-bonding counters gravity  Heat: measure of the total KE die to the motion of particles o Heat depends on volume  Temperature: measure of heat intensity o Average KE regardless of volume  Calorie: amount of heat required to raise the temp. of 1g 2f H O by 1°C  Joule: 1joule=0.239cal / 1cal=4.184J  Heat of vaporization: quantity of heat a liquid must absorb for 1g of liquid to turn into gas  Evaporative cooling: hottest molecules with most KE leave as a gas o As liquid evaporates, the surface of the liquid cools  Crystalline structure is less dense so ice floats b/c of empty space and molecules move too slowly to break H-bonds  Hydration shell: sphere of 2 O molecules around each dissolved ion  Colloid: stable suspension of fine particles in a liquid o Mostly large molecules like cellulose (partial charges can form H-bonds but not dissolve) 3.3 Acidic and Basic Conditions Affect Living Organisms  pH=-log[H ] +  Buffer: substance that accepts H from solution when in excess and donates when depleted o weak acid and conjugate base  Ocean acidification: CO2dissolves in seawater to react wit2 H O to form carbonic acid which lowers pH  Acid precipitation: pH lower than 5.2 Chapter 4: Carbon and the Molecular Diversity of Life 4.1 Organic Chemistry if the Study of Carbon Compounds  Major elements of life: C, H, O, N, S, and P 4.2 Carbon Atoms can Form Diverse Molecules by Bonding to Four Other Atoms  CO d2batable as organic since it lacks hydrogen  Hydrocarbons: organic molecules consisting of only hydrogen and carbon o Undissolvable in H 2 b/c hydrophobic and relatively nonpolar o Can undergo reactions that produce relatively large amounts of energy  Isomers: variation in the architecture of organic molecules 1. Structural: differ in covalent arrangements a. Saturated: fully bonded carbon chain with hydrogens i. > energy with more bonds b. Unsaturated: double bonds present 2. Geometric: arrangement around double bond 3. Optical/mirror/enantiomers: asymmetric carbon 4.3 Few Chemical Groups are Key to the Functioning of Biological Molecules 1. Hydroxyl: alcohols a. Polar b/c oxygen so can form H-bonds that dissolve organic molecules 2. Carbonyl: keytones(within) & aldehydes(end) a. Found in sugars 3. Carboxyl: carboxylic acids/organic acids + a. Acts as an acid b/c can donate H to ionize 4. Amino: amines a. Acts as a base b/c can pick up H from solutions 5. Sulfhydryl: thiols a. 2 sulfhydryl groups form a covalent bond: cross-liking stabilizes protein structures 6. Phosphate: organic phosphates (ATP) a. Potential to react with 2 O 7. Methyl: methylated crystals a. Nonpolar Chapter 5: Structure and Function of Large Biological Molecules 5.1 Macromolecules are Polymers, Built from Monomers  Polymer: long molecule consisting of many similar or identical building blocks linked by covalent bonds  Macromolecules: carbohydrates, proteins, and nucleic acids 5.2 Carbohydrates Serve as Fuel and Building Materials  Carbohydrates: include sugars and polymers of sugars  Monosaccharides: generally have formula that is multiple of CH O 2 o Glucose is most common o Used for cellular respiration and synthesis of amino and fatty acids  Glycosidic linkage: joins a disaccharide with a covalent bond through dehydration o Sucrose  Polysaccharides: polymers with 100s to 1000s of monosaccharides 1. Storage: starch is a polymer of sucrose monomers; glycogen stored in animal liver and muscle cells and hydrolysis of these releases glucose a. Amylose: unbranched b. Amylopectin: branched with 1-6 linkages 2. Structural: build polysaccharides a. Cellulose: major component in tough walls that enclose plant cells b. Chitin: carbohydrate used by arthropods to build exoskeletons 5.3 Lipids are a Diverse Group of Hydrophobic Molecules  Lipids: hydrophobic and are not large enough to be considered macromolecules 1. Fats: glycerol and fatty acids; purpose is to store energy o Glycerol: alcohol that has 3 carbons each with hydroxyl group  Triacylglycerol: 3 fatty acid molecules with glycerol linked by esther  Esther: bond b/w hydroxyl and carboxyl o Fatty acids: 16-18 carbons with carboxyl at one end  Saturated: only single bonds with as many H as possible; unhealthy  Unsaturated: one or more double bonds and has kinks so cannot pack as closely  Cis double bond: causes bonding and prevents solidifying at room temp.  