Protein Biochemistry Flashcards
what are the 4 important versions of amino acid side chains you should be thinking about?
(in terms of the breakdown from dietary protein and stuff)
- Sulfur containing amino acids
- Amino acids with nitrogen in the side chain which are involved in nitrogen transport.
- Branched chain amino acids
- Aromatic amino acids which are precursors for a number of neurotransmitters and hormones.
- Sulfur containing amino acids
What are the specific PTMs on proteins that matter in the land of protein biochemistry?
- Hydroxy-Proline and Hydroxy Lysine which are structural components of collagen, Vitamin C is needed for their synthesis. Vitamin C deficiency causes scurvy because of a failure to synthesize sufficient quantities of these amino acids.
- Gamma carboxyglutamate: Prothrombin uses this to target membranes
- Ornithine: part of the Urea cycle
Describe the process of protein absorption from the gut:
Protein in the diet is broken down in the GI tract by a group of peptidases.
- These enzymes need to be activated in the gut lumen to be functional.
- Once activated, these different peptidases have different specificities for specific types of peptide bonds.
- They are categorized by the type of enzyme they are and the type of bond that they cleave.
- These peptidases work sequentially to break down long peptide chains into their component amino acids which are then absorbed and enter the circulation.
what are the two primary ways proteins are turned over within the cells?
At some point, these proteins will be inactivated and broken down. The half-life and mechanisms by which a protein is broken down will vary depending on the protein. However, there are two intracellular pathways for protein degradation that are particularly important:
- Ubquination which targets proteins for degradation in proteasomes
- Degradation in lysosomes
What is a transaminase reaction? where do they occur?
For an amino acid to be used as a precursor for gluconeogenesis, the NH2 group must be removed.
- For an amino acid to be made from a carbon skeleton, an NH2 group must be added.
- Actually these NH2 groups are transferred from another nitrogen containing molecule to the carbon skeleton, or from an amino acid to an acceptor molecule.
- These so called “transamination reactions” are typically bidirectional depending on the availability of substrates and acceptors.
- These reactions typically take place in the liver (and to a lesser extent in kidney, intestine and muscle).
what is the prototypical transaminase reaction?
In the prototypical reaction, an amino acid donates an NH2 group to alpha-ketoglutarate to produce L glutamate and an alpha-keto acid.
- The enzyme that catalyzes this reaction is an aminotransferase.
- Different aminotransferases have different specificities for different amino acids.
- The nitrogen that has been accepted by alpha-ketoglutarate with the production of glutamate can then be released as NH3 with the regeneration of alpha-ketoglutarate.
- This ammonia is toxic and needs to leave the body. It does so through the process of urea synthesis.
Describe in general the urea cycle
In the first step of the urea cycle, the ammonia that was produced from transamination reactions is converted to carbamoyl phosphate
- The production of carbamoyl phosphate is catalyzed by carbamoyl phosphate synthase 1 which is the key regulated step in protein catabolism.
- KEY ENZYME = carbamoyl phosphate synthase 1
- 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.
*The nitrogen thus transferred from amino acids to urea can then leave the body in urine as urine urea nitrogen. Urinary nitrogen in the form of urea then represents a marker of amino acid catabolism and oxidation
Why is glutamine an important amino acid in the biochemistry of amino acid catabolism?
Glutamine is an important nitrogen containing amino acid (has 2 nitrogen atoms) because it accepts nitrogen from other amino acids in peripheral tissues, carries the nitrogen to the liver and kidney where it is donated to glutamate and from there to alpha-ketoglutarate.
*The conversion of glutamate to alpha-ketoglutarate is catalyzed by glutamate dehydrogenase. This is the second key regulated step in protein catabolism
Why are the sulfur-containing amino acids important?
- Cysteine can form disulfide bridges that change protein conformation.
- S-adenosylmethionine (SAM) is an energy source for a number of important biochemical reactions. In addition, it is a methyl donor for a number of important reactions.
- SAM is a precursor for homocysteine which is important in vascular disease, wound healing, and is involved in B12 and folate metabolism.
- Glutathione is a tri-peptide that contains cysteine, and serves as an important redox buffer, and protects against free radical injury.
When you see vitamin C, what do you think?
ASCORBATE, COLLAGEN, SCURVY
♣ Collagen is the most abundant protein in human body that forms a triple-stranded helix, which is comprised of both hydroxyproline (Hyp) and hydroxylysine (Hyl):
♣ Hyp used in collagen for H-bonding that increases collagen strength. Prolyl hydroxylase converts Pro to Hyp.
♣ Hyl use in collagen for interchain cross-links. Lysyl hydroxylase converts Lys to Hyl.
♣ Prolyl hydroxylase, Lysyl hydroxylase rely on Vit-C (ascorbate) as coenzyme, thus, lack of Vit-C leads to Scurvy (i.e. reduced collagen strength).
What enzyme is responsible for the formation of hydroxyproline?
♣ Hyp used in collagen for H-bonding that increases collagen strength. Prolyl hydroxylase converts Pro to Hyp.
What enzyme is responsible for the formation of hydroxylysine?
Hyl use in collagen for interchain cross-links. Lysyl hydroxylase converts Lys to Hyl.
What is Gla and why is it important?
