AP Biology review sheet - Mariana Cheat Sheet (DRAFT) by MariZL

water -polar molecule -polar colvalent bonds -oxygen end is partial negative and the hydrogens have a partially positive end -cohesive polar covalent bonds -opposite ends of the molecule have opposite charges cohesion -H bonding between H2O creates it (sticky) -allows for the movement of water against gravity -high surface tension -water moves up a tree by transp­iration (helped by ____) adhesion -H2O molecules form H bonds with other substances _{capillary action} meniscus _{water climbs up fiber solvent -water is the universal one -polar water molecules will surround the (+) and (-) ions causing the ions to separate and dissolve -dissolve solutes and create aqueous solutions hydrop­hilic -some molecules have an affinity for water -polar and ionic molecules -ex: cotton, cellulose, paper hydrop­hobic -some substances do not have an affinity for water -nonpolar and non ionic substances -ex: fat, glycerol, oils floats -less dense when it is solid, water ______ -forms crystal lattice structure -important because oceans and lakes do not freeze solid} insulates water below _{seasonal turnover of lakes specific heat -the amount of heat that must be absorbed or lost for 1g to change its temper­ature by 1C -water had high _____ due to H bonding -resists change in temp -moderates temp on earth evapor­ative cooling -organisms use to regulate their temper­ature -ex: sweating -water evaporates through a surface, cooling occurs acidic If [H+]>[-OH] basic If [-OH]>[H+] pH scale -how acidic or basic a solution is -pure water, only 1 molecule in every 554 million is dissoc­iated -most biological fluids have 6-8 -each unit represents a 10-fold difference in H+ and -OH concen­tra­tions neutral -If concen­tration of 2 ions is equal carbon -all life mostly based on this element -important due to its electron config­uration} able to make 4 stable covalent bonds (tetra valence) _{very versatile -tetra­valence allows them to be strung together in chains hydroc­arbons -combi­nations of C and H -nonpolar} not soluble in water _{hydrop­hobic -stable -very little attraction between molecules -gas at room temp isomers -molecules with the same molecular formula but different structures -different chemical properties -different biological functions structural isomers -differ in covalent arrang­ement of atoms geometric isomers -same covalent relati­onships by different spatial arrang­ements enanti­omers -isomers that are mirror images of each other -struc­tural differ­ences create important functional signif­icance functional groups -subst­itute other elements for hydrogen -parts of organic molecules that are involved in chemical reactions -give organic molecules distin­ctive properties -affect reactivity} make hydroc­arbons hydrop­hilic _{increase solubility in water macrom­ole­cules -by joining carbon to other elements, we form the basis of life -smaller organic molecules join together to form larger molecules polymer -a long molecule consisting of similar or identical building blocks -blocks known as monomers -joined through covalent bonds -dehyd­ration synthesis synthesis -joins monomers by "­tak­ing­" H2O out -one monomer donates -OH -other monomer donates H+ -together these form H2O -requires energy and enzymes -conde­nsation reaction digestion -use H2O to breakdown polymers -reverse of dehydr­ation synthesis -cleave off one monomer at a time -H2O is split into H+ and -OH -requires enzymes -releases energy -hydro­lysis carboh­ydrates -composed of C, H, O -function: energy, raw materials, energy storage, and structural storage -monomer: sugars sugars -all have carbonyl group and multiple hydroxyl groups -location determines whether it is an aldehyde or ketone -most names end in -ose -class­ified by number of carbons -when in solution, 5C and 6C structures form rings monosa­cca­rides -simple one monomer sugars -ex: glucose disacc­harides -2 monomer sugars -ex: sucrose polysa­cch­arides -large polymer sugars -ex: starch sugar polymers -costs little energy to build -easily revers­ibl­e=r­elease energy -function: energy storage (starch in plants and glycogen in animals) and structure (cellulose in plants and chitin in arthropods and fungi) starch vs. cellulose -differ in the position of the hydroxyl group on Carbon 1 -S____ has an alpha config­uration (normal bonding of glucose monomers) -C________ has a beta config­uration (every other glucose monomer is upside down) -causes differ­ences in organisms' ability to digest it (S easy, C hard) cellulose -major component of plant walls -most abundant organic compound on Earth -herbi­vores have evolved a mechanism to digest it -most carnivores have not evolved -undig­ested roughage lipids -funct­ions: long term energy storage and concen­trated energy, cushions organs, and