W24 Biological molecules

Question 1

All naturally occurring amino acids have the chirality of..

Answer 1

S (classified as L amino acids)
with the exception of cysteine (R)

Question 2

Difference of LD and RS system

Answer 2

LD is used for fisher diagrams
Used to show placement of OH

Question 3

SN2 Reaction

Answer 3

Inverts the chirality
(configuration of chiral centre)

Question 4

Amino Acids with hydrophobic R groups

Question 5

Amino Acids with polar, uncharged R groups

Answer 5

Serine, Threonine, Asparagine, Glutamine

In the 3-D structure of proteins, the side chains of these amino acids can be
exposed to the external surface, or buried in the inside: they form hydrogen
bonds with water or, if buried, with other polar residues (contributing to
secondary and tertiary protein structure)

The -OH in Ser and Thr can be
phosphorylated (important for
regulating the activity of some
proteins) or attached to
(poly)saccharides (forming
glycoproteins)

Question 6

Amino Acids with charged R groups

Answer 6

In 3-D protein structures, these amino acids are rarely buried: they tend
to be exposed to the outer surface and interact with water
Asp and Glu R groups are always
negatively charged at physiological pH
(~ 7.4)
pKa ≈ 12.1 pKa ≈ 6.0 pKa ≈ 10.7 pKa ≈ 3.7 pKa ≈ 4.2
Arg (guanidinium group) and Lys R
group are always positively
charged at physiological pH (~
7.4)
His R group has a pKa close to
neutral pH: 50% protonated
at physiological pH, acts as
proton donor or acceptor,
depending on environment.
Imidazole ring highly
coordinating.

Question 7

Special Amino Acids

Answer 7

Glycine, Proline, Cysteine
Gly: smallest R group: no contribution to hydrophobic effect, found in flexible protein regions

Pro: cyclic secondary amine (imino acid): rigid
conformation, reduces the flexibility of the protein
region.Often found at bends in protein secondary structures