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Introduction to Biochemistry I

Review of Carbon Atom.

Biochem019
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Introduction to Biochemistry I

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  1. Introduction to Biochemistry Part III – Foundations of Organic Chemistry in Biochemistry

  2. Biochemistry Macromolecules Functional Groups Organic Reactions Carbohydrates

  3. Definitions • Biochemistry is the study of chemical compounds and reactions which occur in living organisms. • It overlaps extensively with organic chemistry since most compounds in living cells contain carbon. • Biochemistry involves the study of carbohydrates, lipids, proteins and nucleic acids, which are the types of molecules involved in the chemistry of living organisms.

  4. Definitions • Hydrogen bonds – ionic and hydrophilic interactions between a polar or ionic molecules and water.

  5. Definitions • Hydrophobic interactions - tendency of nonpolar substances to aggregate in aqueous solution and exclude water molecules.

  6. Macromolecules • All living things contain these organic molecules: carbohydrates, lipids, proteins, and nucleic acids. • These organic molecules are often called macromolecules. • They may be very large, containing thousands of carbon and hydrogen atoms and bonded to other smaller molecules. • They are classified as polar, ionic or non-polar molecules.

  7. Macromolecules • Polarand ionic molecules have either full or partially (dipole) positive or negative charges. • They are attracted to water molecules. • They are said to be hydrophilicbecause they interact with (dissolve in) water by forming hydrogen bonds.

  8. Macromolecules • Nonpolar molecules are neutral (NO dipole). • They are NOT attracted to water or polar molecules. • They are hydrophobicbecause they DO NOT dissolve in water or form hydrogen bonds.

  9. Macromolecules • Nonpolar molecules are hydrophobic. • Polar and ionic molecules are hydrophilic.

  10. Macromolecules • Portions of macromolecules may be hydrophobic and other portions of the same molecule may be hydrophilic. • The chains may be branched or form  rings.

  11. Functional Groups in Biochemistry Hydrocarbons Aromatics Common Functional Groups

  12. Functional Groups • Some functional groups are polar and others can ionize. • For example, if the hydrogen ion is removed from the COOH group, the oxygen will retain both of the electrons and will have a negative charge. • The hydrogen that is removed leaves behind its electron and is now a hydrogen ion (proton, cation, H+).

  13. Functional Groups • If polar or ionizing functional groups are attached to hydrophobic molecules, the molecule may become hydrophilic due to the functional group. • Some ionizing functional groups are: -CO2H, -OH, R2-C=O, and -NH2.

  14. Hydrocarbons

  15. Cycloalkanes

  16. Cycloalkanes

  17. Cycloalkanes

  18. Aromatic Compounds

  19. Aromatic Compounds

  20. Aromatic Compounds

  21. Aromatic Compounds

  22. Common Functional Groups

  23. Common Functional Groups

  24. Summary of Functional Groups

  25. Summary of Functional Groups • Important bond linkages in Biochemistry:

  26. Organic Reactions Classes: Group Transfer REDOX Eliminations, Isomerizations, Rearrangements C-C Bond Making & Breaking Hydrolysis

  27. Group Transfer Reactions • Nucleophilic Substitution • Transfer an electrophile from one nucleophile to another. • Commonly transferred groups: • Acyl • Phosphoryl • Glycosyl • Amino

  28. Group Transfer Reactions: Acyl Group Acylation Reactions

  29. Group Transfer Reactions: Phosphoryl Group Phsophorylation Reaction

  30. Group Transfer Reactions: Glycosyl Group Glycosylation Reactions

  31. Group Transfer Reactions: Amino Group Transamination Reactions

  32. REDOX Reactions • Involve the loss or gain of electrons. • C-H bond cleavage with the loss of electrons. • Use of electron acceptors: • NAD+ • FAD+ • NADP+ • Coenzyme Q • Fe centers in Cytochrome C

  33. REDOX Reactions • Electrons are highly reactive and do not exist on their own in cells. • If oxidation occurs to one molecule in the cell, reduction must immediately to another molecule.

  34. REDOX Reactions

  35. REDOX Reactions

  36. REDOX Reactions

  37. REDOX Reactions

  38. Elimination Reactions • Formation of alkenes • Products are: • Trans (anti) – Major • Cis (syn) • Elimination of: • Water • Ammonia • 1⁰ Amines • Alcohols

  39. Elimination Reactions • Types of Mechanisms: • Concerted • Carbocation Formation: C-O bond breakage • Carbanion Formation: C-H bond breakage • Two Types of Reactions: • Dehydrations • Deaminations

  40. Elimination Reactions: Concerted & Carbocation

  41. Elimination Reactions: Carbanion

  42. Elimination Reactions: Dehydration • Enzyme catalyzed reactions. • Two Types of Enzyme-Catalysis: • Acid: Protonation of OH group • Base: Abstraction of a proton

  43. Elimination Reactions: Dehydradation

  44. Other Dehydration Reactions • Condensation reactions. • Involved in the assembly of all four types of macromolecules. • An H atom is removed from a functional group on one molecule, and an OH group is removed from another molecule. • Products: a larger molecule + water

  45. Condensation of Amino Acids

  46. Condensation of Saccharides

  47. Condensation of Fatty Acids

  48. Elimination Reactions: Deaminations

  49. Elimination Reactions: Deaminations

  50. Isomerization Reactions • Relocation of a = bond. • Intramolecular shift of a proton. • Most common are base catalyzed reactions.

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