Protein Catabolism Flashcards
Describe protein as a dietary component
- Unlike fats and carbohydrates, protein and amino acids cannot be stored in the body.
- Therefore ingested protein is either used to build muscle, or it is converted to carbohydrates, fats, or other compounds, and the nitrogen is excreted.
- Proteins contain nitrogen, and nitrogen in the form of urea is toxic, so must be excreted.
- Normally the amount of nitrogen ingested is balanced by the amount of nitrogen excreted
Show Dietary Protein Digestion
The dietary enzymes responsible for protein breakdown are Peptidases:
(Endopeptidases or Exopeptidases)
Describe how Cellular proteins can also be degraded
- Cells degrade proteins that are no longer required, or because they are misfolded or damaged.
- The first stage is tagging for destruction via the ubiquitin pathway.
- The second stage is the degradation of the tagged protein by the proteasome.
The ubiquitin pathway involves which 3 enzyme types?
E1s = ubiquitin-activating enzymes
E2s = ubiquitin-conjugating enzymes
E3s = ubiquitin ligases
Why are there many E3s?
These provide specificity in recognising the target protein.
How is polyubiquitination achieved?
Polyubiquitination is achieved by conjugating another Ub to Lys48 of the 1st Ub
Describe the ubiquitin pathway
- E1 forms a thioester bond to the ubiquitin.
- The ubiquitin is then transferred from E1 to E2 and is again attached through its C terminus via a thioester bond.
- E3 binds both the target protein and the E2-ubiquitin complex and then transfers the ubiquitin to a lysine side group on the target protein.
Show how the 26S proteasome degrades ubiquitin-tagged proteins
Describe the 26S Proteasome Structure
- The catalytic core of the proteasome is a barrel of 28 subunits, made of:
- 2 x 7 a subunits and
- 2 x 7 b subunits
- arranged in 4 rings (doughnuts).
- A 19 S cap complex fits on each end of the barrel.
Explain the degradation of ubiquitin-tagged proteins in the 26S proteasome
- The 19S cap (lid) recognises polyubiquitin chains and allows the tagged protein (but not the ubiquitin) to pass into the proteasome core.
- Here, the active sites of the b subunits hydrolyse peptide bonds of the tagged protein, to yield short peptides (7-9 aa in length).
- The ubiquitin is cleaved off by the top 19S cap and the proteasome’s contents released on the other side.
- The 7-9 aa peptides can then be degraded to amino acids by other proteases
TRUE or FLASE: The 20S Proteasome can also recognize unfolded or damaged proteins without ubiquitination
TRUE
Show an Overview of cellular protein degradation by the proteasome
TRUE or FALSE: The proteosome is important for suppplyig amino acids for nutrition
FALSE
As well as supplying amino acids for nutrition, the proteasome is also important in immunology for antigen presentation via MHCs.
The fate of amino acids from degraded proteins
Amino acids cannot be stored or excreted. Instead they are used as follows:
- linked to tRNA directly for manufacture of new proteins
- Used to make nitrogen-containing hormones, neurotransmitters, purine/pyrimidine bases, etc.
- Converted into metabolic intermediates such as pyruvate, oxaloacetate, a-ketoglutarate, succinyl CoA and acetyl CoA (2a role, e.g. in starvation).
Hence they are precursors of glucose, fatty acids and ketone bodies (i.e. metabolic fuels).
Amino Acid Breakdown
What are the two main initial processes?
Step 1. Transamination
- The amino group is swapped between molecules
Step 2. Deamination
- Removal of the amino group giving NH4+
These 2 processes work in sequence to remove the amine & allow catabolism of all the amino acids.
Step 1: Transamination
Show the transamination of amino acids to common intermediates
Step 2: Deamination
Some amino acids can be deaminated directly by specific enzymes, producing ammonium ions:
This is used in conjunction with Transamination
Example 1:
Deamination of serine by serine dehydratase
Example 2:
Deamination of glutamate by glutamate dehydrogenase
This reaction is central to amino acid metabolism (both catabolism & synthesis)
Most amino acids are catabolised by transfer of their amino group to α-ketoglutarate to form glutamate, which is then deaminated to release ammonia
Step 1: transamination, Step 2: deamination
Explain why The coenzyme pyridoxal phosphate (PLP) is required for all transaminations & some deaminations
- Pyridoxal phosphate is derived from Vitamin B6
- Its carbonyl group forms a Schiffs base with the amino group of the substrate
- This weakens the bond between the nitrogen and the a-carbon, allowing removal of the amine.
Amino acids to metabolic intermediates
Ammonia is toxic and must be converted to urea for excretion: the Urea Cycle
- Ammonium is activated by reaction with bicarbonate to give carbamoyl phosphate
- This is fed into a cycle by reaction ornithine to give citrulline.
- Arginine is generated and then urea is removed from it by hydrolysis, regenerating ornithine.
- The cycle is energy-dependent: 3 ATPs are consumed
The cleavage of urea from arginine
Diseases of amino acid metabolism: Alcaptonuria
Genetic defect in homogentisate oxidase
Homogentisate quinone accumulates in joints & causes arthritis
Homogentisate is excreted in urine and is oxidized to benzoquinone acetic acid (BQA), a black oxidation product, on contact with air.
Diseases of amino acid metabolism: Phenylketonuria
- Genetic defect in the enzyme phenylalanine hydroxylase
- Phenylalanine accumulation leads to mental retardation.
- It can be treated by a low phenylalanine diet + tyrosine
