UIUC MCB 450 - mcb450 lecture 1 (45 pages)

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mcb450 lecture 1



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mcb450 lecture 1

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Pages:
45
School:
University of Illinois at Urbana, Champaign
Course:
Mcb 450 - Introductory Biochemistry
Introductory Biochemistry Documents
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1 1 MCB 450 Lecture 1 The Unity of Biochemistry Carbon Compounds Stereochemistry Functional Groups Types of Biological Molecules Central Dogma Domains of Life Cellular Organization 1 2 The unity of biochemistry 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 KefiranGel They Metabolize the Sugar Posters i9014831 htm http cosmosmagazine com features the promise regeneration 1 3 The unity of biochemistry 1 x 10 6 m 1m Anything found to be true of E coli must also be true of elephants Jacques Monod Nobel Laureate 1 4 Characteristics 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 DNA into 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 structures are critically dependent on water 1 5 The Elements of Life of total atoms H O C N P S 1 6 Biomolecules Covalent compounds of carbon C forms up to 4 single bonds w other C atoms double triple bonds w other C atoms single bonds w H atoms single double bonds w O N bonds to S P Critical features conferred by covalent bonds atoms are 3 D shape stereochemistry functional groups 1 7 Examples of covalent bonds Two atoms with unpaired electrons in their outer shells can form covalent bonds with each other by sharing electron pairs to fill outer electron shells 1 8 Biologically important covalent bonds formed by carbon free rotation about C C no rotation planar 1 9 D 1 10 Stereochemistry A C containing compound can exist as stereoisomers molecules w the same chemical bonds but different configuration fixed spatial arrangement of atoms Configuration is conferred by either 1 Double bonds no freedom of movement around them 2 Chiral centers groups arranged around a C atom in a specific orientation Stereoisomers cannot be interconverted without temporarily breaking one or more covalent bonds 1 11 cis trans configurations geometrical isomers or cis trans isomers 1 12 Chiral molecules If four different substituents bonded to a tetrahedral C atom they can be arranged in two different ways in space The asymmetric C atom is called a chiral center Chiral molecule Non superimposable mirror images of one another enantiomers Achiral molecule INTERACTIONS BETWEEN BIOLOGICAL MOLECULES ARE ALMOST INVARIABLY STEREOSPECIFIC 1 13 The D and L system a convention for naming stereoisomers The two stereoisomers of the amino acid alanine enantiomers non superimposable mirror images are L Ala and D Ala The terms L and D come from the direction in which crystals rotate plane polarized light The amino acids in proteins exist in the L form 1 14 Conformation Rotation about C C bonds is pretty free allowing substituents on adjacent C atoms to take up many different positions relative to one another conformations No bond breakage and you can t isolate individual conformations Rotation about C C bond in ethane PRESENCE OF BULKY GROUPS WILL RESTRICT ROTATION HENCE CONFORMATIONS 1 15 Functional groups groups of atoms with distinct chemical properties Confer specific chemical properties on the molecule of which it is a component Chemical personality of a compound is determined by the chemistry of its functional groups Common functional groups in biomolecules only C and H CH3 R any substituent can be H typically a C containing moiety Chapter 2 pp 24 26 1 16 Common functional groups in biomolecules containing O IONIZES 1 17 Common functional groups in biomolecules containing N IONIZES IONIZES IONIZES 1 18 Common functional groups in biomolecules containing S a k a thiol IMPORTANT IN PROTEIN 3D STRUCTURE IONIZES 1 19 Common functional groups in biomolecules containing P P P vely charged 1 20 The functional groups in a biomolecule In general Functional groups alter the electron distribution and geometry of neighboring atoms This affects the reactivity of the entire molecule 1 21 Some functional groups can ionize in aqueous solution protonation deprotonation e g the amino acid histidine H COOH H3 N COO H2 N H H N Ionization is important for H Reactivity of the molecule e g catalysis by enzymes Stabilization of protein structure 1 22 Molecular components of an E coli cell Approximate number of building blocks 20 amino acids aa 4 deoxyribonucleotides 4 ribonucleotides 5 monosaccharides 6 fatty acids Inorganics Na K Ca2 Cl Mg2 Fe2 3 Mn2 Co2 Cu2 Zn2 Se 1 23 The four classes of biological molecules Proteins Carbohydrates 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 eliminated 1 24 Proteins are linear polymers of L amino acids that are joined by peptide bonds CAN YOU IDENTIFY THE FUNCTIONAL GROUPS Proteins are built from a repertoire of 20 amino acids H2O Condensation reaction H2O eliminated between COOH of one amino acid NH2 of the next peptide bond 1 25 Polypeptides have a specific sequence of amino acids i e they are informational Amino acids differ in their side chains N terminus SENSE C terminus 1 26 The sequence of a protein s amino acids dictates the final 3 D structure of a protein In addition to the covalent bonds between amino acids many non covalent intramolecular interactions collectively determine how a protein folds into its unique 3 D structure Protein folding is a self assembly process that takes place in water 1 27 Proteins are versatile biomolecules Biological catalysts enzymes Transporters of molecules in out of cells protons and electrons energy generation Structural muscle fibres hair Cell surface receptors for signaling molecules 1 28 Carbohydrates are linear or branched polymers of monosaccharides a k a sugars CAN YOU IDENTIFY THE FUNCTIONAL GROUPS CYCLIZATION 6 carbon hexose 5 carbon pentoses 1 29 Polysaccharides are polymers of sugars that are joined by glycosidic bonds H2O Condensation reaction C 1 C 4 As we ll see in Lecture 6 sugars can be linked to each other in different ways typically between C 1 on one


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