Proteins Flashcards
Amino group
An amino group is a nitrogen bonded to hydrogens or other hydrogen containing groups.
R group
The r group is the side chain of the amino acid group. These side chains have different protperties such as charge and polarity which influence the behavior of the amino acid
Peptide bond
The peptide bond is a dehydration reaction between two amino acids. This bond consists of a carbonyl group and a NH group with their accompanying bonds
pKa
the pKa of an amino acid is how the strength of an acid is measured. Essentially this is the pH of a specific entity like an amino acid.
Isoelectric point
the isoelectric point of an amino acid is the point of a neutral charge. The number of positive and negative charged side chains balances out which gives the overall protein a neutral charge. This is the point at which a protein will precipitate out of solution.
Ampholyte
can act either as an acid or a base depending on the situation. Water is a prime example of this
Zwitter ion
A zwitterion is where an amino acid can have two different charges on the molecule. This means that the molecule could be at its isoelectric point at even charges, but can also have a distinct charge if one charged molecule outweighs another.
Primary structure
The primary structure of an amino acid relates to its sequence. The type and amount of side chains on an amino acid are what dictate the structure in later stages. Each side chain can possess different qualities such as charge distribution, polarity, and therefore influence on solubility. The primary structure is what determines the rest of the structure of the protein.
Secondary structure
Secondary structure makes use of the primary structure of the protein. The most common structures made in a secondary structure form are beta sheets and alpha helices. The sequence of amino acids is held together by hydrogen bonds. The sequence to create an alpha helix in relation to polarity is P-N-P-P-N-N-P. Alternatively the sequence to create a beta sheet is P-N-P-N-P-N. These sequences determine the hydrogen bonding pattern and therefore the shape. The beta-sheet can be oriented with the amino acids in a parallel or antiparallel fashion. The antiparallel fashion makes for bonds that are more straight and shorted which makes them stronger. The secondary structure doesn’t have to stretch the full length of the chain, it just influences sections of it which then form into the designated structure.
Alpha helix
Alpha helices are coil like structures that follow the amino acid polarity sequence; P-N-P-P-N-N-P. The polarity of the side chains is important for the structural integrity of the helix because these determine what sections are attracted to one another and what sections are repelled.
Beta sheet
Beta sheets are created by long strands of protein chain broken up by hairpin turns which then sets another strand of the same chain parallel to the other. The way that the strands line up is important for stability. If the amino acid sections are lines up perfectly and exactly the same as the line before, this is known as parallel. If the amino acid side chains are oriented exactly opposite of the chain above it, this is known as antiparallel. Antiparallel is more stable because the bonds line up better and are therefore shorter.
Tertiary structure
Tertiary structure refers to the combination of beta sheets and alpha helices. This structure level is held together by a lot of different non-covalent forces. The three most important forces are hydrophobic interactions, hydrogen bonding, and disulfide bonds. Hydrophobic interactions are the strongest and most important IMF to the stability of proteins. The hydrophobic groups accumulate in the middle of the protein structure which leaves the hydrophilic groups on the surface to interact with the surrounding water.
Quaternary structure
Quaternary structure is the binding of multiple protein strands together via hydrophobic interactions, hydrogen bonding, intermolecular forces, etc.
Steric strain
This refers to the tendency of chunky charged branches or groups to repel other charged groups. This phenomenon, electrostatic repulsion, prevents certain degrees of rotation around bonds, specifically rotation around alpha carbons of a peptide bond. (psi bond c-c)
van der waals interactions
These electrostatic interactions are some of the weakest but are still able to hold molecules together. They depend of the partial dipoles of molecules to create a weak interactive force between them. Many of these types of bonds however can make a molecule fairly strong
Hydrogen bond
Hydrogen bonds can either be relatively strong or relatively weak depending on the compound. They are the attractive forces that hold a lot of biomolecules together because there is water in biomolecules. Hydrogen bonds requires a donor and an acceptor. It requires a hydrogen that is bonded to a highly electronegative atom like oxygen, nitrogen, or fluorine. It also requires another highly electronegative atom to take advantage of the positively charged hydrogen.
Electrostatic interactions
These are the net charge of all the reactions that exist in a protein. This encompasses most of the interactions and can tell us the overall charge of the molecule.
Disulfide bond
Disulfide bonds are when two thiol or sulfur groups come together to form a covalent bond. These sulfur group bonds can stabilize tertiary and quaternary protein structure.
Denaturation
Denaturation refers to a change from the folded state to an unfolded state because of a change in environment and breaking of bonds. The most common factors that cause denaturation are pH changes, temperature increase, chemicals such as organic solvents, small molecule solvents, and so forth. These can cause a protein to unfold because some type of bond is broken. These could be hydrogen bonds, interacting with hydrophobic interactions, or just physically shaking the bonds apart. Either way, once a few bonds are broken, the whole molecule can unravel.
Two-state transition model
Once a few bonds are broken in the denaturation process, the whole molecule comes unfolded. This means that only two states of proteins, especially globular proteins exist; folded and unfolded. This is the two state transition model.
Temperature denaturation
An increase in temperature can cause a protein to denature because the hydrogen bonds are physically shaken apart. If the high temperature is applied only for a short time, the denaturation of the protein can be reversible. Contrasty, if the heat is applied for a longer amount of time, the denaturation is not reversible and the proteins will remain in an unfolded, disorderly state.
Irreversible denaturation
This refers to denaturation that cannot be reversed or undone. Again, if the protein is denatured by heat for a long amount of time, the protein cannot reform. Additionally if the protein is in high concentrations and a lot has aggregated, it cannot return to its native state.
Reversible denaturation
If the protein in question is not in a super high concentration, has not been heated for long amounts of time, and in many cases has had a smaller pH change, the protein denaturation can be reversed.
