Proteins

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  • FIGURE 5-1 Heme. The heme group is present in myoglobin, hemoglobin, and many other proteins, designated heme proteins. Heme consists of a complex organic ring structure, protoporphyrin IX, with a bound iron atom in its ferrous (Fe2+) state. (a) Porphyrins, of which protoporphyrin IX is only one example, consist of four pyrrole rings linked by methene bridges, with substitutions at one or more of the positions denoted X. (b, c) Two representations of heme (derived from PDB ID 1CCR). The iron atom of heme has six coordination bonds: four in the plane of, and bonded to, the flat porphyrin ring system, and (d) two perpendicular to it.
  • FIGURE 5-6 Comparison of the structures of myoglobin (PDB ID 1MBO) and the β subunit of hemoglobin (derived from PDB ID 1HGA).
  • FIGURE 5-12 A sigmoid (cooperative) binding curve. A sigmoid binding curve can be viewed as a hybrid curve reflecting a transition from a low-affinity to a high-affinity state. Because of its cooperative binding, as manifested by a sigmoid binding curve, hemoglobin is more sensitive to the small differences in O2 concentration between the tissues and the lungs, allowing it to bind oxygen in the lungs (where pO2 is high) and release it in the tissues (where pO2 is low).
  • FIGURE 5-16 Effect of pH on oxygen binding to hemoglobin. The pH of blood is 7.6 in the lungs and 7.2 in the tissues. Experimental measurements on hemoglobin binding are often performed at pH 7.4.
    FIGURE 5-17 Effect of BPG on oxygen binding to hemoglobin. The BPG concentration in normal human blood is about 5 mM at sea level and about 8 mM at high altitudes. Note that hemoglobin binds to oxygen quite tightly when BPG is entirely absent, and the binding curve seems to be hyperbolic. In reality, the measured Hill coefficient for O2-binding cooperativity decreases only slightly (from 3 to about 2.5) when BPG is removed from hemoglobin, but the rising part of the sigmoid curve is confined to a very small region close to the origin. At sea level, hemoglobin is nearly saturated with O2 in the lungs, but just over 60% saturated in the tissues, so the amount of O2 released in the tissues is about 38% of the maximum that can be carried in the blood. At high altitudes, O2 delivery declines by about one-fourth, to 30% of maximum. An increase in BPG concentration, however, decreases the affinity of hemoglobin for O2, so approximately 37% of what can be carried is again delivered to the tissues.
  • FIGURE 5-30 Muscle contraction. Thick filaments are bipolar structures created by the association of many myosin molecules. (a) Muscle contraction occurs by the sliding of the thick and thin filaments past each other so that the Z disks in neighboring I bands draw closer together. (b) The thick and thin filaments are interleaved such that each thick filament is surrounded by six thin filaments.
    FIGURE 5-31 Molecular mechanism of muscle contraction. Conformational changes in the myosin head that are coupled to stages in the ATP hydrolytic cycle cause myosin to successively dissociate from one actin subunit, then associate with another farther along the actin filament. In this way the myosin heads slide along the thin filaments, drawing the thick filament array into the thin filament array (see Figure 5-30).
  • Proteins

    1. 1. Chapter 22: Proteins K. Dunlap Chem 104
    2. 2. Human Proteins • proteins contain C, H, O, and N • Made up of 20 amino acids • amino acids written in blue are essential amino acids, meaning they can not be made and must be consumed
    3. 3. Proteins • Proteins serve many functions: – 1.Structure: collagen and keratin are the chief constituents of skin, bone, hair, and nails. – 2. Catalysts: virtually all reactions in living systems are catalyzed by proteins called enzymes. – 3. Movement: muscles are made up of proteins called myosin and actin. – 4. Transport: hemoglobin transports oxygen from Transport the lungs to cells; other proteins transport molecules across cell membranes. – 5. Hormones: many hormones are proteins, among them insulin, oxytocin, and human growth hormone.
    4. 4. Proteins – 6. Protection: blood clotting involves the protein fibrinogen; the body used proteins called antibodies to fight disease. – 7. Storage: casein in milk and ovalbumin in eggs store nutrients for newborn infants and birds; ferritin, a protein in the liver, stores iron. – 8. Regulation: certain proteins not only control the expression of genes, but also control when gene expression takes place.
