Amino acids & proteins: Primary structure II

Is Cys usually oxidized or reduced in the cell? Outside of the cell?

Inside: Reduced (SH)

Outside: Oxidized (S-S)

What maintains sulfhydryl (reduced) form in vitro?

Reducing agents such as merceptoethanol or dithiothreitol

What is a biological intracellular reducing agent?

Glutathione

What are the two acidic amino acids?

Aspartate and glutamate as they have negatively charged carboxyl side chains at pH 7

What are the two basic amino acids?

Arginine and lysine as they have positively charged side chains at pH 7

What are two other amino acids that have charged side chains at pH 7?

Histidine and cysteine

How are protein sequences written?

From N to C terminus

How do peptide bonds form?

Amino acids can polymerize through a dehydration reaction where water is released and a peptide bond forms between carbon of the carboxyl group and nitrogen

Are amino acids weak acids, bases, or both? What can they act as?

Both and can act as buffers and be protonated or deprotonated

Does each functional group have a different pKa?

Yes

Every time you go through a pKa value does the net charge increase or decrease by one?

It decreases by one (a proton is lost)

When the pKa is greater than the pH is the functional group protonated or deprotonated?

Protonated

When the pH= pKa, what is the functional group?

It is half protonated

When the pKa is less than pH, is the functional group protonated or deprotonated?

It is deprotonated

What is pI?

It is the pH when the molecule has a net charge of 0

How do you find the pI?

1. Draw fully protonated version of the peptide

2. Determine the charge of fully protonated peptide

3. Arrange pKa values from lowest to highest as equilibria from left to right

What does protein solubility depend on?

pH

When the pH is less than pI is the protein soluble or insoluble? Why?

It is soluble because the protein carries a positive charge and there is repulsion between molecules

When the pH is greater than pI is the protein soluble or insoluble? Why?

It is soluble because the protein carries a negative charge and there is repulsion between molecules

When pH=pI is the protein soluble or insoluble? Why?

It has low solubility (aggregation occurs) because the protein is neutral leading to no repulsion. Lowest solubility occurs at the isoelectric point.

When do proteins repel each other? Does this make them more or less soluble?

When carrying a net charge and this makes them more soluble