Amino Acids, Peptides, and Protein Structure

• Amino acids, peptides, and proteins are fundamental molecules in biochemistry.

Learning Objectives

• Recognize and classify amino acid structures.
• Identify essential and non-essential amino acids.
• Understand amino acids as amphoteric molecules.
• Describe peptide bond formation.
• Understand peptide chain/protein synthesis.
• Understand the hierarchy of protein structure: primary, secondary, tertiary, and quaternary.

Summary of Topics

• Amino acid structure and classification
• Essential amino acids
• L- and D-amino acids (stereoisomers)
• Acid-base properties of amino acids
• Peptide bond formation
• Peptide chains, polypeptides, and proteins
• Protein structure (primary & secondary) including alpha-helix and beta-pleated sheet
• Tertiary and Quaternary structures
• Examples of peptides and proteins and their functions

Protein Structure and Function

• Proteins are polymers of amino acids.
• An amino acid sequence is determined by transcription of the genetic code using 3-letter codons.
• Proteins provide structural framework, transport and storage, enzymatic activity, and hormonal regulation.
• A protein's unique three-dimensional structure dictates its function.

Genetic Code

• The genetic code translates DNA codons into amino acids.
• There are 20 amino acids commonly found in proteins with corresponding DNA codons.
• There are 64 possible 3-letter combinations of the DNA coding bases T, C, A, and G.
• These codons specify amino acids or one of three stop codons.

Amino Acid Structure

• An alpha-amino acid consists of a carboxyl group, an amino group, a hydrogen atom, and a functional R group attached to a central alpha-carbon.

Amino acid R-Groups

• Amino acids have different side chains (R-groups).

Classification of Amino Acids

• Amino acids are classified based on their R group: non-polar, polar uncharged, and polar charged.
• Polar amino acids dissolve easily in water.
• Non-polar amino acids don't like to be exposed to water.
• Positively and negatively charged amino acids are easily solvated in water.

Non-Polar Amino Acids

• Non-polar amino acids: Alanine, Valine, Leucine, Isoleucine, Proline, Phenylalanine, Tryptophan, and Methionine
• Alanine, Valine, Leucine, and Isoleucine have non-cyclic alkyl hydrocarbon side chains.
• Proline has an alkyl hydrocarbon in a heterocyclic ring structure and is an imino acid.
• Phenylalanine and Tryptophan have aromatic ring structures.
• Methionine has a linear side chain containing sulphur.

Polar Amino Acids

• Polar amino acids: Serine, Threonine, Cysteine, Tyrosine, Asparagine, and Glutamine
• These are relatively hydrophilic with polar functional groups that can form hydrogen bonds.
• Glycine is included because the H of its R group can H-bond with polar groups.
• Serine, Threonine, and Tyrosine have hydroxyl (OH) groups.
• Asparagine and Glutamine are derived from Asp and Glu, where the carboxyl is modified to become an amide group.
• Cysteine has an SH group and two Cys residues can form a disulphide bridge.

Cystine Formation

• Two oxidized cysteine side chains create a disulphide bridge (-S-S-), forming cystine.
• Three disulphide bridges are used to form peptide hormone insulin

Polar-Charged Amino Acids

• Polar-Charged Amino Acids include basic and - acidic amino acids.
• Basic: Lysine, Arginine, Histidine
• Acidic: Aspartic Acid, Glutamic Acid
• Lysine and Arginine have +ve charged functional groups at pH 7.
• Histidine has an imidazole group and can serve as a proton donor or acceptor.
• Aspartic Acid and Glutamic Acid have carboxyl groups ionized at pH 7.4.

Nomenclature

• Nomenclature consists of three letter and one letter codes for each amino acid.
• Examples:
  • Alanine (Ala, A)
  • Cysteine (Cys, C)
  • Aspartic Acid (Asp, D)
  • Glutamic Acid (Glu, E)
  • Phenylalanine (Phe, F)
  • Glycine (Gly, G)
  • Histidine (His, H)
  • Isoleucine (Ile, I)
  • Lysine (Lys, K)
  • Leucine (Leu, L)
  • Methionine (Met, M)
  • Asparagine (Asn, N)
  • Proline (Pro, P)
  • Glutamine (Gln, Q)
  • Arginine (Arg, R)
  • Serine (Ser, S)
  • Threonine (Thr, T)
  • Valine (Val, V)
  • Tryptophan (Trp, W)
  • Tyrosine (Tyr, Y)

Protein Synthesis

• Proteins are polymers of amino acids.
• The amino acid sequence is determined by transcription of the genetic code.

