Chapter 25: Amino Acids

Question 1

Natural configuration of amino acids

Answer 1

Naturally occuring AA are in the L configuration

When drawn as a Fischer projection the amino group is located on the left

Question 2

Isoelectric focusing

Answer 2

When pI > pH of solution the amino acid is cationic
When pI < pH of solution the amino acid is anionic

If two AA have similar pI’s the larger AA will move more slowly

Question 3

Testing for the presence of an amino acid

Answer 3

Reagents

Ninhydrin

Mechansim

Amino acids are generally colorless, but their presence can often be verified with a ninhydrin color indicator

Question 4

AA syntheses via α-haloacids

Answer 4

Hell-Volhard-Zelinsky Reaction

Reagents

1. Br₂, PBr₃
2. H₂O

followed by

Excess NH₃

Mechanism

Installs a bromine at the α-carbon which is then subsequently replaced by an amine group

Produces a racemic mixture of products

Question 5

Amidomalonate synthesis

Answer 5

Reagents

Starting with diethyl acetamidomalaonate
1. NaOEt
2. RX
3. H₃O⁺ & heat

Mechanism

Similar to malonic ester synthesis; installs the R group from the alkyl halide as the side chain of the AA

Forms a racemic mixture

Question 6

Strecker synthesis

Answer 6

Reagents

1. NH₄Cl (ammonium chloride) & NaCN
2. H₃O⁺

Mechanism

Produces an AA from an aldehyde with the same side chain

Question 7

Edman degredation

Answer 7

Reagents

1. Ph−N=C=S
2. CF₃CO₂H (trifluoroacetic acid or TFA)

Mechanism

Removes an amino acid from the N-terminus of a peptide

Residue can then be determined by analyzing the PTH derivative

• R-group between the carbonyl carbon and nitrogen on the ring

Question 8

What bonds does trypsin cleave

Answer 8

Carboxyl side of lysine (K) and arginine (R)

Question 9

What bonds does chymotrypsin cleave

Answer 9

Carboxyl side of aromatic amino acids (W,Y,F)

Question 10

Protecting the amino side of an amino acid

Answer 10

Di-tert-butyl dicarbonate (Boc)₂O

or

Fmoc

Question 11

Removal of an amino protecting group

Answer 11

Boc protecting group can be removed with CF₃CO₂H (trifluoroacetic acid or TFA)

Fmoc protecting group can be removed with a strong base such as piperdine

Question 12

Protecting the carboxyl side of an amino acid

Answer 12

Carboxyl groups can be protected as an ester

Methyl and benzyl esters are the most popular

Question 13

Removal of an carboxyl protecting group

Answer 13

Esters can be removed using acid or basic conditions

Benzyl esters can be deprotected via hydrogenation to avoid unintended side-reactions

Question 14

Peptide synthesis

Answer 14

Peptide linkage is accomplished by:

1. Install the appropriate protecting groups
2. Couple the protected amino acids using DCC
3. Remove the protecting groups

Question 15

Merrifield synthesis

Answer 15

Also known as solid-phase peptide synthesis (SPPS)

Process builds the amino acid starting with the carboxyl terminus

1. TheC-terminus Boc-protected AA is attached to an insoluable polymer
2. Boc protecting group is removed
3. DCC is used to create a new peptide bond with the next Boc-protected AA
4. These steps are repeated as necessary
5. Final Boc protecting group is removed
6. The protein is removed from the polymer with HF (hydrofluoric acid)