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Transcript
What roles do proteins (polypeptides) play? 1. 2. 3. 4. 5. 6. 7. Enzymes (catalysts) Involved in storage and transport (hemoglobin) Provide support/shape (actin) Allow for movement (flagella) Decoder (DNA, gene expression) Regulators (hormones) Defense (antibodies) What is a protein? • Macromolecule • Polymer of amino acids Only 1 way to link the amino acids together: Peptide bond Sequence of amino acids determine a proteins structure and function Largest human protein is 34350 amino acids (Titan) Smallest human protein is debatable… • 20 standard amino acids All organisms use these 20 amino acids These 20 provide enormous possibilities of combinations For Titan, with 34350 amino acids, there are: (34350)20 combinations = 5.2 x 1090 possibilities!! What is an amino acid? Let’s build an amino acid! 1. C alpha carbon 2. H 3. Amine (NH3+) 4. Acid (COO-) 5. R group (side chain) 6. Backbone Chemistry C483 Fall 2009 Prof Jill Paterson 4-1 Amino acid “backbone” At pH 7.4, the carboxylate group is deprotonated (we will discuss why soon…) giving a negative charge At pH 7.4, the amino group is protonated, giving a positive charge Overall charge of the backbone is 0, [+1 + (-1)] or “zwiterionic” Amino acid side chains • 20 different side groups • Note the stereochemistry (geometry) • 19 of the 20 are chiral Steroisomers • 4 different groups bonded to Cα • These molecules cannot be superimposed (are mirror images of each other) • Therefore they are not identical, and are referred to as stereoisomers. • Using spectrographic instrumentation, the two configurations can be deciphered as either L or D based on how they rotate light (remember, this is different from assigning R- and S-). • Both L- and D- form exist in nature, but only L-forms are used to build proteins (some exceptions with bacteria) Chemistry C483 Fall 2009 Prof Jill Paterson 4-2 R v. S • Assign priority score based on atomic mass (highest being 1) • Orient the molecule with “4” score pointing away • Draw line from 1 to 2 to 3. If Clockwise, the configuration is R If Counterclockwise, the configuration is S Chemistry C483 Fall 2009 Prof Jill Paterson 4-3 Nonpolar amino acids Polar amino acids Chemistry C483 Fall 2009 Prof Jill Paterson 4-4 Glycine (Gly, G) • Nonpolar Aliphatic • Smallest • Leads to flexibility in proteins • Only non-chiral amino acid (Since R group is H, mirror images are superimposable and there is a plane of symmetry) Alanine (Ala, A) • Nonpolar, Aliphatic • Methyl group (β-carbon) Valine (Val, V) • Nonpolar, Aliphatic • Branched, note carbon notations Leucine (Leu, L) • Nonpolar, Aliphatic Isoleucine (Ile, I) • Nonpolar, Aliphatic • An additional chiral C (thus 4 conformations are possible). Chemistry C483 Fall 2009 • Aliphatic amino acids Avoid water Cluster together to keep water out Involved in hydrophobic interactions Prof Jill Paterson 4-5 Methionine (Met, M) • Nonpolar Highly hydrophobic • Contains a sulfur group • Binds to metals • First of most proteins Proline • • • • Nonpolar Only slightly hydrophobic Leads to “kinks” in protein People with naturally curly hair have a high level of Pro Phenylalanine (Phe, F) • Alanine with a phenyl group • Nonpolar • Hydrophobic Tryptophan (Trp, W) • Nonpolar • Less hydrophobic than Phe • Absorbs light at 280 nm Important for spectrophotometric analysis of proteins Serine (Ser, S) • • • • • • Polar, uncharged Slightly hydrophillic Alcohol Can form H-bonds Can be phosphorylated (regulator) Can have sugar attach Chemistry C483 Fall 2009 Prof Jill Paterson 4-6 Threonine (Thr, T) • Polar • Uncharged • Slightly hydrophillic Alcohol • Can form H-bonds • Has an additional chiral center, thus 4 conformations • Can be phosphorylated (regulator) • Can have sugar attach Asparagine (Asn, N) • • • • Uncharged Polar Forms H-bonds Can have sugars attached to form glyco-proteins Glutamine (Gln, Q) • • • • Uncharged Polar Can form H-bonds Can have sugars attach Tyrosine (Tyr, Y) • • • • Uncharged Polar Can form H-bonds absorbs light at 280 nm Important for spectrophotometric analysis of proteins • Can be phosphorylated • Is very slightly hydroPHOBIC, even though this is a polar molecule! Cysteine (Cys, C) • • • • Uncharged Polar Contains a sulfhydryl group Can be oxidized to form disulfide bonds Chemistry C483 Fall 2009 Prof Jill Paterson 4-7 Disulfide bonds These are covalent bonds which can be broken by a reduction reaction. Lysine (Lys, K) • • • • Charged (Positive) Polar Can form H-bonds Basic (we will discuss what this means soon!) Arginine (Arg, R) • • • • Charged (positive) Polar Can form H-bonds Basic Histidine (His, H) • Charged (sometimes positive) • Polar • Can be a proton donor or acceptor, depending on current pH • Known for its ability to bind metals Will we discuss this in detail during the protein purification section Chemistry C483 Fall 2009 Prof Jill Paterson 4-8 Aspartate (Asp, D) • • • • • Charged (negative) Polar Can form H-bonds Acidic Also known as Aspartic Acid Glutamate (Glu, E) • • • • • Charged (negative) Polar Can form H-bonds Acidic Also known as glutamic acid Other amino acids variants will be known to you The hydrophobicity of each amino acid Very hydrophobic Chemistry C483 Slightly hydrophobic Fall 2009 Slightly hydrophilic Prof Jill Paterson Very hydrophilic 4-9 Where do we find these amino acids in proteins? • Charged, hydrophilic amino acids are almost always found on the surface of a protein, interacting with the surrounding water • Polar residues are usually found on the surface of the protein, but can be buried • Non-polar, hydrophobic amino acids are usually buried in a protein, but can be found on the surface Summary • The 20 amino acids have been presented • Each amino acid differs in the side chain, giving each amino acid different chemical characteristics __are nonpolar __ are polar __of the polar are uncharged __of the polar are charged • Each amino acid has a three letter code AND a one letter code • At physiological pH (7.4), the carboxylic acid of an amino acid is deprotonated • At physiological pH, the amino group is protonated • Protonation of the side chains varies, dependent on the chemical group and pH • Some amino acids are characterized as basic, while others are acid Chemistry C483 Fall 2009 Prof Jill Paterson 4-10