Biotech #5 - Liquid Aminos Flashcards
(31 cards)
Structures of alpha amino acids
To the a-carbon of every amino acid are attached:
an amino group
a hydrogen atom
a side chain (“R” group)
a carboxylic acid
pKa of amino/carboxylic group in amino acids
The pKa of the carboxylic acid is about 2
The pKa of the a-amino group is about 10
zwitterionic form
At physiological pH both the carboxylic acid group and the a-amino group will be ionized, to yield the zwitterion form
What two amino acids are encoded genetically but not often used in making proteins?
selenocysteine and pyrrolysine
What is the only achiral amino acid? Why?
Glycine, because its R group is a hydrogen
What are two important consequences L-amino acids in natural proteins?
The surface of any given protein, which is where the interesting biochemistry occurs, is asymmetric. This asymmetry is the basis for the highly specific molecular recognition of binding targets by proteins.
The stereochemistry of the amino acids plays an important role in the formation of so-called “secondary structure” (i.e., a-helices and b-strands) and thereby the overall structure of proteins.
Where are the alipathic amino acids often found?
The more hydrophobic amino acids such as isoleucine are usually found within the core of a protein molecule, where they are shielded from water.
What is special about proline as an alipathic amino acid
Proline, is the only amino acid in this group in which the side chain forms a covalent bond with the a–amino group.
The proline side chain has a primarily aliphatic character; however, it is frequently found on the surfaces of proteins due to its unique structural constraints.
The rigid ring of proline is well-suited to those sites in a protein structure where the protein must fold back on itself (so-called “turns”).
What are serine and cysteine good at?
The –OH group of serine and the –SH group of cysteine are good nucleophiles and often play key roles in enzyme activity.
What is noteworthy about cysteine?
1) The side chain has a pKa = 8.3, so it can ionize at moderately high pH:
2) The oxidation of two cysteine side chains yields a disulfide bond. The product of this oxidation is given the name cystine.
Are methionine and tyrosine hydrophilic or hydrophobic?
Methionine and tyrosine are fairly hydrophobic, but display more hydrophilic character than their aliphatic analogs.
Phenylalanine is one of the most _____ amino acids.
Phenylalanine is one of the most hydrophobic amino acids.
are tyrosine and typrophan hydrophobic?
Tyrosine and tryptophan have some hydrophobic character, but it is tempered by the polar groups in their side chains.
What happens to tyrosine at a high pH?
Tyrosine with a pKa = 10.1 can ionize at high pH.
What is special about the light-absorbing ability of aromatic amino acids?
How is it used in detection of protein?
The aromatic amino acids, like most highly conjugated compounds, absorb light in the near-ultraviolet region of the spectrum.
This characteristic is frequently used for the detection and/or quantitation of proteins, by measuring absorption at 280 nm.
What functional group does arginine have in its side chain? Why is it dank?
The guanidino group of arginine makes it the most basic amino acid due to the resonance stabilization of the protonated side chain.
When histidine is incorporated into proteins, the pKa typically ranges from _____
When histidine is incorporated into proteins, the pKa typically ranges from 6.5–7.4.
What important role does histidine play?
Because the histidine side chain has a pKa near physiological pH, it often plays a role in enzymatic catalysis involving proton transfer.
what are aspartic acid and glutamic acid often referred to as?
Aspartic acid (pKa = 3.9) and glutamic acid (pKa = 4.2) typically carry negative charges at pH 7.
These amino acid residues are often referred to as aspartate and glutamate. (i.e., the conjugate bases rather than the acids).
Unlike their acidic analogs, asparagine and glutamine have ____ ____ side chains.
Unlike their acidic analogs, asparagine and glutamine have uncharged polar side chains.
Where do Asn and Gln tend to be?
Like the basic and acidic amino acids, Asn and Gln are hydrophilic and tend to be on the surface of a protein molecule, in contact with the surrounding water.
Generally, how do ionic properties of amino acids impart ionic properties to proteins
In general these are SURFACE properties (i.e. charged sidechains are on solvent-exposed outside of folded structure)
affect protein-ligand binding (e.g. DNA-binding proteins) or catalysis
For what process is knowing the average charge on a protein an important consideration?
average charge on protein is an important consideration in the design of a purification process
What is an isolelectric point?
For any molecule containing a mixture of ionizable groups that carry formal (+) and/or (-) charges there is some value of pH such that the sum of all full and partial (+) charges is equal to the sum of all full and partial (-) charges.
At this pH the formal net charge on the molecule is zero and we say the pH = pI and define pI as the “isoelectric” point.