Trans fat: formed artificially during hydrogenation of oils 2. Phospholipids: make up cell membranes 3. Steroids: carbon skeleton with 4 fused rings o Cholesterol: animal cell membranes, synthesis of hormones  Viscosity buffer system in phospholipid bilayer 5.4 Proteins Include Diversity of Structures therefore Wide Range of Functions  Polypeptides: polymers of amino acids o Protein: molecule of 1 or more polypeptides  Amino acid: amino and carboxyl group o Side chain determines each amino acid  Acidic aminos have (-) side charge and vice versa  Peptide bond: carboxyl group with amino bond formed through dehydration  Globular or fibrous proteins  Function depends on its ability to recognize and bind to other molecules Levels of Protein Structure: 1. Primary: linked series of amino acids with unique sequence 2. Secondary: alpha helix coils and beta pleated sheet folds (cellulose) that contribute to overall shape a. Interaction between backbone b. Result of H-bonds 3. Tertiary: overall shape of polypeptide from interactions between side chains a. Hydrophobic interaction: as poly folds into shape, nonpolar side chains cluster in middle (hydrophobic) b. Van der Waals hold together nonpolar; H-bonds for polar c. Disulfide bridges: 2 cysteine monomers with sulfhydryl groups brought together 4. Quaternary: overall protein structure from aggregation of polypeptide subunits  Sickle-cell disease: inherited blood disorder b/c substitution of one amino acid for another (valine for glutamic acid) at a particular position in hemoglobin o Abnormal hemoglobin molecules crystalize and deform cells to sickle shape  Denaturation: weak bonds and interactions cause protein to unravel and lose its shape  Chaperonins: crucial to folding process and keeps “bad influences” out o Alzheimer’s and Parkinson’s from accumulation of misfolded proteins  X-ray crystallography: used to determine the 3D structure of proteins  Nuclear magnetic resonance (NMR): spectroscopy that does not require protein crystallization 5.5 Nucleic Acids Store, Transmit, and Help Express Hereditary Info  Gene: discrete unit of inheritance  Nucleic acid: polymers made of nucleotides o Polynucleotides: DNA & RNA  Pyrimidine: cytosine, uracil, thymine  6-membered ring of carbon and nitrogen  Purine: adenine, guanine  6-membered ring fused with 5-member ring  Double helix: 2 polynucleotides  Antiparallel: 2 sugar phosphate backbone run opposite directions 5’→3’  DNA: provide instructions for its own replication, directs RNA synthesis, and controls protein synthesis in ribosomes o RNA: conveys genetic instruction for building proteins from nucleus to cytoplasm  Transfer RNA (tRNA): brings amino acids to the ribosome during polypeptide synthesis nd o Deoxyribose and ribose: deoxyribose lacks an oxygen on 2 carbon in ring Chapter 6: A Tour of the Cell 6.1 Microscopes and the Tools of Biochemistry  Organelles: membrane-enclosed structures in eukaryotic cells  Cell fractionation: takes cells apart and separates major organelles through centrifuge  Electron microscope: focuses a beam of electrons through specimen or onto surface o Resolution varies inversely to wavelength of radiation  Scanning electron microscope: detailed study of topography of a specimen  Transmission electron microscope: internal cell structure viewable by staining with heavy metals to enhance electron density 6.2 Eukaryotic Cells Compartmentalize Their Functions  Cytosol: jellylike substance in which subcellular components are suspended  Nucleoid: region of prokaryotic cells where DNA is not membrane-bound  Microvilli: long, thin