Overview of Protein Biochemistry

Question 1

Different types of categorization of amino acids

Answer 1

• R group properties
• Essential vs. Non-Essential
• Biochemical pathways

Question 2

R group properties of amino acids

Answer 2

• Acidic vs. basic
• Polar vs. Nonpolar
• Chemical constituents of R groups
  
  • Sulfur containing amino acids
  • Amino acids with nitrogen in the side chain
  • Branched chain amino acids
  • Aromatic amino acids

Question 3

Categories of amino acids based on body’s ability to synthesize them

Answer 3

• Essential → cannot be synthesized by the body, so must be obtained from the diet.
• Non-essential → are synthesized from other amino acids.
• Conditionally essential → can be made by the body, but the capacity for their synthesis is limited. In states of high consumption, deficiency may develop.

Question 4

Biochemical pathway definitions of amino acids

Answer 4

• Glucogenic → these amino acids can be used as substrates for gluconeogenesis.
• Ketogenic → when broken down, these amino acids generate acetyl CoA, and cannot participate in gluconeogenesis.
  
  • produce ATP through the TCA cycle OR
  • used in ketone synthesis, similar to the fate of Acetyl CoA derived from β oxidation.

Question 5

Characteristics of protein breakdown @ gut

Answer 5

• gut consumed protein is broken down by a group of peptidases
  
  • peptidases activated @ gut lumen
• Once activated, peptidases are specific different types of peptide bonds
  
  • categorized by the type of bond that they cleave.
• Peptidases work sequentially to break down long peptide chains into their component amino acids which are then absorbed and enter the circulation.

Question 6

Protein breakdown @ tissues

Answer 6

• two intracellular pathways for protein degradation that will be discussed:
  
  • Ubquination which targets proteins for degradation in the proteasome and is ATP dependent
  • Degradation in lysosomes which is ATP independent
• The resulting AAs are then used in the synthesis of new proteins.

Question 7

Generation of ammonia from amino acids

Answer 7

• amino acid donates an NH2 group to an α-ketoglutarate==> L-glutamate + keto acid.
  
  • enzyme = aminotransferase
  • aminotransferases are specific for different amino acids
• glutamate can then released accepted nitrogen as NH3 ==> regenerates the ketoglutarate.
• NH3 (toxic) ==> urea synthesis ==> leave body

Question 8

Characteristics of Urea Cycle

Answer 8

• urea cycle occurs in the liver
• Glutamate, NH3, and aspartate enter the urea cycle

1. ammonia from transamination reactions is ==> carbamoyl phosphate
   
   1. catalyzed by carbamoyl phosphate synthase 1 = key regulated step in protein catabolism
2. The nitrogen from the carbamoyl phosphate enters the urea cycle, and ultimately is combined with an NH3 from aspartate to form urea which contains 2 nitrogen atoms.
3. Urea then leaves the body in urine

Question 9

Overall rxn that leads to urea production

Answer 9

• AA + α ketoglutarate (via aminotransferase) ↔
• Glutamate + α keto acid
• → NH3 → Urea cycle
• → Urea

Question 10

Characteristics of sulfur-containing amino acids

Answer 10

• Sulfur containing → Cysteine and Methionine
• Form disulfide bridges in protein
• S-adenosylmethionine is an important energy source in several reactions and a precursor for cysteine, which is important in wound healing, vascular disease, and folate and B12 metabolism
• Glutathione contains cysteine and is an important buffer and protects against reactive O2 species

Question 11

Characteristics of branched chain amino acids

Answer 11

• require specific enzymes for their breakdown
• deficiencies in these enzymes ==> maple syrup urine disease

Question 12

Characteristics of aromatic amino acids

Answer 12

• used as precursors for a number of important products:
  
  • serotonin
  • niacin (B3)
  • dopamine
  • norepinephrine, epinephrine
  • tetrahydrobiopterin
  • thyroid hormone