Biochemical Foundations of Physiology -1

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Biochemical Foundations of Physiology -1
2014-09-01 18:33:12

Lecture 1
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  1. What is the most abundant and functionally diverse
    molecule in living organisms ?

    What are polymers ?

    All organisms use how many of the
    same Amino Acids  encoded by DNA ?

    What are common or standard Amino
    Acids ?

    They are a sequence of Amino Acids that form a protein , a monomer is a single Amino Acid.

    20 Amino Acids 

    They are the same 20 amino acids used by all organisms
  2. Name the four portions of this Amino Acid ?
    Alpha Carbon 
    Carboxyl Group
    Side Chain (R Group)
    Amino Group 
  3. What part of the Amino Acid determines it's unique property ?
    Side Chain [R]
  4. The standard amino acids have the same general structure, with the exception of which Amino Acid ?
    Proline which has a  2o Amino group

  5. In proteins, almost all of the carboxyl and amino groups are combined through what type of linkages ?
    Peptide Linkages

  6. What is the physiological pH of the body ?
    Approximately 7.4
  7. What is the charge of the Amino group and the Carboxyl and the physiological pH ?
    the carboxyl group is dissociated, forming the negatively charged ion (-COO-), and the amino group is protonated (-NH3+).

  8. What us the amphoteric property of Amino Acids ?
    The ability to act as an Acid or Base due to the Amino and Carboxyl groups changing charges, which is controlled by pH
  9. Neutral molecules that bear an equal
    number of positive and negative charges simultaneously are called ?
  10. What are the 4 properties that the Side Chain [R] can possess ?
    • Nonpolar
    • Uncharged Polar
    • Acidic 
    • Basic
  11. These AAs have a nonpolar side chain that
    promotes (hydrophobic or hydrophobic)  

    Do they have an “oily” or “lipid like” property?

    Where are they Located in proteins when found in aqueous solutions ?

    Where are they found when proteins are in hydrophobic environments ?



    On the outside membranes
  12. Why does proline have a rigid structure ?

    What fibrous tissue structure does it usually contribute to ? 

    Why is it not found in globular proteins ?
    It has a secondary amino group instead of a primary one. 


    The rigid structure often disrupts the a-helices found in globular proteins
  13. Sickle cell anemia, a sickling
    disease of red blood cells, results from the substitution of what Amino Acids at 
    the 6th position in the β-subunit of hemoglobin ?
    Non-polar Valine is switched with Polar Glutamate

  14. Amino acids with polar side chain that
    are hydrophilic, can take part in what type of bonding ?
    • Hydrogen bonding
    • These groups can hyrdrogen bond

  15. The Hydroxyl groups of uncharged polar amino acids  can serve as attachment site for structures such as ?
    Phosphate groups
  16. The Amide and hydroxyl groups of uncharged polar amino acids  can also serve as attachment sites for ?
    oligosaccharide chains in glycoproteins

  17. Sulfhydryl groups of uncharged polar amino acids are important components of the
    active site of ?
  18. At physiological pH what are the acidic amino acids side chains ? Carboxyl groups ?
    Proton donors 

    They are negatively charged
  19. at physiological pH what do basic amino acid side chains do ?
    They are proton acceptors , fully ionized , and have a positive charge
  20. What type of amino acid is Histidine ?
    Weakly Basic  , because it will only be partially ionized at physiological pH
  21. What are the essential amino acids ?

    • Phenylalanine
    • Valine
    • Threonine4.      
    • Tryptophan5.      
    • Isoleucine      
    • Methionine      
    • Histidine      
    • Arginine      
    • Leucine  
    • Lysine
  22. How do you designate an Amino acid as chiral or asymmetrical ?
    It has to have four different groups
  23. What are the two forms that an amino acid can exist in relation to the chiral center ?

    What is the relationship between the D and L versions ?
    D and L

    They are enantiomers or optical isomers
  24. Which amino acid does not have four different groups and does not exhibit a chiral center ?
  25. What are molecules that differ only in spatial arrangement of their atoms ?

    What are molecules that are Mirror images (cannot be superimposed on each other) ?

    What are molecules called that Rotate plane polarized light in opposite directions ?


