Amino Acids and Their Classification Quiz

Amino Acids and Proteins

• Amino acids are acidic organic compounds containing an amine group (NH2).
• The most common amino acids are α-amino acids.
• The COOH and NH2 groups are attached to the same carbon (α-carbon).
• There are only 20 α-amino acids used to produce proteins.
• Amino acids are amphoteric molecules; they can act as acids or bases.

Structure of α-Amino Acids

• α-amino acids (AA) have a common structural motif.
• The α-carbon is linked to four different substituents: the amine group, the carboxyl group, an atom of hydrogen (H), and the R-side chain.
• The R-side chain is variable, and gives each amino acid its unique properties.

Stereochemistry of α-Amino Acids

• Most amino acids are chiral molecules due to the asymmetric carbon atom.
• The α-carbon is linked to four different substituents.
• Only glycine does not have an asymmetric carbon and is therefore not a chiral molecule.

Optical Isomerism

• Amino acids used in humans belong to the L series.
• For any given amino acid, there are two spatial conformations (enantiomers): L and D.
• D-series amino acids are found in bacterial walls and some peptides made by bacteria.

Classification of Amino Acids

• Amino acids are classified according to the chemical nature of their side chains, polarity of the side chains, and dietary importance.
• Seven groups of side chains exist, including aliphatic, hydroxylated, sulfur-containing, basic, aromatic, acidic, and imine groups.

AA with Aliphatic Side Chains

• Glycine (Gly, G)
• Alanine (Ala, A)
• Valine (Val, V)
• Leucine (Leu, L)
• Isoleucine (Ile, I)

Glycine (G or Gly)

• Simplest side chain (one hydrogen atom).
• Not essential in the human diet.
• Lowest molecular weight among all the amino acids.

Alanine (A or Ala)

• Methylated side chain (CH3).
• Not essential in the human diet.

Valine (V or Val)

• Isopropyl side chain.
• Essential amino acid (AA) in the human diet.

Leucine (L or Leu)

• Isobutyl side chain.
• Essential AA in the human diet.

Isoleucine (I or Ile)

• Isobutyl side chain (same chemical formula as leucine).
• Essential AA in the human diet.

AA with Hydroxylated Side Chains

• Serine (Ser, S)
• Threonine (Thr, T)

Serine (S or Ser)

• Side chain with a hydroxyl group (OH).
• Phosphorylation site in many proteins.
• Non-essential AA in the human diet.

Threonine (T or Thr)

• Side chain with a hydroxyl group (OH).
• Phosphorylation site in many proteins.
• Essential AA in the human diet.

AA with Sulfur Side Chains

• Cysteine (Cys, C)
• Methionine (Met, M)

Cysteine (C ou Cys)

• Side chain with sulfhydryl group (thiol: R-SH).
• Amino acid forming disulfide bridges.
• Not essential in the human diet.

Methionine (M ou Met)

• Side chain with a thioether group.
• First amino acid in protein synthesis.
• Essential AA in the human diet.

AA with Basic Side Chains

• Arginine (Arg, R)
• Histidine (His, H)
• Lysine (Lys, K)

Histidine (H ou His)

• Imidazole side chain (aromatic).
• Essential amino acid in human food.

Lysine (K ou Lys)

• Amino side chain.
• Essential amino acid in the human diet.

Arginine (R ou Arg)

• Guanidine group at the end of the side chain
• Always charged (positive) at physiological pH.
• Essential AA in the human diet.

AA with Aromatic Side Chains

• Phenylalanine (Phe, P)
• Tyrosine (Tyr, Y)
• Tryptophan (Trp, W)

Phenylalanine (F ou Phe)

• Aromatic side chain (Phenyl).
• Light absorption in the UV around 280 nm.
• Essential AA in the human diet.

Tyrosine (Y ou Tyr)

• Aromatic side chain (Phenol).
• Light absorption in the UV around 280 nm.
• Phosphorylation site in many proteins. Non-essential amino acid in human food.

Tryptophan (W ou Trp)

• Aromatic side chain (Indol).
• Absorption of light in the UV towards 280nm.
• Essential AA in the human diet.

AA with Acid or Amide Side Chains

• Aspartic acid (Asp, Asp)
• Asparagine (Asn, N)
• Glutamic acid (Glu, E)
• Glutamine (Gln, Q)

Aspartic Acid (D ou Asp)

• Acidic side chain.
• Not essential in the human diet.

Glutamic Acid (E or Glu)

• Acidic side chain.
• Not essential in the human diet.

Asparagine (N ou Asn)

• Side chain with amide group.
• Not essential in the human diet.

Glutamine (Q ou Gln)

• Side chain with amide group.
• Most abundant amino acid in the blood.
• Not essential in the human diet.

Imine Acid

• Proline (Pro, P)
• Only AA with a bond between R and NH2
• Cyclic side chain
• Not essential in the human diet.

Classification according to Polarity

• Non-polar (hydrophobic) R groups (e.g., Glycine, Alanine)
• Uncharged polar groups (hydrophilic) (e.g., Serine, Threonine)
• Polar groups charged (hydrophilic) (negatively charged=acidic, positively charged=basic) (e.g., Aspartic Acid, Glutamic Acid)

Classification according to Dietary Importance

• Essential amino acids (must be obtained through diet).
• Non-essential amino acids (can be synthesized by the body).

Zwitterions

• Amino acids in aqueous solution exist as dipolar ions (or zwitterions): a positive charged amino group and a negatively charge carboxyl group.
• Zwitterions have no net charge, due to the positive and negative charges balancing each other out.
• The isoelectric pH (pHi) is the pH at which a zwitterion of an amino acid in solution has a net charge of zero.

