AMINO ACID and PEPTIDES

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Author:
RolandoBijasa
ID:
304231
Filename:
AMINO ACID and PEPTIDES
Updated:
2015-07-19 05:18:53
Tags:
Biochemistry
Folders:
Biochemistry
Description:
Lecture 1: Amino Acid and peptides
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  1. Compound that contains both an amino group and a carboxyl group
    Amino Acid
  2. Building blocks of protein
    Amino Acid
  3. It gives the identity to amino acid
    Side chain (R)
  4. α-amino acid has an ___________ amino group attached to the carbon adjacent to the carboxyl group
    Amino group
  5. Two steroisomers to amino acid based on similarity to glyceraldehyde
    L- or D-
  6. pH when Amino Aid is zwitter ion
    neutral
  7. di-polar ionic structure with net charge 0
    zwitter ion
  8. 4 different groups attached to AA
    • -COOH (carboxyl)
    • -NH2  (amino)
    • -H 
    • -R (Side Chain)
  9. Where amino and carboxyl group are attached
    α-carbon atom
    • 1. non ionized form
    • 2. ionized form
  10. It does not undergo process of ionization
    Side Chain
  11. NHlocated at left
    L- AA
  12. NH2 located at right
    D- AA
  13. Found in cell wall of bacteria and peptide antibiotics
    D- isomers
  14. Found in proteins
    L- isomers
  15. Properties of Amino Acid
    • 1. asymmetry/ chirality
    • 2. optical activity
  16. both have same physical properties and chemical properties but differ in direction in w/c they rotate polarized lght
    optical activity
  17. 2 isomers result because of this chiral C (L AA and D AA)
    asymmetry/ chirality
  18. example of not asymmetric AA
    Glycine
  19. have both polar and nonpolar region
    amphiphatic
  20. example of amphiphatic AA
    tyrosine
  21. Classification of AA as to structure of the side chain
    • 1. hydrophobic or non polar (aliphatic and aromatic)
    • 2. polar
  22. AA with side chains that do not like to reside in aqueous environment. These AA buried within the hydrophobic core of the protein
    Hydrophobic (Non-Polar)
  23. AA with side chains that prefer to reside in an aqueous environment and can be generally found exposed on the surface of a protein
    Polar
  24. Hydrophobic group that contains only carbon or hydrogen atoms
    Aliphatic
  25. contains aromatic ring system
    aromatic
  26. the simplest amino acid, although placed under nonpolar and aliphatic its small H do not contribute much to hydrophobic interaction
    Glycine (gly)
  27. an example of imino acid
    Proline (pro)
  28. Sulfur containing AA
    • Cysteine (Cys)
    • Methionine (Met)
  29. Gly
  30. Ala
  31. cys
  32. ile
  33. leu
  34. met
  35. phe
  36. pro
  37. trp
  38. tyr
  39. val
  40. asn
  41. ser
  42. gln
  43. thr
  44. arg
  45. lys
  46. his
  47. glu
  48. aspartate
  49. Side chain of tyr
    phenol
  50. Side chain of trp
    indole
  51. Side chain of asp
    carboxyl
  52. Side chain of arg
    guanidino
  53. Side chain of asn
    amide
  54. Side chain of cys
    thiol/ sulfhydyl
  55. Side chain of Met
    thio-ether
  56. Side chain of phe
    benzene
  57. Side chain of his
    imidazole ring
  58. Side chain of  thr
    hydroxyl
  59. Side chain of lys
    epsilon amino
  60. derived from phe by hydroxylation
    tyrosine
  61. simplest AA
    glycine
  62. S containing AA that is essential
    methionine
  63. S containing AA that is not essential
    cysteine
  64. essential for children
    Arginine
  65. gives histamine when decarboxylated
    histidine
  66. precursor of cathecolamines
    tyrosine
  67. cathecholamines
    Dopamine, Epinephrine, Norepinephrine
  68. abundant in milk
    tryptophan
  69. precursor of Serotonin, Melanin and Niacin
    tryptophan
  70. positive at pH = 7
    Lysine
  71. negative at pH = 7
    Aspartic
  72. polar
    lys, aspartic
  73. aromatic
    phe, trp
  74. will give adrenalin
    tyrosine
  75. will form dopa (precursor of dopamine)
    tyrosine
  76. inhibitory hormone
    GABA
  77. excitatory hormone
    Glutamate
  78. secreted when there is emergency
    adrenaline, noradrenaline
  79. essential amino acid
    • (PVT TIM HALL)
    • phe
    • val
    • trp
    • thr
    • ile
    • met
    • his
    • arg
    • lys
    • leu
  80. uclassifiable
    gly
  81. precursor of GABA
    glutamic acid
  82. precursor of Histamine
    histidine
  83. precursor of Dopamine
    tyrosine
  84. precursor of throxine
    thyrosine
  85. combination of two AA
    Dipeptide
  86. Function of AA
    • Synthesis of pretein
    • precursor of N-bases of nucleic acid
    • function as chemical messenger / neurotransmitter
    • glucose synthesis
    • buffer
    • detoxification reaction (gly,cys,met)
  87. neutralizes acid and base
    buffer
  88. regulates mood appetite and sleep
    Serotonin
  89. controls the sleep and wake cycle
    melatonin
  90. ketogenic AA
    Leu, lys
  91. AA in solution at certain pH are predominantly in di polar form, fully ionized but without net charge due to COO- and NH3+
    Isoelectric point
  92. the ionization constant of ionizable groups
    pK
  93. joins amino acids in proteins formed by removal of water from a carboxyl group of one amino acid and a amino group of another
    Peptide bond
  94. reaction used in peptide bond
    dehydration reaction or condensation reaction
  95. combination of 2 or more AA
    Dipeptide
  96. combination of three AA
    tripeptide
  97. many AA are joined
    Polypeptide
  98. could have thousands of AA residues
    protein
  99. covalent bonds
    • peptide
    • disulfide
  100. non-covalent bond
    • H-bond
    • hydrophobic interaction (van der waals)
    • ionic bond
  101. cut peptide bond
    protease/ peptidase
  102. all peptide bonds in proteins occur in what configuration
    trans configuration
  103. make peptide bond planar and rigid
    partial double bond character
  104. only part on peptide ionized
    N-terminal and C-terminal
  105. released by α-cells when lower blood sugar (hypoglycemic effect)
    glucagon
  106. released by β-cells when blood sugar is high (hyperglycemic effect)
    Insulin
  107. Structures of protein
    • Primary
    • Secondary
    • Tertiary
    • Quaternary
  108. includes a description of all covalent bonds (peptide and disulfide bonds) linking AA in the polypeptide chain. determines how a protein folds into unique 3D- structure
    primary (covalent)
  109. refers to stable arrangements of AA residues giving rise to recurring structural patterns. refers only in interactions of the peptide backbone
    Secondary (H-bond)
  110. Describes all aspects of 3D folding of a peptide. 3D-arrangement of all atom
    Tertiary (covalent and noncovalent)
  111. describes the arrangement in space of a protein consisting of 2 or more subunits
    Quaternary (noncovalent interactions)
  112. it determines the function of AA
    shape
  113. arrangement
    conformation
  114. Protein secondary structure
    • alpha helix
    • beta pleated sheets
    • beta turns
    • random coil
  115. a helix breaker
    Pro
  116. hydrogen bonds are parallel to the helical axis
    α-helix
  117. more stable than left handed helix
    right hand alpha helix
  118. organizes polypeptide into sheets, extended zigzag conformation of protein backbone
    β-pleated sheet
  119. Protein backbones are arranged side by side through ________
    H-bonds
  120. the side chain of β-sheets adjacent AA protrude in ______
    opposite direction
  121. β-keratin
    silk fibroin and fibroin of spider webs
  122. protein backbone of β-sheets can be either _________
    parallel or anti-parallel
  123. more stable because the H-bonds are colinear
    anti-parallel
  124. H-bonds are ________ to the backbone direction
    perpendicular
  125. core of many protein
    β-sheets
  126. reverse the direction of a polypeptide, connects the ends of two adjacent segments of antiparallel sheet
    β-turns
  127. residues often occur in β-turns
    glycine and proline
  128. connected regions of turns and loops
    Turns and Loop
  129. short region of non α and non β conformation
    turns
  130. larger stretches with no structure, often disordered. aka "random coil"
    loops
  131. Formation of domain: section of protein structure sufficient to perform a particular chemical or physical task
    Tertiary structure
  132. Highest order of monomeric protein
    Tertiary structure
  133. stabilized by weak non covalent interactions
    Tertiary structure
  134. found in interior or core
    nonpolar
  135. outside because they can interact with water
    polar
  136. each polypeptide chain in the protein is called a
    subunit
  137. Important peptides
    [EAGOV]