♣ g-Carboxyglutamate (Gla) used to target proteins to membranes via Ca chelation. G-glytamyl carboxylase converts Glu to Gla, which is Vit-K dependent.
While there are too many aminotransferases to know, what are some pretty dang important ones? what co-factor do they use/depend upon?
¬ For protein degradation, aminotransferases move nitrogen to Asp & ammonia for Urea Cycle.
¬ Two specific aminotransferases are:
♣ Alanine aminotransferase (Alt)
♣ Aspartate aminotransferase (Ast)
¬ Pyridoxal phosphate (PLP) is a derivative of Vit-B6 and is used by aminotransferases to “hold”/transfer the amino groups.
What is the overall reaction of the urea cycle?
3ATP + HCO3- + NH4+ + aspartate –> 2ADP + AMP + 2Pi + PPi + fumarate + urea
what are the two entry points for nitrogen into the urea cycle?
¬ There are two entry points for Nitrogen in urea cycle:
1) Aspartate.
2) Free ammonia (incorporated into carbamoyl phosphate
When arginine is made into ornithine, what is released?
UREA. this is part of the urea cycle
what molecule is moved from the mitochondria to the cytoplasm during the urea cycle?
citrulline. Ornithine and carbamoyl phosphate are the substrates of the reaction that makes citrulline
What catalyzes the conversion of glutamate to alpha-ketoglutarate? Is this a regulated reaction?
*The conversion of glutamate to alpha-ketoglutarate is catalyzed by glutamate dehydrogenase. This is the second key regulated step in protein catabolism
What are the 4 steps of the Urea Cycle?
• Ornithine –> citrulline
○ Carbamoyl phosphate synthetase I
○ Citrulline + Aspartate –> argininosuccinate
§ Arginonosuccinate synthase
○ Argininocussinate –> arginine
§ Argininosuccinate lyase
○ Arginine –> Ornithine + urea (catalyzed by arginase)
What is important about the reaction catalyzed by Carbamoyl phosphate synthetase I?
• This is the initial step in the Urea Cycle, and is what creates the species for ENTRY into the cycle
• Found in the mitochondria
• Bicarbonate + ammonia –> carbamoyl phosphate
○ Uses 2 of the 3 ATPs used in Urea Cycle
• N-acetylglutamate is an allosteric activator of Carbomoyl phosphate synthetase I
• Arginine is an activator of N-acetylglutamate synthase
○ Acetyl CoA + glutamate –> N-acetylglutamate
○ Which in turn will potentently stimulate the action of CPS-I which initiates the urea cycle
Describe in general the transport of ammonia through the body
¬ Ammonia cannot be transported through blood, so alternative mechanisms are needed such as those that rely on urea.
¬ Glutamine serves as a means of transport, since it can “hold” two ammonia groups.
¬ Glu dehydrogenase serves as a regulator modulator for protein metabolism specifically by controlling the direction of either nitrogen removal or incorporation into amino acids
¬ Most tissues use glutamine synthetase to convert glutamate to glutamine for transport to the liver (to enter the urea cycle).
*Muscle is different where alanine is used instead of glutamine for transport in the Alanine-Glucose Cycle. This is because in muscle there is a build-up of pyruvate from glycolysis and pyruvate can be converted to alanine for transport to liver (transamination). The liver, in turn, can use the alanine to convert back to pyruvate (transamination) and glucose remade (gluconeogenesis) can then be delivered back to the muscle
What amino acid functions as a “transport” molecule for ammonia?
Glutamine - it can “hold” two ammonia groups
*¬ Most tissues use glutamine synthetase to convert glutamate to glutamine for transport to the liver (to enter the urea cycle).
Many tissues use glutamine as a way to transport ammonia back to the liver. What does muscle tissue do?
- short = alanine instead of glutamine b/c it can be used in gluconeogenesis
- Muscle is different where alanine is used instead of glutamine for transport in the Alanine-Glucose Cycle. This is because in muscle there is a build-up of pyruvate from glycolysis and pyruvate can be converted to alanine for transport to liver (transamination). The liver, in turn, can use the alanine to convert back to pyruvate (transamination) and glucose remade (gluconeogenesis) can then be delivered back to the muscle
Describe the role of arginine in nerve and muscle tissue (ammonia handling and energy production)
¬ NO synthase converts arginine –> citrulline to produce NO, an important molecule used as a neurotransmitter. (nerve tissue) - this is essentially a shortcut through the urea cycle that bypasses the mitochondrial phase
¬ In the urea cycle, arginine –> ornithine can either be catalyzed by arginase or alternatively can be catalyzed by several enzymes to produce creatine phosphate for energy (muscle).
Creatine Phosphate is used by what tissue for energy, and where does this reactant come from?
¬ In the urea cycle, arginine –> ornithine can either be catalyzed by arginase or alternatively can be catalyzed by several enzymes to produce creatine phosphate for energy (muscle).
*different from nerve tissue when arginine is often converted into citrulline to produce NO
Give an example of a glucogenic amino acid metabolism
♣ Glucogenic: Oxaloacetate in Kreb Cycle comes from aspartate transamination
Give an example of a ketogenic amino acid metabolism reaction
Ketogenic: Lysine and leucine are the ketogenic amino acids since breadown gives Acetyl-CoA (i.e. only 2 carbons
