BIOCHEMISTRY

1. BIOCHEMISTRY

2. Our targets: • Explain life processes in the molecular level • Success in tests and exams • Prepare for the USMLE Exam Step 1

3. Useful References: • Lippincott’s Biochemistry, 4th or 5th edition • Mark’s Basic Medical Biochemistry, 2nd ed

4. Scope of Biochemistry Structure BIOMOLECULES Function BIOCHEMISTRY Anabolism METABOLIC PATHWAYS Catabolism

5. Scope of Biochemistry feed/fast insulin/glucagon obesity INTEGRATION OF METABOLISM nutrition vitamins BIOCHEMISTRY Replication Transcription Translation Central Dogma Biotechnology

7. Central dogma of molecular biology Replication Transcription Translation DIET phenotype PROTEINS NORMAL FUNCTION ENV family

8. Amino Acids: Building Blocks of Proteins

9. Proteins are abundant and functionally moloecules in living systems • It is a “Macromolecule” ie: it is made up of many small subunits called “Monomers” • Monomers in protein are amino acids and are called , Residues • Amino acids →Peptides (2-9 AA) →Oligopeptides(10-20 AA)→ Polypeptides(>20 AA) →Proteins • Proteins are Linear and unbranched , constructed from 20 different AA that are encoded in DNA of Genome

10. Proteins - functionally diverse molecules e.g. 1)Enzymes 2) Immumity – Antibodies 3) Hormones 4)Control of Gene expression- Activators and Repressors 5)metabolism, 6)transport and storage, 7)cell communication movement 8)Structural element- Collagen, Cytoskeleton “scaffolding”

11. Amino Acid Structure All amino acids has a Carboxyl group “COOH”, an Amino group ”NH2“ , a side chain /group known as the “R” group , a hydrogen atom all attached to an α- carbon. This configuration is called a Primary Amino acids

12. α- Amino Acid

13. Exception • Proline is a secondary amino acid consider to be an IMINO ACID Has an Imino Group NH Its side chain and the α amino N forms a five membered ring structure • Disrupts protein secondary structures . E.g.: α helix • Forms fibrous structures e.g. collagen

14. Primary vs. Secondary

15. Properties of Amino acids • A) All AA contain an asymmetric/ chiral carbon This makes them optically active Exception : Glycine Has two hydrogen attached to carbon • B) Enantiomers- aa exists as stereoisomers called Enantiomers. Designated L (Levorotatory) D(Dextrorotatory) L – Amino acids found in Proteins D- Amino Acids are found in Bacterial products and Antibiotics

16. L-Amino acids are those with the -amino group on the left, and D-amino acids have the -amino group on the right.

17. Enantiomers

18. C) Amphoteric Molecule Has both basic and acidic groups At pH 7.4 (physiological pH), amino acids exist in zwitterionic form (positive NH3+ and negative COO- charges). Net charge = 0

19. At low ph (High [H+ ]) Carboxyl group accepts H+ and losses it charge Net molecular charge = + • At high ph (low [H+ ]) , the amino group loses it H+ and become uncharged Net molecular charge is negative

20. pKa =  2.0 Free amino acids are zwitterionic at physiological pH.

21. Amino Acids Classification • Classified based on side chain (R) group: Nonpolar, Polar, Charged (acidic or basic)

22. 20 Common Amino Acids found in proteins CLASSIFICATION-based on side chain • Non-polar amino acids (hydrophobic) • Polar, uncharged amino acids (hydrophilic) • Polar, charged amino acids (hydrophilic) -Acidic amino acids -Basic amino acids

23. Hydrophobic, Non Polar, Aliphatic

25. A. Amino acids with non-polar side chains • do not bind nor give protons • do not form hydrogen bonds • have hydrophobic interactions • 1. Location of non-polar (hydrophobic) amino acids in proteins • In soluble proteins (aqueous environment), found in the interior of proteins (shielded from environment) • In membranes or other hydrophobic environments, found on protein surface.

27. Hydrophilic amino acids

29. B. Amino acids with uncharged polar side chains • 2. Side chains as sites of attachments for other compounds: • Ser, Thr & Tyr contain polar –OH group – site of attachment for PO4- group, for e.g. Ser side-chain important active site component in many enzymes • -CONH2 group of Asn and –OH group of Ser & Thr serve as site of attachment of oligosaccharide chains in glycoproteins

30. 1. Disulfide bond: • Side chain of Cys contains –SH group – important active site of enzymes • Proteins with 2 –SH groups can form a disulphide bridge or cystine dimer (-S-S- , intermolecular or intramolecular). • Disulfide bonds help to stabilize Tertiary Protein structures • Destroying bonds denature protein • Methionine is another sulfur containing amino acid

32. C. Amino acids with acidic side chains • Asp & Glu are proton donors. • At neutral pH (physiological), side chains fully ionized or dissociated (COO-) and carry a net negative charge. • Contribute a negative charge to proteins . • Aspartate (aspartic acid) and glutamate (glutamic acid). • R groups typically have a pK< 7

34. D. Amino acids with basic side chains • Side chains of basic amino acids accept protons • At physiologic pH, side chains of Lys and Arg are fully ionized – positively charged ( NH3+) • Contribute a positive charge to proteins that contain them • Have a pK value>7 ( histones have an abundance of Arg and lys, net +ve charge) • His -- weakly basic and partially positively charged at physiologic pH- good buffering capacity • In proteins, can be +ve or –ve depending on environment of protein (important role in proteins like myoglobin).

36. Several Amino Acids Occur Rarely in Proteins Hydroxylysine, hydroxyproline - collagen -Carboxyglutamate - blood-clotting proteins Phosphorylated amino acids (serine, threonine, tyrosine) – a signaling device Hormones – epinephrine Allergic response - histamine

37. E. Abbreviations and symbols for commonly occurring amino acids 3-letter abbreviation and one-letter symbol 1. Unique first letter

38. 2. Most commonly occurring amino acids have priority

39. 3. Similar sounding names

40. 4. Letter close to initial letter:

41. Abbreviations and symbols for amino acids

42. Why know the nature of the R groups? The R group of an amino acid dictates its properties and reactivity.

43. The Henderson- Hasselbalch Equation Buffers are solutions which resist change in pH following the addition of an acid or base

44. REVIEW OF UNDERGRADUATE CHEMISTRY: Amino acids are weak acids The acid dissociation constant is given by: 1. HA  H+ + A- Ka = [ H + ] [ A - ] [HA] 2. ph = -log[H+] The larger the Ka, the stronger the acid. 3. pH < pKa protonated pH > pKa deprotonated

45. III. Acid/Base Properties of Amino acids • A. Henderson-Hasselbalch equation • Derivation of equation: Weak acid proton salt or base Ka = dissociation constant

46. acid conjugate base Henderson-Hasselbalch equation Buffers resist change in pH.

47. Henderson-Hasselbalch equationderivation - Log [HA] + pKa = pH [A-] Log [A-] + pKa = pH [HA]

48. Henderson-Hasselbalch equationderivation Ka = [H+][A-] [HA] [HA] Ka = [H+] [A-] - Log [HA] - Log Ka = - Log [H+] [A-] - Log [HA] + pKa = pH [A-]

49. Buffers • Buffer: solution that resists change in pH following addition of acid or base • Combination of weak acid and conjugate base in equal concentrations [HA] =[A-] ; pH = pKa • Effective buffer when pH = pKa ± 1 • Henderson-Hasselbalch equation can be used to calculate pH of a solution after addition of strong acid or base • Titration curve of acetic acid (a weak acid ).