    5. 5. Amino Acids •Have an alpha- carbon attached to: • an amino group • carboxyl group • a hydrogen • an R group
    6. 6. Each R group determines the properties of the amino acid R groups can be polar, nonpolar, acidic, basic
    7. 7. Each R group determines the properties of an amino acid R groups can be polar, nonpolar, acidic, basic
    8. 8. Chirality of Amino Acids • With the exception of glycine, all proteinderived amino acids have at least one stereocenter (the α-carbon) and are chiral. – The vast majority of protein-derived amino acids have the L-configuration
    9. 9. Zwitterions • amino acids can act as acids and bases • • Amino acids exist in solution as dipolar ions (Zwitterions) Like buffers, AA’s can act as proton donors or acceptors – “Amphoteric” compounds or “amphoteric electrolytes” • Isoelectric point – pH at which all the molecules have equal positive and negative charges
    10. 10. Proteins are made of 20 amino acids
    11. 11. proteins
    12. 12. Peptides: how aa are linked • proteins are long chains of amino acids joined by amide bonds. peptide bond: – amino acids become linked together to form peptide bonds with the elimination of water – The reaction takes place between the -COOH of one amino acid and the -NH2
    13. 13. formation of peptide bonds Peptides and proteins are polymers of amino acids • Two amino acids are covalently joined in condensation reaction N-terminal C-terminal
    14. 14. Peptides – Peptide: A short polymer of amino acids joined by Peptide peptide bonds; they are classified by the number of amino acids in the chain. – Dipeptide: containing two amino acids joined by a Dipeptide peptide bond. – Tripeptide: containing three amino acids joined by Tripeptide peptide bonds. – Polypeptide: chain containing up to 50 amino acids Polypeptide – Protein: A biological macromolecule containing at Protein least 30 to 50 amino acids joined by peptide bonds.
    15. 15. 4 levels of protein structure • Primary – sequence of amino acids • Secondary – interactions between adjacent amino acids • Tertiary – 3D folding of the polypeptide • Quaternary – arrangements of multiple polypeptides
    16. 16. Levels of Structure • Primary structure: the sequence of amino acids • Secondary structure: conformations of amino acids in localized regions of a polypeptide chain; examples are α-helix, β-pleated sheet, and random coil. • Tertiary structure: the complete threedimensional arrangement of atoms of a polypeptide chain. • Quaternary structure: the spatial relationship and interactions between subunits in a protein that has more than one polypeptide chain.
    17. 17. 1) Primary Structure • the sequence of amino acids in a polypeptide chain. • The number peptides possible from the 20 protein-derived amino acids is enormous. – the number of peptides possible for a chain of n amino acids is 20n. – for a small protein of 60 amino acids, the number of proteins possible is 2060 = 1078
    18. 18. Primary Structure • The hormone insulin consists of two polypeptide chains held together by two interchain disulfide bonds.
    19. 19. Primary Structure • Just how important is the exact amino acid sequence? – Human insulin consists of two polypeptide chains having a total of 51 amino acids. – In the table are differences between four types of insulin. A Chain p ositions 8-9-10 B Chain p osition 30 H uman Cow -Thr-Ser-Ile-A la-Ser-Val- -Thr -Ala H og -Thr-Ser-Ile- -Ala Sh eep -Ala-G ly-Val- -Ala
    20. 20. Primary Structure – Vasopressin and oxytocin are both nonapeptides but have quite different biological functions. – Vasopressin is an antidiuretic hormone. – Oxytocin affects contractions of the uterus in childbirth and the muscles of the breast that aid in the secretion of milk.
    21. 21. proteins range in size
    22. 22. 2) Secondary Structure • conformations of amino acids in localized regions of a polypeptide chain. – The most common types of secondary structure are α-helix and β-pleated sheet. α-Helix: a type of secondary structure in which a section of polypeptide chain coils into a spiral, most commonly a right-handed spiral. β-Pleated sheet: a type of secondary structure in which two polypeptide chains or sections of the same polypeptide chain align parallel to each other
    23. 23. α-Helix • The α-helix structure: held together by hydrogen bonds
    24. 24. α-Helix • In a section of α-helix; – The C=O group of each peptide bond is hydrogen bonded to the N-H group of the peptide bond four amino acid units away from it. – All R- groups point outward from the helix.
