Protein metabolism
This mRNA sequence contains codons: 3 nucleotide long segments that code for a specific amino acid.
The amino acids are joined by peptide bonds making a polypeptide chain.
These amino acids are absorbed into the bloodstream to be transported to the liver and onward to the rest of the body.
Essential amino acids require intermediates not present in the human body.
In order to initiate transcription, the DNA segment that is to be transcribed must be accessible (i.e. it cannot be tightly packed).
During the initial transcription phase, the RNA polymerase searches for a promoter region on the DNA template strand.
Once the RNA polymerase binds to this region, it begins to “read” the template DNA strand in the 3’ to 5’ direction.
Proteins bound to these regions can either directly halt or allow RNA polymerase to read the DNA strand or can signal other proteins to halt or allow RNA polymerase reading.
Each 3-base-pair-long segment of mRNA is a codon which corresponds to one amino acid or stop signal.
The second reaction cleaves the aminoacyl-AMP producing the energy to join the amino acid to the tRNA molecule.
After translational initiation (which is different in prokaryotes and eukaryotes), the ribosome enters the elongation period which follows a repetitive cycle.
For example, a protein called eukaryotic initiation factor-2 (eIF-2) can bind to the smaller subunit of the ribosome, starting translation.
Common biological methods of modifying peptide chains after translation include methylation, phosphorylation, and disulfide bond formation.
The R groups on these amino acids can be methylated multiple times as long as the bonds to nitrogen does not exceed 4.
This adds a negative charge on the R groups and will thus change how the amino acids behave in comparison to their standard counterparts.
The fact that all amino acids contain R groups with different properties is the main reason proteins fold.
One way they do this is to cleave enzymes in pathways that do not need to be running (i.e. gluconeogenesis when blood glucose concentrations are high).
Futile cycles occur when the catabolic and anabolic pathways are both in effect at the same time and rate for the same reaction.
Proteases are also nonspecific when binding to substrate, allowing for great amounts of diversity inside the cells and other proteins, as they can be cleaved much easier in an energy efficient manner.
[21] Exopeptidases are enzymes that can cleave the end of an amino acid side chain mostly through the addition of water.
They are present in all lifeforms and are crucial for survival since they do many cellular tasks in order to maintain stability.
These three amino acids are known as the catalytic triad which means that these three must all be present in order to properly function.
Both are produced as zymogens, meaning they are initially found in their inactive state and after cleavage though a hydrolysis reaction, they becomes activated.
[6] Cellular proteins are held in a relatively constant pH in order to prevent changes in the protonation state of amino acids.
A significant change in pH may even disrupt many interactions the amino acids make and denature (unfold) the protein.
Hydrogen bonds and hydrophobic interactions are important stabilizing forces in proteins.
The amount of heat applied determines whether this change in protein is permanent or if it can be transformed back to its original form.
