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BCH210H1 (352)


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Charles Deber

Biochemistry Exam review Lecture 1 to 3 Properties of the protein components: the amino acids  20 commonly – occurring residues  They are zwitterionic as monomers- neutral overall but within the molecule there is a separation in charge (positive and negative)  Joined together through peptide bonds- peptide bonds are through dyhydration (removal of h20) C=O attach to NH  Amino acids usually have a chirality center (except Gly) The L isomer is usually found in proteins  The side chains of amino acids are either hydrophobic (non-polar) or hydrophilic (polar charge)  Hydrophobic amino acids occur usually in the interior of globular proteins  Hydrophilic (polar) amino acids occur on the protein surface (interacts with water)  Some residues- especially Gly and Pro have structural functions in protein chains. Amino Acids Beta- branched- the second carbon is a CH Disulfide bridge-two cysteine= form a cystine 1. Glycine (Gly) G 2. Alanine (Ala) A 3. Valine (Val) V Beta-branched 4. Leucine (Leu) L Beta- branched 5. Isoleucine (Ile) I 6. Serine (Ser) S 7. Threonine (Thr) T Beta branched 8. Phenyl-alaine (Phe) P 9. Tyrosine (Tyr) Y 10. Triptophan (Trp) W Indole ring 11. Cystine (Cys) C - form disulfide bonds = can form dimers 12. Methionine (Met) M 13. Aspartic acid (Asp) D 14. Glutamic acid (Glu) E 15. Asparagine (Asn) N 16. Glutamine (Gln) Q 17. Lysine (Lys) K 18. Arginine (Arg) R Guani-dinium group 19. Histidine (His) H imidazole ring 20. Proline (Pro) P –imino acid Hydrophobic Amino Acids= Ala, Cys, Ile, Leu, Met, Phe, Val Hydrophilic (polar) amino acids= Basic: Arg, Lys Acidic: Asp, Glu Polar: Asn, Gln, His Mid- range amino acids= Ser, Thr, Tr, Trp, Gly, Pro PKa values of amino acid side chains  Pka= The ph of protonation or de-protonation Pka Values Propanated  Terminal COOH = 3  Side- chain COOH =4  Histidine =6.5  Red Cell=7  Terminal NH2 and cysteine =8  Tyrosine and Lysine= 10  Arginine=12 Depropanated  The amino acid side chain I protonated when the Ph is lower than its PKA value and deprotonated when the pH is above its pKa value  If right on an animo acids pKa value= equilibrium Interactions Stabilizing Protein Structures 1) Electro static forces- attractions between oppositely charged species (+,-) especially between positive NH3 and negative COO- -also between one fully positive or negative species and one polar species (C=O, OH, NH, SH) 2) Hydrogen Bonds- stabilizing, attractive interaction between a proton (often part of a polarizable bond such as NH, OH or SH) and an electron donation species often C=O -hydrogen bonds are the biggest stabilizing force in secondary structures -each H bond is 3 to 6 Kcal -electron density is donated from carbonyl group to form H-Bond, the stronger the H-bond the weaker the C=O 3) Hydrophobic interactions- attractive interactions between pairs or clusters of non-polar side chains which cause them to associate -the driving force is so that the side chains have minimal interactions with water -the non-polar side chains of amino acids cannot replace intermolecular stabilization of organized water molecules (cannot fo
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