Isoelectric pH (pHi)

• The zwitterion has no net charge at its isoelectric pH (pHi)

Determination of pKa

• Amino acids with non-ionizable side chains are characterized by two ionization constants, pKa1 (α-COOH) and pKa2 (α-NH3+).

Titration Curve

• A titration curve is a graph that plots the pH of a solution as a function of the amount of titrant added.
• It can be used to determine the pKa values of an amino acid.

Absorbance of Amino Acids

• Aromatic amino acids absorb UV light around 280 nm.
• Absorption can be used to measure amino acid concentrations, based on Beer-Lambert law.

Electrical Properties of Amino Acids

• Electrophoresis is a method used to separate ions under the effect of an electric field. Anions migrate to the anode, cations migrate to the cathode, and uncharged molecules don't migrate.

Protein Separation (SDS-PAGE)

• SDS-PAGE is a denaturing technique used to separate proteins based on their molecular weight. SDS coats proteins and charges them negatively.

Estimation of Molecular Weight

• The mobility of proteins in SDS-PAGE is inversely proportional to their molecular weight. A calibration curve of known proteins can be used to estimate the molecular weight of unknown proteins.

The Proteins

• Proteins are macromolecules composed of L-amino acids linked by peptide bonds.
• Poly peptides are chains of 10 to 100 amino acids.
• Oligopeptides contain up to 10 amino acid residues.
• Proteins are polymers of at least 100 amino acids, typically, up to several thousand.

Classification of Proteins

• Holoproteins: proteins made up solely of amino acids.
• Heteroproteins: proteins that contain non-protein components (prosthetic groups, e.g. metals, carbohydrates, or lipids)

Fibrous vs. Globular Proteins

• Fibrous proteins: long, parallel polypeptide chains; insoluble in water; stable structures; structural support roles
• Globular proteins: coiled and folded polypeptide chains; spherical shape; soluble in water; variable three-dimensional structures; metabolic functions (e.g., enzymes, hormones, receptors).

Classification of Proteins by Function

• Structural proteins (e.g., keratin, collagen)
• Catalytic proteins (enzymes) (e.g., oxidoreductases, transferases)
• Transport proteins (e.g., hemoglobin)
• Defense proteins (e.g., immunoglobulins)

Reserve Proteins

• Some proteins function as a reservoir of nutrients, e.g., casein in milk

Regulatory Protein

• Some proteins control the expression of genes and regulate the type and timing of protein synthesis, e.g., hormones such as Insulin.

Peptide Bond

• Peptide bonds are covalent bonds between the carboxyl group of one amino acid and the amino group of another.
• The formation of a peptide bond involves the elimination of a water molecule.

Stereochemistry of Peptide Bond

• The peptide bond structure is planar due to resonance.
• The C=O and N-H groups are parallel and lie in the same plane.

Conformation of Peptide Bond

• Peptide bonds primarily exist in the "trans" conformation, with the alpha carbons on opposite sides of the bond.

Primary Structure of Proteins

• The primary structure is the linear sequence of amino acids in a polypeptide chain.
• N-terminal end: the amino acid at the beginning.
• C-terminal end: the amino acid at the end.

Secondary Structure of Proteins

• Secondary structural elements (e.g., alpha helix, beta pleated sheet) are stabilized by hydrogen bonds.

Alpha Helix

• Main chain spirals to the right.
• Hydrogen bond between -C=O and -N-H groups in the peptide backbone.

Beta-pleated Sheet

• Peptide chain is in a zigzag form
• Hydrogen bonds between C=O and N-H groups in different segments of the polypeptide chain.

Tertiary Structure of Proteins

• Overall three-dimensional structure of a polypeptide chain, stabilized by various interactions between amino acid side chains.

Quaternary Structure of Proteins

• Assembly of two or more polypeptide chains; held together by hydrophobic interactions, hydrogen bonding, or disulfide bridges. Can be identical monomers (homo-multimer), or different monomers (hetero-multimer).

Hemoglobin

• A protein in red blood cells responsible for oxygen transport.
• Consists of four polypeptide chains (two alpha and two beta): quaternary structure
• Each chain associated with a heme group.

Post-Translational Modifications of Proteins

• A protein's activity can be modified after translation from the nucleic sequence.

Glycation

• The non-enzymatic process of sugar attaching to proteins.
• Increased with rising blood glucose levels.
• Can lead to complications in diabetes by forming AGEs (advanced glycation end products).

Protein Glycosylation

• Enzymatic addition of glycans (sugar chains) to proteins.
• Important for protein function.
• Occurs in the endoplasmic reticulum and Golgi apparatus.

N-Glycosylation

• Co-translational attachment of glycans to the amide nitrogen of an asparagine residue
• Sugar immediately attached to the asparagine is N-acetylglucosamine.

O-Glycosylation

• Post-translational attachment of glycans to the oxygen of a serine or threonine side chain hydroxyl group

Acylation of Proteins

• Covalent attachment of fatty acids to proteins.
• Important for protein localization and function. Four main types: Myristoylation, Palmitoylation, Glypiation, Farnesylation/Geranylation.

Phosphorylation/Dephosphorylation

• Covalent attachment of a phosphate group to the hydroxyl group in serine, threonine, or tyrosine residues.
• A reversible modification that may activate or inactivate a protein.

Protein Solubility

• Solubility is affected by factors such as pH, ionic strength, and the presence of organic solvents.

Protein Purification

• Techniques such as precipitation with ammonium sulfate and electrophoresis can be used to purify specific proteins.

Test your knowledge of amino acids with this quiz that covers functional groups, classifications, and essential amino acids. You'll be asked to recognize characteristics, identify essential amino acids, and match them to their groups. Perfect for students of biochemistry or molecular biology!