Secondary protein structure refers to only the spatial arrangements of the polypeptide backbone that does not include the sided chain conformations. 
The most common secondary structures include:
-	Alpha helix
-	Beta sheets
- Turns

Secondary Protein Structure

Primary structure refers to the amino acid sequence, or multiple sequences of a protein. Each amino acid in a primary structure is known as a residue. Because the 20 amino acids have individual chemical and physical properties, they influence the 3D structure, the function of the protein and its chemical properties. i.e. hydrophobic and hydrophilic properties. 

Ions can additionally be found in the primary structure. Zinc and calcium ions can form complexes that are present in the protein's primary structure. 

Primary Protein Structure 

Quaternary structure refers to the proteins that are multisubunit, more than 100 kilo Daltons, and form a specific geometry. These subunits are usually linked non-covalently. 

Quaternary Protein Structure

Tertiary protein structure combines the folding of the secondary back bone structure and includes the positions of the side chains of each amino acid. 

Tertiary Protein Structure

Protein structure is the 3-dimensional assembly caused by the string of amino acids translated from RNA . Protein structures varies immensely due to the assembly of the amino acids.
There are four subdivisions of proteins structures:
- Primary structure
- Secondary structure
- Tertiary structure 
- Quaternary structure 

Grand Valley State University

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

Voet, D., Voet, J. G., &amp; Pratt, C. W. (2013). Chapter 5: Protein: Primary Structure. In Fundamentals of biochemistry: Life at the molecular level (4th ed., pp. 93-126). Hoboken, NJ: Wiley. Retrieved January 05, 2021, from archive.org.

Fundamentals of biochemistry: Life at the molecular level, 4th edition: Chapter 5

- Enzyme: Glutamate dehydrogenase
- 1. Oxidation (NAD+ or NADP+) of glutamate to yield Schiff-base intermediate
- 2. Hydrolysis deamination of intermediate to make alpha-ketoglutarate
- Glutamate -> alpha-ketoglutarate and ammonium
- Mitochondrial enzyme: NH4+ is toxic
> Reactions close to equilibrium

> Usually pulled forward by loss of NH4+


Oxidative deamination of amino acids to yield glutamate in liver

- 1st amino group from ammonium, second amino group from aspartate, carbon comes from bicarbonate
- ** Fumarate is formed from the breakdown of argininosuccinate in the urea cycle, and links the urea cycle with the TCA cycle
- First reactions occur in the mitochondrial matrix

OVERVIEW
- Carbamoyl Phosphate synthesis
- Formation of Citrulline (in mitochondrial matrix)
- Formation of Argininosuccinate (cytoplasm)
- Formation of Fumarate
- Cleavage

- Eventually converted to OAA, cycle can start again


Urea Cycle

- Phenylketonuria (PKU)
- Alkaptonuria
- Maple-Syrup urine disease

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