    Optical isomers
  26. What make up standard buffers ?
    • Weak acid and conjugate base 
  27. AAs in aqueous solution contain
    (weakly or strong )  acidic α-carboxyl groups and (weakly or strong)  basic α-amino groups ? Does this make Amino acids good buffers ?
    • Weakly 
    • Weakly 

  28. Explain the Bronsted - Lowry theory ?
    • Acids are proton donors
    • Bases are proton acceptors 

  29. What is the dissociation constant of an acid ?
    What does the ka mean if it is larger ?
    What does the ka mean if it is smaller ?
  30. What is the equation for pka of an acid ?
    what does the pKa mean ?

  31. What is the Henderson Hasselbach Equation ?
  32. In relation to the Henderson Hasselbalch equation
    [A-] > [HA] : pH > pKa
    (log of > 1 is positive)
  33. In relation to the Henderson Hasselbalch equation 

     [A-] < [HA] : pH < pKa
    (log of <1 is negative)
  34. In relation to the Henderson Hasselbalch equation 
    [A-] = [HA] : pH = pKa
    (log of 1 is zero)
  35. The pH of buffer should be within how many pH unit of the acid’s pKa value ?
    +/- 1
  36. When does maximum buffering effect occur ?
    When [A-] = [HA]
  37. What is a buffer ?
    a solution that resists change in pH following the addition of an acid or base
  38. When does maximum buffering capacity occur ?
    pH =pka
  39. If pH < pKa what happens ? 

    If pH > pKa what happens ?
    protonated acid form (HA) predominates

    deprotonated base form (A-) predominates.
  40. What is the isoelectric point ? 

    State the equation ?
    It is the pH that the amino acid is neutral.

  41. What is the linear sequence of amino acids ?
    Primary Structure
  42. What are peptide bond ?

    How can they be hydrolyzed nonenzymatically ?
    Amide linkages between the carboxyl group and amino group

    by being exposed to a strong acid or base , at high temperature

  43. What are peptidases (proteases) ?
    They are enzymes that hydrolyze peptide bonds.
  44. What are Exopeptidases ? 

    What are Aminopeptidases?

    What are Carboxypeptidases ?
    Cuts the ends of proteins 

    Cuts amino end 

    Cuts carboxyl end
  45. What are endopeptidases ?
    Enzyme that cleaves proteins from the inside
  46. How do you read peptides?
    From the N end to the C 

    New to Closing
  47. What is each portion of a peptide called  (each amino acid )
  48. When AA residues are named in a polypeptide they have their suffixes (-ine, -an, -ic, or –ate) changed to what
  49. How do you name the tripeptide composed of an N-terminal valine, a glycine, and a C-terminal leucine ?
  50. A peptide bond is usually (cis or trans ) ?
    Trans large part because of steric interference of the R-groups when in the cis position
  51. What two groups bring about the structure of amino acids in the peptide chains ?
    the carboxyl and amino
  52. What shape is the secondary structure Alpha helix ?

    Where do the side chains extend (inside or outside) of the helix ?

    How many AA's are in an Alpha Helix turn ?


    3.6 AA's per turn
  53. What amino acid disrupts an α-helix because its secondary amino group is not geometrically compatible with the right hand spiral of the α-helix. It inserts a
    kink in the chain ?
  54. What Protein contain α-helices ?
    keratins; components of hair, nails and skin
  55. Is Myoglobin is also highly α-helical or beta pleated ?
  56. 2 or more segments of polypeptide
    chains that are lined up side by side this describes an a-helix or b-sheet ?
  57. What is each individual segment of a beta sheet  referred to as ?
    a β-strand and it is fully extended
  58. How are beta pleated sheets stabilized ?
    They are stabilized by H-bonds that form between the polypeptide backbone N-H and C=O groups of adjacent chains
  59. Can beta pleated sheets be parallel and anti-parallel ?

  60. What is Tertiary structure ?

    How is the Tertiary structure held together ?
    A description of the way the polypeptide chain folds itself into its final 3-dimensional shape

    Held together by interactions between the side chains ( R groups).