insulates body -not a true polymer and not large enough to be a macrom­olecule -big molecules made up of smaller subunits -not a continuous chain -all mix poorly in water (hydro­phobic) -include waxes, pigments, fats, pils, phosph­oli­pids, and steroids -struc­ture: a glycerol (3 Carbons) and a fatty acid chain triacy­lcg­lycerol (trigl­yce­ride) -three fatty acid chains linked to a glycerol -combine by an Ester linkage (hydroxyl and carboxyl) -dehyd­ration synthesis saturated fats -all carbons are bonded to hydrogens -there are no carbon to carbon double bonds -long, straight chain -most animals fats -solid at room temp. (contr­ibutes to cardio­vas­cular disease, athero­scl­erosis) unsatu­rated fats -contains carbon to carbon double bonds in the fatty acids -C=C double bonds in the fatty acids -plant and fish fats -vegetable oils -liquid at room temp (the kinks made by double bonded C prevent the molecules from packing tightly together) -mono- and poly- phosph­olipids -struc­ture: glycerol + 2 fatty acids + PO4 (negat­ively charged) -contains a head and a tail region -fatty acids tails are hydrop­hobic -PO4 head is hydrop­hilic -in water, assembles into a bubble (forms a bilayer) -create a barrier for water and define "­out­sid­e" vs. "­ins­ide­" -make up the cell membrane steroids -struc­ture: carbon skeleton of four fused rings with different chemicals attached -with a different functional group attached you create a new one -ex: choles­terol and sex hormones choles­terol -important cell component -animal cell membranes -helps keep membrane fluid, flexible and mobile -precursor of all other steroids} including vertebrate sex hormones -high levels in blood may contribute to cardio­vas­cular disease proteins -most struct­urally and functi­onally diverse group -function: involved in almost everything _{enzymes (pepsin, DNA polyme­rase)} structure (keratin, collagen) _{carriers and transport (hemog­lobin, aquaporin)} cell commun­ication (signals and receptors) _{defense (antib­odies)} movement (actin and myosin) _{storage (bean seed) -struc­ture:} monomer amino acids _{polymer polype­ptide -can be one or more polype­ptide chains folded and bonded together -large and complex molecules -complex 3D shape amino acids -struc­ture: central carbon (alpha carbon) -amino group -carboxyl group (acid) -R group (side chain)} variable group _{different for each} confers unique chemical properties -physical and chemical properties based on R groups attached peptide bonds -covalent bond between NH2 (amine) of one amino acid and COOH (carboxyl) of another -C-N bond protein structure -a polype­ptide chain that has been folded, twisted and coiled into unique shapes -performed as soon as the polype­ptide is formed by creating bonds between parts of the chain -the specific structure determines the function primary structure -unique sequence of amino acids -amino acid sequence determined by gene (DNA) -slight change in amino acid sequence can affect protein's structure and its function secondary structure -localized folding or pleating of parts of the protein chain -result of H bonds between repeating structures of polype­ptide -weak bonds -α helix and β pleated sheets tertiary structure -whole molecule folding -inter­actions between distant amino acids -hydro­phobic intera­ctions _{cytoplasm is water-­based} nonpolar amino acids cluster away from water -H bonds and ionic bonds -disulfide bridges _{covalent bonds between sulfurs in sulfhy­dryls (S-H)} anchors 3D shape quaternary structure -more than one polype­ptide chain bonded together -only then does polype­ptide become functional protein -hydro­phobic intera­ctions denatu­ration -although proteins fold as they are made, under certain condit­ions, these proteins will not fold properly -can be caused by heat, change in pH, change in solution, or salinity -will be inactive -some proteins will be able to regain their original structure by removing the elements nucleic acid -function: genetic material -stores inform­ation; genes, blueprint for building proteins -transfers inform­ation; blueprint for new cells and next generation -monomer: nucleo­tides RNA -nucleic acid -single helix -controls protein synthesis DNA -nucleic acid -double helix -controls its own synthesis and protégé's as well as instru­ctions for reprod­uction from one generation to the next nucleo­tides -made up of three parts -nitrogen (C-N ring) -pentose sugar (5C) _{ribose in RNA} deoxyr­ibose in DNA -phosphate (PO₄) group -two types: purines and pyrimi­dines purines -double ring N base -adenine (A) and guanine (G) pyrimi­dines -single ring N base -cytosine (C), thymine (T), uracil (U) phosph­odi­ester bond -new base added to sugar of previous base -polymer grows in one direction metabolism -the totality of an organism's chemical reactions -each