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by: Hannah B.


Hannah B.
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This is the completed study guide for Dr. Bowling's FRO 1
Principles of Biology
Scott Anthony Bowling
Test Prep (MCAT, SAT...)
Auburn University, auburn, BIOL 1020, BIOL, Bio, Biology, Bowling, Principles of biology
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This 19 page Test Prep (MCAT, SAT...) was uploaded by Hannah B. on Thursday February 4, 2016. The Test Prep (MCAT, SAT...) belongs to BIOL 1020 at Auburn University taught by Scott Anthony Bowling in Summer 2015. Since its upload, it has received 34 views.

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Date Created: 02/04/16
Group 1: Scientific Method – know the general sequence of the scientific method and what makes a good hypothesis; distinguish deductive reasoning from inductive reasoning DEDUCTIVE REASONING: general reasoning -> specific reasoning INDUCTIVE REASONING: specific reasoning -> general reasoning Characteristics of Living Matter – know the characteristics of living things - made up of cells - regulate their metabolism - grow and develop - perceive and respond to stimuli
 - reproduce Page 1 of 19 Information Transfer in Living Systems – know the general methods of information exchange between cells and between cell generations Cells “talk” to each other through cell signaling via special molecules (such as hormones and neurotransmitters) Organisms signal state via behavior Diversity of Biological Organisms – know the classification scheme (Dashing King Phillip....DKPCOFGS), the relationships (and the basis for them) between the widely accepted 3 domains and 6 kingdoms; and how to write species names Taxonomy: the science of classifying and naming organisms Carolus Linnaeus: 18th century Swedish botanist; developed a system of classification that is the basis of what is used today Dashing King Phillip Came Over For Great Sex - Species: basic unit of classification or taxonomy Genus: group of closely related species Family: group of related genera Order: related families Class: related orders Phylum: related classes; also known as division Kingdom: related phyla or divisions Domain: related kingdoms; highest level of classification Domain Archaea - Kingdom Archaebacteria bacteria found in extreme environments Domain Bacteria - Kingdom Eubacteria very diverse group; pretty much all but archaebacteria Page 2 of 19 Domain Eukarya - Kingdoms Anamalia, Protista, Plantae, and Fungi Protista: single celled and simple multicellular; have nuclei; protozoa, algae, water molds, and slime molds Fungi: organisms with cell walls consisting of chitin; mostly multicellular, multi-tissued, decomposers; molds, yeasts, and mushrooms Plantae: multicellular organisms w/ tissues and organs; cell walls made of cellulose; producers; nonvascular (mosses) and vascular (ferns, conifers, flowering plants) Anamalia: multicellulars that depend on other organisms for nourishment; lack cell walls; organs and organ systems; most forms are motile Domain Archaea and Bacteria are prokaryotes: organisms with no true cellular nucleus Domain Eukarya is made of eukaryotes: organisms with discrete cellular nucleus Life Depends on Energy – know how energy flows through ecosystems, and the particular roles of producers, consumers, and decomposers To maintain existing cellular structures and components (replacement of damaged or worn out materials within the cell) To produce materials to support growth, development, and reproduction To support movement (either of the cell itself or of materials into and out of the cell), signaling responses (such as hormone production and perception, nerve impulses, etc.), other forms of cell work (symbiotic relationships with other organisms, defense against pathogens) Producers (autotrophs): manufacture their own food from simple materials Consumers (heterotrophs): obtain energy by eating other organisms (producers) Decomposers (heterotrophs): obtain energy by breaking down the waste products, by products, and dead bodies of producers and consumers Photosynthesis: Carbon Dioxide + Water + Light Energy ——> Carbohydrate (food) + Oxygen Respiration: how energy is released from food Carbohydrate (food) + Oxygen ——> Carbon dioxide + Water + energy Page 3 of 19 Group 2: Elements andAtoms – know the 12 elements commonly found in living organisms by name and chemical symbol; C,H, O, and N make up 96% of living organisms; interpret atomic diagrams for such things as atomic number, isotopes, numbers of protons, neutrons, and electrons, etc.; role of valence shell/electrons in chemistry (rule of 8) Oxygen, Carbon, Hydrogen, Nitrogen, Calcium, Phosphorus, Potassium, Sulfur, Sodium, Chlorine, Magnesium, Iron