Chem 3653 Semester

non-spontaneousPositive delta GKeq greater than 1Favors productsKeq less than 1Favors reactantsgain of electronsReductionloss of electronsOxidationExperiment that modeled Earth's primordial atmosphere in the lab and produced amino acids. (i.e. organic matter from Earth's primordial conditions)Miller experimentA component of nucleic acids, energy-carrying molecules such as ATP, and certain coenzymes. Chemically, it is a purine base.Adenineadds adenine nucleotides to the 3' endpolyA polymeraseBacteria and ArchaeaProkaryotesanimals, plants, fungi, protistsEukaryotesWhat is the difference between nucleotides and nucleosides?Nucleotides have a phosphate group.clockwise rotationR configurationcounterclockwise rotationS configurationsimplest aldose the reference compound for the D, L systemGlyceraldehyde10^-10 measurementAngstromVolume of a sphere4/3πr³Surface area of a sphere4πr²Volume of a cubeV=s³Strongest type of bondcovalent bondbetween oppositely charged side chains in the interior of a protein also stabilize protein structurecharge-charge interactionsattractions between oppositely charged regions of polar moleculesdipole-dipole interactionsAre noncovalent interactions reversible?YesThe exclusion of nonpolar molecules by polar molecules, which drives biological processes such as the formation of cell membranes and the folding of proteins. Nonpolar molecules aggregate togetherhydrophobic effectA molecule having both hydrophobic (nonpolar) and hydrophilic (polar) regionsamphiphilic moleculesa two-layered arrangement of phosphate and lipid molecules that form a cell membrane, the hydrophobic lipid ends facing inward and the hydrophilic phosphate ends facing outward.phospholipid bilayerPhysiological ph7.35-7.45Henderson-Hasselbalch equationpH = pKa + log [A-]/[HA]graph showing how the pH of a solution changes as acidic and basic solutions are added togethertitration curvediscovered nucleic acids from bandaid pusFriedrich Mieschergenetic material could be transferred between dead bacteria and living bacteria, experiment done with miceGriffith's experimentProved that DNA is the hereditary material -without it, death occursAvery, MacLeod, McCartyconfirmed that DNA is the genetic material because only radiolabeled DNA could be found in bacteriophage-infected bacteriaHershey-Chase ExperimentDeveloped the double helix model of DNA.Watson and CrickWoman who generated x-ray images of DNA and provided Watson and Crick with key data about DNARosalind Franklin2 strands of DNA, held together throughout their length by hydrogen bonds between bases on opposite strands. A-T G-CWatson-Crick pairingDifference between ribose and deoxyriboseribose has a 2'-OH group and deoxyribose has a 2'-Ha nucleoside; a combination of ribose and adenine; serves as a neuromodulator in the brainAdenosineWhich form predominates between Keto and Enol?KetoAlanine, Ala, AGlycine, Gly, GIsoleucine, Ile, ILeucine, Leu, LProline, Pro, PValine, Val, VPhenylalanine, Phe, FTryptophan, Trp, WTyrosine, Tyr, YAspartic acid, Asp, DGlutamic acid, Glu, EArginine, Arg, RHistidine, His, HLysine, Lys, KSerine, Ser, SThreonineCysteine, Cys, CMethionine, Met, MGlutamine, Gln, QAsparagine, Asn, Nelectromagnetic radiation absorption for nucleic acids~ 260 nmWhat gets deaminated into uracil?CytosineMethod of DNA replication in which parental strands separate, act as templates, and produce molecules of DNA with one parental DNA strand and one new DNA strandSemiconservative replicationWhy is DNA better than RNA?more stable and is able to store genetic material DNA has no 2' OH so it is not prone to hydrolysis like RNA istype of RNA that carries instructions from DNA in the nucleus to the ribosomemRNAtype of RNA that makes up part of the ribosomerRNAtype of RNA that carries amino acids to the ribosometRNAEnzyme involved in DNA replication that joins individual nucleotides to produce a DNA moleculeDNA polymeraseEnzyme that links together the growing chain of RNA nucleotides during transcription using a DNA strand as a templateRNA polymeraseWhat direction are strands to be assumed?5' to 3'The DNA strand that provides the template for ordering the sequence of nucleotides in an mRNA transcript.template strandthe strand of DNA that is not used for transcription and is identical in sequence to mRNA, except it contains uracil instead of thyminecoding strandThe existence of multiple genes in the genome of an organism that perform the same function. Multiple codons can code for the same amino acidgene redundancyStop codonsUAA, UAG, UGAStart codonAUGdirection DNA is synthesized5' to 3'Charge of CathodeNegativeCharge of AnodePositiveThe order of nucleotides from DNA sequencing forms a strand that is in what direction and what strand is it?It is a 5' to 3' coding strand because it is complementary to the templateenzyme that cuts DNA at a sequence of