Sheet 3 Lecture 5 2/7/2018 (9:15-10:30)

1. Sheet 3 Lecture 5 2/7/2018 (9:15-10:30) Done By Laith Obeidat Edited By Saeed Ashraf If you come by any error (whether it be spelling, grammar or scientific) while browsing this sheet, kindly report it to the academic team 2023od@gmail.com

2. Biochemistry by Mary K. Campbell & Shawn O. Farrell

3. The Three-Dimensional Structure of Proteins

4. Protein Structure 1° structure: the sequence of amino acids in a polypeptide chain, read from the N-terminal end to the C-terminal end • Amino acid sequence (1° structure) of a protein determines its 3D structure which determines its properties and its biological function. • A striking example of the importance of primary structure is sickle-cell anemia, a disease caused by a change in one amino acid in each of two of the four chains of hemoglobin(HbS the β-chain of sickle cell Hb a valine residue has replaced a glutamic acid residue at position 6).

5. In the primary structure the amino acid sequence determines the secondary and tertiary structures • The bonds between amino acids in the polypeptide chain are called Peptide bonds

6. 2° structure: the ordered 3-dimensional arrangements (conformations) in localized regions of a polypeptide chain; refers only to H-bonded arrangement of the peptide backbone e. g., -helix and -pleated sheet In Alzheimer’s disease patients, levels of β-amyloid become elevated, and this protein undergoes a conformational transformation from a soluble α helix–rich state to a state rich in β sheet and prone to self-aggregation.

7. In Alzheimer’s disease the (α-helix) becomes (β-amyloid), the brain shrinks and the communication function will seize

9. -Helix Characteristics: • coil of the helix is clockwise or right-handed • there are 3.6 amino acids per turn • full turn distance is 5.4 Å (pitch) • each peptide bond is trans and planar • C=O of each peptide bond is hydrogen bonded to the N-H of the fourth amino acid away • C=O…...H-N hydrogen bonds are parallel to helical axis • all R groups point outward from helix • R groups are not involved in the H-bonds

10. -Helix

11. -Pleated Sheet • polypeptide chains are folded back on itself • polypeptide chains lie adjacent to one another; may be parallel or antiparallel • R-groups alternate, first above and then below plane • each peptide bond is trans and planar • C=O and N-H groups of each peptide bond are perpendicular to axis of the sheet • C=O…...H-N hydrogen bonds are between adjacent sheets and perpendicular to the direction of the sheet

12. -Pleated Sheet antiparallel parallel • Reverse turn: allows peptide chain to reverse (bend) direction • Proline and glycine are prevalent

13. Tertiary (3°) structure: the 3D arrangement in space of all atoms in a polypeptide chain • Bonds stabilize the 3° structure: Metal ion coordination, side chain H-bond, electrostatic attraction, disulfide bond, and hydrophobic interaction • Quaternary (4°) structure: the association of polypeptide chains. • Proteins are divided into two large classes based on their three-dimensional structure. Protein Classifications according to shape : • fibrous proteins • globular proteins

14. A single polypeptide chain does not have a function, but when it binds with another polypeptide chain this gives it functionality and is called the Quaternary Structure, for example hemoglobin consists of 4 polypeptide chains

15. Fibrous Proteins • Fibrous proteins: contain polypeptide chains organized approximately parallel along a singleaxis. They • consist of long fibers or large sheets • tend to be mechanically strong • are insoluble in water and dilute salt solutions • Play an important structural roles in nature

16. Secondary Structures and Properties of Fibrous Proteins

17. Collagen triple helix Collagen has an unusual amino acid composition and sequence: Glycine is found at almost every third residue Proline (Pro) makes up about 17% of collagen Collagen contains two uncommon derivative amino acids not directly inserted during translation. These amino acids are found at specific locations relative to glycine and are modified post-translationally by different enzymes, both of which require vitamin Cas a cofactor.