reaction will follow a pathway -what manages the material being used and formed and the energy needed for the changes metabolic pathway -a specific molecule is altered resulting in a product (needs enzymes in order to be changed) catabolism -breaking down of complex molecules to simpler compounds -releases energy -known as hydrolysis or digestion anabolism -uses energy in order to form bonds/ molecules -go through biosyn­thetic pathways -dehyd­ration synthesis bioene­rgetics -the study of how organisms manage their energy resources energy -the capacity to cause change kinetic energy -the energy of an object due to its motion light energy -energy from the sun that cane converted to solar energy, or chemical energy through photos­ynt­hesis thermal energy (heat) -energy associated with the random movement of atoms and molecules potential energy -energy not in use, but that an object possesses due to its location or structure chemical energy -the potential of a substance to undergo a chemical reaction and transform, thus releasing energy thermo­dyn­amics -the study of energy transf­orm­ation First Law of Thermo­dyn­amics -energy is constant -can change forms, but cannot be created or destroyed -just like matter -"pr­inciple of conser­vation of energy­" Second Law of Thermo­dyn­amics -all energy transf­orm­ations increase the entropy of the universe -entropy is the measure of disorder or randomness free energy -measures the portion of a system's energy that can perform work while temper­ature and pressure are uniform -shows if a process or change will be sponta­neous or if energy is needed for a change to occur _{negati­ve=­spo­nta­neous} positive or 0=not sponta­neous exergonic reactions -release of free energy from a chemical reaction -ex: digesting polymers endergonic reaction -chemical reaction that requires an input of energy -absorbs free energy from surrou­ndings -ex: building polymers cell work -3 main types _{mechanical (muscle contra­ctions)} transport (diffu­sio­n/t­ran­sport) _{chemical (ender­gonic reactions) -coupling reactions to save energy energy coupling -use exergonic (catab­olic) reactions to fuel endergonic (anabolic) reactions -allows for the energy that organisms need to live ATP -adenosine tripho­sphate -modified nucleotide -adding phosphates is endergonic -P groups unstable, excellent energy donor phosph­ory­lation -released P can transfer to other molecules} destab­ilizing them enzymes -speed up reactions by lowering the energy barrier -regulate the movement of molecules through metabolic pathways -a catalytic protein -needed by all reactions for completion -do not change ∆G -hasten a reaction that would occur eventually -selec­tive, determine which chemical processes will occur at any time -substrate specific -catalyze reactions only at the active site -unchanged by a reaction -can catalyze or anabolize a substrate (work towards equili­brium in reactants and products) catalyst -a chemical agent that changes the rate of a reaction without begin consumed by the reaction energy of activation -makes the reactants unstable, increases the speed of the reactant molecules, and creates more powerful collisions -the amount of energy necessary to push the reactants over an energy barrier -at the summit the molecules are at an unstable point, the transition state ∆G -the difference between the free energy of the products and the free energy of the reactants cofactors -nonpr­otein enzyme helpers -bind perman­ently to the enzyme or reversibly -ex: zinc, iron, and copper coenzymes -organic cofactors include vitamins or molecules derived from vitamins inhibitors -binding prevents enzymes from catalyzing reactions -binding involving covalent bonds, often irreve­rsible -if weak, reversible compet­itive inhibition -if the inhibitor binds to the same site as the substrate, it blocks the substrate noncom­pet­itive inhibition -if the inhibitor binds somewhere other than the active site, it blocks the substrate -binding causes the enzyme to change shape, rendering the active site unrece­ptive at worst or less effective at catalyzing the reaction ^%$The attraction between a hydrogen of one water molecule and the oxygen of another water molecule Carbon atoms covalently bonded to each other Carboh­ydr­ate­-co­nta­ining layer at the surface of the plasma membrane Glycocalyx The major component of the fluid bilateral of a plasma membrane Phospo­lipid Carrier molecule in the plasma membrane Protein Steroid affecting the fluidity of the plasma membrane Choles­terol ATP synthase (synth­etase) in the inner mitoch­ondrial and chloro­plast membrane Trigly­ceride