    25. 25. secondary structure • Note the position of the purple R groups relative to the backbone of the polypeptide
    26. 26. all α helices are right handed • But some supramolecular complexes are left handed (keratin, collagen) right-handed = clockwise
    27. 27. β sheet secondary structure • More extended • H-bonds may occur between amino acids some distance from one another • Adjacent chains can run parallel or anti-parallel to each other
    28. 28. β-Pleated Sheet • In a section of β-pleated sheet; – The C=O and N-H groups of peptide bonds from adjacent chains point toward each other so that hydrogen bonding is possible between them. – All R- groups on any one chain alternate, first above, then below the plane of the sheet, etc.
    29. 29. Pleated Sheet Structure of Proteins
    30. 30. secondary structure and function
    31. 31. 3) Tertiary Structure • the overall conformation of an entire polypeptide chain. • Tertiary structure is stabilized in four ways: – Covalent bonds, as for example, the formation of disulfide bonds bonds between cysteine side chains. – Hydrogen bonding between polar groups of side chains, as for example between the -OH groups of serine and threonine. – Salt bridges, as for example, the attraction of the -NH3+ bridges group of lysine and the -COO- group of aspartic acid. – Hydrophobic interactions, as for example, between the interactions nonpolar side chains of phenylalanine and isoleucine.
    32. 32. Cysteine • The -SH (sulfhydryl) group of cysteine is easily oxidized to an -S-S- (disulfide).
    33. 33. the permanent wave that isn’t Heat + New S-S bonds
    34. 34. Tertiary Structure • Forces that stabilize 3° structure of proteins
    35. 35. Tertiary Structures of Proteins • the three dimensional shape of proteins that results from further crosslinking, folding and interaction between R groups 1) disulfide linkages (-S-S-) b/w cysteins 2) dipole dipole interactions b/w polar groups 3) hydrogen bonding on side chains 4) London forces
    36. 36. relative compactness of proteins • Hypothetical chain length of a protein if it were to appear either as an α helix or β sheet
    37. 37. 4) Quaternary Structure • the arrangement of polypeptide chains into a noncovalently bonded aggregation. – The individual chains are held together by hydrogen bonds, salt bridges, and hydrophobic interactions. • Hemoglobin – Adult hemoglobin: two chains of 141 amino acids each, and two chains of 146 amino acids each. – Each chain surrounds an iron-containing heme unit.
    38. 38. Hemoglobin • The 4° structure of hemoglobin: made up of 4 subunits
    39. 39. Denaturation • the process of destroying the native conformation of a protein by chemical or physical means. – Some denaturations are reversible, while others permanently damage the protein.
    40. 40. Protein Function • Protein function often includes reversible binding interactions with other molecules. • Complementary interactions between proteins and ligands are the basis of self vs non-self recognition by the immune system. • Specific protein interactions modulated by chemical energy are the basis of muscle movement.
    41. 41. oxygen-binding proteins have a heme prosthetic group
    42. 42. oxygen-binding proteins have a heme prosthetic group hemoglobin http://www.youtube.com/watch?
    43. 43. Hemoglobin Binds O2 is a cooperative process. Binding affinity of Hb for O2 is increased by the O2 saturation of the molecule with the first O2 bound influencing the shape of the binding sites (conformation change) for the next O2
    44. 44. hemoglobin-O2 binding allosterically modulated by 2,3-bisphosphoglycerate BPG reduces the affinity of Hb for O2. BPG binds at a site distant from the O2-binding site and regulates the affinity of Hb for O2.
    45. 45. immune responses are mediated by protein interactions that distinguish self and non-self Cellular immune response - T cells destroy host cells infected by viruses Humoral immune response – B cells produce antibodies or immunoglobulins against bacteria, viruses and foreign molecules
    46. 46. muscle contraction is also based on protein interactions and conformational changes Muscle contraction occurs by the sliding of the thick (myosin) and thin (actin) filaments past each other Conformational changes in the myosin head are coupled to ATP hydrolysis http://www.sci.sdsu.edu/movies/
    47. 47. 1. What 2 functional groups are present in all amino acids? 2. Name the simplest amino acid. Is it a chiral molecule? 3. Approximately how many amino acids are needed to make the proteins found in the body? 4. What element is present in proteins but not in sugars or fats?
    48. 48. 5. What is meant by the primary, secondary and tertiary structures of proteins? 6. What type of bonds are responsible for the helix structure of some proteins?

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