nucleotidesrestriction enzymesA method of producing thousands of copies of DNA segment using the enzyme DNA polymerase Temperature adjusting higher and lower repeatedly -Kary Mullispolymerase chain reaction (PCR)a targeted and specific change in a genesite-directed mutagenesisWhy is hydrolysis an exergonic reaction?Because although energy is invested to break the bond, the bonds formed give off more energy.Average weight of amino acids110 amuStrong chemical side bonds formed when the sulfur atoms in two adjacent protein chains are joined together.disulfide bondssequence of amino acidsprimary structureEither an alpha helix or beta pleated sheet.secondary structureIrregular contortions of a protein molecule due to interactions of side chains involved in hydrophobic interactions, ionic bonds, hydrogen bonds, and disulfide bridges.tertiary structureThe overall protein structure that results from the aggregation of two or more polypeptide subunits.quarternary structure1-Fluoro-2,4-dinitrobenzene is a chemical that reacts with the N-terminal amino acid of polypeptidesSanger's reagentWhere does trypsin cleave?at the carboxyl end of arginine and lysineWhere does chymotrypsin cleave?at the carboxyl end of phenylalanine, tryptophan, and tyrosineWhere does carboxypeptidase cleave?Cleaves all at carboxy terminusWhere does aminopeptidase cleave?Cleaves all at amino terminusWhere does cyanogen bromide cleave?carboxyl side of methionine residuesAmino acids at the amino terminusWhere does edman degradation cleave?N-CphiC-CpsiHow many residues per turn?3.6 residues per turnIndicator of relatedness, as species diverge, so do DNA sequences.DNA resolutionA method of determining molecular structure that uses the relative position of carbons and hydrogens determined by the relative shielding and spins of electrons observed when a molecule is exposed to a magnetic fieldNMR spectroscopyside chain of histidine aromatic ring with two nitrogens pka of side chain is 6 - so at a physiological pH the side chain is neutral amide then will be protonated at a higher pHImidazolerelies on porous beads; larger molecules elute first because they are not trapped in small poressize exclusion chromatography-stationary phase is made of either negatively or positively charged beads (attract & bind compounds that have opposite charge) -salt is added to elute proteins stuck to columnion exchange chromatographycodon specifies biochemically similar amino acidconservative mutationchemical properties of mutant amino acid are different from original amino acidnonconservative mutationAn oxygen-storing, pigmented protein in muscle cells.Myoglobiniron-containing protein in red blood cells that carries oxygen for delivery to cellsHemoglobinone of four polypeptide chains in the quaternary structure of hemoglobinheme groupThe product of a reaction that is formed favorably at a higher temperature because thermal energy is available to form the transition state of the more stable product.thermodynamic productThe product of a reaction that is formed favorably at a lower temperature because thermal energy is not available to form the transition state required to create a more stable thermodynamic product.kinetic productdiamagneticparamagneticDoes a paramagnetic magnetic orbital have low spin or high spin?High spin Deoxy HbDoes a diamagnetic magnetic orbital have low spin or high spin?Low spin Oxy HbLess affinitive curve shiftCurve shifts to the rightMore affinitive curve shiftCurve shifts to the lefta decrease in the amount of oxygen associated with hemoglobin and other respiratory compounds in response to a lowered blood pH resulting from an increased concentration of carbon dioxide in the blood.Bohr effectCompound that lowers hemoglobin's affinity to oxygen, thereby freeing up oxygen for use by tissues2,3-bisphosphoglycerateFetal hemoglobin is (more or less affinitive) to oxygen?moreWhat protein structure is conserved in hemoglobin?TertiaryWhat amino acid mutation results in sickle cell anemiaGlutamate into ValineWhich side of the polymer binds things faster?(+) sideMicrotubules are made oftubulinMicrofilaments are made ofActinoften abbreviated as Gly-X-Y, where X is often Pro and Y is often HypCollagenWhy does Collagen have high tensile strength?Strength of collagen is provided by tight packing of collagen molecules into bundles via hydrophobic interactions between moleculesThe contractile protein that makes up the thick filaments of muscle fibersMyosintheory that actin filaments slide toward each other during muscle contraction, while the myosin filaments are stillSliding filament theoryRole of calcium in muscle contractionsThe muscle contraction cycle is triggered by calcium ions binding to the protein complex troponin, causes tropomyosin to move, exposing the active-binding sites on the actin.motor proteins in anterograde transportKinesinmotor proteins in retrograde