MCB 450Lecture 1The Unity of BiochemistryCarbon Compounds & StereochemistryFunctional GroupsTypes of Biological MoleculesCentral DogmaDomains of LifeCellular Organization1-1The unity of biochemistry1-2• The cell is the basic unit of life.• All cellular processes can be explained by basic chemical principles.• Fundamental molecular building blocks are the same.• One cell differs from another cell, but it's all a variation on a theme.http://www.allposters.com/-sp/Yeasts-and-Bacteria-Live-in-Kefir-Grains-Embedded-in-Kefiran-Gel-They-Metabolize-the-Sugar-Posters_i9014831_.htmhttp://cosmosmagazine.com/features/the-promise-regeneration/Anything found to be true of E. coli must also be true of elephants.- Jacques Monod, Nobel LaureateThe unity of biochemistry1-3~ 1 x 10-6m ~ 1 mCharacteristics of Living Systems• All living cells can divide• All living organisms can replicate their genetic material "replicated molecule" = DNA (deoxyribonucleic acid)• All living organisms convert information stored in DNAinto protein (via RNA = ribonucleic acid)• Proteins allow cells to…• transform energy and use it to power biochemical reactions• make the biomolecules that they themselves are made of• replicate themselves• All cells respond to their environment• Cellular processes and self-assembly of cellular structuresare critically dependent on water1-4The Elements of Life% of total # atoms1-5H, O, C, N, P, SBiomolecules= Covalent compounds of carbonC forms... up to 4 single bonds w. other C atomsdouble & triple bonds w. other C atomssingle bonds w. H atomssingle & double bonds w. O & Nbonds to S & PCritical features conferred by covalent bonds & atoms are...3-D shape/stereochemistryfunctional groups1-61-7 Examples of covalent bondsTwo atoms with unpaired electrons in their outer shellscan form covalent bonds with each other bysharing electron pairs to fill outer electron shellsBiologically important covalent bonds formed by carbonfree rotation about C-Cno rotation, planar1-8)D1-9A C-containing compound can exist as stereoisomers,= molecules w. the same chemical bonds,but different configuration (= fixed spatial arrangement of atoms)Stereochemistry1-10Configuration is conferred by either...1. Double bonds - no freedom of movement around them2. Chiral centers - groups arranged around a C-atomin a specific orientation Stereoisomers cannot be interconvertedwithout temporarily breaking one or more covalent bondscis & trans configurations= geometrical isomers or cis-trans isomers1-11Chiral molecules1-12If four different substituents bonded to a tetrahedral C-atom, they can bearranged in two different ways in space.The asymmetric C atom is called a chiral center.Chiral molecule: Achiral molecule:INTERACTIONS BETWEENBIOLOGICAL MOLECULESARE ALMOST INVARIABLYSTEREOSPECIFICNon-superimposable mirror imagesof one another = enantiomersThe D and L system, a convention for namingstereoisomers1-13The two stereoisomers of the amino acid alanine(enantiomers, non-superimposable mirror images)are L-Ala and D-AlaThe terms L and D come from the direction in which crystals rotateplane-polarized light.The amino acids in proteins exist in the L-formConformation1-14Rotation about C-C bonds is pretty free, allowing substituents on adjacentC-atoms to take up many different positions relative to one another= conformationsNo bond breakage, and you can't isolate individual conformationsRotation about C-C bond in ethane:PRESENCE OFBULKY GROUPSWILL RESTRICTROTATION, HENCE# CONFORMATIONSFunctional groups: groups of atoms with distinctchemical properties1-15• Confer specific chemical properties on the molecule of which it isa component• Chemical personalityof a compound is determinedby the chemistry of its functional groupsCommon functional groups in biomolecules- only C and H:R = any substituent(can be H, typicallya C-containing moiety)-CH3Chapter 2, pp. 24-26Common functional groups in biomolecules- containing O:1-16IONIZESCommon functional groups in biomolecules- containing N:1-17IONIZESIONIZESIONIZESCommon functional groups in biomolecules- containing S:1-18IMPORTANT INPROTEIN 3D STRUCTUREIONIZES(a.k.a. thiol)Common functional groups in biomolecules- containing P:1-19-P, P-vely chargedThe functional groups in a biomolecule1-20In general:Functional groups alter the electron distribution andgeometry of neighboring atoms.This affects the reactivity of the entire moleculeSome functional groups can ionizein aqueous solution (protonation-deprotonation)1-21Ionization is important for:Reactivity of the molecule, e.g. catalysis by enzymesStabilization of protein structuree.g. the amino acid histidine:N+HH+COO-H+H3N+H+H2NCOOHInorganics:Na+, K+, Ca2+, Cl-,Mg2+, Fe2+/3+, Mn2+, Co2+,Cu2+, Zn2+, Se1-224 deoxyribonucleotides20 amino acids (aa)4 ribonucleotides>5 monosaccharides~6 fatty acidsApproximatenumber of buildingblocksMolecular components of an E. coli cellThe four classes of biological molecules1-23ProteinsCarbohydrates(poly- & oligosaccharides)Lipids(fatty acids)Nucleic acids(DNA & RNA)When the monomeric units (building blocks) in proteins, carbohydrates,& nucleic acids are joined, the elements of H2O are eliminated1-24 Proteins are linear polymers of L-amino acidsthat are joined by peptide bondsCondensation reaction:H2O eliminated betweenCOOH of one amino acid& NH2of the nextpeptide bondH2OProteins are builtfrom a repertoireof 20 amino acidsCAN YOU IDENTIFYTHE FUNCTIONALGROUPS??N-terminus C-terminus1-25SENSEPolypeptides have a specific sequence of amino acids i.e. they are informationalAmino acids differin their side chainsThe sequence of a protein's amino acidsdictates the final 3-D structure of a proteinIn addition to the covalent bonds between amino acids, manynon-covalent intramolecular interactions collectively determinehow a protein folds into its unique 3-D structureProtein folding is a self-assembly process that takes place in water1-26Ø Biological catalysts (= enzymes)Ø Transporters of: molecules in & out of cellsprotons and electrons (energy generation)Ø Structural (muscle fibres, hair)Ø Cell surface receptors for signaling moleculesProteins are versatile biomolecules1-271-28Carbohydrates are linear or branched polymersof monosaccharides (a.k.a. sugars)CYCLIZATION6-carbon "hexose" 5-carbon "pentoses"CAN YOU IDENTIFYTHE FUNCTIONALGROUPS??Condensation reactionH2O1-29 Polysaccharides are polymers of sugarsthat are joined by glycosidic bondsAs
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