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Unformatted text preview: BIO 202 FINAL EXAM REVIEW SHEET Chapter 2: The Chemical Context of Life Matter: anything that takes up space and has mass (all organisms made of matter) ● Element : substance that cannot be broken down to other substances by chemical reactions ○ Essential elements : elements required for organisms to live healthy life and reproduce ○ Trace elements : elements required by organisms in only minute quantities ○ Atom : smallest unit of matter that still retains properties of an element ■ Composed of s ubatomic particles : protons (+), neutrons, electrons (­) ● Atomic nucleus: protons and neutrons closely packed together at center ● Electron cloud: negatively charged cloud surrounding positive nucleus ○ Isotope : atom of a given element that has a different number of neutrons ■ Radioactive isotope : isotope where nucleus decays spontaneously, giving off energy and particles ● If number of protons changes, it decays into a different element ● Compound : substance consisting of 2 or more elements in a fixed ratio ○ Has characteristics different from those of its elements Energy : capacity to cause change (ie. doing work) ● Potential energy : energy that matter possesses because of its location/structure ● Electron shell : location of electrons, each with a characteristic average distance and energy level ○ Energy level correlates to average distance from nucleus (closer to nucleus = less energy) ■ Valence shell = outermost = most potential energy (houses v alence electrons ) ○ Orbital : 3D space where electrons are found 90% of the time ■ Only 2 electrons per orbital Chemical Bonds : attraction from interactions between valence electrons of atoms that hold them together ● Covalent bond : sharing of a pair of electrons between 2 atoms ○ Molecule : two or more atoms held together by covalent bonds ■ Single bond : 1 pair of shared electrons; d ouble bond : 2 pairs of shared electrons ○ Valence : bonding capacity (number of bonds an atom can form) ○ Electronegativity : attraction of an atom for electrons of another atom ■ Nonpolar : electrons shared equally between atoms ■ Polar : one atom has stronger attraction to electrons ­ electrons not shared equally ● Ionic bond : bond formed by two ions after transfer of electrons ○ ion = charged atom (cation = +, anion = ­) ○ Ionic compounds/salts : compounds formed by ionic bonds ● Hydrogen shells : hydrogen atoms bonded to one electronegative atom is attracted to another electronegative atom nearby ● Van der waals : ever­changing regions of positive and negative charges on an atom enable them to stick to another atom ○ Intermolecular forces ­ weak ○ Only occur when atoms/molecules are close together Chemical reactions : making and breaking of chemical bonds (conversion of reactants to products) ● BREAK IN MAKE OUT ­ breaking bonds requires energy in, making them releases energy ● Equilibrium : point in which forward reaction equals reverse reaction ○ Concentration of products and reactants not changing Chapter 3: Water and Life Water = p olar molecule that creates V shape ­ Highly polar ­ unequal sharing of electrons creates positive end near hydrogens and negative end near oxygen ­ C ohesion : binding of water molecules with one another due to hydrogen bonding ● Attractions between molecules ­ hydrogen bonds often form, break, and re­form ● Adhesion : clinging of one substance to another (counters downward pull of gravity) ● Surface tension : measure of difficulty to stretch or break surface of liquid (because of hydrogen bonding of molecules) ­ Moderates air temperature by absorbing large amounts of heat with slight change in its own temperature (because of constant breaking and making of Hydrogen bonds) ● Kinetic energy : energy of motion ○ Heat : form of energy ­ total kinetic energy due to motion of molecules ● Water = h igh specific heat (amount of heat that must be absorbed for 1g of substance to change its temperature by 1o C) ­ h eat of vaporization : quantity of heat a liquid must absorb for 1g of it to be converted to gaseous state ● Evaporative cooling : as liquid evaporates, the surface of the liquid that remains cools down ● Water’ h igh heat of evaporation causes stability of temperature and ability to regulate temperature ­ ice less dense than liquid ­ allows life to exist because only top layer of water freezes ­ very versatile s olvent because of polarity ­ can dissolve many other things ● Solution : liquid that is a completely homogenous mixture of 2 or more substances ○ Solvent dissolves s olute (substance being dissolved) ● Hydration shell : sphere of water molecules around each dissolved ion (because of polarity) ● Hydrophilic : any substance that has affinity for water ○ Colloid : stable suspension of fine particles in a liquid (can’t dissolve because of size, but remains suspended in aqueous conditions) ● Hydrophobic : substances that not only do not have affinity towards water, but also see to repel it ○ Nonionic and nonpolar substances ­ m olecular mass : sum of masses of all atoms in a molecule (used to calculate number of molecules) ● Molarity : number of moles of solute per liter of solution (unit of concentration) ­ a cid : substance that increases hydrogen ion concentration of a solution ­ donates H+ ­ b ase : substance that decreases hydrogen ion concentration of a solution ­ accepts H+ ­ p H scale : measures H+ ions/acidity over orders of magnitude ● 0­14, water = 7 = neutral, product of [H + ] and [OH ­ ] will always be 10 ­14 ● H 3 O + : hydronium, H+ binds to another water molecule ­ acidic ­ b uffers : substances that minimize pH changes ­ accepts or donates H+ ions when they’re in excess/depleted ● Contributes to pH stability ­ a cidification : threat to water quality posted by human activities ● Ocean acidification : when CO 2 dissolves in water, it reacts with water to form carbonic acid, which lowers ocean pH ● Acid precipitation : precipitation with pH lower than 5.2 can damage life in lakes and streams and affect plants by changing soil chemistry ○ Result of burning fossil fuels Chapter 4: Carbon and the Molecular Diversity of Life Organic chemistry : branch of chemistry that specializes in the study of carbon compounds ● Carbon = v ersatility : 4 valence electrons vary in number of bonds, bond length, branching, double bond position, and presence of rings ● Hydrocarbon : organic molecule consisting of only carbon and hydrogen Isomers : variation in structure of organic molecules that have the same molecular formula ● Structural isomer : differ in covalent arrangement of atoms (ie. branched vs straight) ● Geometric isomers differ in spatial arrangement of atoms ○ Trans isomer : atoms on different sides of carbon, C is isomer : atoms on same side ● Enantiomer : isomers that are mirror images of one another Functional groups : chemical groups that participate in chemical reactions in a characteristic way Functional Groups Structure Name of Compound Properties Hydroxyl ­OH alcohols (ends in ­ol) Carbonyl ­C=O ketones (carbonyl w ithin ­ ketones and aldehydes are carbon chain) isomers of each other aldehydes (carbonyl at ­ commonly found in sugars end of carbon chain) Carboxyl organic acids ­ polar ­ has acidic properties (source of H+ ions) amines ­ acts as a base ­ can pick up H + ions in solutions ­ N very electronegative thiols ­ two sulfhydryls can react to form covalent bond. This c ross­linking helps stabilize protein structure ­ not that polar organic phosphates ­ contributes negative charge to molecule of which it is a part of ­ molecules containing phosphate groups have potential to react with water, releasing energy ­ incredibly negative charge methylated compounds ­ affects expression of genes, shape & function of sex hormones ­ ways for cells to modify molecules for easy recognition Amino ­ polar ­ can form hydrogen bonds w/ water to dissolve organic compounds Sulfhydryl ­SH Phosphate Methyl ­CH 3 ATP : adenosine triphosphate: adenosine attached to 3 phosphate groups, incredibly negative charge, reaction with water releases energy that can be used by cell Chapter 5: The Structure and Function of Large Biological Molecules : Macromolecule : large biological molecules w/ properties that arise from orderly arrangement of atoms ● Polymer : long molecule consisting of monomers (similar building blocks) linked by covalent bonds ○ Put together by d ehydration synthesis (releases water) and broken down by h ydrolysis (requires water molecule) ○ Polymerization : dehydration synthesis reaction makes many monomers into a polymer ● Enzyme : specialized macromolecules (usually proteins) that speeds up reactions (catalysts) Carbohydrates : sugars and polymers of sugars ● Converted into g lycogen in liver and muscle cells ● Monosaccharide : monomer of larger carbohydrates (generally have multiple of the unit CH 2 O) ● Disaccharide : two monomers linked together by g lycosidic linkage (covalent bond by dehydration synthesis reaction) ● Polysaccharide :polymer with many monosaccharides linked together by g lycosidic linkage ○ Starch : polymer of glucose that stores excess sugars ■ Storage of energy in p lants in granules inside chloroplasts ○ Glycogen : stored in liver and muscle cells ­ releases glucose when there is demand ■ Highly branched, ONLY way for a nimals to store energy ○ Cellulose : part of tough wall that encloses plant cells ■ Strength and ability to bear weight come from h ydrogen bonds ○ Chitin : used by arthropods to build exoskeletons (hard case to protect soft animal) ɑ­glucose: 1­4 linkage = OH in SAME direction, ­OH on bottom: starch and glycogen (storage) β­glucose: 1­4 linkage = ­OH in OPPOSITE direction, ­OH on top: cellulose (strength) ● Flipped orientation of β 1­4 linkages form s traight polymers stabilized by hydrogen bonds ○ Can align parallel to one another ­ hydrogen bonds give structure, stability, and ability to support weight (important for cellulose fibers) Lipids : compounds that mix poorly, if