    • 1) Hydrogen bonds
    • 2) Disulfide bonds
    • 3) Ionic interactions
    • 4) Hydrophobic
    • interactions
  61. As a peptide folds, its AA side chains are attracted and repulsed according to their ?
    chemical properties
  62. In reference to Tertiary structure ,What are Chaperones ?
    • specialized group of proteins required for the
    • proper folding of many species of proteins.
  63. In regards to tertiary structure , what are the step involved in protein folding ?
    (hint -3 steps )
    • 1.Formation of secondary structures
    • 2.Formation of Domains
    • 3.Formation of final protein monomer
  64. What is the Denaturation process ? Do the individual peptides get hydrolyzed ?
    results in the unfolding and disorganization of the proteins secondary and tertiary structures,

    Not accompanied by hydrolysis of peptide bonds.
  65. What are some Denaturing agents ?
    • -Heat 
    • -Organic solvents
    • -Mechanical mixing
    • -Strong acids or bases
    • -Detergents
    • -Ions of heavy
    • metals such as lead and mercury
  66. Is denaturation reversible or irreversible ?
    It depends on the protein
  67. What is the Quaternary structure ?
    • The 3D structure formed by interaction
    • of more than one polypeptide chain
  68. How does the Quaternary subunits maintain it's form ?
    Subunits are held together by noncovalent interactions.

    • Hydrophobic interactions
    • H-bonds
    • ionic bonds
  69. Do the subunits of the Quaternary structure function independently or cooperatively ?
    • Both , subunits may either function
    • independently or cooperatively
  70. What are Isoforms ?

    What are Isozymes ?
    Proteins that perform the same function but have different primary structures

    Protein isoforms that function as enzymes
  71. What is protein misfolding ?
    • Protein folding is a complex, trial and error process that can sometimes
    • result in improperly folded molecules
  72. How does the body remove misfolded proteins ?

    What happens if they are not removed ?

    What diseases can be caused by misfolding?
    • Misfolded proteins are usually tagged and
    • degraded by the cell

    However the control system is not perfect and aggregates of misfolded proteins can accumulate, particularly as we age. 

    • 1) amyloid disease and
    • 2) prion disease.
  73. What is amyloid disease ? Does it involve a-helix or b-pleated sheets?

    What specific age related disease is it usually seen in ?
    Disease in which there is an accumulation of insoluble,spontaneously aggregating proteins, called amyloids consisting of β–pleated sheets

    β–pleated sheets

    Alzheimer's disease.

  74. What is Prion disease ?

    Explain prion disease in terms , how to break it down and it's tissue make up ?
    Disease caused by the prion protein (PrP).

    The infectious PrP is highly resistant to proteolytic degradation, and tends to form insoluble aggregates of fibrils, similar to the amyloid found in some other diseases of the brain.
  75. Are prions Implicated as the causative agent of transmissible spongiform encephalopathies (TSE) ? This also includes what other three diseases ?

    • - Creutzfeldt-Jakob disease in humans
    • - Scrapie in sheep
    • - Bovine spongiform encephalopathy in cattle (madcow disease)
  76. What are globular heme proteins ?

    Does heme bind reversibly or irreversibly ?
    • Specialized group of proteins that
    • contains the prosthetic  group, heme.

    • Hemoglobin
    • Myoglobin
  77. What are the four structures associated withe heme ?
    • hemeprotein 
    • heme
    • O2
    • Histidine

  78. Where is Myoglobin found ? 

    What are it's two functions ?
    Heart and skeletal muscle 

    • 1) A reservoir for oxygen
    • 2) An oxygen carrier that increases the rate of transport of O2 within a muscle cell
  79. How many peptide chains make up myoglobin ?

    Does myoglobin tissues their red color ?
    1 chain

  80. Where is Hemoglobin found and what is it's function ? 

    What does it transport ?
    In red blood cells where its main function is to transport O2 from the lungs to the capillaries of tissues.

    O2 , H+ , and CO2
  81. How many bonds can iron /heme form ? what does it bind with ?
    6 bonds 

    4 porphyrin nitrogens and plus 2 additional bonds O2 and histidine
  82. How many molecules of O2 can Hemoglobin hold  ?

    How many molecules of oxygen does myoglobin ?
    4 molecules 

    1 molecule
  83. What is the major Hemoglobin (A or B) 
    hemoglobin in adults,
    How many peptides make up Hemoglobin A ?
    is composed of _ polypeptide chains -2α and 2β chains held together by non covalent interactions.
  84. How many peptides make up Hemoglobin A ?

    What are there make up in terms of alpha and beta units ?

    What type of interactions hold it together ?