2 organelles that contain their own DNA separate from the chromosome Mitoch­ondria and chloro­plast What domains fall under prokar­yotic cells? Bacteria and archaea What are the basic features of all cells? Membrane, cytoplasm, chromo­somes, ribosomes This organelle synthe­sizes lipids, metabo­lizes carboh­ydr­ates, detoxifies poison, and stores calcium Smooth ER This cell is charac­terized by having DNA in a nucleus that is bound by a nuclear envelope and membrane bound organelles Eukaryotic cell This is a membranous sac of hydrolytic enzymes that can digest macrom­ole­cules Lysosome The __________ is a selective barrier that allows oxygen, nutrients, and wastes to service the volume of every cell Plasma membrane Ribosomes use the inform­ation from the DNA to make what Proteins This cell type is charac­terized by having no nucleus, but instead a nucleoid, and no membrane bound organelles Prokar­yotic cell Diffusion through protein channels is known as what? Facili­tated diffusion Site of ribosomal RNA synthesis Nucleolus What happens to a plant cell when placed in pure water (hypotonic solution)? It becomes turgid, cell wall protects from bursting Site of photos­ynt­hesis chloro­plast These vacuoles pump excess water out of the cell Contra­ctile This ER lacks ribosomes Smooth ER This organelle modifies products of the ER, manufa­ctures certain macrom­ole­cules, sorts and packages materials into transport vesicles Golgi apparatus What kind of amino acids will anchor proteins into the membrane? Non-polar What is it called when cells are moving molecules against its concen­tration gradient, from an area of low concen­tration to an area of high concen­tra­tion? What does it require to do this? Active transport, requires ATP Site of cellular respir­ation Mitoch­ondria These types of vacuoles are formed by phagoc­ytosis Food The logistics of carrying out cellular metabolism sets a limit on the size of cells. The ________ to _______ ratio of a cell is critical. Surface area to volume Both animals and plants have _________ that allow molecules to pass readily between adjacent cells without crossing plasma membranes. Cell junctions These vacuoles are found in many mature plant cells and they hold organic compounds and water Central What are the 3 main types of membrane receptors? G-protein linked, tyrosine kinases, ion channel Oxidative organelles Peroxi­somes What happens when you put a red blood cell in pure water (hypotonic solution)? Why? The cell will burst because water rushes into the cell. The ________ is continuous with the nuclear membrane ER membrane Which part of the phosph­olipid bilayer is considered hydrop­hobic? Fatty acid tail Which part of the phosph­olipid bilayer is considered hydrop­hilic? Phosphate head How does the membrane become semipe­rmeable to polar molecules? Protein channels _______ is a water channel in bacteria. Aquaporin This is the movement of molecules from a HIGH concen­tration to a LOW concen­tra­tion. What type of transport is this? Diffusion, passive transport What is osmosis? Diffusion of water across a semi permeable membrane What does hypertonic mean? More solute, less water What does hypotonic mean? Less solute, more water What does isotonic mean? Equal solute, equal water What happens when you water plants with salt water? Why? It will wilt because water will leave the plant and go toward the hypertonic solution (salt water). Signal transd­uction pathways serve to convert signals on a cell's surface into cellular ________. Responses A _______ is a chemical released by a cell in one part of the body, that sends out messages that affect cells in other parts of the organism. Hormone What are plant hormones called? Phytoh­ormones How are hormones transp­orted? In the blood What are the 3 stages of cell signaling? Reception, transd­uction, response Reception occurs when a ________ molecule binds to a ______ protein, causing it to change _____. Signal, receptor, shape Membrane receptors that attache phosphates to specific amino acids in proteins are called Receptor tyrosi­ne-­kinases The activation of this pathway occurs when a GTP displaces the GDP. G-protein linked receptor pathway Part of the receptr on the cytopl­asmic side serves as an enzyme which catalyses the transfer of phosphate groups from ATP to a certain amino acid on a substrate protein. This is an example of what signal transd­uction pathway? Tyrosine kinase receptor pathway This pathway requires formation of a dimer. Tyrosi­ne-­kinase pathway The signal molecule that binds to a receptor is typically called a what? Ligand What needs to happen to a receptor to initiate the transd­uction of a signal? Confor­mat­ional change (change in shape) What is the formula for solute potential? Ys=-iCRT What is the ionization constant for sucrose? What about NaCl? Sucrose = 1 NaCl = 2 What types of cells typically have a pressure potential? What is this due to? Plant cells due to a cell wall what is the pressure potential of an open beaker? 0 How is temper­ature measured in the water potential equation? Kelvin If the temper­ature was 39 degrees C, what is the temper­ature in Kelvin? 312K What is the cell junction of a plant called? Plasmo­desmata What is the cell junction of an animal cell called? Gap junction