projections that increase surface area w/o much increase in volume 6.3 Eukaryotic Genetic Instructions in Nucleus and Carried Out by Ribosomes  Nucleus enclosed by nuclear envelope o Double membrane with pore complex that regulates entry/exit of proteins  Nuclear lamina: netlike array of protein filaments that hold nucleus shape o Chromatin: complex of DNA and proteins that make up chromosomes  Nucleolus: ribosomal RNA synthesized from imported proteins  Ribosomes: made of rRNA and proteins 1. Free: suspended in cytosol; make proteins for function in cytosol 2. Bound: attached to outside 6.4 Endomembrane System Regulates Protein Traffic and Performs Metabolic Functions  Endoplasmic reticulum: network of membranes o Important for ER to make new components b/c ER shrinks every time vesicles departs o ER lumen/cisterna space: internal compartment of the ER o Glycoproteins: proteins that have carbohydrates 1. Rough: studded with ribosomes; protein synthesis 2. Smooth: outer surface lacks ribosomes, metabolic processes and enzymes; storage of ions, detox, fats production  Golgi apparatus: warehouse for receiving, sorting, and o Cis face: receiving; vesicles can add their contents to cis face by fusing with Golgi o Trans face: shipping; vesicles that pinch off and travel to other sites  Lysosome: membranous sac of hydrolytic enzymes used to digest (hydrolyze) macromolecules; acidic  Phagocytosis: intercellular digestion of smaller organisms of food particles o Autophagy: use of hydrolytic enzymes to recycle cell’s own organic material  Vacuole: large vesicles derived from ER and Golgi o Food: formed by phagocytosis o Contractile: pump excess H O out of cell to maintain concentration 2 o Central: coalescence of smaller vacuoles that contains inorganic ions; only in plant cells 6.5 Mitochondria and Chloroplasts Change Forms of Energy  Mitochondria: sites of cellular respiration; uses oxygen to generate ATP by extracting energy from sugars and fats o Mitochondrial matrix: enclosed by the inner membrane and contains mitochondrial DNA and ribosomes; respiration proteins  Chloroplasts: 2 phospholipid bilayers and composed of thylakoid o Thylakoids: flattened, interconnected sacs; stacked like poker chips  Granum: each stack of thylakoids  Stroma: fluid outside thylakoids  Cristae: foldings in the inner membrane  Plastids: one of a family of closely related organelles that include chloroplasts o Amyloplast: colorless organelle that stores starch o Chromoplast: orange and yellow pigments  Peroxisomes: metabolic compartment bounded by single membrane o H2O 2s toxic so enzyme converts H2O2to H 2 2 o Glyoxysomes: fat-storing tissues of plant seeds  Fatty acid to sugar for energy until self-sufficient with photosynthesis 6.6 Cytoskeleton is a Network of Fibers that Organizes Structures and Activities  Cytoskeleton: network of fibers through cytoplasm o Microtubules: hollow rods of alpha and beta tubulin  Dimer: molecule made of 2 subunits  Centrosome: microtubule organizing center  Centrioles: 1 pair per centrosome  Flagella and cilia: microtubule-containing extensions  Basal body: anchors microtubule assembly  Dyneins: large motor protein that connects doublets o Microfilaments: solid rods of twisted double chain of actin to hold shape  Cortex: outer cytoplasmic layer supported by network  Myosin: motor protein by means of projections that walk on actin filaments  Pseudopodia: “false foot”; extension by actin subunits o Intermediate filaments: named for diameter; bears tension and fixes organelle positions 6.7 Extracellular b/w Cells Help Coordinate Cellular Activities  Middle lamella: thin layer of pectins that glues adjacent cells together  Plasmodesmata: perforated channels b/w cytoplasm of adjacent cells  Extracellular matrix (ECM): glycoprotein and other carbohydrates o Collagen most abundant glycoprotein  Proteoglycan molecules: core protein with carbs attached  Proteoglycan complexes: PG molecules join with long