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Transcript
The Molecules of Life Biochem! Chapter 9 Biochemistry Carbohydrates, lipids, proteins, and the nucleic acids All built from simple precursors How they are put together is the key to their activity Carbohydrates Polymers built from repeating sugar molecules Carbohydrates Glucose – most common • Assembled one way = starch – our main E source • Assembled a different way = cellulose – main ingredient in wood and most plentiful organic substance on earth! Lipids Polymers built from long hydrocarbon chains of fatty acids Proteins Constructed from 20 different kinds of amino acids • Great structural and functional variability Types of Proteins – major component of tendons, skin, and bones Hemoglobin – transports O2 in the blood stream Enzymes – catalyst that speeds up rxn’s in all living organisims Collagen Biochem History Until early 19th century, it was thought that living things had something called “vital forces” that was unique to only living things. 1828 – German Scientist Freidrich Wöhler synthesized Urea from ammonium cyanate (a mineral) • Urea is a waste product of animal metabolism • NH4OCH H2NCONH2 Current Realizations Any compound that exists in a living organism can be synthesized in a lab Rxn’s of biomolecules depend on the functional groups Functional Groups Table of functional groups Also, carbon containing derivatives of phosphoric acid [esters and anhydrides of phosphoric acid ADP, ATP Amino Acids 20 A.A’s - usually found in proteins General structure in common with variations in side chains Amino acids contins amino groups (RNH2, R2NH, R3N) and a carbonyl group (RCOOH) Amino Acids Both groups are bonded to the same carbon atom and labeled α carbon = the one next to the carbonyl group Amino Acids Carbon atoms in the R group are labeled using the Greek alphabet starting w/the C adjacent to the carbonyl group α β γ δ ε Alpha beta gama delta epsilon Amino Acids Identity of the amino acids depends on the nature of the Rgroup. Monosaccharides Carbohydrates have the general formula Cn(H2O)n • All carbohydrates are not just hydrates of water Simple sugars (monosaccharides) are cmpds that contain a single carbonyl group & 2 or more hydroxyl groups • Either polyhydroxyaldehydes or polyhydroxyketones Monosaccharides The ones that contain aldehydes=aldases The ones that conatin ketones = ketoses 6 Carbon sugars are most abundant in nature but 2, 5 carbon sugars (ribose and deoxyribose) occur in the structures of RNA and DNA The Structure of Nucleic Acid Monomers The 2 kinds of nucleic acids are DNA and RNA There are diffs and sims b/t the two They are macromolecules (very large molecules) formed by polymerizing monomer units (nucleotides = monomer units of nucleic acids) The Structure of Nucleic Acid Monomers Nucleotides have a base, a sugar, and a phosphoric acid residue covalently bonded together Nucleic acids can be hydrolyzed to their constituent nucleotides by acids, bases, or enzymes The Structure of Nucleic Acid Monomers The main distinction between the nucleotide monomers of DNA and RNA is the sugar portion DNA = deoxyribose RNA = ribose Nucleotide Base The Structure of Nucleic Acid Monomers 1. 2. Nucleic acid bases (aka nucleobases) = nitrogen-containing aromatic compounds that fall into 2 categories Pyrimidines – cytosine (in RNA&DNA)/thymine (DNA in rarely in RNA)/uracil (only in RNA) Purines adenine (RNA/DNA)/guanine (RNA/DNA) Lipid Examples Insoluble in H2O and soluble in organic solvents Glycerol esters of fatty acids (long chain carbox.acids) & derivatives of these esters are imoportant examples of lipids Another example = steroids Biochem Part II Amino Acids We know that proteins are long chain of amino acids linked together by peptide bonds between a + charged N (amino) group at one end and a – charged carbonyl group at the other end. • Along the chain is a series of side chains that are different for each of the 20 amino acids Amino Acids Dipeptide = 2 amino acids Tripeptide = 3 The sequence of the amino acids is most important • There are 8,000 ways to arrange them • In a protein chain of 100 amino acids, there are more ways to arrange them than there are atoms in the universe Of all the possible AA’s, only 20 are usually found in proteins! General structure of an AA involves an amino group, a carboxyl group & both are bonded to the α C • The α C is also bonded to a H • and an R group (side chain) The R group determines the identity of the AA Amino Acids One of the most important properties of a AA is its 3-d shape (stereochemistry) • Mirror images that are superimposable = achiral • Mirror images that aren’t superimposable = chiral • Many important molecules are chiral • Frequently, chiral center is a C atoms bonded to 4 different groups Amino Acids Glycine is the only AA that doesn’t have a chiral center (it’s R group is a single H, giving it 2H’s out of 4 groups) All other AA have 2 stereoisomers Amino Acids Dashed lines show behind the plane, solid triangles show out of the plane Amino Acids In biochemistry, we don’t use R&S designations, instead D & L are used L (laevus) and D (dexter) meaning left and right For AA, D=amino group on right side, L = amino group on the Left side Amino Acids AA in proteins are all L Structures and Properties of the Individual AA’s R group (thus the amino acids) are classified according to several criteria (two very important) Polar or nonpolar nature of the side chain Presence of an acidic or basic group in the side chain Group 1 – AA Nonpolar side chains Alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophan, methionine Group 2 - AA With electrically neutral polar side chains (neutral pH) Serine, threonine, tyrosine, cysteine Group 3 – AA - carboxyl groups in their side chains Glutamic acid and aspartic acid Carbonyl group can lose H+ (forming carboxylate ion) so they are – charged at neutral pH They frequently bond to –NH2 to form side chain amide groups yielding analogous AA glutamine & asparagine Group 4 – AA With basic side chains [+ charged at or near neutral pH Histidine Lysine Arginine Others Some other AA’s are known to occur in some, but not all proteins Derived from common AA and are produced by the modification of the parent AA after the protein is synthesized by the organism Others Hydroxyproline and hydroxylysine have extra –OH groups on the side chain Thyroxine (from tyrosine) has an extra Iodine containing aromatic group on the side chain (found only in thyroglobuin, a protein in the thyroid) The Peptide Bond AA are linked by covalent bonds joining the α – carboxyl group with the α-amino group) splitting out an H2O After the H2O elimination, the groups are linked amino acids residues A bond formed this way is called a peptide bond (aka: amide bond) Peptide Bond The Peptide Bond In a protein many AA (usually more than 100) are linked by peptide bonds to form a polypeptide chain • A peptide is a compound formed by liking smaller #’s of amino acids (two several dozen) • The bond is a single bond with partial double bond character (resonance)