Isotopes: # of protons same, # of neutrons different Radioisotopes: most unstable isotopes Atoms: protons = electrons Orbitals: electron energy levels, locations probabilities Electron Shell: orbitals with similar energies; valence is highest-energy electrons Atomic Combinations – recognize different ways of writing chemical formulas; understand the mole and molecular mass Molecule: has covalent bonds, smallest unit of molecular substance (ex. O2, H2O) Compound: two+ different elements combined, may have ionic bonds (ex. Sodium, Chlorine) Page of 19 Chemical Formula:# of atoms of each element; molecular formula (ex. H2O, O2, C6H12O6) Structural Formula: arrangement of atoms (ex. Water = H—O—H, Carbon dioxide = O==C==O) Molecular mass: sum of the atomic masses in a molecule Mole: # molecules for gram amount to = atomic mass Avagadro’s number: 6.02 x 10^23 atoms Chemical Bonds – recognize different bonds in diagrams; know what these bonds are (ionic = opposite charges coming together, covalent = shared electron pair, etc.); know relative bond strengths (covalent>ionic>hydrogen) Covalent bonds: electrons shared in pairs (1= single covalent bond); carbon forms four total Nonpolar: equal sharing Polar: unequal sharing j Ionic bonds: ions of opposite charge; polar substances, such as water, tend to dissolve ionic compounds Hydrogen bonds: weak interaction but very strong collectively; positive and negative (usually positive is H); common and important in living things; water forms them Bond Strengths: covalent > ionic > hydrogen Page 5 of 19 Chemical Equations – know how to interpret chemical equations; know equilibrium as reactions occurring simultaneously and at the same rate in both directions Reactants and Products: reactants on left, products on right Arrows: shows direction; double shows equilibrium but different lengths shows one is favored Redox – know what is oxidized and what is reduced in the rusting example; know how the terms relate to electron movement, and that energy goes with electrons when they are moved (thus a reduced atom or molecule has more energy than it did before it was reduced) Oxidation: a chemical process in which an atom, molecule, or ion loses an electron Oxygen is a common oxidizing agent Reduction: an electron is gained Example is rusting…. 4Fe + 3O2 —> 2Fe2O3 4Fe —> 4Fe^3+ + 12e- 3O2 + 12e- —> 6O^2- Group 3: Properties of Water – know the unusual properties of water due largely to hydrogen bonding, such as heat stability (heats or cools slowly compared to most other substances), ice floating, adhesion and cohesion and their consequences, roles of water in living organisms and the biosphere as a temperature buffer and as a solvent Four properties of water: (1) water is the principal solvent in living things highly polar = excellent solvent for other polar substances, and for ionic compounds Page of 19 hydrophilic substances = interact readily with water hydrophobic substances = do not interact readily with water; non polar (2) water exhibits both cohesive and adhesive forces cohesive forces = attraction of water molecules to each other give water a high surface tension adhesive forces = water molecules to be attracted to other kinds of molecules; how things are made wet capillary action = water moving through narrow tubes even against gravity; results from cohesion and adhesion; living organisms take advantage of this (3) water helps maintain a stable temperature high specific heat of water —> temperature stability specific heat = energy to raise the temperature of 1 gram of something 1C hydrogen bonds make water specific heat high…. 1 calorie/gram C heat of vaporization = energy to move 1 gram from liquid to gas (4) ice (solid water) floats in liquid water liquid water becomes denser as it cools, but only up to a point Acids and Bases – recognize likely acids and bases from chemical formulas (HA– acid; – base; whereAcan be any anion, B any cation); basis of pH scale, its logarithmic nature and directionality (pH 7 is neutral, pH 5 is acidic, pH 4 is 10x more acidic than pH 5, etc.); recognize a pH buffer from its effects Acids: proton donors; dissociates to yield hydrogen ions (H+) in a solution HA (an acid) <—> H+ + A- (an anion) when the atom loses its electron to become a hydrogen ion, all that remains is the nucleus —> sometimes referred to as proton —> any substance that yields a proton is an acid, or an acid is a proton donor Bases: proton acceptors; dissociates to yield hydroxide ions NaOG <—> Na+ + OH- ; B (a base) + HOH <—> BH+ + OH- Page 7 of 19 Buffers: minimize pH changes; weak acids and weak bases Solvent: a liquid into which a substance dissolves Solute: the dissolved substance Solution: solvent + solute Salts: form from acids and bases; water is formed Electrolytes: salts, acids, or bases that form ions in water and thus can conduct an electrical current when dissolved in water (pure water is a poor conductor of electricity, but put salt and it becomes an excellent conductor) Mixtures: a mixture of two or more elements and/or compounds; they can be broken down into elements and compounds by simple physical means; heterogeneous vs. homogeneous Group 4: Organic Compounds – role of carbon in organic compounds; diversity of organic compounds Organic Compounds have at least one carbon atom covalently bound to either another carbon atom or to hydrogen Carbon is not a strongly electron seeking element and it does not readily give up its electrons therefore: carbon does not readily form ionic bonds and it almost always forms covalent bonds Carbon can form up to four covalent bonds (typically forms all four) Hydrocarbons contain only hydrogen and carbon Single carbon-carbon bonds allow rotation around them and lend flexibility to molecules Isomers – recognize different isomer types from examples; importance of isomers in biology (isomers often have different compound natures, essentially only L-amino acids are used, etc.) Isomers have the same molecular formula, have different structures, are either structural or stereoisomers Structural Isomers: substances with the same molecular formula that differ in the covalent arrangement of their atoms; example = ethanol and dimethyl ether Stereoisomers: substances with the same arrangement of covalent bonds, but the order in which the atoms are arranged in space is different; types are enantiomers and diastereomers Page 8 of 19 Cis-Trans Isomers: diastereomers associated with compounds that have carbon-carbon double bonds; larger items together = cis; larger items opposite = trans Enantiomers: substances that are mirror imaged of each other and that cannot be superimposed on each other; sometimes called optical isomers Functional Groups – recognize different functional groups by name; recognize natures of these groups (polar, , weakly basic or acidic) Functional groups: groups of atoms covalently bonded to a carbon backbone that give properties different from a C-H bond determines the major classes of organic molecules Hydroxyl group: polar; found in alcohols Carbonyl group: polar; found in aldehydes and ketones Carboxyl group: weakly acidic; found in organic acids (such as amino acids) Amino group: weakly basic; found in suck things as amino acids Sulfhydryl group: essentially non polar; found in some amino acids Phosphate group: weakly acidic; found in such things as phospholipids and nucleic acids Methyl group: nonpolar (thus hydrophobic); found in such things as lipids, other membrane components Page 9 of 19 Polymers – roles of hydrolysis (breaks with water) and condensation (joins monomers, removes equivalent of water) Polymers: long chains with repeating subunits (monomers) proteins - amino ac;dsnucleic acids - nucleotides Macromolecules: very large polymers (100s of subunits) Hydrolysis: “break with water” Condensation: dehydration synthesis Groups 5 and 6: Lipids, Carbohydrates; Proteins and related compounds; Nucleic Acids and related compounds
 For both of these groups, know the names of types of compounds placed in each class (DNA, steroid, starch, etc.); be able to classify a compound into one of these based on a diagram of the compound; be able to distinguish between a carbohydrate and a lipid based on chemical formula alone; know the subunit building blocks where appropriate (monosaccharides, glycerol + 3 fatty acid chains, amino acids, nucleotides, etc.); know special bond names and what type of polymer uses them (peptide bond in proteins, phosphodiester bond in nucleic acids, etc.); know the roles associated with molecules from each group (phospholipid bilayer in biological membranes,ATPas energy currency, etc.); know the roles of amino acid variable groups (R-groups) in amino acids; given an image of an R group, be able to classify it as polar/charged/nonpolar and hydrophobic/hydrophilic; be able to distinguish between protein structure levels; know the differences between DNAand RNA; know the basepairing rules for both DNAand RNA Page 0 o 9 Carbohydrates: carbon, hydrogen, and oxygen ; ratio typically (CH2O)n ; sugars, starches, cellulose main molecules of life for energy storage; consumed for energy production monosaccharides: single monomer; 3-7 carbons; glucose and galactose are diasteromers disaccharides: two monosaccharide units joined by a glycosidic linkage or bond condensation maltose, sucrose, lactose polysaccharides: number of subunit varies (typically thousands); branched or unbranched starch, glycogen, cellulose starch: main energy storage of carbohydrate of plants amylose: unbranched starch ; amylopectin: branched starch (branched usually 1-6 linkages) ; amyloplasts: a type of plastid for starch storage glycogen: main energy storage carbohydrate of animals; very highly branched; more water-soluble; in not stored in an organelle; mostly found in liver and muscle cells cellulose: major structural component plant cell walls; cannot be digested by most organisms; major constituent of cotton, wood, and paper; ~50% of the carbon found in plants Lipids: defined by solubility, not structure ; oily or fatty compounds lipids are principally hydrophobic (mainly carbon and hydrogen, some do have polar and non polar regions, some oxygen and/or phosphorus, mainly in polar regions) roles include serving as: membrane structural components, signaling molecules, energy storage molecules triacylglycerols: glycerol + 3 fatty acids glycerol: 3C sugar alcohol w/ 3 (-OH) groups fatty acid: long, unbranched hydrocarbon chain w/ (-COOH) at end most abundant, important sources of energy saturated fatty acids: no carbon-carbon double bonds (solid at room temperature) unsaturated fatty acids: one or more double bonds (liquid at room temp) Page 1 1 of 9 phospholipids: a diacylglycerol molecule, a phosphate group esterified to the third -OH group of glycerol, an organic molecule (such as choline) esterified to the phosphate amphipathic: polar end (the phosphate and organic molecule) and nonpolar end (the two fatty acids) terpenes: long-chained lipids built from 5-carbon isoprene units ; include natural rubber and essential oils steroids: terpene derivatives that contain four rings of carbon atoms; ex. is cholesterol, testosterone Proteins: macromolecules formed from amino acid monomers; great structural diversity and preform many roles, including enzyme catalysis, defense, transport, structure/support, motion, regulation; structure determines function amino acids consist of a central or alpha carbon bound to….hydrogen, amino group, carboxyl group, variable side chain peptide bond: joins the carboxyl group of one amino acid to the amino group of another by a condensation reaction two amino acids fastened together by a peptide bond is called a dipeptide, several amino acids fastened together by a peptide bonds are called a polypeptide primary structure: (1degree) of a protein is the sequence of amino acids in the peptide chain Page 1 2 of 9 secondary structure: (2degree) of a protein results from hydrogen bonds involving the backbone, where the peptide chain is held in structures tertuary structure: (3degree) of a protein is the overall folded shape of a single polypeptide chain; determined by secondary structure combined with interactions between R groups quaternary structure: (4degree) of a protein results from interactions between two or more separate polypeptide chain denaturation: unfolding of a protein disrupting 2, 3, and 4 structure enzymes: biological substances that regulate the rated of the chemical reactions in living organisms Nucleic Acids: hereditary information DNA(carried the genetic information-AGCT); RNA(functions in protein synthesis-AGCU) ATP: adenosine triphosphate; important energy carrying compound cAMP: cyclic adenosine monophosphate; hormone intermediary compound NAD+: nicotinamide adenine dinucleotide; electron carrier (metabolic redox) Group 7: Cell Theory – know the statements of cell theory All living organisms are composed of cells smallest building blocks of all multicellular organisms all cells are enclosed by a surface membrane that separates them from other cells and from other cells and from their environment specialized structures with the cell are called organelles; many membrane-bound All new cells arise from existing cells All presently living cells have a common origin all cells have basic structural and molecular similarities, all cells share similar energy conversion reactions, all cells maintain and transfer genetic information in DNA, the genetic code is essentially universal Page 1 3 of 9 Surface-to-Volume Limitation – know why surface area is needed and how the ratio limits cell size; interpret diagrams or word problems relating to surface area and volume Cell size is limited - surface area to volume ratio puts a limit on cell size food and/or other materials must get into the cell, waste products must be removed from the cell, cells need a high surface area to volume ratio VOLUME increases faster than surface area as cells grow larger Studying Cells – know importance of resolution in microscopy, the reason for resolution limits (wavelength of light or electrons), relative resolving power of LM and EM, differences in TEM and SEM; use of cell fractionation and centrifugation