Atomic Structure and Chemical Bonds Flashcards
Describe the basic structure of an atom?
An atom contains a nucleus which contains protons and neutrons.
These are surrounded by an orbit of electrons.
The nucleus is tiny, however as protons and neutrons are heavy and account for 99.9% of the atoms mass.
Different elements contain different numbers of protons.
What are neutrons and protons made up of?
Neutrons and protons are collectively made up of Fermions.
Fermions can be categorised as quarks (which are charged) or leptons (which are neutral).
Quarks and leptons interact via force carrying particles known as bosons.
How are electrons distributed in an atom?
Electrons are in orbitals around the nucleus of an atom.
These orbitals are on different energy levels.
The lowest energy level orbital is 1.
Orbitals can be spherical denoted by an S.
Or they can be denoted by the letter P where there shape resembles ∞ with the 2 orbital lobes either side of the orbital node at the nucleus.
What is a photon?
A photon is an elementary particle which makes up a quantum (tiny proportion) of an electromagnetic field.
What happens when electrons change to a higher energy level obital?
As electrons become excited they will jump to a higher energy level orbital, as an electron transitions back to its original energy orbital a photon is emitted.
This occurs as one of the key features of quantum mechanics is that matter acts as both a particle and a wave.
What is an isotope?
An isotope is an atom of the same element which contains a different number of neutrons.
I.e. Carbon 12 is the most abundant form or carbon it contains 6 protons, 6 neutrons and 6 electrons.
Carbon 14 is an isotope of Carbon and contains 6 protons, 8 neutrons and 6 electrons.
Note an element is dictated by the number of protons it contains. Protons = electrons as charges are balanced.
What is an Ionic bond?
A type of intramolecular bond.
Atoms want to be stable and therefore will tend towards there lowest energy orbital and want to have a full orbital. Because of this they either donate/receive electrons OR share electrons.
Ionic Bonds: are when an intramolecular bond is formed when one atom donates an electron and the other receives an electron, there is then an electrostatic force holding the 2 atoms together. E.g. NaCl (In this example Na is the electron donor and Cl the electron receiver)
What is a Covalent bond?
A type of intramolecular bond.
Atoms want to be stable and therefore will tend towards there lowest energy orbital and want to have a full orbital. Because of this they either donate/receive electrons OR share electrons.
Covalent bonds occur when to atoms share a pair of electrons forming a intramolecular bond. The more pairs of electrons that are shared the stronger the bond.
Covalent bonds are stronger and less reversible than ionic bonds.
How can covalent bonds be broken down in the body?
Covalent bonds are strong and stable and therefore are not involved in many drug interactions.
However enzymes can break them down. The intermediates from the breakdown can form new bonds which can have clinical consequences.
What occurs in paracetamol overdose?
Paracetamol is a covalently bonded molecule.
As paracetamol is metabolised 3 metabolites are formed.
Two of which are non toxic the third is N-acetyl-p-benzoquinone imine (NAPQI), which is produce in very small quantities.
When a therapeutic dose of paracetamol is taken the NAPQI undergoes glutathione-dependent conjugation reactions to two non-toxic metabolites.
However in overdose the glutathione becomes deplete so that the NAPQI cannot be metabolised. Leading to hepatoxicity.
N- Acetyl Cysteine (NAC) is used as a treatment as it acts as a glutathione donor preventing NAPQI accumulation.
How do organophosphate compounds cause toxicity (pesticides/nerve gas)?
They form covalent bonds with cholinesterases, leading to excess ACh at the neuromuscular junction and a cholinergic crisis.
What are the different types of intermolecular forces?
Hydrogen Bonds:
This is when a hydrogen atom (+ve) covalently binds to a more electronegatively charged atom to create the initial strong dipolar
attractive force.
Hydrophobic bonds:
Interaction between non-polar molecules to exclude water molecules between them. This occurs to allow molecules to achieve a lower energy state.
Van der Vaals:
These are attractions that occur between the electron clouds of neighbouring atoms that aren’t very strong.
Repulsive Forces:
Electrostatic and dipole repulsion both influence the shape of molecules. RBCs cannot aggregate as their charge keeps them apart.
Electrostatic/ionic binding:
Results from binding of oppositely charged molecules. The pH of the environment affects the
acidity/alkalinity of a molecule (proton donor/acceptor respectively)
