A residue is a monomeric unit that results when two or more amino acids combine and release a water molecule during dehydration synthesis. The primary structure of a protein, which is a peptide chain, is composed of these amino acid residues.

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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

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- 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

Inborn Errors of Amino Acid Catabolism

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 

Protein Structure 

An amino acid is an organic molecule containing a hydrogen atom, a carboxyl group ($$-\text{COOH}$$), and an amino group ($$-\text{NH}_2$$) bonded to a central carbon atom, called the $$\alpha$$ carbon. The fourth group attached to the $$\alpha$$ carbon is the variable side chain (R group) that defines the amino acid's identity.

Amino Acid Structure

Amino Acid Residue

A side chain, or residue (represented as $$\text{R}$$ in structural formulas), is the variable fourth group bonded to the central $$\alpha$$ carbon of an amino acid. These groups are composed primarily of carbon, hydrogen, oxygen, nitrogen, and sulfur in the form of hydrocarbons, acids, amides, alcohols, and amines. Their unique chemical properties allow them to form hydrogen, ionic, and disulfide bonds, along with polar/nonpolar interactions that are essential for folding proteins into secondary, tertiary, and quaternary structures.

Side Chain

A peptide bond is a covalent chemical bond formed when the carboxylic acid group of one amino acid reacts with the amine group of another, releasing a water molecule in a dehydration synthesis process.

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