Chapter1
GLOSSARY
Biochemistry:Biochemistryistheapplicationofchemistrytothestudyofbiologicalprocessesatthecellularand molecularlevel. Bioenergetics:Thestudyofenergychangesinbiologicalsystems Biomolecule:anymolecule,especiallyamacromolecule,thatoccursinorisformedbylivingorganisms Biopolymer:Abiologicalmacromoleculeinwhichmanyidenticalorsimilarsmallmoleculesarecovalentlylinkedto [Link],polysaccharidesandnucleicacidsarebiopolymers. Condensation Reaction: A reaction involving the joining of the two or more molecules accompanied by the eliminationofwater,alcoholorothersimplesubstance Degradation:theprocessesbywhichorganicsubstancesarebrokendownbylivingorganisms EnthalpyChange:Athermodynamicstatefunctionthatdescribesthechangeofheatcontentofasystem FreeenergyChange:Athermodynamicquantitythatdefinestheequilibriumconditionintermsofthechangesin enthalpyandentropyofasystematconstantpressure.G=[Link] measureoftheenergyavailablewithinasystemtodowork Hydrolysis:Cleavageofabondwithinamoleculebygrouptransfertowater Metabolism:Thesumtotalofbiochemicalreactionscarriedoutbyanorganism Monomer: 1. A small compound that becomes a residue when polymerized with other monomers. 2. A single subunitofamultisubunitprotein Residue: A single component within a polymer. The chemical formula of a residue is that of the corresponding monomerminustheelementsofwater. Synthesis: the forming or building of a more complex substance or compound from elements or simpler compounds
10^1 10^2 10^3 10^6 10^9 10^12 10^15 10^18 deci centi milli micro nano pico femto atto d c m u n p f a
Chapter1 Activesite:Theportionofanenzymethatcontainsthesubstratebindingsiteandtheaminoacidresiduesinvolved [Link] proteinsorinindentationsontheproteinsurfaces. ADP: Adenine diphosphate. A ribonucleoside monophosphate in which two phosphoryl groups are successively [Link] adenosinetriphosphateortoadenosinemonophosphate. ATP:Adenosinetriphosphate.Aribonucleosidetriphosphateinwhich3phophorylgroupsaresuccessivelylinked to the 5 oxygen atom of adenosine. The phosphoanhydride linkages of ATP contain considerable chemical potential energy. By donating phosphoryl groups, ATP can transfer that energy to intermediates that then participateinbiosyntheticreactions. Carbohydrate: Loosely defined as a compound that is a hydrate of carbon in which the ration of CHO is 1:2:1. [Link]. Catalyze:Tomodify,especiallytoincrease,therateof(achemicalreaction)bycatalysis Chromatin:ADNAproteincomplexinthenucleiofeukaryoticcells Chromosome: A single DNA molecule containing many genes. An organism may have a genome consisting of a singlechromosomeormany. DNA:Apolymerconsistingofdeoxyribonucleotideresiduesjoinedby35phosphodiesterlinkages Enzyme: A biological catalyst, almost always a protein. Some enzymes may require additional cofactors for [Link] Genome:[Link] chromosomes (haploid) Mitochondria and chloroplasts have genomes separate from that in the nucleus of eukaryoticcells. Hydrophilic:Acompoundinteractswithwaterwaterloving Hydrophobic:AcompoundthatissolubleinnonpolarsolventsandisinsolubleinwaterWaterhating Invitro:Occurringunderartificialconditions,suchasinalaboratory Invivo:Occurringwithinalivingcellororganism Lipid:Awaterinsolubleorganiccompoundfoundinbiologicalsystemswhichcanbeextractedbyusingrelatively nonpolarorganicsolvents Monosaccharide:Asimplesugarofthreeormorecarbonatomswiththeempiricalformula(CH2O)n Mr(relative molar mass): The mass of a molecule relative to 1/12 of the mass of 12C. There are no units associatedwiththisvalue Nucleic acids: A polymer composed of nucleotide residues linked in a linear sequence by 35 phosphodiester [Link].
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Chapter1 Polypeptide:Apolymerofmanyaminoacidresidueslinkedbypeptidebonds(usually20) Polysaccharide:[Link] belinearorbranched. glycosidicbond:atypeofcovalentbondthatjoinsacarbohydrate(sugar)moleculetoanothergroup,whichmay ormaynotbeanothercarbohydrate. Protein: A biopolymer consisting of one or more polypeptide chains. The biological function of each protein moleculedependsnotonlyonthesequenceofcovalentlylinkedaminoacidresiduesbutonitsthreedimensional structure(conformation)aswell.
