Amino Acid L1

Question 1

What is an AMINO ACID?

Answer 1

molecules that form the building blocks of proteins.

Question 2

AMINO ACID Structure:
4.

Answer 2

1. CENTRAL CARBON ATOM (which is called the a-carbon; Ca),
2. bonded a PRIMARY AMINO group
3. CARBOXYL group
4. Also attached to the alpha carbon is a SIDE CHAIN (we call this the
   R group).

Question 3

Explain why Amino acids are chiral…

Answer 3

1. ALPHA-CARBON is tetrahedral
   - 4 different SUBSTITUENTS bonded to it
2. TWO possible CONFIGURATIONS in 3 dimensions.

3.We say there are two
ENANTIOMERIC FORMS (2
enantiomers – R and S) which are mirror images of each
other

Question 4

There is only ONE AMINO ACID which is NOT CHIRAL…WHAT IS IT AND WHY?

Answer 4

GLYCINE

• it DOES NOT HAVE 4 different SUBSTITUENTS BONDED to the alpha CARBON ATOM.

Question 5

How do you decide which enantiomer is R and which is S ?

= 6

Answer 5

1. H with the LOWEST PRIORITY GROUP, pointing away from you
2. CLOCKWISE ORDER OF PRIORITY = R
3. ANTICLOCKWISE ORDER OF PRIORITY = S
4. Reason for Priority: ATOMIC NUMBER (higher the number the MORE PRIORITY)
5. then,
   Carbon double bond to O (treated as 2 oxygens),
   COH
   CNH
   CH
6. Carbon to Oxygen, C-N, C-C, CH, H

Question 6

FOR CHIRALITY = with amino acids the nomenclature….4

Answer 6

1. L- = S (ANTICLOCK WISE)
   D- = R (CLOCKWISE)
2. is used and this is based on the relationship of the amino acid stereochemistry to D- and L-glyceraldehyde:
3. Although most L-amino acids are S-, Cys is
   R-
   (because the -CH2-SH has higher priority than –COO-)
4. ALMOST ALL BIOLOGICALLY OCCURING AMINO ACIDS ARE THE L-enantiomer.

Question 7

Biological Importance of Chirality

Answer 7

1. ORGANISMS Distinguish between ENANTIOMERS OF MOLECULES.
2. most biological reactions are CATALYSED by ENZYMES which have BINDING SITES for REACTANTS in their ACTIVE SITE.
3. These binding sites RECOGNISE and BIND SPECIFIC CHEMICAL GROUPS on the REACTANTS.
4. Binding sites are POSITIONED so that ONLY ONE ENANTIOMER of the REACTANT BINDS CORRECTLY in the ACTIVE SITE.

Question 8

Amino acids are Zwitterions = 5

Answer 8

1. AAs have at least 2 TITRATABLE groups
   —- The amino group (NH2)
   —–The carboxylic aid group (COOH)
2. Depending on the pH, each group can exist in two possible states
3. The amino group can be positively charged or neutral
   (uncharged)
4. The carboxylic acid group can be negatively charged or neutral
   (uncharged)
5. COMBINATIONS of these DIFFERENT CHARGED STATES on the molecule are also possible GENERATING 3 DIFFERENT STRUCTURES.

Question 9

Amino acids are Zwitterions AT WHAT pH do they exist?
= 4

Answer 9

1. At MEDIUM pHs (≈ 5 – 8) the amino acids exist in a ZWITTERIONIC form

2 — has a protonated α-amino group
and

3 —- a deprotonated α-carboxyl group

4…. and thus has a NET CHARGE of 0 contributed by these groups.

Question 10

How many common amino acids?

needed for?

Answer 10

These 20 common amino acids are coded for by the DNA sequence –
the genetic code

Question 11

How do they 20 common amino acids differ?

Answer 11

—- They differ in
* Size
* Shape
* Charge
* Hydrogen bonding capacity
* Hydrophobic character
* Chemical reactivity

• The “R” group of the amino acid attaches to the a-carbon atom.

There are 20 different “R” groups

• 3 letter codes and 1 letter codes

Question 12

What are the
SMALL HYDROPHOBIC
Amino Acids?

