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.

Conjugated Protein

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.

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The genetic code refers to mRNA transcripts translated into amino acids to make proteins. This occurs due to the nucleotide triplets called codons that code for amino acids.

The Genetic Code

There are many types of macromolecules such as: 

- carbohydrates
- lipids
- proteins
- nucleic acids

Types of Macromolecules

https://www.khanacademy.org/science/biology/macromolecules

Macromolecules

The number of codons possible is more than the number of amino acids. This means there is redundancy in the genetic code for multiple codons to translate for one amino acid. In most cases, the first two codons dictate the amino acid while the third position is the wobble position is less important for the amino acid that is incorporated.

Redundancy in the Genetic Code

• DNA is the hereditary material of the cell  
• It is mostly formed in antiparallel DNA strands in a double helix with a 5' and 3' end. 

• DNA contains major and minor grooves. 

• DNA is formed from hydrogen bonds between the base pairs adenine and thymine and cytosine and guanine bases, respectively.

Deoxyribonucleic Acid (DNA)

RNA is involved in protein synthesis and regulation. It also has catalytic properties.
RNA is typically found in the single stranded form.
RNA is formed from hydrogen bonds between the base pairs adenine and uracil and cytosine and guanine bases, respectively.

Ribonucleic Acid (RNA)

Proteins

Carbohydrates are macromolecules that are composed of carbon, hydrogen, and oxygen in the ratio C:2H:0.  

Carbohydrates

Nucleic acids are macromolecules that are composed of subunits called nucleotides.  They are responsible for the transfer of genetic information from an organism's genome and turning it into proteins.  Nucleic acids exist in two forms:

- deoxyribonucleic acid (DNA)
- ribonucleicacid (RNA)

Nucleic acids are built using nitrogen, and thus need a nitrogen source to undergo nitrogen fixation

Nucleic Acids

Lipids are a broad, chemically diverse class of molecules composed primarily of carbon and hydrogen, but which can also contain oxygen, nitrogen, sulfur, and phosphorus. They perform a variety of biological functions, serving as nutrients, carbon and energy storage molecules, and structural components of hormones and cellular membranes.

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