Dietary Protein Breakdown

Endogenous protein breakdown is the catabolism of a cell's own proteins, occurring primarily in proteasomes and lysosomes.

Reasons for degrading endogenous protein:
- Regulation through turnover: degrade the right protein at the right time.
- Quality control: misfolded, mistranslated, or error-containing proteins. Chaperones first attempt correction; if that fails, lysosomes and proteasomes degrade the protein.
- Source of amino acids: released amino acids serve as fuel and as anabolic precursors.

Sequence features influence protein half-life:
- The N-terminal residue affects longevity (e.g., an N-terminal serine gives a long half-life of >20 hours, whereas aspartate gives a very short one of <3 minutes).
- A PEST sequence (rich in proline (P), glutamate (E), serine (S), and threonine (T)) marks a protein for rapid turnover; its residues may be phosphorylation sites that promote recognition by the ubiquitination machinery.

Key step: ubiquitination tags the target protein for proteasomal degradation.

Endogenous Protein Breakdown

Michigan State University

Proteins are macromolecules composed of amino acid subunits. When a large number of amino acids link together, or when multiple polypeptides assemble, they form proteins of various sizes. These molecules serve many vital biological functions, acting as structural components of cells and subcellular entities, as nutrient sources, as storage reservoirs for atoms and energy, and as functional agents such as enzymes, receptors, transport molecules, and hormones.

Proteins

Enzymes are proteins that function as biological catalysts, meaning they can increase the rate of a reaction without being consumed.  

Enzymes

Amino acids make up every protein. There are 20 total amino acids each with a unique side-chain group. Some additional amino acids are listed, but only 20 are coded from DNA directly. These side-chains allow for chemical interactions like sulfide bonds, hydrogen bonds, and ionic bonds. Amino acids are further divided by being non-polar, polar, and charged. They link together with a peptide bond making a string of amino acids a polypeptide. Finally, each amino acids is assigned a name, a three-letter symbol and a one-letter symbol. 


Amino Acids are involved in many systems and issues with its breakdown can cause diseases: 
- In the liver: major site of urea production in the urea cycle
- Alpha-keto acids can deliver amino groups to the liver 
- Ammonium is toxic: lethargy, headache, vomiting, seizures, death
- Seen in compromised liver


Amino Acids

- Defense protein are also known as immunoglobins (Ig) 
- Antibodies are produced by the B lymphocytes which are in the bone marrow cells. 
- Involved in humoral immunity (fluid). 
- Structurally diverse proteins

Defense Proteins (Antibodies)

Methods of Visualizing Proteins

A protein's structure is organized into four hierarchical levels that determine its three-dimensional conformation and function:

1. Primary structure: The specific sequence of a chain of amino acids.
2. Secondary structure: The local folding of the polypeptide chain into shapes such as helices (like the $$\alpha$$-helix) or sheets (like the $$\beta$$-pleated sheet).
3. Tertiary structure: The three-dimensional folding pattern of a single polypeptide chain due to interactions between side chains.
4. Quaternary structure: The configuration formed when a protein consists of more than one polypeptide chain (subunit).

Levels of Protein Structure

A conjugated protein is a class of protein that contains a nonprotein component attached to its polypeptide chain.

Conjugated Protein

The nearly unlimited diversity in the types of proteins that can be formed is due to the continuously variable length of these biopolymers, combined with the variety of possible side chains ($$\text{R}$$ groups) on each amino acid.

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