Describe the enzyme mediated process. Key words, ideas, or phrases: Substrates have same charge and shape as active site of enzyme. Causes an induced fit on substrate to enzyme Anabolic versus catabolic Enzymes can do this process over and over Bonus: Example Identify TWO enviro­nmental factors the impact enzymatic activity. pH temper­ature Explain the effect of the two factors you identi­fied. pH: outside of its optimum pH range....the enzymes hydrogen and ionic bonds are disrupted enzymes are proteins so therein structure is disrupted and therefore function is negatively impacted Temper­ature: An increase of temper­ature, to a certain degree, increases the reaction rates on the enzymes but past the optimum range of temper­atures causes denatu­ration, which then means the enzyme functions little if at all. A decrease in temper­ature outside the optimum range will not cause denatu­ration but will slow reaction rates. Identify THREE components of the ATP molecule. Adenine base sugar (such as ribose) 3 Phosphate groups Explain phosph­ory­lation. Phosph­ory­lation is the addition or removal of a phosphate group from either ADP or ATP. High energy bond is between second and third phosphate group, when broken energy is released Bonus: example Explain why we see plants as green We see plants as green because to chloro­phyll, green visible light is the least useful to the plant and therefore is reflected rather than absorbed. The colors of visible light most useful to the plant are red and blue light and therefore these colors of light are absorbed rather than reflected. What is the equation of photos­ynt­hesis? 6CO2 + 6H2O ---solar energy­---­---­-> C6H12O6 +6O2 Where do the reactants and products of photos­ynt­hesis come from? Carbon dioxid­e-from the air through stomata on underside of plant's leaves. Water from the soil absorbed through the roots on the plant use cohesion adhesion and transp­ira­tional pull through xylem vein to get to chloro­plasts in leaves. Glucose made in the Calvin Cycle Oxygen made from the splitting of the water molecules. Identify which organisms utilize glycol­ysis. All living organisms Bonus: Why? Because all living organisms have cytoplasm which is where this process takes place. This is a highly conserved process. Identify the location of glycol­ysis. Cytoplasm Explain the signif­icance of a highly conserved process and provide an example (from the lecture). The signif­icance of a highly conserved process is that it is retained over time, the same enzymes and its charac­ter­istic to all forms of life. Bonus: Example Glycolysis What is substr­ate­-level phosph­ory­lation? Substr­ate­-level phosph­ory­lation is the synthesis of ATP from ADP and PI, through an enzyme­-ca­talyzed reaction. Bonus: example Glycolysis and Krebs Cycle What is oxidative phosph­ory­lation? Oxidative phosph­ory­lation is where ATP is made from ATP and PI, driven by chemio­smosis, or the flow of protons through the ATP synthase. Bonus: This is the last stage of cell respir­ation. What is the final electron acceptor of photos­ynt­hesis? NADP What is the final electron acceptor in cell respir­ation? Oxygen Describe the process of lactic acid fermen­tation. Lactic acid fermen­tation is the process where NADH is oxidized back into NAD+, requiring the pyruvate molecules to reduce to lactic acid molecules. This process begins with glucose, it goes through normal glycol­ysis, creating ATP and 2 pyruvate molecules. The pyruvate molecules then go through a chemical reaction that change then to lactic acid molecules, all the while oxidizing NADH back into NAD+. Bonus: mentioning substrate level phosph­ory­lation when talking about glycol­ysis. Explain the selective advantage of lactic acid fermen­tation vs oxidative phosph­ory­lation. The selective advantage of lactic acid fermen­tation over oxidative phosph­ory­lation is the fact that oxygen does not have to be present for ATP to be made from ADP and PI. This means that if oxygen is not available to the cell that it can still create ATP. Explain the advantage of oxidative phosph­ory­lation. The advantage of oxidative phosph­ory­lation is the amount of ATP it creates over lactic acid fermen­tation. Oxidative phosph­ory­lation makes 34-38 ATP molecules whereas lactic acid fermen­tation only makes 2 ATP molecules. Identify what oxidative phosph­ory­lation requires, which fermen­tation does not require. Oxygen Identify the inputs and outputs of glycol­ysis. Inputs: glucose, takes 2 ATP to get going, 2 NAD+ Outputs: 2 pyruvate molecules, net 2 ATP, 2 NADH.