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Flashcards in Protein Biochemistry 1 Deck (15)
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Amino acids with nonpolar R group (9)

  • Glycine
  • Alanine
  • Valine
  • Leucine
  • Isoleucine
  • Phenylalanine
  • Tryptophan
  • Methionine
  • Proline


Amino acids with uncharged polar R group (6)

  • Serine
  • Threonine
  • Tyrosine
  • Asparagine
  • Glutamine
  • Cysteine


Amino acid with acidic R group (1)

  • Aspartic acid


Amino acids with basic R group (3)

  • Histidine
  • Lysine
  • Arginine


Examples of post-translational modifications

  • Hydroxylation of proline and lysine --> collagen
  • Carboxylation --> glutamic acid
  • Amination
  • Glycosylation
  • Phosphorylation
  • Methylation


Hydroxylation of proline and lysine --> collagen

  • Collagen is most abundant protein in human body
  • Forms triple stranded helix made of hydroxyproline (Hyp) and hydroxylysine (Hyl)
    • Hydroxyl group/modification --> increases tensile strength of collagens due to intra-strand hydrogen bonds
  • Hyp --> used in collagen for H-bonding to increase collagen strength
    • Pro --> Hyp conversion by prolyl hydroxylase
  • Hyl --> used in collagen for interchain crosslinks
    • Lys --> Hyl conversion by lysyl hydroxylase
  • Hyp/Hyl: covalent crosslink repeat --> additional strength


Carboxylation --> glutamic acid (glu)

  • Glutamate (glu) modified by transmembrane protein (gamma glutamyl carboxylase) --> gamma-carboxyglutamate
  • Gamma-carboxyglutamate (gla) used to target proteins to membranes via Ca2+ chelation (ex. prothrombin)
  • N-terminal domain of prothrombin (Gla domain) binds to Ca2+ --> alters the conformation of prothrombin --> allows it to embed into membrane --> allows thrombin to cleave off, become active
  • Gamma-glutamyl carboxylase: vitamin K dependent



  • Results in reduced collagen strength
  • Hyp and hyl enable helical formation, increase tensile strength of collagen by H-bonding at core of collagen
  • Enzymes catalyzing hydroxylation of proline/lysine dependent on vitamin C as cofactor
  • No vitamin C --> no hydroxylation of proline/lysine --> weak collagen --> scurvy
  • Symptoms: reduced vascular endothelium --> hemorrhages --> loss of RBCs: swollen gums, bruising, anemia


Vitamin C as cofactor

  • Vitamin C (C = collagen)
  • Used for hydroxylation of proline and lysine
  • Important for collagen formation


Vitamin K as cofactor

  • Vitamin K (K = koagulation)
  • Cofactor for gamma-glutamyl carboxylase
  • Helps prothrombin embed itself into membranes by forcing negative charges to face in at Ca2+
  • Allows nonpolar residues to face outward


Vitamin B6 as cofactor

  • Vitamin B6 (B Six = Schiff Base)
  • B6 converted into PLP (pyridoxyal phosphate) --> flips amino group over
  • Important cofactor for aminotransferases - holds amino group during transfer reaction
  • In resting state: PLP forms Schiff base with aminotransferase --> PLP bound to aminotransferase
  • B6 also involved in glycogen phosphorylase, cystathionine synthesis, heme synthesis, required for synthesis of niacin from tryptophan


Cellular aspects of protein degradation

  • Ubiquitin-protease system
    • ATP dependent pathway
    • Enzyme crosslinks protein to ubiquitin repeatedly, resulting in multiple ubiquitin bound to single protein
    • Ubiquitinated proteins sequestered to proteasome (giant cellular trash can), proteolytic activity breaks down proteins
  • Lysosomal path
    • ATP independent
    • Used primarily to engulf extracellular proteins or live pathogens
    • Proteins broken down by acid hydrolysis, other lysosomal proteins (i.e. cathepsins)


Proteases in protein degradation

  • Covert zymogen (inactive enyzme) --> active enzyme
  • Pepsin (stomach):
    • Pepsinogen cleaved by HCl to produce pepsin that cleaves proteins to pieces (pepsin is endopeptidase)
  • Enteropeptidase (intestine):
    • Cleaves trypsinogen
    • Activated by several proteases including trypsin
  • Trypsin (produced in pancreas, goes to small intestine)
    • Trypsinogen cleaved by enteropeptidase to produce trypsin
    • Trypsin cleaves all other zymogens in small intestine (including chymotrypsinogen to chymotrypsin, and procarboxypeptidases to carboxypeptidases)


Classes of proteases

  • Aspartic protease
    • Pepsin
  • Serine proteases
    • Trypsin
    • Chymotrypsin
  • Metallocarboxypeptidases
    • Carboxypeptidases-A: hydrolyzes C-terminal of hydrophobic amino acids (Ala, Ile, Leu, Val)
    • Carboxypeptidase-B: hydrolyzes C-terminal of basic residues amino acids (Arg, Lys)


General goal of urea cycle

  • Purpose: to get rid of ammonia by forming less toxic compounds (i.e. urea)
  • Why: we do not store ammonia/nitrogen (it's toxic)
    • Hyperammonemia can cause cerebral edema, coma, and death
  • 3 ATP + HCO3 + NH4 + aspartate --> 2 ADP + AMP + 2Pi + PPi + fumarate + urea