to separate cell components based largely on density Most cells are large enough to be resolved from each other with light microscopes (LM) cells were discovered by Robert Hooke who saw the remains of cell walls in cork with a LM, had about 30x magnification -> modern LMs can reach up to 1000x LM resolution is limited about 1 μm due to the wavelength of visible light; only about 500x better than the human eye Resolution of most subcellular structure requires electron microscopy (EM) electrons have much smaller wavelength than light (resolve down to under 1nm); magnification up to 250k or more; resolution 500k better than human eye transmission electron microscopy (TEM) electron passes through a sample, need very thin samples (100nm or less), embedded in plastic and sliced with a diamond knife scanning electron microscopy (SEM) samples are gold-plated; electrons interact with the surface; imaged have a 3D appearance Page 1 4 of 9 Eukaryotic vs. Prokaryotic – differences between these cell types (internal membranes or not; differences in usual size); similarities (both have DNA, ribosomes, plasma membrane) Prokaryotic Cells do not have internal membranes (thus no nuclear membrane) main DNA molecule (chromosome) is typically circular; its location is called the nuclear area other small DNA molecules (plasmids) are often present, found throughout the cell plasma membrane is typically enclosed in a cell wall, often covered with a sticky layer of proteins and/or sugars called a capsule do not completely lack organelles; have plasma membrane and ribosomes Eukaryotic Cells have internal membranes and a distinct, membrane enclosed nucleus; 10-100 μm Groups 8 and 9: Nucleus, Ribosomes; Endomembrane System (ER, Golgi, vesicles, lysosomes, vacuoles, microbodies); Energy Organelles and Endosymbiont Theory
 Be able to recognize specific organelles from diagrams or descriptions (structure); also know their roles (functions) in the cell (ribosomes in protein synthesis, etc.). Take advantage of the summary of information presented in Figure 6.8. Compartments in Eukaryotic Cells Two general regions inside the cell are cytoplasm (everything outside the nucleus and within the plasma membrane - contains fluid cytosol and organelles) and nucleoplasm (everything within the nuclear membrane) membranes separate cell regions - have non polar regions that help form a barrier between aqueous region and allow for some selection in what can cross a membrane (more details later) Nucleus — the control center of the cell typically large (~5 μm) and singular Page 1 5 o 9 nuclear envelope: double membrane surrounding the nucleus nuclear pores: protein complexes that cross both membranes and regulate passage chromatin: DNA-protein complex have a granular appearance; easily stained for microscopy (“chrom-“ = color); “unpacked” DNA kept ready for message transcription and DNA replication; proteins protect DNA and help maintain structure and function; chromosomes: condensed or “packed” DNA ready for cell division (“-some” = body) nucleoli: regions of ribosome subunit assembly appears different due to high RNA and protein concentration (no membrane); ribosomal RNA (rRNA) transcribed from DNA there; proteins (imported from cytoplasm) join with rRNA at a nucleolus to form ribosome subunits; ribosome subunits are exported to the cytoplasm through the nuclear pores Ribosomes: the sites of protein synthesis ribosomes: granular bodies with three RNA strands and about 75 associated proteins; two main subunits, large and small; perform the enzymatic activity for forming peptide bonds, and serve as the sited of translation of genetic information into protein sequences prokaryotic ribosome subunits are both smaller than the corresponding subunits in eukaryotes; in eukaryotes, the two main subunits are formed separately in the nucleolus and transported separately to the cytoplasm and some are free in the cytoplasm while others are associated with the endoplasmic reticulum (ER) Endomembrane system: set of membranous organelles that interact w/ each other via vesicles includes ER, Golgi apparatus, vacuoles, lysosomes, micro bodies, and in some definitions the nuclear membrane and the plasma membrane Endoplasmic reticulum (ER): membrane network that winds through the cytoplasm ER lumen: internal aqueous compartment in ER smooth ER: primary site of lipid synthesis, many detoxification reactions, and sometimes other activities rough ER:ribosomes that attach there insert proteins into the ER lumen as they are synthesized; ribosome attachment directed by a signal peptide at the amino end of the polypeptide; a protein/RNA signal recognition particle (SRP) binds to the signal peptide and pauses translation proteins are transported from