Amino Acids, Peptides, and Proteins – Part 1

Why are they important?

Main Agents of Biological Function
• Catalysis
– enolase (in the glycolytic pathway)
– DNA polymerase (in DNA replication)
• Transport
– hemoglobin (transports O2 in the blood)
– lactose permease (transports lactose across the cell membrane)
• Structure
– collagen (connective tissue)
– keratin (hair, nails, feathers, horns)
• Motion
– myosin (muscle tissue)
– actin (muscle tissue, cell motility)
–
What should you know from this chapter?
• Structure and naming of amino acids
• Structure and properties of peptides
• Ionization behavior of amino acids and peptides
• Methods to characterize peptides and proteins

Introduction

The protein keratin, formed by all vertebrates, is the chief structural component of hair, scales,
horn, wool, nails, and feathers. The black rhinoceros is nearing extinction in the wild because of
the belief prevalent in some parts of the world that a powder derived from its horn has
aphrodisiac properties. In reality, the chemical properties of powdered rhinoceros horn are no
different from those of powdered bovine hooves or human fingernails.

Can you speculate what protein(s) the other images are referring to?

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Amino Acids
• Proteins are linear heteropolymers of -amino acids
• Amino acids have properties that are well-suited to carry out a variety of biological
functions
– Capacity to polymerize
– Useful acid-base properties
– Varied physical properties
– Varied chemical functionality

Amino acids share many features, differing only at the R substituent!

This structure is common to all but one of the α-amino acids. (Proline, a cyclic amino acid, is the
exception.) The R group, or side-chain (red), attached to the α carbon (blue) is different in each
amino acid.

Most -amino acids are chiral

• The -carbon always has four substituents and is tetrahedral
• All (except proline) have:
– an acidic carboxyl group
– a basic amino group
– an -hydrogen connected to the -carbon
• The fourth substituent (R) is unique
– In glycine, the fourth substituent is also hydrogen

Amino Acids: Atom Naming

• Organic nomenclature: start from one end
• Biochemical designation:
– start from -carbon and go down the R-group

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All amino acids are chiral (except glycine)
Proteins only contain L amino acids. What does the L stand for and how is it used?

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Common amino acids can be placed in five basic groups depending on their R substituents:
• Nonpolar, aliphatic (7)
• Aromatic (3)
• Polar, uncharged (5)
• Positively charged (3)
• Negatively charged (2)

There are some Uncommon Amino Acids in Proteins

• Not incorporated by ribosomes
 except for Selenocysteine
• Arise by post-translational modifications of proteins
• Reversible modifications, especially phosphorylation, are important in regulation and
signaling

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Ionization of Amino Acids
• At acidic pH, the carboxyl group is protonated and the amino acid is in the cationic form.
• At neutral pH, the carboxyl group is deprotonated but the amino group is protonated. The
net charge is zero; such ions are called Zwitterions.
• At alkaline pH, the amino group is neutral –NH2 and the amino acid is in the anionic
form.
Cation  Zwitterion  Anion

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Chemical Environment Affects pKa Values
The pKa values for the ionizable groups in glycine are lower than those for simple, methyl-
substituted amino and carboxyl groups. These downward perturbations of pKa are due to
intramolecular interactions. Similar effects can be caused by chemical groups that happen to be
positioned nearby—for example, in the active site of an enzyme.

Amino acids with uncharged side chains, such as glycine, have two pKa values:
• The pKa of the -carboxyl group is 2.34
• The pKa of the -amino group is 9.6

It can act as a buffer in two pH regimes. On the bottom image of page 5 where are these?

Amino acids carry a net charge of zero at a specific pH (the pI)

• Zwitterions predominate at pH values between the pKa values of the amino and carboxyl
groups
• For amino acids without ionizable side chains, the Isoelectric Point (equivalence point,
pI) is

At this point, the net charge is zero

– AA is least soluble in water
– AA does not migrate in electric field

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Ionizable side chains can show up in titration curves
• Ionizable side chains can be also titrated
• Titration curves are more complex
• pKa values are discernable if two pKa values are more than two pH units apart

Why is the side chain pKa so much higher?

How to Calculate the pI When the Side Chain is Ionizable

• Identify species that carries a net zero charge
• Identify pKa value that defines the acid strength of this zwitterion: (pK2)
• Identify pKa value that defines the base strength of this zwitterion: (pK1)
• Take the average of these two pKa values

What is the pI of histidine?

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Peptides

• Peptides are small condensation products of amino acids

• They are “small” compared to proteins

The α-amino group of one amino acid (with R2 group) acts as a nucleophile to displace the
hydroxyl group of another amino acid (with R1 group), forming a peptide bond. Amino groups
are good nucleophiles, but the hydroxyl group is a poor leaving group and is not readily
displaced. At physiological pH, the reaction shown here does not occur to any appreciable
extent. Can you elaborate more on this?

Peptide ends are not the same

Numbering (and naming) starts from the amino terminus
AA1 AA2 AA3 AA4 AA5

Name:

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Peptides: A Variety of Functions
• Hormones and pheromones
– insulin (think sugar)
– oxytocin (think childbirth)
– sex-peptide (think fruit fly mating)
• Neuropeptides
– substance P (pain mediator)
• Antibiotics
– polymyxin B (for Gram – bacteria)
– bacitracin (for Gram + bacteria)
• Protection, e.g., toxins
– amanitin (mushrooms)
– conotoxin (cone snails)
– chlorotoxin (scorpions)

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Proteins
Proteins are:
• Polypeptides (covalently linked -amino acids) + possibly:
• cofactors
 functional non-amino acid component
 metal ions or organic molecules
• coenzymes
 organic cofactors
 NAD+ in lactate dehydrogenase
• prosthetic groups
• covalently attached cofactors
• heme in myoglobin
• other modifications

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What to Study about Peptides and Proteins
 What is its sequence and composition?
 What is its three-dimensional structure?
 How does it find its native fold?
 How does it achieve its biochemical role?
 How is its function regulated?
 How does it interacts with other macromolecules?
 How is it related to other proteins?
 Where is it localized within the cell?
 What are its physico-chemical properties?

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