Chemistry of Life: Protons, Neutrons, and Electrons

Matter is composed of various elements.
There are four primary elements essential to life:
- 1. Carbon ( $C$ )
- 2. Hydrogen ( $H$ )
- 3. Oxygen ( $O$ )
- 4. Nitrogen ( $N$ )
These four elements together constitute $96.1\%$ of all living matter.
The specific properties of an element are determined by its unique atomic structure.

The atom is the smallest unit of an element.
Atoms are composed of three subatomic particles:
- Protons: Carry a positive charge ( $+$ ). The number of protons determines the atomic number ( $Z$ ).
- Neutrons: Carry no charge (neutral). They contribute only to the atomic mass.
- Electrons: Carry a negative charge ( $-$ ).
An atom is considered neutrally charged when the number of electrons is equal to the number of protons.

Different isotopes of an element vary in their number of neutrons.
Because isotopes vary in neutron count, they also vary in mass.
A "heavier" isotope is one that contains a greater number of neutrons.
Atomic Number: This value represents the number of protons in an atom. In the case of Carbon ( $C$ ), the atomic number is $6$ .
Atomic Mass: This value is the average mass of all naturally occurring isotopes of an element. In the case of Carbon ( $C$ ), the atomic mass is $12.011$ .

Electrons exist in specific layers known as shells.
- The first shell can hold a maximum of $2$ electrons.
- The second and third shells can each hold a maximum of $8$ electrons.
Valence Shell: This is the outermost electron shell of an atom.
The behavior of an atom is dictated by its valence electrons:
- Full Valence Shell: The atom is unreactive (stable).
- Incomplete Valence Shell: The atom is reactive.
When atoms interact to form chemical bonds, they share valence electrons.
Interaction only occurs between unpaired valence electrons.

Definition of Electronegativity: The tendency of an atom to attract electrons toward itself when it forms a chemical bond.
Electronegativity is primarily determined by atomic radius, not just the number of electrons.
Smaller atoms tend to possess higher electronegativity. This occurs because the bonding/valence electrons sit physically closer to the positive nucleus.
Factors influencing pull:
- More rings of electrons results in less positive pull on the outer shells due to increased distance from the nucleus.
- A higher number of protons creates a stronger positive pull on electrons.

Ionic bonding is characterized by the complete transfer of an electron from one atom to another.
This process involves an "electron thief"—the atom with significantly higher electronegativity.
Cation: An atom that has lost an electron and remains with a full positive ( $+$ ) charge. A specific case is Hydrogen ( $H$ ), which, upon losing its single electron, is essentially just a proton.
Anion: An atom that has gained an electron and remains with a full negative ( $-$ ) charge.
One atom becomes fully positive while the other becomes fully negative.
Biological Application: Protective folding in proteins can occur so that a full positive charge can interact with a full negative charge part of the protein through an ionic bond.
Example Case: Ammonium ( $NH_4^+$ ) is a cation. While Nitrogen typically forms only three bonds, this represents a special case where it forms four.
Cations and anions can form ionic bonds with each other, though an ionic bond is not strictly required to exist as a cation or anion.

Covalent bonding is defined by the sharing of electrons between atoms rather than a full transfer.
The goal of covalent bonding is for both participating atoms to end up with full valence shells.
Partial Charges: These are denoted as partial positive ( $\delta+$ ) and partial negative ( $\delta-$ ) and are based on the electronegativity difference between the bonded atoms.
In covalent bonds, the electronegativity difference is not large enough to cause a complete transfer, but both atoms still exert a pull to fill their shells.
Hydrogen ( $H$ ) can form covalent bonds with itself ( $H-H$ ) or with other elements like Chlorine ( $Cl$ ) to form $HCl$ .

Q: How many valence electrons are in Carbon?
- A: Carbon has $4$ valence electrons.
Q: Based on unpaired valence electrons, how many bonds would Nitrogen ( $N$ ) typically form?
- A: Nitrogen typically forms $3$ bonds.
Note on Hydrogen ( $H$ ): If Hydrogen loses its single bonded electron, it is referred to simply as a "proton."
Note on Nitrogen ( $N$ ): Although Nitrogen typically makes 3 bonds, in the case of ammonium figures, it is shown making four bonds, which is noted as a special case.