18. Collagen triple helix means it has three (rod like structures) polypeptide chains overlapping one other • Glycine and Alanine are small amino acids • These small amino acids help in coiling the chains • The skin becomes abnormal if there is no collagen

19. Hydroxyproline (Hyp), derived from proline. Hydroxylysine(Hyl), derived from lysine (Lys). Depending on the type of collagen, varying numbers of hydroxylysines are glycosylated (mostly having disaccharides attached). Cortisol stimulates degradation of (skin) collagen into amino acids.

20. The best-known defect in collagen biosynthesis is Scurvy, a result of a dietary deficiency of vitamin C required by prolyl and lysyl hydroxylases. • The resulting deficit in the number of hydroxyproline and hydroxylysine residues undermines the conformational stability of collagen fibers, leading to bleeding gums, swelling joints, poor wound healing, and ultimately to death. • Menkes’syndrome, characterized by kinky hair and growth retardation, reflects a dietary deficiency of the copper required by lysyl oxidase, which catalyzes a key step in formation of the covalent cross-links that strengthen collagen fibers. • ``

21. Genetic disorders of collagen biosynthesis include : • several forms of osteogenesis imperfecta, characterized by fragile bones. In Ehlers-Dahlos syndrome, a group of connective tissue disorders that involve impaired integrity of supporting structures, defects in the genes that encode α collagen-1, procollagen N-peptidase, or lysyl hydroxylase result in mobile joints and skin abnormalities.

23. Globular Proteins • Globular proteins: proteins which are folded to a more or less spherical shape • they tend to be soluble in water and salt solutions • most of their polar side chains are on the outside and interact with the aqueous environment by hydrogen bonding and ion-dipole interactions • most of their nonpolar side chains are buried inside • nearly all have substantial sections of -helix and -sheet • Example • Myoglobin

24. Myoglobin

25. Myoglobin • Function in O2 storage in muscles • a single polypeptide chain of 153 amino acids • Compact with a single heme group in a hydrophobic pocket • 8 regions of -helix; no regions of -sheet • most polar side chains are on the surface • nonpolar side chains are folded to the interior • two His side chains are in the interior, involved with interaction with the heme group

26. Heme is a prosthetic group made from one protoporphyrin ring and iron in the center protoporphyrin ring is made from 4 pyrrole rings Fe(II) of heme has 6 coordinates sites; 4 sites interact with N atoms of protoporphyrin , 1 with N of a His side chain, and 1 with either an O2 molecule or an N of the second His side chain

27. Heme structure

28. Myoglobin • In the presence of globin, Fe(II) affinity to O2 increases and its affinity to CO decreases. • In the absence of globin, Fe(II) has high affinity to CO while low affinity to O2 . • In the absence of globin, Fe(II) can be easily oxidized to Fe(III) which has no affinity to O2

29. Fe(ll) affinity for CO is 210-folds more than its affinity for O2 • CO gas has no smell and it causes headache and dizziness

31. A free heme group has an affinity for CO = 25000 folds its affinity for O2 • E7 means polypeptide #7, the Hemoglobin (or myoglobin ) has 8 polypeptide chains with E7 • The (His E7) is close to (His F8) (which is in contact with the heme group) and forms a gate which prevents CO from connecting with the right angle of the heme group, this decreases the affinity of heme for CO from 25000 to 210 folds of its affinity for O2

32. Globular Protein Subunits Alcohol dehydrogenase 2 Triosephosphate isomerase 2 Aldolase 3 Hemoglobin 2 + 2 Lactate dehydrogenase 4 Pyruvate kinase 4 2 Insulin Quaternary Structure • Quaternary (4°) structure: the association of polypepetide monomers into multisubunit proteins (dimer, trimer, tetramer, etc) • examples we will see in this course

