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Amino acids & proteins

Draw and recognize the general structure of amino acids.

α-carbon is asymmetric ( has four different substituent) except in glycine.

R group (side chain) is distinctive for each amino acid.

Classify amino acids on the basis of their side chain

Polar:

Contain HO and HN bonds.

Uncharged “ No charge in side chain “.

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 Non-polar:

Contain only carbon and hydrogen.

Charged [-ve] acidic:

R group has negative charge (carboxyl group).

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 Charged [+ve] basic:

R group has positive charge (amino group).

Essential amino acids:

Amino acids not produced by our bodies, taken by diet .

Relate the structure of amino acids to their function, and understand how it
will affect the protein structure

amino acids with different side chains (polar, non-polar, acidic, basic and
so on) might be involved in different types of reactions.

They will affect the overall protein structure as bonding/interactions

between these side chains (ionic, hydrogen, disulfide and hydrophobic)
are the ones making the tertiary level of protein structure.

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 Define pKa value and relate it to the acidic and basic properties of amino
acids.

Ka: dissociation constant.

pKa:

PH

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 Use the pKa values to calculate the pI of any amino acid.

Isoelectrical point (pI): it is the PH at which amino acid has no electrical

charge or (-ve) and (+ve) charges are equal.

pKa 1 : for carboxyl group.

pKa 2 : for amino group.

pK R : for R group.

pI of neutral amino acid:

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 pI of acidic and basic amino acids:
Has 3 ionizable functional groups, so:

Acid:

pI = average of two lowest pKa.

Base:

pI = average of two highest pKa.

pKa and pI of amino acid:

The amino group and carboxyl group will start buffering if pH is 1 of their
pKa.
1 neutral amino acid:

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 Example:

pKa 1 range= 1.3 - 3.3

- at this range carboxyl group start buffering.

- became protonated.

- when pH < 1.3 : all carboxyl groups are protonated.

- when pH > 3.3 : all carboxyl groups are deprotonated.

- Net charge = 1 ( pH < 3.3 ).

pKa 2 range= 8.1 - 10.1

- at this range amino group start buffering.

- became deprotonated.

- when pH < 8.1 : all amino groups are protonated.

- when pH > 10.1 : all amino groups are deprotonated.

- Net charge = 1 ( pH > 8.1 ).

pI = 5.7

- ( 2.3 + 9.1 ) / 2 = 5.7

- from 3.3 - 8.1, amino acid is neutral.

- neutral/ uncharged.
- Net charge = 0.

2 acidic amino acid:

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 pK :

- 3 pKa = 3 ionizable groups.

- each pKa has its range (1 pKa).

- pH < 1.9 : net charge = 1

- pH 1.9 - 3.9 : net charge = 0

- pH 3.9 - 9.2 : net charge = 1

- pH > 9.2 : net charge = 2 “more negative”.

pI :

- average of two lowest values.

- 1.9 + 3.9 / 2 = 2.9

- small range at which amino acid is neutral.

3 basic amino acid:

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 pK :

- 3 pKa = 3 ionizable groups.

- each pKa has its range (1 pKa).

- pH < 2.2 : net charge = 2.

- pH 2.2 - 8.8 : net charge = 1.

- pH 8.8 - 1.6 : net charge = 0.
- pH > 10.6 : net charge = 1.

pI :

- average of two highest values.

- 10.6 + 8.8 / 2 = 9.7

- small range at which amino acid is neutral.

Note the charge is depending on number of carboxyl and amino groups.

Summary:

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 Neutral

Acidic

Amino acids & proteins 10

 Basic

Draw a peptide bond and the general reaction for its formation.

Describe the properties of a peptide bond.

Covalent bond “strong bond”.

Linking carboxyl group of an amino acid with amino group of another

amino acid.

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 R group not involved.

Describe and distinguish between the various levels of protein architecture.

Primary structure:

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 - amino acid sequence

- AA linked by peptide bond.

- mutation in this level may affect the final structure 3 , 4 ).

Secondary structure:

- contain: α-helix , β-sheet , β-bend , Non-repetitive structure.

- formed by hydrogen bonds: hydrogen atom with electronegative atom ( O

, N ).

Tertiary structure:

- 3 dimensional structure.
- formed by interactions between side chains.

- bonds:
-hydrogen bonds: hydrogen with negative atoms.
-hydrophobic interactions: polar groups away from water.

-ionic bonds: between -ve and +ve charged side chain.

-disulphide bond: between S — S

Quaternary structure:

- two or more polypeptide chains ( each polypeptide = subunit).

- bonds: hydrogen bonds, hydrophobic interactions, ionic bonds.

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 Relate the primary structure of a protein to DNA mutations and isoforms of
proteins

Hb-A :

- 4 subunits make quaternary structure [2 α subunits & 2 β subunits].

- carrying oxygen.
- molecules don’t associate with one another.

Hb-S :

- 4 subunits.
- change in glutamate in primary structure.
- the change affects tertiary and quaternary structure.
- molecules interact with one another.
- capacity to carry oxygen is reduced.

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 Normal cell vs. Sickle cell

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 Briefly describe protein folding and the factors contributing to it.

Protein is only biologically active when it has its right folding (3D
structure).

Formed by non covalent ( primarily) and covalent bonds.

Explain how protein denaturation is caused and distinguish between it and

protein digestion.

Denaturation:

 Complete loss of organized structure 3D in a protein.

 Loss of secondary and tertiary structures and biological function.

 Reversible, by renaturation .

 peptide bonds are not broken.

 Denatured enzyme cannot bind to its substrate.

 Denaturating agents: Heat, organic solvents, strong acids and bases,

detergents, ions of heavy metals (e.g: lead).

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 Digestion:

 From proteins to peptides (by proteases) to amino acids (by peptidases).

 Free amino acid, peptide bonds are broken.

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 List some diseases associated with protein misfolding.

Prion diseases:

- the infectious PrP causes the normal PrP to form into the infectious form.
- the new one will convert normal PrP into the infectious form and so on.
- affect cells in the brain.

Creutzfeldt-Jakob disease:

- causes by prion molecules.

- cause brain to shrink.

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 videos:
1 https://youtu.be/9ssCKw-7OvQ
2 https://youtu.be/Bsk9hvXDJp8
3 https://youtu.be/DwBxI2QPsZU
4 https://youtu.be/a7wOprWcYXA

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