Dietary Protein Breakdown

- primarily in proteosomes and lysosomes
- catabolism of cellular protein
- Reasons
- Regulation through turnover
- Quality control: errors, mistranslated, misfolded
> Chaperons make an attempt at correction, but lysosome and proteasomes degrade

- Source of amino acids: fuel and anabolic metabolites
> Use proteins for fuel and anabolic reactions

- Can also use proteins as anabolic precursors
- Some N-terminal sequences can affect protein longevity
- Serine is long (>20 hours), aspartate very short (< 3 minutes)
- PEST sequence has short halflife
> Proline (P), Glutamate (E), Serine (S), Threonine (T)
> May be sites for phosphorylation that allows its recognition by ubiquitination machinery 
- Make sure we degrade the right protein at the right time
STEPS
- Ubiquitination
- Transamination


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

Protein Degradation

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.

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