Chemistry of Amino Acids

L24 - Chemistry of Amino acids,L25 - Making and breaking biological outcomes

Why are proteins important in pharmacokinetics?

• Drug metabolism is controlled by proteins

• Proteins transport drugs in the body

• Plasma protein binding affects distribution and half life

What are α-amino acids?

The monomers from which proteins are built

What does ionisation state mean?

The ionisation state describes the overall electrical charge a functional group or molecule has at a given pH (tells you how many e^- an atom has lost, gained, or shared, compared to its neutral form).

What does pKa mean relative to 0?

The acid with the LOWER pKa is the STRONGER acid

• pKa value less than 0 is a very strong acid

  • HCl has a pKa of -6

• pKa value around 0 is a strong acid

• pKa value higher than 0 is a weaker acid

What are the ionisation states of glycine?

Explain this

It shows how protonation states change with pH.

• Low pH: –NH₃⁺ / –COOH (net +1)

• Mid pH: –NH₃⁺ / –COO⁻ (zwitterion, net 0)

• High pH: –NH₂ / –COO⁻ (net –1)

• Carboxyl group deprotonates first (lower pKa), amino group deprotonates last (higher pKa).

Define a zwitterion

A molecule with functional groups, of which at least one has a positive and one has a negative charge. The net charge of the molecule is zero.

What is the isoelectric point (pI)?

The pH at which a particular molecule carries no charge

What does ionisation of side chains mean?

• Refers to whether the R group gains or loses H⁺ at a given pH

• Each ionisable side chain has its own pKa, which determines the pH at which it gains or loses H⁺

Are amino acids chiral molecules?

Yes

What is L/D nomenclature?

L/D nomenclature tells you whether the NH₂ is on the left (L) or right (D) in a Fischer projection.

What is the reference molecule for L/D nomenclature?

Glyceraldehyde

Draw L-lysine and D-lysine

How are peptide bonds formed?

Carboxyl group of one amino acid reacts with the amino group of another amino acid

What is an amino acid unit in a peptide/polypeptide chain called?

A residue

What geometric isomers are possible for peptide bonds?

Cis / trans

Why do peptide bonds prefer trans conformation?

In the cis form, there are unfavourable steric clashes

What is hydrogen bonding?

The electrostatic attraction between a lone pair of electrons on an electronegative atom and a hydrogen atom bonded to an electronegative atom.

H bond donor Vs H bond acceptor

What is the hydrophobic effect in proteins?

Hydrophobic regions of a protein cluster together to minimise interactions with water.

Are proteins clustering together to minimise interactions with water an entropic effect or a formal interaction?

Entropic effect

How does entropy increase with hydrophobic regions in proteins clustering together?

• At first, it is ordered, has lower entropy, and this is disfavoured. There’s a limited number of conformations for water molecules to maintain hydrogen bond network

• Then it is less ordered, higher entropy, and this is favoured. Reduction in size of hydrophobic water interface leads to fewer ordered water molecules

What are Van der Waals interactions?

• The interaction between uncharged atoms held in proximity

• Many weak interactions produce significant cumulative stability

• Facilitates the dense packing of protein hydrophobic cores

What are ionic interactions?

Oppositely charged amino acid sidechains held in proximity will form electrostatic interactions

What are disulfide bonds?

• Covalent bond linking together 2 cysteine residues

• Not every cysteine in a protein forms a disulfide

What are Pi-interactions?

Non covalent interaction involving the electron density of aromatic rings

• Phe, Tyr, and Trp residues in proteins

What type of Pi-interactions exist?

• Pi stacking

• Cation-Pi interactions

What is cation-pi interactions?

When a positively charged group interacts with the electron density of an aromatic ring

What does PTMs stand for?

Post-translational Modifications

What are PTMs?

• Chemical changes which occur after a protein has been synthesised

• The change in protein structure alters the function, stability, and / or cellular localisation

Are PTMs typically reversible?