    -2αlpha and 2βeta

    Non-covalent interactions
  85. Each subunit has stretches of (α-helical or beta sheets ) structure,and a heme binding pocket similar to that of myoglobin ?
  86. 1. Oxygenated form =  
    2. Deoxygenated form = 

    R (relaxed) state
    T (taut) state
    • R (relaxed) state 
    • T (taut) state
  87. What does the O2 dissociation curve of hemoglobin and myoglobin look like ?
    • Myoglobin has a hyperbolic shape
    • Hemoglobin has a sigmoidal shape
  88. When the first O2 binds to the hemoglobin, the binding of additional O2 to the same molecule is (enhanced or not enhanced) by cooperative binding ?
  89. In the lungs where O2 tension is high, hemoglobin is not quickly
    saturated ? T or F
    F - In the lungs where O2 tension is high, hemoglobin is quickly saturated
  90. In tissues depleted of O2, hemoglobin gives up
    about half its O2 ? T or F

  91. How does the bohr effect change hemoglobin ?
    other ligands bind and stabalize the Taut form
  92. How does  H+ (pH) effect oxygen affinity of hemoglobin ?
    When there is increased H+ it decreases the affinity for O2  , so the affinity for CO2 is increased .

  93. What is the Effect of 2,3-Bisphosphoglycerate
    on the oxygen affinity of hemoglobin ?
    It decreases the affinity for O2 , then it increases the affinity for CO2.

  94. What is the Effect of CO2 on the oxygen
    affinity of hemoglobin ?
    Increased CO2 decreases the affinity of O2

  95. How does CO (Carbon monoxide) effect the affinity for O2 ?
    It increases the affinity for Oxygen in the other heme sites make it difficult to release oxygen. (It is to tight , can cause death)

    When CO binds to one or more of the 4 heme sites, hemoglobin shifts to the R state causing the other heme sites to bind O2 tightly
  96. Explain the hemoglobinopathy Sickle cell anemia (Hb S) ?
    glutamate is substituted with valine
  97. Explain the hemoglobinopathy Hemoglobin C (Hb C) disease ?
    glutamate is substituted with lysine
  98. Explain the hemoglobinopathy Hemoglobin SC disease - (Hb S + Hb C) ?
    Sickle cell anemia (Hb S) – glutamate is substituted with valine


    Hemoglobin C (Hb C) disease – glutamate is substituted with lysine
  99. Explain the hemoglobinopathy Thallassemia syndrome ?
    decreased production of normal hemoglobin
  100. Fibrous proteins typically contain high proportions of what type of structures ?
    regular secondary structures such as α–helices or β–pleated sheets.
  101. What are some examples of most structural proteins that are fibrous ?
    • 1) Collagen
    • 2) Elastin
    • 3) α–keratin
    • 4) Silk fibroin
  102. What is the most abundant protein in the body ?
  103. What is collagen composed of (how many helices) ?
    Composed of 3 polypeptide helices that are twisted around each other to form a right-handed triple helix.

  104. What structures are made by Type 1 collagen ?
    teeth, bone, skin and tendons
  105. How much of collagen is made up of glycine ? 

    Proline and 4-Hydroxyprooline make up what percentage of collagen  ?
    1/3 of the AA's

  106. If Hydroxyproline and hydroxylysine are present in an unknown structure , what is it most likely to be ?
  107. What are the major steps in the Biosyenthsis of Collagen ?
    3.Proline and Lysine are hydroxylated

    • 4.Some hydroxylysine are glycosylated with glucose
    • and galactose

    6.Triple helix is formed and procollagen is produced

    (Outside of Golgi apparatus)

    • 8.The N-terminal and C-terminal are
    • cleaved making tropocollagen

    • 9.Self-assembly of the tropocollagen to a mature
    • collagen
  108. What is the collagen defect Ehlers-Danlos syndrome (EDS) ?
    results in fragile stretchy skin and loose joints

  109. What is the collagen defect Osteogenesis imperfecta (OI) ?
    results in bones that easily bend and fracture

  110. What is Elastin ?

    Where can they be found in reference to the body ?

    What is it's special ability ?
    Elastin is a connective tissue protein with rubber-like properties.

    • 1)Lungs
    • 2)Walls of large arteries
    • 3)Elastic ligaments.

    • They can be stretched to several times their
    • normal length, but recoil to their original shape when the stretching
    • force is relaxed.

  111. Where can keratin be found ?

    What is it composed of ?
    Keratin is found in hair, wool, skin, horns and fingernails

    Composed of α–helical polypeptides