Chemical basis: Bonding

1. Chemical basis: Bonding • Covalent Bonds: sharing of e- • One pair shared = single bond C C • Two pairs = double bond C C • Three pairs = triple bond C C • Electronegativity (EN) is the ability of an atom to attract electrons to itself • C = 2.5 N = 3.0 O = 3.5 H = 2.1 • Sharing is unequal between different atoms in a molecule • Polar molecules have significant EN differences • H2O, CH3COOH • Nonpolar molecules have little EN differences • CH3(CH2)nCH3 • Amphipathic molecules have different EN characteristics at different positions • CH3(CH2)nCOOH

2. Chemical basis: Bonding • Noncovalent Bonds: attractive forces between atoms of opposite charge • Ionic: fully charged Na+ Cl- • Strength dependent on environment (salt crystal vs aqueous) • Hydrogen: partial charge (polar molecules)

4. Chemical basis: Bonding • Noncovalent Bonds: continued… • Van der Waals: transient dipole interactions • Hydrophobic: water fearing • Hydrophilic: water loving

5. H2O • Can form 4 hydrogen bonds • High energy barrier to liquid --> gas phase transition • Highly polarized • Asymmetric structure - both H atoms on one side • Can dissolve many compounds

6. H2O • Can dissolve many compounds • Acids: can release H+ • Bases: can accept H+ pH = - log [H+] • Pure H2O pH = 7 , [H+] = [OH-] = 10-7 M • Why are reactions so pH sensitive? • Amino acid functional groups can change state based on pH

7. The importance of water in protein structure

8. Carbon, Chirality and Stereoisomerism Carbon is central to the chemistry of life. Carbon forms four covalent bonds, with itself or other atoms. Carbon-containing molecules produced by living organisms are called biochemicals. Chirality and Stereoisomerism: Asymmetric carbons bond to four different groups. Molecules with asymmetric carbons can exist in two mirror-image configurations called enantiomers or stereoisomers Enantiomers can be either D- or L-isomers Natural amino acids are almost all L-isomers Natural carbohydrates are almost all D-isomers

9. Stereoisomerism

10. Classes of molecules • Miscellaneous co-factors • Vitamins, ATP, NADPH, etc • Metabolic intermediates • Glycolysis, TCA cycle, etc • Monomers • Amino acids • rNTPs = rATP, rGTP, rCTP, rUTP • dNTPs = dATP, dGTP, dCTP, dTTP • Sugars • Macromolecules

11. Four types of macromolecules

12. Classes of molecules • Macromolecules • Lipids • Fats = glycerol esterified with 3 fatty acids • Saturated, unsaturated, cis, trans • Phospholipids = glycerol + 2 fatty acids + 1 phosphate • Steroids = cholesterol and derivatives

13. Classes of molecules • Macromolecules • Lipids • Fats = glycerol esterified with 3 fatty acids • Saturated, unsaturated, cis, trans • Phospholipids = glycerol + 2 fatty acids + 1 phosphate • Steroids = cholesterol and derivatives

14. Classes of molecules • Macromolecules • Lipids • Fats = glycerol esterified with 3 fatty acids • Saturated, unsaturated, cis, trans • Phospholipids = glycerol + 2 fatty acids + 1 phosphate • Steroids = cholesterol and derivatives

15. Classes of molecules • Macromolecules • Lipids • Fats = glycerol esterified with 3 fatty acids • Saturated, unsaturated, cis, trans • Phospholipids = glycerol + 2 fatty acids + 1 phosphate • Steroids = cholesterol and derivatives

16. Monomers and polymers

17. Classes of molecules • Macromolecules • Carbohydrates • ( CH2O )n • At n ≥ 5 self-reaction to form rings • C5 = ribose • C6 = glucose

18. Classes of molecules • Macromolecules • “Nutritional” sugars: • Glycogen = branched alpha 1-4 linkage, dense granules in cell cytoplasm in animals • Starch = helical and branched alpha 1-4 linkage, within membrane bound plastids in plants alpha 1 --> 4 glycogen, starch beta 1 --> 4 cellulose

19. Classes of molecules • Macromolecules • “Nutritional” sugars: • Glycogen = branched alpha 1-4 linkage, dense granules in cell cytoplasm in animals • Starch = helical alpha 1-4 linkage, within membrane bound plastids in plants plastid

20. Classes of molecules • Macromolecules • “Structural” sugars: • Cellulose = long and unbranched, beta 1-4 linkage, resist tensile (pulling) forces, plants • Chitin = unbranched, N-acetylglucosamine, invertebrates • Glycosaminoglycans = components of extracellular matrix for cartilage and bone, repeating (A-B)n structure

