User:Tiffanyhu/sandbox

use chemdraw for biological molecules - under wikiproject:chemistry: also tells you how to do it

under chemdraw: file: apply from document: use first one: ACS

PAY ATTENTION TO:

- specific and intentional use of scientific words: like "and" when you mean "or"

- assume very minimal science understanding: HS understanding: explain

- careful to bias vs neutrality: "most", "best", "more important", "least": implication must be backed up bold bold bold

Protein catabolism is the breakdown of proteins into amino acids and simple derivative compounds, for transport into the cell through the plasma membrane and ultimately for the polymerisation into new proteins via the use of ribonucleic acids (RNA) and ribosomes. Protein catabolism, which is the breakdown of macromolecules, is essentially a digestion process.

Protein catabolism is most commonly carried out by non-specific endo- and exo-proteases. However specific proteases are used for cleaving of proteins for regulatory and protein trafficking purposes. One example is the subclass of proteolytic enzymes called oligopeptidase.

The amino acids produced by catabolism may be directly recycled, used to make new amino acids, or undergo amino acid catabolism to be converted to other compounds via the Krebs cycle.[1]

Purpose
The primary reason for protein catabolism is so organisms can convert proteins into a form of energy that they can use or store. For organisms such as bacteria or soil microorganisms, through protein catabolism, proteins are able to be broken down into its amino acids and are used to form bacterial proteins. As for other organisms, such as humans, the proteins are still first broken down into amino acids, then, typically, deaminated so that they can be processed into the Krebs/Citric Acid (TCA) Cycle. By proceeding into the Citric Acid Cycle, the original proteins will be converted into usable energy for the organism.

There are also other processes to convert amino acids into usable molecules to enter the TCA cycle, such as transamination, decarboxylation, and dehydrogenation.

Protein Degradation
The first step to protein catabolism is breaking the protein down into amino acids by cleaving their peptide bonds, also known as proteolysis. The peptide bonds are broken up by the protein, proteasome. The proteasome is able to hydrolyze the peptide bonds by using ATP energy. This process is further helped through the use of enzymes called proteases. The proteases help cleave off the remaining peptide residues to produce individual amino acids, ready to be converted into usable molecules for either glycolysis or the TCA cycle, to produce energy for the organisms.

Use this source: https://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/protease.htm

Talk more about how proteins can break down into amino acids

Also add in a photo of how amino acids can feed into the TCA cycle

Also add a section on what determines the rate of protein catabolism: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1392602/pdf/jphysiol01472-0013.pdf

Transamination
This process leads to the same end result as deamination: the remaining acid will undergo either glycolysis or the TCA cycle to produce energy that the organism's body will use for various purposes. This process, which is reversible, transfers the amino group instead of directly losing the amino group to be converted into ammonium. The amino group is transferred to alpha-ketoglutarate, so that it can be converted to glutamate. Then glutamate transfers the amino group to oxaloacetate. This transfer is so that the oxaloacetate can be converted to glutamine or aspartate. Eventually, this product will also proceed into oxidative deamination to once again produce alpha-ketoglutarate, an alpha-keto acid that will undergo the TCA cycle, and ammonium, which will eventually undergo the urea cycle.

Transaminases and aminotransferases are enzymes that help catalyze the reactions that take place in transamination. They help catalyze the reaction at the point when the amino group is transferred from the original amino acid, like glutamate to alpha-ketoglutarate.

Oxidative deamination[edit | edit source]
This is the first step to breaking down the amino acids so that they can be converted to sugars. The process begins by losing the amino group of the amino acids. The amino group becomes ammonium as it is lost and later becomes urea, which will be released by the liver, where it undergoes the urea cycle, into the blood stream. It is then transferred to the kidneys, which will secrete the urea as urine.[2][3] The remaining portion of the amino acid becomes oxidized, resulting in an alpha-keto acid. The alpha-keto acid will then proceed into the TCA cycle, in order to produce energy. The acid can also enter glycolysis, where it will be eventually converted into pyruvate. The pyruvate is then converted into acetyl-CoA so that it can enter the TCA cycle and convert the original pyruvate molecules into ATP, or usable energy for the organism.