33. Aldolase and Lactate dehydrogenase are found in muscles

34. Hemoglobin (Hb)

35. Oxygen Binding of Hb • Hb is a tetramer of two -chains (141 amino acids each) and two -chains (153 amino acids each); a2b2 • each chain has 1 heme group; hemoglobin can bind up to 4 molecules of O2 • binding is cooperative; when one O2 is bound, it becomes easier for the next O2 to bind (positive cooperativity) • the function of hemoglobin is to transport oxygen • the structure of oxygenated Hb (loaded) is different from that of unoxygenated Hb (unloaded) • H+, CO2, Cl-, and 2,3-bisphosphoglycerate (BPG) affect the ability of Hb to bind and transport oxygen

36. Hemoglobin is the carrier of O2 in the blood , and Myoglobin is the storage site of O2 in muscles

37. Fig. 4-28, p.106

38. The difference between oxygenated and non oxygenated Hemoglobin is that : The chains in oxygenated hemoglobin are more compacted together (less space between the chains).

39. Oxygen Binding of Hb O2 binding of hemoglobin and myoglobin hyperbolic sigmoidal

40. Myoglobin can bind with O2 at any pressure (hyperbolic) and will be fully saturated because muscles need a lot of O2 to function properly • When the O2 concentrationrises the saturation of hemoglobin increases , so it displays an S (sigmoidal)-shape in the previous figure • Myoglobin does not need as much O2 to become saturated (can be saturated at lower pressures of O2) whereas hemoglobin needs a fair amount to become as saturated with oxygen

41. Oxygen Binding of Hb • The effect of pH on the oxygen-binding ability of Hb is called the Bohr effect • as pH decreases (more acidic), oxygen is released • Hb has lower affinity to O2 under  [H+] • CO2 promotes release of O2 from HbO2

42. Oxygen Binding of Hb The Bohr effect

43. Actively Metabolizing Muscle Lungs + Higher pH than actively Lower pH due to production of H metabolizing tissue Hemoglobin binds O Hemoglobin releases O 2 2 + + Hemoglobin releases H Hemoglobin binds H Oxygen Binding of Hb Summary of the Bohr effect

44. Hemoglobin (Hb) • Hemoglobin in blood is bound to BPG • interaction is electrostatic, between negative charges on BPG and positive side chains (e.g., Lys, Arg) of hemoglobin • BPG promotes O2dissociation • Hb stripped of BPG remains saturated with O2

45. Fig. 4-32, p.108

46. Fig. 4-33, p.109

47. Fetal Hemoglobin, Hb F • has a higher affinity for O2 than maternal Hb A • structure is a2g2 • binds less strongly to BPG than does Hb A Oxygen binding capacity of Hb F

48. Adaptation to High Altitude • Physiologic changes that accompany prolonged exposure to high altitude include an increase in the number of erythrocytes and in their concentrations of hemoglobin and of BPG. • Elevated BPG lowers the affinity of HbA for O2 (decreases P50), which enhances release of O2 at the tissues.

49. BIOMEDICAL IMPLICATIONS Myoglobinuria • Following massive crush injury, myoglobin released from damaged muscle fibers colors the urine dark red. • Myoglobin can be detected in plasma following a myocardial infarction. Anemias • Anemias, reductions in the number of red blood cells or of hemoglobin in the blood, can reflect impaired synthesis of hemoglobin (eg, in iron deficiency; or impaired production of erythrocytes (eg, in folic acid or vit.B12 def.)

50. Glycosylated Hemoglobin (HbA1c) When blood glucose enters the erythrocytes it glycosylates the amino group of lysine residues and the amino terminals of hemoglobin. The fraction of hemoglobin glycosylated, normally about 5%, is proportionate to blood glucose concentration. Since the half-life of an erythrocyte is typically 60 days, the level of glycosylated hemoglobin (HbA1c) reflects the mean blood glucose conc.over the preceding 6–8 weeks. Measurement of HbA1c therefore provides valuable information for management of diabetes mellitus.