transportDyneinturnover number (molecules catalyzed per second in optimal conditions) Vmax / [E]Kcatconverts pyruvate to acetyl-CoApyruvate dehydrogenaseenzyme only bonds to one substrate due to shape of active siteenzyme specificityA nonprotein molecule or ion that is required for the proper functioning of an enzyme. Inorganic.cofactorIf the cofactor is an organic molecule.CoenzymeA non-protein, but organic, molecule (such as vitamin) that is covalently bound to an enzyme as part of the active site.prosthetic groupthe reduced form of NAD+; an electron-carrying molecule that functions in cellular respirationNADHA molecule that stores energy for harvest by the electron transport chain.FADH2An enzyme that catalyzes a chemical reaction during which one or more hydrogen atoms are removed from a molecule. Molecule gets oxidized as a result.DehydrogenaseHow does a catalyst work?By lowering the Activation Energy of a reactiona molecule other than water plays the role of a proton donor or acceptorgeneral acid-base catalysisthe active site contains a nucleophile that is briefly covalently modifiedcovalent catalysismetal ion in the active site participates in catalysismetal ion catalysisHow does pH affect enzyme activity?The most favorable pH value is known as the optimum pH. Extremely high or low pH values generally result in complete loss of activity for most enzymes. Middle ground.enzyme that catalyzes the reaction between carbon dioxide and water to form carbonic acidcarbonic anhydraseWhat two types of catalysis does Chymotrypsin use?General acid-base catalysis & Covalent catalysisIs Lock and key fit or Induced fit better?Induced fit It allows better binding and catalytic effectshydrogen may choose which atom to bond with. advantages- greater stability of active site (enzyme-enzyme) Shorter and stronger than normal H bondsLow barrier hydrogen bondsHow are entropy and enthalpy affected by an enzyme binding to a substrate?The substrate is put in a place where the most energy can be taken from it. (decrease entropy) The energy released makes reactions favorable and makes up for the lack of entropy in the system. (increase enthalpy)How do Subtilisin and (Chymotrypsin, Trypsin, and elastase) compare?Different overall structures Similar active sitesProcess by which unrelated organisms independently evolve similarities when adapting to similar environmentsconvergent evolutionwhen two or more species sharing a common ancestor become more different over timedivergent evolutionHow is chymotrypsin activated?Trypsin cleaves a bond between an Arginine and Isoleucine. Two peptides resultWhat is the clotting cascade?1)Platelet finds exposed collagen 2)Platelets to adhere to each other (platelet plug) 3)Collected platelets and damaged tissue both released thromboplastin 4) Thromboplastin and calcium and vit.K converts inactive prothrombin to its active form thrombin 5) Thrombin converts fibrinogen into fibrin 6) fibrin threads coat damaged area and trap blood cells to form clotHow are clots dissolved?Plasminogen turns into plasmin Plasmin dissolves clotsRole of vitamin K in carboxylation?Uses vitamin K epoxidation to convert Glu to carboxylated GlaRole of calcium in coagulationClotting also requires: calcium ions Ca2+ which is why blood banks use a chelating agent to bind the calcium in donated blood so the blood will not clot in the bag.Reaction rate measured over a period of time during which the substrate concentration has not decreased enough to affect the rate.Initial reaction velocityv = (vmax [S])/(Km + [S])Michaelis-Menten equationSubstrate concentration at 1/2 VmaxKmWhat is the lineweaver burk plot-double reciprocal of michaelis menten -x int: is -1/Km -y int: 1/vmaxinhibitor bonds noncovalently to the active site and prevents substrate from bindingreversible inhibitionactive site is made unavailable for prolonged period of time or enzyme is permanently alteredirreversible inhibitionsubstance that resembles the normal substrate competes with the substrate for the active site Raises Kmcompetitive inhibitioninhibitor binds only to enzyme-substrate complex locks substrate in enzyme preventing its release (increasing affinity b/w enzyme and substrate so it lowers Km) Lower Km and Vmaxuncompetitive inhibitionIn noncompetitive inhibition, the inhibitor binds with the enzyme at a site other than the active site and inactivates the enzyme by altering its shape. Lowers Vmaxnoncompetitive inhibitionA method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway.feedback inhibitionDoes Phosphoenolpyruvate (PEP) inhibit or increase enzyme activity?Phosphoenolpyruvate (PEP) inhibitsKinase vs Phosphatase?Kinase- adds phosphate Phosphatase- removes phosphateA fatty acid in which all carbons in the hydrocarbon tail are connected by single bonds, thus maximizing the number of hydrogen atoms that can attach to the carbon skeleton.saturated