polysaccharides o Fibronectin: bind to cell-surface receptors called integrins  Integrins: cell surface receptor proteins  Gap junction: connects cytoplasm and communicates with intermediate filaments  Tight junction: bands that circle all the way around and limit leakage  Desmosome: adhere with plaques of proteins Chapter 7: Membrane Structure and Function 7.1 Cellular Membranes are Fluid Mosaics of Lipids and Proteins  Integral proteins: penetrate hydrophobic interior of bilayer  Peripheral proteins: appendages bound loosely to membrane surface Protein Functions: 1. Transport: selectively permeable hydrophilic channel; may change shape to accommodate 2. Enzymatic activity: protein built into membrane may be an enzyme 3. Signal transduction: membrane protein receptor has shape that fits a specific chemical message 4. Cell-cell recognition: glycoproteins serve as i.d. tags that are specifically recognized by membrane proteins 5. Intercellular joining: membrane proteins of adjacent cells hook together in gap or tight junctions 6. Attachment to cytoskeleton and ECM: microfilaments or other elements noncovalently bind to membrane proteins to maintain cell shape and stabilize location  Glycolipids: covalent bond of carb and lipid o Glycoprotein: covalent bond of protein and lipid 7.2 Membrane Structure Results in Selective Permeability  Transport proteins: allow hydrophilic or polar ions t pass through membrane o Channel proteins: have hydrophilic channel for molecules o Carrier proteins: hold passengers and change shape to pass membrane 7.3 Passive Transport is Diffusion of a Substance w/o Energy Investment  Concentration gradient: represents PE and density  Tonicity: ability of a surrounding solution to cause a cell to gain/2lose H O o Isotonic, hypertonic, hypotonic o Plants are happiest in hypotonic environment  Osmoregulation: control of the concentration of the solute’s an2 H O balance o Turgor pressure: back pressure on cell that opposes further H O uptake 2  Turgid and flaccid  Plasmolysis: as plant cell shrivels, plasma membrane pulls away from the cell wall 7.4 Active Transport Uses Energy to Move Solutes against Gradients  Sodium-potassium pump: exchanges Na for K across plasma membrane to induce protein to change shape that translocates a solute bound to protein across the membrane  Membrane potential: voltage from -50 to -200m with cytoplasmic side: (-) so favors cations in o Drives diffusion  Electrogenic pump: generates voltage across membrane o Proton pump: plant version; H out of cell; uniport: one direction o Cotransport: single port that transports specific solute and indirectly drives active transport of other solutes 7.5 Bulk Transport across Plasma Membrane by Exocytosis and Endocytosis 1. Phagocytosis: cell engulfs a particle by wrapping pseudopodia 2. Pinocytosis: cell engulfs droplets 3. Receptor-mediated: enables cell to acquire in specific bulk  Ligands: low-density lipoproteins: molecules that bind specifically to a receptor site on another molecule Chapter 8: An Intro Into Metabolism 8.1 An Organism’s Metabolism Transforms Matter & Energy Subject to the Law of Thermodynamics  Metabolism: totality of an organism’s chemical reactions o Cell at metabolic equilibrium is dead o Metabolic pathway: specific and organized; allows for amplification  Catabolic: release energy by breaking don molecules  Cellular respiration: glucose broken down with O to form CO + H O 2 2 2  Anabolic: consumes energy to build complicated molecules  Photosynthesis  Synthesis of amino acids and then synthesis of proteins from amino acids  Energy: capacity to cause change; ability to rearrange a collection of matter o Thermal energy: KE associated with random movements of atoms and molecules  Thermodynamics: study of energy transformations o Isolated systems: unable to exchange energy or mater with its surroundings o Open system: able to exchange 1. First Law: energy transferred, not created nor destroyed 2. Second