Lecture 4: Amino Acids & Peptides

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What are amino acids?

They are building blocks of proteins consisting of an amino group, carboxyl group and a side chain.

What is Peptide?

It’s a oligomer of amino acids (2 - 40 amino acids) that are connected by amide bonds and can also have cross-link S-S bonds.

What are proteins?

They are long chains (>40 amino acids) of amino acid residues

What are hydrophobic amino acids?

They are amino acids with hydrocarbon fragments as side chains.

What does it mean that amino acid has cationic form?

It means that amino acid under physiological conditions carries a net positive charge.

What does it mean that amino acid has anionic form?

It means that amino acid under physiological conditions carries a net negative charge.

How does electrophoresis tehnique work?

It separates amino acids from solution based on their movement in an electric field.

How does Ion-exchange Chromatography method work?

It separates amino acids from solution based on their charge interactions with solid materials.

What happens in condensation reaction?

A carboxyl group of one amino acid and the amine group of another react thus creating peptide bond between the two molecules and releasing water.

What is Brønsted Acid?

It’s a substance that can donate a proton (H+) in an acid-base reaction.

What is Brønsted Base?

It’s a substance that can accept a proton (H+) in an acid-base reaction.

What is amine?

It’s a functional group that contains a nitrogen atom bonded to one or more alkyl or aryl groups.

What is carboxylic acid?

It’s an organic compound that contains a carboxyl group (–COOH).

What can be done with Dicyclohexyl-carbodiimide (DCC)?

It can used for the activation of free carboxylic acid in peptide synthesis

What is Solid-Phase Peptide Synthesis?

It’s a method for synthesizing peptides by attaching amino acids to a solid support and going through repetitive coupling and deprotection process.

What does increasing rotational barrier provide?

Stiffness

What is the function of structural proteins?

They provide strength and micro-/macroscopic structure to organisms

What are examples of structual proteins?

Collagen, keratin and silk

Where can keratin be found?

In hairs and feathers

what protective proteins provide?

They provide defense mechanisms against attack by other organisms or mechanical damage

What are examples of protective proteins

Antibiotics, antibodies and toxins

What are enzymes?

They are natural compounds, that work as catalysts, which maintain metabolic functions and signal transmissions

What are examples of enzymes?

cholinesterase, a-glycosidase and cytochrome P450

What does bacterial b-glycosidase do?

It breaks down cellulosic plant biomass

What Hormones do?

They are proteins that provide regulatory functions and works as intracellular communication tools

What are examples of hormones?

Insuline and luteinizing

What does luteinizing do?

It regulates the menstrual cycle

What do proteins with other physiological functions do?

They provide functions, that are neither catalytic nor regulatory

Examples of Proteins with other physiological functions

Albumin and hemoglobin

What is an amino acid?

It’s a molecule that has carbonate and amine group

What all 20 Alpha-amino acids share?

They all are L-alpha amino carboxylic acids

What is isoelectric point (Pl)

It’s the pH where given amino acids positive and negative charges are balanced (no net charge)

How can amino acids be seperated?

By electrophoresis and Ion-exchange chromatography methods

Why is activation of carboxylic acid beneficial?

It enables reaction with other amino acids

What is peptide bond?

It’s molecule where two amino acids are connected by amide

What is peptide?

It’s a oligomer of amino acids with peptide bonds.

What can peptide bonds do?

They can create Pi bond with nitrogen

Where in peptides are rotational points located?

At CO - C (α) and N - C (α)

What peptide bond has cis structure?

Proline

What kind of structure most peptide bonds have?

Trans structure

What is important when making peptides?

Choosing the right activating agents

What automated solid-phase peptide synthesis consists of?

Repeated DCC activation and deprotection

Name all nine hydrophobic alpha-amino acids?

alanine, valine, leucine, isoleucine, methionine, Phenylalanine, Tyrosine, tryptophane and proline

Name all five alpha-amino acids with polar charged groups?

lysine, arginine, histidine, aspartic acid and glutamic acid

Name all five alpha-amino acids with polar uncharged groups?

Serine, threonine, asparagine, glutamine and cysteine