Amino Acid 2.2

Question 1

How many amino acids have READILY IONIZABLE SIDE CHAINS?

Answer 1

7/20
= Arg, Asp, Cys, Glu, His, Lys, Tyr

• have readily ionizable side chains
• able to DONATE OR ACCEPT PROTONS in ENZYMATIC REACTIONS
  able to FORM IONIC BOND

Question 2

pH scale

Answer 2

1. measures how acidic an object is.
2. Higher Number = More Basic
   lower Number = More Acidic
3. BASIC means = more Oh, Less H+ in solution
   ACIDIC = more H+, less OH

Question 3

How to Calculate pH?

Answer 3

pH = -log10[H+]
= -log10[H3O+]
= log10(1/[H+])
= log10(1/[H3O+]

Question 4

Explain what Each WEAK ACIDS AND BASES DO?

Answer 4

1. STRONG ACIDS
   - ionise completely
2. WEAK ACIDS
   - do Not ionise completely
3. STRONG BASES
   - ionise completely
4. WEAK BASES
   - do not completely ionise.

Question 5

Important biological buffers are weak acids & bases

Answer 5

HCO3– (aq) + H+ (aq) ,<—> H2CO3 (aq)

H2PO4– (aq) + H+ (aq) <—> H3PO4 (aq)

Question 6

Understanding Ka and pKa

Answer 6

• help to determine whether a species will donate or accept protons at a specific pH value.

They describe the degree of ionization of an acid and are thus an indicator of the strength of an acid

Question 7

The equilibrium constant is given by the following equation

Answer 7

HA + H2O <—-> A- + H3O+

K = ( [A-][H3O+] / [HA][H2O]

— if too large eg 55.49M then calculate

pKa

Ka = K [H2O] = ([A-]*[H3O+]/[HA]

pKa = -log10Ka

Question 8

Understand the Hendersen-Hasselbalcj Equation ….

Answer 8

Calculations…

Question 9

Amino Acid Ionisable Groups – α-Amino and αCarboxyl

Answer 9

1. α-carboxyl group
   pKa = 1.82 to 2.38 depending on the amino acid
2. α-amino groupp
   Ka = 8.80 to 10.96 depending on the amino acid

Question 10

What Affects protein Charges?

Answer 10

In Proteins Mainly the Ionisable Side Chain Groups of Amino Acids Contribute to Charges on Proteins

Question 11

In Proteins Mainly the Ionisable Side
Chain Groups of Amino Acids Contribute to
Charges on Proteins….EXPLAIN

Answer 11

1. When the amino acids are part of a
   protein, nearly all of the α-amino and αcarboxyl groups have formed peptide bonds

— to join the amino acids together in the polypeptide chain and so do not undergo ionisation and do not contribute to the charge on a protein.

—– The charge on a protein is mainly contributed by the amino acid side chains.

Answer 12

1. In a protein there is (typically) only:
   —- one free α-amino and

—- one free αcarboxyl group in a protein,

—— all the other α-groups are used in peptide bond formation.

• In some proteins, which are POST=TRANSLATIONALLY PROTEOLYICALLY CLEAVED, there are 2 or MORE free α-groups.

Question 13

Amino Acid Ionisable Groups – Side Chains

***Nonpolar amino acids:

Answer 13

do not have ionisable groups in their side chains,
so do not contribute any charge to peptides and proteins.

Question 14

Amino Acid Ionisable Groups – Side Chains

**Polar basic amino acids: 3

Answer 14

1 * Protonated form (acid) is positively charged, deprotonated form
(conjugate base) is neutral.

2 * If pH &laquo_space;pKa then side chains will be in PROTONATED form and therefore POSITIVELY CHARGED.

3 * If pH&raquo_space; pKa then side chains will be in DEPROTONATED form and therefore NEUTRAL.

pKa ~ 10.5 (free amino acid) pKa ~ 6.00 (free amino acid)
pKa ~ 12.5 (free amino acid)

Question 15

Amino Acid Ionisable Groups – Side Chains:
Polar acidic amino acids:

Answer 15

pKa ~ 3.6 (free amino acid) pKa = 4.25 (free amino acid)

Question 16

Amino Acid Ionisable Groups – Side Chains

Polar uncharged amino acids:

Answer 16

Protonated form (acid) is neutral, deprotonated form (conjugate base) is negatively charged.

If pH &laquo_space;pKa then side chains will be in PROTONTATED form and therefore NEUTRAL

If pH&raquo_space; pKa then side chains will be in DEPROTONATED form and
therefore NEGATIVELY CHARGED charged

pKa ~ 8.1 (free amino acid) pKa ~ 10.0 (free amino acid)

Question 17

• Know the structures of the ionisable groups of amino acid side chains and their approximate pKas and know the charge on the conjugate acid and conjugate base forms of the ionizable groups.

Answer 17

Asp/Glu: –COOH < –> COO + H+

Lys: -NH3+ <–> -NH2 + H+

Cys: -SH <—> -S- + H+