fatty acidA fatty acid possessing one or more double bonds between the carbons in the hydrocarbon tail. Such bonding reduces the number of hydrogen atoms attached to the carbon skeleton.unsaturated fatty acidButyric acidCaproic acidCapryllic acidLauric acidMyristic acidPalmitic acidStearic acidArachidic acidMyristoleic acidPalmitoleic acidOleic acidLinoleic acida-linoleic acidArachidonic acidthree fatty acids linked to one glycerol moleculetriaglycerolEthanolamineCholineGlycerolGlycerophospholipidSphingolipidlipids characterized by a carbon skeleton consisting of four fused ringsSteroidsA steroid that forms an essential component of animal cell membranes and acts as a precursor molecule for the synthesis of other biologically important steroids, such as many hormones.Cholersterol-at low temperatures, cholesterol interferes with the crystal structure of the cell membrane and occupies space between phospholipid molecules → increases fluidity -at high temperatures, it restricts excessive movement of phospholipids → decreases fluiditycholesterol and membrane fluidityCholesterol is the metabolic precursor to what hormones?Cortisol Aldosterone Testosterone B-EstradiolWhat plant is a good source of vitamin A?carrotsRetinolVitamin ATocopherolVitamin EThe heads of the phospholipid are hydrophilic and will want to be by the water, the tails are hydrophobic and want to be away from the waterphosphlipid bilayerslow shift of a polar head to the other side of the bilayerTransverse diffusion (flip-flop)rapid, side to side shift of polar headsLateral diffusion of lipidsA protein embedded in the lipid bilayer of a cell. These are typicallly cell surface receptors, channels, or pumps.Integral membrane proteinproteins associated with but not embedded within the plasma membraneperipheral membrane proteinsProteins that have been covalently modified by the addition of one or more lipid groups.Lipid-linked proteinsdoes not use a transporter proteinnonmediated transporttransport of molecules across a membrane utilizing transmembrane proteinsmediated transportWhat characteristics do molecules that go through the membrane via passive diffusion have?Small and nonpolarThe diffusion gradient of an ion, which is affected by both the concentration difference of an ion across a membrane (a chemical force) and the ion's tendency to move relative to the membrane potential (an electrical force).electrochemical gradientA transport protein in the plasma membrane of a plant or animal cell that specifically facilitates the diffusion of water across the membraneAquaporinsWhat transport channel does GLUT 1 have?Uniporta substance which initiates a physiological response when combined with a receptor.agonisttype of receptor ligand or drug that blocks or dampens a biological response by binding to and blocking a receptor rather than activating itantagonistmembrane receptors that attach phosphates to tyrosinesreceptor tyrosine kinasesA signal receptor protein in the plasma membrane that responds to the binding of a signaling molecule by activating a G protein. Also called a G protein-linked receptor.G-protein coupled receptorsA series of chemical reactions in which a single hormone has the cascade effect which triggers the production or activation of up to a billion enzymesEnzyme amplifcationReceptor activation that triggers a feedback to shut of the receptor or kick off signal.Enzyme desensitizationalso known as the "7TM receptor"G protein coupled receptorWhat are the alternative names for epinephrine and norepinephrine?Epinephrine- adrenaline Norepinephrine- noradrenalineconverts ATP to cAMPadenylate cyclaseWhat is protein kinase A (PKA)?family of enzymes whose activity is dependent on cellular levels of cyclic AMP (cAMPWhat is the effect of cAMP on PKA?activated by the binding of cyclic AMP (cAMP), which causes it to undergo a conformational change. PKA then goes on to phosphoylate other proteins in a phosphorylation cascade.What is PKA regulated by?Phosphorylationthe process by which one molecule of the tyrosine kinase receptor dimer phosphorylates its partnerautophosphorylationRas is activated when GTP is bound activates map kinase activates AP1Ras pathwayAre lipid hormones polar or nonpolar?Nonpolar

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For the overall reaction $\left[\mathrm{Cu}\left(\mathrm{H}_2 \mathrm{O}\right)_6\right]^{2+}+4 \mathrm{NH}_3 \rightleftharpoons$ $\left[\mathrm{Cu}\left(\mathrm{H}_2 \mathrm{O}\right)_2\left(\mathrm{NH}_3\right)_4\right]^{2+}+4 \mathrm{H}_2 \mathrm{O}$ , a tabulation of formation constants lists the following $\log _{10} K$ values: $\log _{10} K_1$ $=4.25, \log _{10} K_2=3.61, \log _{10} K_3=2.98$ , and $\log _{10} K_4$ $=2.24$ . What is the overall formation constant $\beta_4=K_f$ for $\left[\mathrm{Cu}\left(\mathrm{H}_2 \mathrm{O}\right)_2\left(\mathrm{NH}_3\right)_4\right]^{2+}$ ?