the ER in transport vesicles Page 1 6 of 9 vesicles: small, membrane-bound sacs; buds off an organelle and transports contents Golgi apparatus: a stack of flattened membrane sacs (cisternae) where proteins further processes, modified, and sorted (the “post office” of the cell) cis face: near ER and receives vesicles from is; current model holds that vesicles actually coalesce to continually form new cis cisternae medial region: as a new cis cisterna is produced, the older cistern mature and move away from the ER trans face: nearest to the plasma membrane; a fully matured cisterna breaks into many vesicles that are set up to go to the proper destination taking their contents with them lysosomes: small membrane-bound sacs of digestive enzymes; serves to confine the digestive enzymes and their actions vacuoles: large membrane-bound sacs that perform diverse roles; have no internal structure central vacuole: typically single, large sac in plant cells that can be 90% of the cell volume tonoplast: membrane of the plant vacuole food vacuole: present in most protozoa and some animal cells; usually bud from plasma membrane and fuse with lysosomes for digestion contractile vacuoles: used by many protozoa for removing excess water microbodies: small membrane-bound organelles that carry out specific cellular functions peroxisomes: sites of many metabolic reactions that produce hydrogen peroxide, which is toxic to the rest of the cell glyoxysomes: in plant seeds, contains enzymes that convert stored fats into sugar Energy Converting Organelles mitochondria: the organelles where chemical energy is placed in a more useful molecule; the site of aerobic respiration inner membrane is highly folded, forming cristae; provides a large surface area inside the inner membrane is the matrix, analogous to the cytoplasm of a cell have their own DNA, division process, leak electons into the cell, play a role in initiating apoptosis (programmed cell death) Page 1 7 of 9 plastids: organelles of plants and algae that produce and store food amyloplasts (for starch storage), chromoplasts (for color, often found in petals and fruits), chloroplasts (for photosynthesis) chloroplasts: plastids where light energy is captured during photosynthesis; double membrane endosymbiont theory: mitochondria and plastids evolved from prokaryotic cells that took residence in larger cells and eventually lost their independence; the cells containing the endosymbionts become dependent upon them for food processing, and in turn provide them with a protected and rich environment Group 10: Cytoskeleton – know roles of cytoskeleton; components, roles, and relative sizes of the different types of proteins fibers involved; associated proteins and structures such a motor proteins, flagella; recognize 9x3 structures and 9+2 arrangements and know where they occur Cytoskeleton: a dense network of protein fibers that provides needed structural support; composed of microtubules, microfilaments, and intermediate filaments Page 1 8 o 9 Microtubule-Organizing Centers (MTOCs) serve as anchors centrosome in animal cells; has two centrioles in a perpendicular arrangement; nine sets of three attached microtubules forming a hollow cylinder play an organizing role for microtubule spindles in cell division motor proteins (such as kinesin or dynein) attach to organelle and to microtubule cilia and flagella are made of microtubules stalk has two inner microtubules surrounded by nine attached pairs of microtubules Outside the Cell – know what types of materials are associated with the outsides of cells from different organisms (plants – cellulose in cell wall; fungi – chitin in cell wall; animals – ECM with carbohydrates and proteins, mainly collagen, fibronectins, and integrins); roles of material outside cell in structure, signaling Most prokaryotes have a cell wall, an outer envelope, and a capsule (capsule is also called glycocalyx or cell coat) Plants have thick, defined cell walls made primarily of cross-linked cellulose fibers Fungi typically have thinner cell walls than plants, made primarily of cross-linked chitin fibers Animals do not have cell walls, but their cells secrete varying amounts of compounds that can produce a glycocalyx and an extracellular matrix (ECM) glycocalyx: polyscaccharides attached to proteins and lipids on the outer surface of the plasma membrane ECM: a gel of carbohydrates and fibrous proteins; several different molecules can be involved main structural protein is tough, fibrous collagen fibronectins are glycoproteins in the ECM that often bind to both collagen and integrins (proteins in the plasma membrane that typically receive signals from the ECM) Page 1 9 of 9


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