Biochemistry MCAT

Amino Acids

Building Blocks of Proteins

Amino acids with long alkyl chains are hydrophobic, and those with charges are hydrophilic; many others fall somewhere in between.

Amino Acid Structure

1. Carboxyl Group (COOH)

2. Amino Group (NH3)

2. Hydrogen (H)

2. R Group (Varies)

Alkyl Chains

Amino acids with long alkyl chains are hydrophobic,

• Alkyl chains are hydrocarbon chains, meaning they are composed primarily of carbon and hydrogen atoms.

• Amino acids with alkyl side chains are classified as Aliphatic and they include:

  1. Alanine

  2. Valine

  3. Leucine

  4. Isoluecine

Aliphatic

Amino Acids with side chains consist of carbon and hydrogen atoms, forming straight or branched hydrocarbon chains

Amphoteric

Amino acids can accept or donate protons.

Zwitterion

At pH near the pI of the amino acid, the amino acid is a neutral

L/D Configurations

All Amino Acids in Human Body are “L”

R/S Configuration

All Amino Acids are “S” Except Cystine “R”

Protonation OR Depronation Of AA

Amino acids exist in different forms at different pH values;

• At low (acidic) pH, the amino acid is fully protonated (More H+)

• At high (alkaline) pH, the amino acid is fully deprotonated (More OH-)

  • If pKa is higher than pH, a molecule is Protonated

  • If pKa is less than pH, a molecule is deprotonated

Pka’s

PKa of a group is the pH at which half of the species are deprotonated (OH-); [HA] = [A − ] and half are protonated (H+)

• Carboxylic Group (COOH) ≈ 2

• Amine Group (NH3) ≈ 10

• R - Group ( Varies)

Pka Equation

Non Polar, Aliphatic "R" Groups

1. Glycine Gly (G)

2. Alanine Ala (A)

3. Proline Pro (Pro)

4. Valine Val (V)

5. Leucine Leu (L)

6. Isoleucine Ile (l)

7. Methionine Met (M)

Glycine

Gly (G)

R — H

Not a Chiral/Not Enantiomer

Very Small, Too Flexible and disturbs alpha Helix

Alanine

Ala (A)

Non Polar

Alkyl Chain

Proline

Pro (P)

Non - Polar

Too Rigid

Creates Kinks Alpha helix and Beta Sheets and that distubs them

Valine

Val (V)

Non- Polar

Alkyl Chains

Leucine

Leu (L)

Non-polar

Alkyl Chains

Isoleucine

Ile (I)

Non- Polar

Alkyl Chains

Methionine

Met (M)

Non-Polar

Start of three letter Amino Acids and can also be found at other pistions

Contains Sulfide Group (Can be Oxidized)

Polar, Uncharged R groups

1. Serine Ser (S)

2. Threonie Thr (T)

3. Cysteine Cys (S)

4. Asparagine Asn (N)

5. Glutamine Gln (Q)

Serine

Ser (S)

Polar

Hydroxyl group (OH)

Capable of Phosphorylation

Threonine

Thr (T)

Polar

Hydroxyl group (OH)

Capable of Phosphorylation

Cysteine

Cys (C)

Thiol Group (—SH)

Covalent Bonds Between two Cysteine; Disulfide Bonds

Can be Oxidized

Asparagine

Asn (N)

Amide Side Chain

Glutamine

Gln (Q)

Amide Side Chain

Aromatic R Groups

1. Phenylalanine

2. Tyrosine

3. Tryptophan

Phenylalanine

Phe (F)

Nonpolar

Aromatic Group

Tyrosine

Tyr (Y)

Aromatic Group

Neutral Polar - more Polar than nonpolar because of Hydroxyl group (OH)

Capable of Phosphorylation

Tryptophan

Trp (W)

Nonpolar

Aromatic Group

Positively Charged “R” Groups/ Basic Polar

1. Lysine

2. Arginine

3. Histadine

Lysine

Lys (K)

Basic Polar

Pka ≈

Arginine

Arg (R)

Basic Polar

Pka ≈

Histadine

His (H)

Basic Polar

Pka ≈ 7

Negativaly Charged “R” Groups/ Acidic Polar

1. Asparatate

2. Glutamate

Aspartate

Asp (D)

Acidic Polar

Pka ≈

Glutamic Acid

Glu (E)

Acidic Polar

Pka ≈

Amino Acids that can H-Bond

Any amino acid with a

Hydroxyl side chain (Serine, Threonine and Tyrosine),

Amide (Asparagine, Glutamine)

Amine group (Lysine, Arginine and histidine)

Amino Acids With Hydroxyl (OH) side chain

1. Serine

2. Threonine

3. Tyrosine

Amino Acids With Amide Side Chain

1. Asparagine

2. Glutamin

Amino Acids With Amine Side Chain

1. Lysine

2. Arginine

3. Histidine)

Peptides

Composed of amino acid subunits, Called residues

Dipeptides

Two Residues of Amino Acids

Tripeptides

Three Residues of Amino Acids

Oligopeptide

Amino Acids up to 20 residues

Polypeptides

Long Chain more than 20 residues of AA

Peptide Bond (Amide)

Residues in peptides are joined together through peptide bonds, a specialized form of an amide bond, which form between the −COO− group of one amino acid and the NH3+ group of another amino acid.

Peptide Bond Formation

Condensation/Dehydration Reaction occur; a water molecule (H₂O) is removed from two or more molecules, forming a new bond between them

Peptide Bond Hydrolysis (Breakage)

A water molecule (H₂O) is added to the peptide bond. 

The oxygen atom from the water attacks the carbon atom of the carbonyl group in the peptide bond, and the hydrogen atom of the water attacks the nitrogen atom.