Biotech #5 - Liquid Aminos

Question 1

Structures of alpha amino acids

Answer 1

To the a-carbon of every amino acid are attached:

an amino group
a hydrogen atom
a side chain (“R” group)
a carboxylic acid

Question 2

pKa of amino/carboxylic group in amino acids

Answer 2

The pKa of the carboxylic acid is about 2

The pKa of the a-amino group is about 10

Question 3

zwitterionic form

Answer 3

At physiological pH both the carboxylic acid group and the a-amino group will be ionized, to yield the zwitterion form

Question 4

What two amino acids are encoded genetically but not often used in making proteins?

Answer 4

selenocysteine and pyrrolysine

Question 5

What is the only achiral amino acid? Why?

Answer 5

Glycine, because its R group is a hydrogen

Question 6

What are two important consequences L-amino acids in natural proteins?

Answer 6

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.

Question 7

Where are the alipathic amino acids often found?

Answer 7

The more hydrophobic amino acids such as isoleucine are usually found within the core of a protein molecule, where they are shielded from water.

Question 8

What is special about proline as an alipathic amino acid

Answer 8

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”).

Question 9

What are serine and cysteine good at?

Answer 9

The –OH group of serine and the –SH group of cysteine are good nucleophiles and often play key roles in enzyme activity.

Question 10

What is noteworthy about cysteine?

Answer 10

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.

Question 11

Are methionine and tyrosine hydrophilic or hydrophobic?

Answer 11

Methionine and tyrosine are fairly hydrophobic, but display more hydrophilic character than their aliphatic analogs.

Question 12

Phenylalanine is one of the most _____ amino acids.

Answer 12

Phenylalanine is one of the most hydrophobic amino acids.

Question 13

are tyrosine and typrophan hydrophobic?

Answer 13

Tyrosine and tryptophan have some hydrophobic character, but it is tempered by the polar groups in their side chains.

Question 14

What happens to tyrosine at a high pH?

Answer 14

Tyrosine with a pKa = 10.1 can ionize at high pH.

Question 15

What is special about the light-absorbing ability of aromatic amino acids?

How is it used in detection of protein?

Answer 15

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.

Question 16

What functional group does arginine have in its side chain? Why is it dank?

Answer 16

The guanidino group of arginine makes it the most basic amino acid due to the resonance stabilization of the protonated side chain.

Question 17

When histidine is incorporated into proteins, the pKa typically ranges from _____

Answer 17

When histidine is incorporated into proteins, the pKa typically ranges from 6.5–7.4.

Question 18

What important role does histidine play?

Answer 18

Because the histidine side chain has a pKa near physiological pH, it often plays a role in enzymatic catalysis involving proton transfer.

Question 19

what are aspartic acid and glutamic acid often referred to as?

Answer 19

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).

Question 20

Unlike their acidic analogs, asparagine and glutamine have ____ ____ side chains.

Answer 20

Unlike their acidic analogs, asparagine and glutamine have uncharged polar side chains.

Question 21

Where do Asn and Gln tend to be?

Answer 21

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.

Question 22

Generally, how do ionic properties of amino acids impart ionic properties to proteins

Answer 22

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

Question 23

For what process is knowing the average charge on a protein an important consideration?

Answer 23

average charge on protein is an important consideration in the design of a purification process

Question 24

What is an isolelectric point?

Answer 24

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.

Question 25

Calculating pI for amino acids with non-ionizing R group:

Answer 25

pI = (pKa[a-NH3+] + pKa[a-COO-]) / 2

Question 26

at pH = pI the net charge of the molecule =

Answer 26

at pH = pI the net charge of the molecule = 0;

S[-] = S[+]

Question 27

at pH > pI the net charge of the molecule =

Answer 27

at pH > pI the net charge of the molecule = (-);

S[-] > S[+]

Question 28

at pH < pI the net charge of the molecule

Answer 28

at pH < pI the net charge of the molecule = (+);

			 S[-] < S[+]

Question 29

Electrostatic Repulsion between macroions

Answer 29

DNA molecules, with many negative charges, strongly repel one another in solution.

Question 30

Electrostatic attraction

Answer 30

If DNA is mixed with a positively charged protein, these molecules have a strong
tendency to associate.

Question 31

What two properties are major determinants of peptide conformation

Answer 31

Stereochemistry (all biosynthetic proteins made up of L-isomer)

Hydropathy (partitioning between polar and nonpolar solvents as indicator of polarity)