Answer 12

1. GLYCINE (Gly, G)
   R = H
2. ALANINE (Ala, A)

R = CH3

Question 13

What are the
LARGER HYDROPHOBIC
Amino Acids?

Answer 13

1. Valine (Val, V)
2. Leucine (Leu, L)
3. Isoleucine (Ile, I)
4. Methionine (Met, M)

Question 14

Property of HYDROPHOBIC AMINO ACIDS?

Answer 14

• Hydrophobic
• Cluster together
• Hydrophobic effect

Question 15

Whats so Special about PROLINE? = 3

Answer 15

Pro, P

1. Cyclic
2. Conformationally Restricted
3. Strategically important in SHAPING PROTEIN STRUCTURE.

Question 16

What are the UNcharged Polar Amino Acids?

AND THEIR PROPERTIES

Answer 16

1.Serine (Ser, S)

2. Threonine (Thr, T)

• Contain a hydroxyl group
• ## Hydrogen bond donor and acceptor

3. Asparagine (Asn, N)
4. Glutamine (Gln, Q)

• Contain an amide group
• Hydrogen bond donor and acceptor

5. CYSTEINE (Cys, C)

• Contains a ‘thiol’ group
• Sulfhydryl group is more reactive than an OH group
• Can form disulfide bond with another cysteine – intra and intermolecular

Question 17

Threonine has an

Answer 17

extra chiral centre

Question 18

Aromatic Amino acids =

Answer 18

1. Phenylalanine (Phe, F)
2. Tyrosine (Tyr, Y)
3. Trptophan (Trp, W)

Question 19

Charged Polar Amino Acids AND THIER PROPERTIES …

Answer 19

1. Arginine (Arg, R)
   - guanidinium group
   pKa = 12.5
2. Lysine (Lys, K)
   - butylammonium group
   pKa = 10.5
3. Histidine (His, H)
   - immidazolium group
   - pKa = 6.0 physiological pKa
   - participates in many enzymatic reactions
4. Asparagine (Asp, D)
   CH2 - carboxylate group
   pKa = 3.9
   normally negatively charged at physiological pH
5. Glutamine (Glu, E)
   CH2CH2 - carboxylate group
   pKa = 4.1
   normally negatively charged at physiological pH

Question 20

Some Amino Acids Have More Than One Stereogenic Centre WHICH ONES ARE THEY?

Answer 20

Leucine
Isoleucine
Threonine
Allothreonine

Question 21

Basic amino acids (Lys, Arg, His) have different basic groups in their side
chain, but are

Answer 21

but are uncharged when deprotonated and positively charged when
protonated.

Question 22

Ser, Thr, Tyr all have a

Answer 22

a hydroxyl group (-OH) in their side chain.

Question 23

The special amino acids:

Answer 23

Gly – H as a side chain, achiral;

Cys has a sulphydryl
group (-SH/-S-
) in its side chain and is uncharged when protonated and
negatively charged when deprotonated.

Question 24

Hydrogen Bonds And Amino Acid Side Chains:

Answer 24

1. A H- bond is a special dipole-dipole electrostatic interaction
2. where the positive end of the dipole is a proton attached to an electronegative atom such as oxygen or nitrogen, which forms the
   negative end of the dipole

Question 25

Water can form electrostatic interactions

Answer 25

(hydrogen bonds) with amino acid side chains

Question 26

Hydrogen Bonds and Ionic Bonds Between
Polar Amino Acid Side Chain:

NON IONIC VS IONIC interactions

Answer 26

NON IONIC =
H-O,
H-N,
C-H

IONIC =
O-
N+

Question 27

Hydrophobic (Nonpolar) Amino Acids and Interaction with Water

Answer 27

1. Hydrophobic amino acids prefer not to interact with polar molecules such as water – interactions between polar and non
   polar molecules is energetically unfavourable (“like seeks like”)
2. Thus hydrophobic amino acids tend to cluster together (called
   the “hydrophobic effect”)
3. In the context of a large protein molecule, hydrophobic amino
   acids tend to cluster together in the centre of proteins, away
   from the aqueous environment