    • enkephalins
    • aspartame
    • glutathione
    • oxytocin
    • vasopressin
  138. naturally occuring analgesic, similar to action of opiates
    enkephalins
  139. atificial sweetener, nutrasweet
    aspartame
  140. a tripeptide, cellular reducing agent, side effect is inhibition of melanin synthesis
    glutathione
  141. uterine contraction and milk ejection
    oxytocin
  142. reduces oxidized glutathione, powerful reducing agent
    NADPH
  143. antidiuretic (antihypertensive) hormone, makes kidney retain water, regulates BP
    Vasopressin
  144. make up 15% of the cell
    Protein
  145. function of protein
    • enzymes (catalytic)
    • structural (collagen, keratin, fibroin, elastin)
    • transport and storage (Hb, albumin, Mb
    • cell signaling (insulin receptor)
    • immune protection (immunoglobulins)
    • Hormones (insulin, glucagon)
    • coordinated motion (actin, myosin)
    • special function
  146. repeating sequence of polypeptide backbone
    N-Cα-C-N-Cα-C-N-Cα-C
  147. classification of protein
    • simple
    • conjugated
  148. composed only of amino acid (albumin, histones, protamines)
    Simple protein
  149. containsa non protein group/prosthetic group
    conjugated
  150. example of conjugated protein
    • glycoproteins
    • lipoproteins
    • metalloproteins
    • phosphoprotein
    • chromoprotein
  151. protein shape is determined by ______ of AA
    sequence
  152. final shape and has the lowest free energy possible
    conformation
  153. process of unfolding the protein
    Denaturation
  154. denaturing agents
    • heat
    • pH
    • chemical compounds (alcohol, urea, acids and bases)
  155. protein turns like a spiral fibnrous proteins (hair nails, horns)
    C
  156. protein folds back on itself as in a ribbon-globular protein
    β-sheet
  157. core of many protein
    β-sheet
  158. can be parallel or anti parallel and form rigid structures with the H-bond
    β-sheet
  159. formed by a H-bond between every 4th peptide bond -C=O to N-H
    α-helix
  160. a framework for structural protens such as the hair, nails and skin
    coiled-coil shape
  161. types of protein
    • globular
    • fibrous
  162. example of globular protein
    enzymes, transport proteins, immunoglobulins, hormones, myoglobin
  163. soluble in water in water, 2° structure is a mixture of α β & loop structures
    Globular protein
  164. usually span a long distance, insoluble in water
    fibrous protein
  165. example of fibrous protein
    collagen, keratin, silk fibroin, elastin

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