Essential Amino Acids

• Humans must obtain essential amino acids through diet.
• Essential amino acids can't be synthesized by the body.
• Essential amino acids: Valine, Phenylalanine, Tryptophan, Isoleucine, Threonine, Histidine, Methionine, Leucine, and Lysine.
• Cysteine can partially meet the need for methionine.
• Tyrosine can partially substitute for phenylalanine.

Mnemonic for Essential Amino Acids:

• Use "Very Full With Milk" :
  • Valine
  • Phenylalanine
  • Tryptophan
  • Isoleucine
  • Threonine
  • Histidine
  • Methionine
  • Leucine
  • Lysine

Other Amino Acids

• More than 200 amino acids occur in nature.
• Some amino acids can be chemically altered post-translationally where proline is oxidised to hydroxyproline.
• Chemically modified derivatives: Glutamic acid converted to γ-aminobutyrate (GABA), a neurotransmitter.
• Dopamine is a neurotransmitter synthesized from tyrosine.
• Taurine in bile acts as an emulsifier for lipids and supports neurological development in babies.

Post-Translational Modifications

• Common modifications include acetylation, amidation, phosphorylation, hydroxylation, methylation, acylation, palmitoylation, and sulphation.

Chirality of Amino Acids

• With the exception of glycine, all amino acids have chiral carbons and exist as L and D isomers.
• These isomers are mirror images of one another.
• All amino acids except glycine have four different groups attached to the alpha-carbon
• The alpha-carbon is chiral, or asymmetric

Amino Acids as Stereoisomers

• Chirality describes a molecule's "handedness", which is the ability to rotate polarized light.
• L-form amino acids are incorporated into proteins in mammalian cells.
• Chiral molecules and their mirror images are stereoisomers.
• Enantiomers are non-superimposable mirror images.

Acid-Base Properties of Amino Acids

• The α-COOH and α-NH2 groups in amino acids can ionize, as do the acidic and basic R groups.
• Amino acids are amphoteric molecules.
• At physiological pH (7.4), the carboxyl group will be unprotonated (-ve charged) and the amino group will be protonated (+ve charged).
• The net charge of an amino acid, peptide, or protein depends on the pH of the surrounding aqueous environment.
• Net zero charge of an amino acid or protein is called its isoelectric point (pl).

Ionization of Glycine

• Ionization occurs at different pH levels.
• At ph 2.35, pKa1 of glycine is reached.
• At pH 9.78, pKa2 of glycine is reached.

Titration Curve of Glycine

• Isoelectric point is the point where the net charge is zero

Zwitterion Structure

• A zwitterion is an amino acid with both + and - charges
• Amino Acid Structure contains:
  • amine (H2N-C-C-OH)
  • acid group (H2N-C-C-OH)
  • and an R group attached to the central a-carbon

Peptide Bond

• A peptide bond links amino acids through a covalent bond between the alpha-carboxyl end and the alpha-amino end.
• Peptide bond formation is a condensation reaction where water is lost.

Peptide Bonds with Glycine and Alanine

• In the formation of a peptide bond, a water molecule (H2O) is lost. This is also called a condensation reaction.
• Hydrolysis is involved when a water molecule is added.

Key Characteristics of a Peptide Bond

• Planar due to resonance.
• Has a flat structure

Dipeptide Formation

• Happens when you bond two amino acids together
• Water molecule is released

Peptide Classification

• A string of amino acids held together by peptide bonds
• In a peptide of length (n) amino acids there are (n-1) peptide bonds.

Linus Pauling and Robert Corey

• They analyzed the geometry of peptide bonds to discover that the four atoms to which the C and N atoms are directly linked form a flat or planar structure.
• A peptide's C–N bond length is 10% shorter than that found in usual C–N amine bonds due to resonance, so it demonstrate some double bond character (40%).
• Free rotation takes place about the aC-N and the aC-C bonds, permitting adjacent peptide units to be at different angles
• Hydrogen atom of the amino group is nearly always on the opposite side (trans)

Polypeptide Backbone Conformation

• The backbone conformation of a polypeptide is specified by torsion angles about the aC-N and aC-C bonds (phi and psi angles).
• The conformational range of phi and psi are restricted by steric hindrance.

