Protein Biochemistry 1

Question 1

Amino acids with nonpolar R group (9)

Answer 1

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

Question 2

Amino acids with uncharged polar R group (6)

Answer 2

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

Question 3

Amino acid with acidic R group (1)

Answer 3

• Aspartic acid

Question 4

Amino acids with basic R group (3)

Answer 4

• Histidine
• Lysine
• Arginine

Question 5

Examples of post-translational modifications

Answer 5

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

Question 6

Hydroxylation of proline and lysine –> collagen

Answer 6

• 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

Question 7

Carboxylation –> glutamic acid (glu)

Answer 7

• 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

Question 8

Scurvy

Answer 8

• 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

Question 9

Vitamin C as cofactor

Answer 9

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

Question 10

Vitamin K as cofactor

Answer 10

• 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

Question 11

Vitamin B6 as cofactor

Answer 11

• 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

Question 12

Cellular aspects of protein degradation

Answer 12

• 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)

Question 13

Proteases in protein degradation

Answer 13

• 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)

Question 14

Classes of proteases

Answer 14

• 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)

Question 15

General goal of urea cycle

Answer 15

• 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