Medicinal Chemistry: Cell Structure

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Questions and Answers

What is the main function of the nucleus in a cell?

To synthesize proteins

To provide energy for the cell

To store carbohydrates

To act as the control center for the cell (correct)

Which of the following is NOT a type of protein that can be a drug target?

Receptors

Cell surface carbohydrates (correct)

DNA polymerase

Structural proteins

What is the typical molecular weight of a drug?

Several thousand atomic mass units

A few atomic mass units

Several million atomic mass units

A few hundred atomic mass units (correct)

What is the process by which a drug interacts with a macromolecular target?

Binding Signup and view all the answers

What is the typical bond strength of a covalent bond formed between a drug and a macromolecular target?

200-400 kJ mol^(-1) Signup and view all the answers

What is the function of the mitochondria in a cell?

To provide energy for the cell Signup and view all the answers

What is the typical strength range of ionic or electrostatic bonds?

20-40 kJ/mol Signup and view all the answers

What is a characteristic of hydrogen bond donors and acceptors?

They can act as both donors and acceptors Signup and view all the answers

Which of the following is an example of a macromolecule?

DNA Signup and view all the answers

What is the purpose of the binding site on a macromolecule?

To allow the drug to bind Signup and view all the answers

What is the typical nature of the binding sites of macromolecules?

Hydrophobic Signup and view all the answers

What is the result of the interaction between the orbital containing the lone pair of electrons and the atomic orbitals involved in the covalent bond?

A weak form of sigma (σ) bonding Signup and view all the answers

What is the typical environment where ionic interactions are stronger?

Hydrophobic environments Signup and view all the answers

What is the typical element that is electron-rich and has a lone pair of electrons?

Oxygen Signup and view all the answers

What is the term given to the characteristic of functional groups that can act as both hydrogen bond donors and acceptors?

Hydrogen bond flip-flop Signup and view all the answers

What is the typical type of bond that forms between the electron-rich heteroatom and the electron-deficient hydrogen?

Hydrogen bond Signup and view all the answers

What is the reason why fluorine does not participate in hydrogen bond interactions?

It clings tightly to its lone pairs of electrons Signup and view all the answers

Which of the following statements is true about phosphate ions?

They can act as good hydrogen bond acceptors Signup and view all the answers

What is the impact of electron density on a heteroatom's ability to act as a hydrogen bond acceptor?

The greater the electron density, the stronger the hydrogen bond Signup and view all the answers

Which functional groups are typically involved in moderately strong hydrogen bonds?

Ethers, alcohols, phenols, amides, amines, and ketones Signup and view all the answers

What is unique about the electron density in π systems?

It is diffuse Signup and view all the answers

Under what conditions can aromatic rings and alkynes act as significant hydrogen bond acceptors?

When interacting with a strong hydrogen bond donor Signup and view all the answers

What is the comparative ability of an aliphatic tertiary amine and an amide to act as a hydrogen bond acceptor?

The aliphatic tertiary amine is a better hydrogen bond acceptor Signup and view all the answers

What is the impact of the functional group on the ability of a carbonyl group to act as a hydrogen bond acceptor?

The functional group has a significant impact Signup and view all the answers

What is the primary difference between covalent bonds and intermolecular bonds?

Covalent bonds are stronger than intermolecular bonds Signup and view all the answers

What is the role of functional groups in the drug-target interaction?

They are involved in forming intermolecular bonds with the target binding site Signup and view all the answers

What is the term used to describe the study of how drugs interact with their targets through binding interactions?

Pharmacodynamics Signup and view all the answers

What is the significance of the number of intermolecular bonds involved in drug-target interaction?

It determines the duration of action of the drug Signup and view all the answers

What is the role of the carbon skeleton of the drug in binding to its target?

It is involved in forming intermolecular bonds with the target through van der Waals interactions Signup and view all the answers

What is the term used to describe the specific regions where intermolecular bonds take place between the drug and its target?

Binding regions Signup and view all the answers

What is the primary factor that determines the strength of intermolecular bonds?

The structure of the drug Signup and view all the answers

What is the outcome of the equilibrium between the drug being bound and unbound to its target?

The drug remains bound to its target for a certain period of time Signup and view all the answers

What is the optimal angle for the strongest hydrogen bonds?

180° Signup and view all the answers

What is the typical bond distance for hydrogen bonds?

1.5–2.2 Å Signup and view all the answers

What is the primary factor affecting the strength of a hydrogen bond?