STUDYQUESTIONS:
1. What were the earliest examples of experimental evidence that molecules from living cells can be synthesizedoutsideoflivingcells,andwhydidthesediscoveriesleadtothefieldofbiochemistry? in 1828, Friedrich Whler published a paper on the synthesis of urea, proving that organic compounds can be createdartificially. TheidentificationofenzymesbyBuchnershowedthatextractsofyeast cellscouldcatalyze fermentationofthe sugarglucosetoalcoholandcarbondioxide,priorscientistsbelievedonlylivingcellscoulddothis. 2. Brieflyexplainhowbiochemistryrelatestootherfieldsofthelifesciences
Bioinformaticsisasubdiciplineofbiochemistry,whichisbiologyusingcomputerstodolargecalculations. Another major breakthrough, the identification of nucleic acids, has allowed us to understand DNA as genetic material,[Link], 3. In broad terms, what are the foremost contributionsbiochemistry has made to theunderstanding of livingorganisms?
Thediscoveryoftherolesofenzymesascatalystsandtheroleofnucleicacidsasinformationcarryingmolecules werehugebreakthroughs.Thefirstproteinstructuresweresolvedinthe1950sandsincethen1000sofproteins havebeendeterminedandareinthreedimentionalunderstanding.
Chapter1 4. Listthesixsocalledorganicelementsthattypicallymakeupabout97%ofthemassoflivingorganisms
Oxygen,Hydrogen,Carbon,Phosphorus,Nitrogen,Sulfur 5. List the five metal ions that are generally considered to be essential to all species and the 5 trace elementsrequiredbymostspecies
Sodium,Calcium,Potassium,Magnesium,Chlorine 6. 7. 8. HowmanynanogramsofDNAaretherein10pictogramsofDNA 0.01nanograms=10picograms Drawthestructuresofhydroxylandcarboxylatefunctionalgroups Drawthegeneralformulaforanalcoholandforacarboxylicacid
9. Brieflyexplainthefollowingterms a) Biomolecule [Link] "macromolecules," 1)proteins 2)nucleicacids 3)carbohydrates(orpolysaccharides) 4)lipids
b) CondensationReaction A type of chemical reaction in which two simple molecules combine to form a third more complex molecule,withtheeliminationofasimplesubstance.(iewater)
Chapter1 10) Manyimportantbiomoleculesarepolymersofmonomericmetabolites:proteinsarepolymersofamino acids;DNAandRNAarepolymersofnucleicacids;[Link] reasonsastowhythisstrategymayhaveevolved. In this experiment, gases that were in the atmosphere, boiling waterandsparks(likelightning)[Link] timepassed,aminoacidswereformed! All cells on earth appear to have evolved from a common ancestor that existed more than 3 billion years ago. Evidenceiscommonbiochemicalbuildingblocks,thesamegeneralmetabolismandacommongeneticcode. Simple organic molecules(nucleotides), are the building blocks of life and must have been involved in its origin. Experiments suggest that organic molecules could have been synthesized in the atmosphere of early Earth and [Link] simplenucleotides. anewpropertyofRNAwasdiscovered:somekindsofRNAcancatalyzechemicalreactionsandthatmeansthat RNA can both store genetic information and cause the chemical reactions necessary to copy itself. This breakthrough tentatively solved the chicken and egg problem: nucleic acids (and specifically, RNA) came first andlateron,lifeswitchedtoDNAbasedinheritance 13)ClinicalQuestion Somepoisons,suchascarbonmonoxide,[Link],whatwouldbe theeffectofcarbonmonoxideexposure? Carbon monoxide binds to cytochrome oxidase with less affinity than oxygen, so it is possible that it requires significant intracellular hypoxia before binding. This binding interferes with aerobic metabolism and efficient adenosine triphosphate synthesis. Cells respond by switching to anaerobic metabolism, causing anoxia, lactic acidosis,andeventualcelldeath Followingabsorption,carbonmonoxidebindstohemoglobin,whichistheprincipaloxygencarryingcompoundin blood; this produces a compound known as carboxyhemoglobin. The traditional belief is that carbon monoxide toxicity arises from the formation of carboxyhemoglobin, which decreases the oxygencarrying capacity of the bloodandinhibitsthetransport,delivery,[Link] andcarbonmonoxideisapproximately 230timesstrongerthantheaffinitybetweenhemoglobinandoxygenso carbonmonoxidebindstohemoglobininpreferencetooxygen.