at all, with water (nonpolar covalent bonds = no polarity = no affinity for water) ● Fats : constructed of glycerol and fatty acids, insoluble ­ keep things out of cell ○ Glycerol: hydrophilic, alcohol with 3 carbons, each of which bear a carboxyl group ○ Fatty acid: hydrophobic, long carbon skeleton with a carboxyl group ○ Glycerols linked to fatty acids through e ster linkage ● Saturated fat : hydrocarbon chains w/ single bonds (flexibility allows tails to pack together tightly) ● Unsaturated fats : hydrocarbon chain with naturally occurring cis double/triple bonds ○ Kinks in cis bonds prevent molecules from packing closely enough to solidify at room temp ● Trans fat : unsaturated fat containing one or more trans double bonds ● Phospholipid : two fatty acids connected to 1 glycerol, third hydroxyl group of glycerol connected to phosphate group (incredibly negative) ○ Makes up cell membranes (hydrophilic head and hydrophobic tails keep things out) ○ Phospholipid micelle allows body to absorb fat­soluble vitamins ● Steroid : lipids characterized by carbon skeleton consisting of 4 fused rings (distinguishable by what’s attached to the rings) ­ CAN DIFFUSE ○ Amphipathic : contains both hydrophobic and hydrophilic elements ○ Cholesterol : common component of animal cell membranes ■ Precursor for which other steroids are synthesized Proteins : biologically functional molecule that consists of one or more polypeptides ● Polypeptide : amino acids joined together by p eptide bonds (dehydration synthesis) and coiled into a unique shape ○ Bond forms between carboxyl and amino groups of two adjacent amino acids ● amino acid : organic molecule with both amino group & carboxyl group ● R group = side chain = variable group (differs w/ each amino acid) ● denaturation ­ can unravel or lose natural shape due to changes in pH, salt concentration, temperature, or other aspects of environment ● essential amino acids ­ body can’t create, absorbed through diet ● MANY functions, including enzymatic activity, defense (protection against disease), storage, transport, hormonal coordination of organism's activities, receptors to respond to chemical stimuli, movement from motor proteins, and support in structural proteins Primary sequence of amino acids Secondary regions stabilized by hydrogen bonds ­ sequence of amino acids that folds and coils within itself ● forms either α­helix (coil) or β­pleated sheet (pleated) Tertiary 3­D shape ­ sequence of amino acids folds within itself and forms a globule ● hydrophobic amino groups coil when in contact with water ● disulfide bridges reinforce structure Quaternary two or more polypeptide chains aggregated into one macromolecule ­ R ­groups on amino acids determine characteristics ● Hydrocarbon R­groups = nonpolar = hydrophobic ● charged/polar R­groups = hydrophilic Gene: u nit of inheritance Nucleic Acids : polymers consisting of many nucleotides ● DNA/ RNA allow living organisms to reproduce and pass complex components to next generation ● DNA = genetic material inherited from parents that programs cell activities ­ provides directions for replication and directs RNA synthesis ● RNA codes off DNA and synthesizes proteins in ribosomes ● Flow of genetic information = DNA→ RNA → protein DNA ­ double helix, a ntiparallel spiral of 2 sugar­phosphate backbones (complementary strands) running in opposite directions (5’ to 3’) ­ base pairing provides mechanism for DNA replication ­ deoxyribose (lacks oxygen on second C of ring) ­ Nitrogenous Bases: Adenine + thymine, cytosine + thymine RNA ­ single stranded ­ ribose ­ Nitrogenous Bases: Adenine + uracil, cytosine + thymine ­ can base pair with itself (folding, can create a loop) or other RNA strands ­ 3 different polymers: mRNA, tRNA, rRNA Nucleotide : monomers of polynucleotides/nucleic acids ● Structure: phosphate group + 5­carbon sugar + nitrogenous base ○ Purine : larger, 6­membered ring fused to a 5­membered ring (d ouble ring ) ■ Adenine and guanine (Ag = silver = pure element) ○ Pyrimidine : 1 6­membered ring of 4 carbon and 2 nitrogen atoms ■ Cytosine, thymine, uracil Bonding: A­T: 2 H bonds = easier to break, C­G: 3 H bonds = harder to break Strands of DNA held together by HYDROGEN BONDING Nucleotides linked by PHOSPHODIESTER bonds between 5’ (phosphate group) & 3’ (carbon ring) ends Enzymes : catalysts that speed up chemical reactions (usually proteins) ● Catalysts : chemical agents that selectively speed up chemical reactions without being consumed by reaction (not used up in reaction = can be used again) ● Reactions WILL ALREADY SPONTANEOUSLY OCCUR ­ enzymes only speed up reactions ● Induced­fit model : substrate approaches, enzyme’s shape slightly altered Chapter 6: A Tour of the Cell How to Study Cells : Light microscope : visible light passed through specimen and then through glass lenses ● Lenses refract (bend) light in such a way that image of specimen is magnified ● Magnification : ratio of object’s image to real size ● Resolution : measure of clarity of image ○ resolution barrier of light microscopes prevented study of organelles ● Contrast : accentuates differences in parts of sample Electron microscope : focuses a beam of electrons through the specimen or onto its surface ● Resolution higher than light microscopy, BUT cannot observe living cells (preparation kills cells) ● Scanning electron microscope : useful in studying topography (surface) of specimen ● Transmission electron microscope : used to study internal structure of cells (cross­structure) Cell Fractionation : takes cells apart and separates major organelles and other subcellular structures from one another using a centrifuge (larger components sink to the bottom) Prokaryotic vs Eukaryotic Cells : Both bounded by selective barrier ­ p lasma membrane (phospholipid bilayer) ● Cytosol : jellylike substance in which organelles and other components are suspended in ● Cytoplasm : interior of either type of cell Eukaryotic ­ most of DNA found in double bound nucleus ­ membrane­bound organelles suspended in cytoplasm that performs s pecialized functions ● internal membranes divide the cell into Prokaryotic ­ DNA concentrated in n ucleoid , not membrane bound ­ membrane bound organelles absent ­ generally smaller than eukaryotic cells → cannot compartments → organelles perform cellular metabolism as effectively ­ need for s urface area : many cells in narrow, elongated shape → exchange materials with surroundings ● Compartmentalization reduces diffusion distances and separates “incompatible” reactions ● Large organisms usually do not have larger cells, just MORE cells (more surface area) Nucleus: Information Central ­ n ucleus contains most of genes in eukaryotic cell ● Chromatin complex of DNA and proteins makes up eukaryotic c hromosomes (balances extremely negative DNA with positively charged proteins) ● chromosomes : structures that carry genetic information (coiled to allow it to fit in nucleus) ­ enclosed by n uclear envelope (double membrane ­ two phospholipid bilayers ­ that protect DNA by separating it) ● nuclear pore complex : multi­protein structure forming a channel through nuclear envelope, allowing selected molecules to move between nucleus and cytoplasm ­ n uclear lamina : lining on side of envelope that contains protein filaments to maintain s hape of nucleus ­ n ucleolus : mass of densely stained granules and fibers adjoining part of the chromatin ● ribosomal RNA synthesized from instructions in DNA ● proteins imported from cytoplasm to assemble ribosomal subunits Ribosomes: Protein Factories ribosome : complex made of ribosomal RNA and protein that carry out p rotein synthesis ● free ribosomes suspended in cytosol while b ound ribosomes are attached to outside of endoplasmic reticulum or nuclear envelope ○ bound and free ribosomes can rotate between the two roles Endomembrane system: regulates protein traffic and performs metabolic functions endomembrane system : c arries out many tasks, including protein synthesis, transport of proteins into organelles or out of cell, metabolism and movement of lipids, and detoxification of poisons endoplasmic reticulum : biosynthetic factory : extensive network of membranes that account for more than half of total membrane in many eukaryotic cells ● network of membranous tubules and sacs called c isternae ● separates internal compartment of ER (E R lumen ) from cytosol ● two distinct, interconnected regions → smooth (appearance) and rough (has ribosomes) ● smooth ER : diverse metabolic processes (synthesize lipids, metabolize carbohydrates, detoxification by adding ­OH to flush out toxins from body, store Ca for cellular activity ○ synthesis of lipids → enzymes synthesize and secrete hormones + steroids ○ metabolism of carbohydrates ○ detoxification of drugs/poisons → enzymes function to detoxify, usually in liver cells ■ usually involves adding hydroxyl groups to drugs → makes them more soluble and easier to flush from body ■ excess consumption of drugs/toxins lead to increased rate of detoxification → body builds increase tolerance to drugs ● barbiturate abuse → can lead to resistance of useful drugs ○ stores calcium ions → when muscle cell is stimulated by nerve impulse, calcium rushes back to cytosol to trigger contraction of muscle cell ■ triggers different responses in different parts of body ● rough ER : ribosomes attached to it c reate proteins → as a polypeptide chain is formed, it gets threaded into ER lumen through pore formed by protein complex ○ as it is threaded into ER lumen, polypeptide chain coils/forms into its natural shape ■ secretory proteins, usually g lycoproteins (proteins that have carbohydrates covalently bonded to it) ■ transitional ER : specialized region where membranous vesicles are made so secretory proteins can leave ER ● membrane factory for the cell → adds membrane proteins and phospholipids to own membrane ○ ○ enzymes in ER membrane can assemble phospholipids transport vesicles move parts of ER memb...
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