Molecular Weight of a Peptide

• Add the mass of amino acids and then calculate the molecular mass by subtracting the mass of a water molecule (H2O) for each peptide bond formed.

Protein Structure

• There are four levels of structure in proteins: primary, secondary, tertiary, and quaternary.

Primary Structure

• Primary structure is the linear sequence of amino acids joined by peptide bonds and is determined by sequencing the nucleotide bases in the gene encoding the protein.

Secondary Structure

• Secondary structure refers to the amount of structural regularity or shape in a polypeptide chain.
• A natural polypeptide chain will spontaneously fold into a regular and defined shape.
• Includes alpha helices and beta pleated sheets.

Alpha Helix

• The polypeptide folds by twisting into a right handed screw, forming hydrogen bonds.
• The ability of a protein to fold into a helix is influenced by the amino acids and the R side chains that they possess.
• A Pro residue and consecutive Asp or Glu residues can destablise the helix.
• There are 3.6 residues per turn and the rise/residue is 1.5 Å units.
• Hydrogen bonds are formed between the C=O of residue n to the H-N of residue n+4.
• Peptide bonds have a dipole moment.

Beta-Pleated Sheet

• The polypeptide chains stretch and align side by side, forming H-bonds between lengths.
• H-bonds form from amino and carboxyl groups.
• The strands of peptide chains can run in opposite (antiparallel) or same (parallel) directions.
• Extended polypeptide chain beta-sheets tend to be twisted.

Tertiary Structure

• Tertiary structure is about how the secondary structure units associate within a single polypeptide chain to give a three-dimensional structure.
• Interactions include disulphide bridges, hydrogen bonding, salt bridges, and hydrophobic interactions.

Quaternary Structure

• Quaternary structure describes how two or more polypeptide chains associate to form a native protein structure.
• Proteins with multiple polypeptide chains are oligomeric.
• An active native conformation of a protein is maintained by hydrophobic interactions, electrostatic forces, Van der Waals forces, hydrogen bonding and disulphide bonds.

Functional Properties

• Haemoglobin transports oxygen in the blood stream from red blood cells to tissues.
• Myoglobin is in skeletal muscles as an extra storage protein to enable muscle cells to have a readily available supply of oxygen.
• Both proteins contain "haem" and the center is the Fe+2 metal ion.
• Globular proteins are relatively spherical in shape and examples include egg albumin, haemoglobin, myoglobin, insulin, and serum globulins.

Hemoglobin vs. Myoglobin

• Haemoglobin consists of four protein chains and four haem groups that carry oxygen from the lungs to the tissue cells.
• Myoglobin consists of a single protein chain with 153 amino acids and one haem group that stores oxygen in the muscle cells.
• Myoglobin has a stronger affinity for oxygen than haemoglobin.

Examples of Human Proteins

• Sarcolipin: Calcium ion transport into muscle cells
• Somatotropin: Growth hormone
• Ribonuclease A: Breakdown of RNA molecules
• Carbonic anhydrase: Removes carbon dioxide from tissues.
• Beta-globin: Component of hemoglobin, carries oxygen in the bloodstream.
• Myoglobin: Utilizes oxygen in muscle tissue
• Tissue plasminogen activator: Blood clotting system
• Hsp70: Molecular chaperone, helps other proteins adopt correct structures.
• Keratin II: Component of hair and cytoskeleton
• Collagen 1: Component of tendons, ligaments and bones.
• Dystrophin: Part of the internal skeleton of muscle cells.
• Titin: Structural component of muscle.

Insulin Structure

• Contains 2 peptide chains (A and B chains) linked by disulphide bonds
• Proinsulin starts as a single chain molecule and enzymes process it into the finaly insulin product.

Examples of Other Peptides

- Met-enkephalin and Leu-enkephalin (pain killers)
- Glucagon Like Peptide (diabetes medication)

Consequences of Mutations

• Single amino acid changes can cause diseases.
• Example: sickle cell anemia