Peptide Structure and Synthesis

Introduction

• Overview of 3D structures of peptides, peptide synthesis, and the significance of functional group reactivity.

• Focus on the directionality of amino acids and peptides, emphasizing the N-terminus on the left.

• Establishes a connection to DNA and RNA structure.

The Amide (Peptide) Bond

• Clarifies the distinction between an amide bond and a peptide bond, noting that a peptide bond is a specific type of amide bond within a peptide.

• Explains how amino acids are linked by peptide bonds to create peptide polymers.

• Provides an example of a dipeptide, highlighting the importance of the N-terminus and C-terminus for peptide identification.

Peptide Synthesis

Chemical Synthesis vs. Biological Synthesis

• Contrasts the enzymatic assembly of peptides in the body with chemical synthesis methods.

• Notes the necessity of a coupling reagent to facilitate amide bond formation from an amine and a carboxylic acid in chemical synthesis.

• Identifies this reaction as a nucleophilic acyl substitution.

Why a Coupling Reagent is Necessary:

• Explains that carboxylic acids are poor electrophiles because they have a less reactive carbonyl carbon.

• Describes how, without a coupling reagent, an acid-base reaction occurs, preventing the desired nucleophilic attack.

Acid-Base Reaction

• Details the acid-base reaction where the amine takes a hydrogen from the carboxylic acid, leading to charged nitrogen and oxygen atoms.

• Explains that the nitrogen loses its nucleophilic properties in this reaction.

• Clarifies that adding acid as a catalyst is ineffective because it protonates the amine, preventing it from acting as a nucleophile.

• Reviews lectures 3 & 5: how $H^+$ polarizes the carbonyl carbon but fails due to amine protonation.

Role of Coupling Reagent

• Describes how the coupling reagent activates the carboxylic acid, transforming it into a good leaving group for nucleophilic attack by the amine.

• Compares this activation process to converting the carboxylic acid into an acid chloride.

• Emphasizes that the amine remains a free base, allowing it to attack the carbonyl carbon effectively.

Synthesis Tactics and Protecting Groups

Problem with Unprotected Amino Acids

• Highlights the issue of multiple reactive functional groups leading to unwanted side reactions.

• Illustrates how alanine and glycine, with four reactive sites, can produce several dipeptide products.

• Lists $Ala-Ala$, $Gly-Gly$, $Ala-Gly$, and $Gly-Ala$ as possible products from unprotected alanine and glycine with a coupling reagent.

• Notes that $Ala-Gly$ and $Gly-Ala$ are distinct compounds with different properties.

Protecting Groups

• Explains that protecting groups are used to block reactivity at unwanted sites.

• States the goal of forming predominantly one product to simplify separation.

• Describes the characteristics of protecting groups: they form covalent bonds, block reactivity, remain stable during amide bond formation, and are easily removed afterwards.

Schematic Representation

• Uses P1 and P2 to represent protecting groups.

• Explains that protecting the amine on alanine (with P1) and the carboxylic acid on glycine (with P2) results in a single dipeptide product.

• Describes global deprotection as the simultaneous removal of all protecting groups after the coupling reaction.

• Points out that protecting group chemistry is essential due to the high functionality of amino acids and peptides.

Structure of the Amide Bond

Resonance

• Explains that resonance in the amide bond results in partial double bond character between the carbon and nitrogen atoms.

• Notes that this restricts rotation, making peptides rigid and planar.

• Indicates that the resonant structure is a stable form for an amide.

Implications for Peptide Structure

• Explains that restricted rotation gives peptides a well-defined shape.

• Defines peptides as polymers of amino acids, with specific names for dipeptides, tripeptides, and polypeptides.

• Differentiates between a peptide and a protein based on the number of amino acids (more than 50 is typically considered a protein).

Directionality and Properties of Peptides

Directionality

• Explains that peptides have a directional sense similar to RNA and DNA.

• States that the N-terminus is always written on the left.

• Notes that $Alanine-Glycine$ is different from $Glycine-Alanine$.

• Mentions that the R-groups and side-chains determine the properties of the peptide.

Peptide Properties

• Specifies that peptide properties depend on the amino acids and their side chains (R-groups), which influence chemistry, shapes, and reactivity.

• Notes that functional groups on side chains (e.g., cysteine with a thiol) affect peptide properties.

• Mentions the ionization of side chains at physiological pH.

• Indicates that side chains influence hydrogen bonding.

Peptide Structure: Primary, Secondary, Tertiary, and Quaternary

Levels of Structure

• Defines the primary structure as the amino acid sequence (single-letter code).

• Describes secondary structures as localized, well-defined structures like alpha helices and beta sheets.

• Explains the tertiary structure as the arrangement of secondary structure elements.

• Defines the quaternary structure as the arrangement of multiple peptide chains (subunits).

• Mentions that hydrogen bonding stabilizes secondary structures and contributes to water solubility.

Secondary Structure: Alpha Helix

• Explains that the organization and stability of secondary structure are determined by the R-groups of the amino acids.

• States that polar side chains face the solvent, while nonpolar side chains are buried.

• Notes that hydrogen bonds between the carbonyl oxygen of one amide bond and the $N-H$ of another stabilize the structure.

• Describes the $i$ to $i+4$ hydrogen bonding pattern in alpha helices.

• Mentions that repeating hydrogen bonds provide strength.

• Notes that the carbonyl oxygen hydrogen bonds to the $N-H$ four amino acids up the chain.

• Indicates that eight to ten or more amino acids are needed to stabilize the alpha helix.

Sickle Cell Anemia - Impact of Amino Acid Change

Mutation

• Explains that a single amino acid change (e.g., glutamic acid to valine) can cause genetic diseases.

• Notes that sickle cell anemia is caused by valine replacing glutamic acid in hemoglobin.

• Mentions that glutamic acid is ionized at physiological pH.

Resulting Changes

• Indicates that valine has different properties than glutamic acid.

• Explains that this change alters protein shape and red blood cell structure.

• Notes that the nonpolar side chain causes aggregation and reduces hydrogen bonding.

Disulfide Chemistry and Protein Structure

Disulfide Bonds

• Explains that disulfide bonds (bridges) stabilize tertiary structure.

• Describes how two thiols ($R-SH$) react to form a disulfide ($R-S-S-R$).

• Notes that cysteine side chains form reversible disulfide bonds.

• Mentions that our bodies control disulfide bonds during oxidation and reduction.

Function

• Explains that disulfide bonds can be within the same peptide or between two different peptides.

• Notes that they form a reversible covalent bond.

• States that the bonds bring remote parts of a peptide together and are important for biological activity.

Insulin Example

• Describes insulin as consisting of two peptide chains (A and B) connected by three disulfide bonds.

• Notes the presence of one intra-chain and two inter-chain disulfide bonds.

• States that disulfide bonds stabilize insulin's structure and are crucial for its activity.

• Concludes that disulfide bonds stabilize peptides.