21. Classes of molecules • Macromolecules • Nucleic Acids • Nucleotide monomers (rNTPs, dNTPs) • Storage and transmission of genetic information • Phosphate + 5C ribose sugar + nitrogenous base RNA DNA H

22. Classes of molecules • RNA is usually single stranded and DNA is usually double stranded. • RNA may fold back on itself to form complex three dimensional structures, as in ribosomes. • RNA may have catalytic activity; such RNA enzymes are called ribozymes. • Adenosine triphosphate (ATP) is a nucleotide that plays a key role in cellular metabolism • Guanosine triphosphate (GTP) serves as a switch to turn on some proteins.

27. Classes of molecules • Macromolecules • Proteins • Amino acid monomers • Peptide bond formation • N-terminus versus C-terminus • Backbone is common, side chains (R) differ

28. Classes of molecules • Macromolecules • Proteins • Backbone is common, side chains differ • 4 categories of amino acid side chains • Polar charged D, E, K, R, H • Polar uncharged S, T, Q, N, Y • Nonpolar A, V, L, I, M, F, W • Unique G, C, P • Post-translational modifications: Phosphorylation

29. Classes of molecules • Macromolecules • Proteins • Backbone is common, side chains differ • 4 categories of amino acid side chains • Polar charged D, E, K, R, H • Polar uncharged S, T, Q, N, Y • Nonpolar A, V, L, I, M, F, W • Unique G, C, P • Post-translational modifications: Phosphorylation

30. Classes of molecules • Macromolecules • Proteins • Backbone is common, side chains differ • 4 categories of amino acid side chains • Polar charged D, E, K, R, H • Polar uncharged S, T, Q, N, Y • Nonpolar A, V, L, I, M, F, W • Unique G, C, P • Post-translational modifications: Phosphorylation

31. Classes of molecules • Macromolecules • Proteins • Backbone is common, side chains differ • 4 categories of amino acid side chains • Polar charged D, E, K, R, H • Polar uncharged S, T, Q, N, Y • Nonpolar A, V, L, I, M, F, W • Unique G, C, P • Post-translational modifications • Phosphorylation

32. Hydrophobic and hydrophilic amino acid residues in the protein cytochrome c

33. Classes of molecules • Macromolecules • Proteins • Structure • Primary • Sequence of the polypeptide chain H3N-MQWERTYIPASDFGHKLCVN-COOH H3N-Met Gln Trp Glu Arg Thr Tyr Ile…

34. Classes of molecules • Secondary • Alpha-helix (collagen) • Beta-sheet (spider silk) • Side-chain dependence to which form is adopted but stabilization comes from backbone - backbone hydrogen bonding interactions

35. Classes of molecules • Tertiary • Side-chain dependent and mediated packing of the secondary elements • Fibrous proteins = elongated, often structural roles • Globular = compact, often enzymes • Domains • Conformational changes

36. Protein structure • Protein Domains • Domains occur when proteins are composed of two or more distinct regions. • Each domain is a functional region

37. Protein structure • Dynamic Changes within Proteins • May occur with protein activity. • Conformational changes are non-random movements triggered by various events (e.g. binding, chemical mods…)

38. Classes of molecules • Quaternary • Interactions between 2 or more distinct polypeptide chains

39. Protein Structure • Protein-Protein Interactions • Results from large-scale studies can be presented in the form of a network. • A list of potential interactions can be elucidate unknown processes.

40. Disease Sickle cell anemia E --> V mutation in hemoglobin

41. Classes of molecules • Macromolecules • Proteins • Protein folding • Anfinsen RNase A experiment • Denature (unfold) protein in urea and observe loss of activity • Dialyze the urea away and observe refolding and regain of activity Demonstrated structure info is inherent to protein sequence Fold to the lowest energy state Follow a folding pathway

42. Two alternate pathways for protein folding

43. Classes of molecules • Macromolecules • Proteins • Protein folding • Molecular Chaperones • HSP70 during translation of nascent peptide • Chaperonins assist post-translation

44. GroEL-GroES-assisted folding of a polypeptide

45. Classes of molecules • Macromolecules • Proteins • Protein folding • CJD (Mad Cow) & Alzheimers Disease • PrPC --> PrPSc --> plaque • APP --> Ab42 --> plaque

46. Classes of molecules • Macromolecules • Proteins • Protein folding • CJD (Mad Cow) & Alzheimers Disease • PrPC --> PrPSc --> plaque • APP --> Ab42 --> plaque