Yes

What are a few examples of PTMs?

Protein function can be modulated by PTM such as:

• Addition of small chemical groups like phosphorylation

• Glycosylation, which is the addition of sugar molecules which can alter protein folding

How does TFEB activity and function get regulated in cells?

• TFEB is a transcription factor that controls autophagy.

• Its activity is regulated by cellular signalling, which determines whether it is active or inactive.

• Post-translational modifications (like phosphorylation) change TFEB’s structure.

• Structural changes alters where a protein is located in the cell, which affects its function.

• Phosphorylation increases TFEB’s binding affinity, influencing its activity.

Protein dysfunction is a common cause of what?

disease

Other than PTMs, what else can change the physicochemical properties of proteins?

Mutations and environmental damage

What is “binding specificity” in amino acids?

A protein only binds molecules that fit its shape and match its chemical properties

How do amino acids in the binding site determine binding specificity?

• The binding site has a specific shape

• It also has favourable interactions (i.e. hydrogen bonds, ionic interactions, hydrophobic contacts)

• Only molecules that complement these features can bind effectively.

DHFR reduces dihydrofolate to tetrahydrofolate using NADPH.

How is the substrate binding stabilised?

• Hydrogen bond network (enzyme–substrate–water)

• π-stacking with an active-site phenylalanine

• Ionic interaction between substrate carboxylate and arginine

What is protein dysfunction?

Proteins must fold correctly and maintain chemical properties to perform biological function

Protein dysfunction leads to disease, since it changes stability, structure, activity, binding, and / or abundance

What 3 ways do mutations affect proteins?

• Loss of function

• Gain of function

• Altered expression

How can mutations lead to a loss of function?

Changes in amino acids lead to a loss of catalytic activity, reduced binding, or structural destabilisation

How can mutations lead to a gain in function?

Changes in amino acids lead to new interactions or aggregation

How do mutations lead to altered expressions?

Too much or too little protein activity alters the biochemical pathways

Name the factors of the environment that damages proteins

• Oxidation

• UV

• Reactive metabolites

• pH changes

Environmental damage (oxidation, UV, reactive metabolites, pH changes) do what to proteins?

Produces altered protein chemistry

What is the structure of haemoglobin?

• Quaternary structure

• 4 subunits

• Each subunit contains a haem group that binds oxygen

What is the function of haemoglobin?

It is an oxygen transport protein located in red blood cells

How does the mutation in sickle cell disease affect haemoglobin and red blood cells?

• Sickle cell disease is caused by a single amino acid substitution, where glutamic acid is replaced by valine (E6V).

• The substitution creates a hydrophobic patch on the surface of haemoglobin

• The hydrophobic patch causes abnormal protein–protein interactions

• As a result, haemoglobin aggregates and forms polymeric fibres

• These fibres distort the red blood cells into a sickle cell shape, blocking capillaries and reducing oxygen delivery

Why do drugs act on proteins?

Drugs act on proteins in order to:

• Antagonise overactive proteins

• Agonise underactive proteins

• Degrade overexpressed proteins

• Prevent/reverse misfolding

• Rebalance signalling pathways

How can somatostatin biology be used for targeted cancer therapy?

• Somatostatin is an inhibitory peptide hormone that signals through specific somatostatin receptors

• These receptors are overexpressed in some neuroendocrine tumours

• A somatostatin-like peptide can be used to target tumour cells

• When this peptide is linked to a radionuclide, it delivers localised radiation, allowing selective cancer cell killing whilst sparing the tissue

Explain how DPP-4 inhibitors improve glucose control in type 2 diabetes.

• GLP-1 suppresses glucagon (this is good)

• DPP-4 degrades GLP-1

• Therefore, DPP-4 inhibitors prevent GLP-1 breakdown, prolonging GLP-1 action

• This increases insulin release and improves glucose homeostasis

• Demonstrates targeting a regulatory enzyme rather than the primary defect