Module 3

Why are amino acids called such

Called like such because:

• Have and amino group

• Have an acid( carboxyl group)

How do each amino acid differ?

The difference between each amino acid is with the R or chain

What are the structures common to all amino acids?

• hydrogen

• amino group

• carboxyl group

• central alpha carbon

What determines the different properties in amino acids?

The properties of their side chains

List the different categories based on grouping AAs by side chain properties

• Non-polar aliphatic

• Aromatic

• Polar, uncharged

• Polar, positively charged

• Polar negatively charged

Main components of non-polar aliphatic AA/ where it’s found

• Mainly hydrocarbon side chains

  -no charge

  -no h-bond capacity (hydrophobic)

• Found in the core of a protein

_____ is often found at polypeptide turns due to its unique ______ formation.

Proline, cyclic

________ is the smallest amino acid and is usually found after ____ for a tight turn.

Glycine, proline

Main components of aromatics AA/ where it’s found

• Contains a ring within its side chain

Role of phosphorylation in biomolecules?

A mechanism to regulate protein function; usually reversible

Which type of AA can be phosphorylated?

Amino acids with hydroxyl groups

What is Post-Translational Modification?

Protein modification after they have been made

• phosphorylation

Explain basics of phosphorylation and enzymes involved

The addition of phosphoryl groups added to AA containing a hydroxyl group

• kinase recognizes and adds the phosphoryl groups to OH ends

• phosphatase removes the phosphoryl groups from AA

Which AA is the largest?

Tryptophan

Main components of polar uncharged AA/ where it’s found

• Contains dipoles ready to h-bond

What are the two AA containing sulfur?

Methionine, Cysteine

What are two examples of post-translational modification?

• phosphorylation

• disulfide bond formation

How are disulfide bonds formed?

Formed through the oxidation of the sulfhydryl groups of two cysteines that will form a covalent bond

• AA needs to be close within the molecule

• Can be inter or intramolecular

What is the function of a disulfide bond?

Function to stabilize protein structure

Main components of polar charged AA/ where it’s found

• Always carry a +1 charge at physiological pH

• h-bond capability

What’s special about histidine?

Can change its protonation state within the body

• Some will be of protonated and the rest unprotonated form within the body

• Usually serves as a proton donor/ acceptor

When will be the charge of the imidazole group in histidine in its protonation states?

• protonated state [A-]: positive charge

• unprotonated state[HA]: negative charge

What is histodine’s pKa?

6

What is meant by “protonated” form?

When a functional group has an extra proton/ H+ ion.

Where is the protonated form of a function group found in terms of the pKa?

Under the pKa,

Where is the unprotonated form of a function group found in terms of the pKa?

Over the pKa

Zwitterion

When an AA has opposite charges ( net sum is zero) in both ions

Isoelectric point pI

The pH where the net charge of the molecule is zero

How do you calculate pI?

Taking the average on either sides (pKa points) of where the net charge of the molecule equals zero.

How many pIs are allowed per molecule?

1 pI

Which letters in the alphabet are not attributed to an amino acid code?

JOB