Elements, Atoms, and Atomic Structure

• Matter is anything with mass that takes up space.
• Elements are substances that cannot be broken down by chemical reactions and make up matter.
• Examples of elements include gold, copper, carbon, and oxygen.
• 25 of the 92 natural elements are essential for human life, and 17 are essential for plant life.

Key Elements

• Carbon (C), Oxygen (O), Hydrogen (H), and Nitrogen (N) make up 96% of an organism's mass.

Atomic Structure

• An element can't be broken down/converted into another substance
• The smallest unit of an element that retains its properties is known as the Atom
• 'C' represents both the element and the carbon atom.
• Subatomic particles include protons, neutrons, and electrons.
• Mass number represents the sum of protons and neutrons in an atom.
• Atomic number represents the number of protons in an atom

Atomic Components

• Number of protons is unique to each element
• Orbitals are 3D spaces where electrons are found in an atom.
• Each electron shell, also known as principal energy level, has a unique orbital structure and contains a fixed number of electrons.
• Different atoms contain varying numbers of electrons which fill electron shells starting from the nucleus outwards.
• Valence electrons are in the outermost of the electron shell (valence shell).
• The octet rule states that atoms of main-group elements tend to combine in a way that each has 8 valence electrons.

Compounds

• A compound contains two or more different elements combined in a fixed ratio.
• Examples of compounds include methane (CH4) and water (H2O).

Covalent Bonds

• Covalent bonds involve the sharing of electron pairs between atoms.
• Molecules consist of two or more atoms held together by covalent bonds.

Electronegativity

• Electronegativity measures an atom's attraction for electrons in a covalent bond.
• The higher the electronegativity, the stronger the pull an atom has on shared electrons.
• Electronegativity values (Pauling Scale) order: O > N >> S = C ≃ H = P

Covalent Bond Types

• Nonpolar covalent bonds occur when atoms have similar electronegativity, and electrons are shared equally.
• Polar covalent bonds occur when one atom is bonded to a more electronegative atom, resulting in unequal sharing of electrons.

Ionic Bonds

• Ionic bonds form when one atom strips an electron from another due to significant electronegativity differences.
• An ion is a charged molecule
• A cation is a positively charged molecule.
• An anion is a negatively charged molecule.
• Ionic bonds are formed via attraction between cations and anions.

Hydrogen Bonds

• Hydrogen bonds are non-covalent attractions between a slightly positive hydrogen atom in one molecule and a slightly negative atom in another.

Water Properties

• Water molecules have a polar arrangement of oxygen and hydrogen atoms.
• Hydrogen has a positive electrical charge and oxygen has a negative charge
• Water molecules dissociate with ionic compounds and break the ionic bond forming ions
• Water molecules (solvent) surround solute molecules (NaCl), forming hydrogen bonds, which leads to a hydration shell.
• Non-ionic molecules that are important to life can also be dissolved in water (proteins, polysaccharides, nucleic acids), but not lipids.
• Polar molecules have an uneven distribution of charges and can form hydrogen bonds.

Hydrophilic vs Hydrophobic

• Hydrophilic substances have an affinity for water, include ionic or polar substances, such as sugars and cellulose
• Hydrophobic substances do not have an affinity for water, include nonionic and non-polar substances with lots of C-C or C-H bonds.

Chemical groups

• Organic compounds contain carbon and hydrogen atoms.
• Organic chemistry known as "carbon based life"
• Carbon has 4 valence electrons in its outermost shell that can hold up to 8 electrons.
• Carbon usually shares electrons in covalent bonds
• The properties of an organic molecules depends on the arrangement of its carbon skeleton, as well as the chemical groups attached.
• ATP is crucial for energy in cellular processes and stands for Adenosine TriPhosphate.
• Hydrolysis is the process of breaking chemical bonds by adding water.

Important Chemical Groups

• The seven most important chemical groups in biological processes are:
• Hydroxyl
• Carbonyl
• Carboxyl
• Amino
• Sulfhydryl
• Phosphate
• Methyl