The electronegativity of the hydrogen bond acceptor Signup and view all the answers

Which of the following atoms is a weak hydrogen bond acceptor due to its larger and more diffuse orbitals?

Sulfur Signup and view all the answers

How many hydrogen bonds can oxygen typically accept?

Two Signup and view all the answers

What is the typical strength range of hydrogen bonds in drug–target interactions?

10–60 kJ mol−1 Signup and view all the answers

Why is fluorine a weak hydrogen bond acceptor despite being highly electronegative?

Its orbitals are larger and more diffuse Signup and view all the answers

What is the primary characteristic of a good hydrogen bond acceptor?

High electronegativity Signup and view all the answers

Study Notes

Cell Structure

The nucleus is the 'control center' of the cell, containing the genetic code (DNA) that acts as a blueprint for constructing proteins.
Other structures within a cell include mitochondria, Golgi apparatus, and endoplasmic reticulum.
Different drugs act on molecular targets located in different parts of the cell.

Drug Targets

Lipids: Cell membrane lipids
Proteins: Receptors, Enzymes, Transport proteins, Structural proteins
Nucleic acids: DNA & RNA
Carbohydrates: Cell surface carbohydrates, Antigens and recognition molecules

Drug Targets at the Molecular Level

Main molecular targets for drugs are proteins (enzymes, receptors, and transport proteins) and nucleic acids (DNA and RNA).
These macromolecules have molecular weights in the order of several thousand atomic mass units.
Typical drugs have a molecular weight in the order of a few hundred atomic mass units.

Drug/Macromolecular Target Interactions

The interaction of a drug with a macromolecular target involves binding.
Binding takes place at a specific area of the macromolecule, known as the binding site.
Some drugs react with the binding site and become permanently attached via a covalent bond (200-400 kJ/mol).
Most drugs interact through weaker forms of interaction, including intermolecular bonds.

Intermolecular Bonds

Intermolecular bonds are weaker than covalent bonds and can be formed and broken again.
Equilibrium takes place between the drug being bound and unbound to its target.
The length of time the drug remains at its target depends on the number of intermolecular bonds involved.

Binding Groups

Functional groups present in the drug can be important in forming intermolecular bonds with the target binding site.
Carbon skeleton of the drug also plays an important role in binding through van der Waals interactions.
The target binding site contains functional groups and carbon skeletons that can form intermolecular bonds with the drug.

Pharmacodynamics

The study of how drugs interact with their targets through binding interactions and produce a pharmacological effect is known as pharmacodynamics.

Intermolecular Bonding Forces

There are several types of intermolecular bonding interactions, including:
- Electrostatic or ionic bonds (20-40 kJ/mol)
- Hydrogen bonds (16-60 kJ/mol)
- Van der Waals interactions
- Dipole-dipole interactions
- Hydrophobic interactions

Electrostatic or Ionic Bonds

Ionic or electrostatic bonds are the strongest of the intermolecular bonds.
They take place between groups that have opposite charges, such as a carboxylate ion and an ammonium ion.
Strength of the interaction is inversely proportional to the distance between the two charged atoms and depends on the nature of the environment.

Hydrogen Bonds

Hydrogen bonds vary in strength (16-60 kJ/mol) and take place between an electron-rich heteroatom and an electron-deficient hydrogen.
Electron-rich heteroatom has a lone pair of electrons and is usually oxygen or nitrogen.
Hydrogen bond strength depends on the nature of the hydrogen bond acceptor and donor.
Optimum orientation is where the X-H bond points directly to the lone pair on Y (180°).

Hydrogen Bonds and Biological Systems

Nitrogen and oxygen are the most common atoms involved as hydrogen bond acceptors in biological systems.
Nitrogen has one lone pair of electrons and can act as an acceptor for one hydrogen bond; oxygen has two lone pairs of electrons and can act as an acceptor for two hydrogen bonds.
Sulphur is a weak hydrogen bond acceptor due to its large and diffuse orbitals.
Fluorine is a weak hydrogen bond acceptor due to its high electronegativity.

Hydrogen Bonds: General Features

Any feature that affects the electron density of the hydrogen bond acceptor affects its ability to act as a hydrogen bond acceptor.
Phosphate ions can act as good hydrogen bond acceptors.
Pi (π) systems present in alkynes and aromatic rings can act as weak hydrogen bond acceptors.

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Description

Learn about the structure of cells, including the nucleus, mitochondria, Golgi apparatus, and endoplasmic reticulum, and their roles in cellular functions.