APR ASSIGNMENT. Comprehensive Notes on Atomic Structure, Bonding, Organic Molecules, Electrolytes, and Enzymes
Atoms and Atomic Structure
An atom is the smallest particle of an element that retains the properties of that element.
Subatomic particles:
Protons: positively charged, +1.
Neutrons: neutral, no charge.
Electrons: negatively charged, −1; move around the nucleus in concentric regions called electron shells or energy levels.
The central nucleus contains protons and neutrons; electrons occupy regions around the nucleus.
An element is uniquely defined by the number of protons in its atoms.
Example: only carbon atoms have 6 protons; only potassium atoms have 19 protons.
The atomic number Z is the number of protons in an atom of a particular element.
In a neutral atom, the number of protons equals the number of electrons, so the overall charge is zero.
Atomic mass is the sum of an atom’s protons and neutrons:
A = Z + N
The number of neutrons (N) can vary for a given element, giving different atomic masses (isotopes).
Isotopes: atoms with the same atomic number Z but different atomic weights (A) due to differing numbers of neutrons.
Electron shells are filled in fixed numbers:
1st shell (closest to the nucleus) holds a maximum of 2 electrons: 2
2nd shell holds up to 8 electrons: 8
3rd shell can hold up to 18 electrons: 18
Subsequent shells can hold higher numbers.
The outermost shell is the valence shell and holds a maximum of 8 electrons (octet rule).
The electrons in the valence shell determine an atom’s chemical bonding properties.
Stable structures: atoms with filled valence shells (e.g., helium) are chemically inactive.
Atoms with partially filled valence shells tend to lose, gain, or share electrons to achieve a stable valence electron count.
Bond formation basics:
Ionic bonding: octet is formed by transferring valence electrons from one atom to another, creating ions that are held together by electrostatic attraction.
Covalent bonding: octet is formed by sharing valence electrons between atoms.
Key example: ionic bonding (Na and Cl)
Sodium (Na) has one valence electron, chlorine (Cl) has seven valence electrons.
If Na transfers one electron to Cl, both achieve an octet and form ions: ext{Na}
ightarrow ext{Na}^+ + e^- \ ext{Cl} + e^-
ightarrow ext{Cl}^-The resulting ionic bond is the electrostatic attraction between ext{Na}^+ and ext{Cl}^- in the compound NaCl.
Covalent bonding examples:
Nonpolar covalent bond: sharing of electrons equally; electron density is symmetrical. Example: ext{Cl}_2 (two chlorine atoms share electrons equally).
Polar covalent bond: one atom attracts the bonding electrons more strongly (higher electronegativity), leading to an unequal sharing and partial charges. Example: hydrogen chloride (HCl): chlorine is more electronegative, so the electrons spend more time near Cl, giving:
partial negative charge on Cl (δ⁻)
partial positive charge on H (δ⁺)
Hydrogen and electronegativity concept:
Hydrogen has only one valence electron (and seeks a second to complete its valence shell, like helium).
In H–Cl, chlorine’s greater attraction for electrons creates a polar covalent bond with unequal electron sharing.
Bonding summary:
Ionic bonds form when electrons are transferred to achieve octets, with electrostatic attraction between ions.
Covalent bonds form when electrons are shared to achieve octets; can be nonpolar (equal sharing) or polar (unequal sharing).
The number and type of bonds an atom forms depend on the valence electrons needed to fill the valence (outer) shell.
Electrons, Bonding, and Electronegativity in Water and Ions
The distribution of electrons around atoms in a bond influences polarity and reactivity.
The most electron-rich region is often represented as red, while electron-poor regions may appear blue in visualizations (conceptual).
Hydrogen–chlorine examples illustrate two extremes:
Nonpolar covalent bond (e.g., Cl–Cl): electrons shared equally; no permanent dipole.
Polar covalent bond (e.g., H–Cl): electrons drawn toward the more electronegative atom (Cl), creating partial charges and a dipole.
In any given bond, electronegativity differences drive bond type and polarity, affecting molecular interactions and properties in solution.
Organic Molecules and Biological Macromolecules
Organic molecules are compounds found in or produced by living things and typically contain carbon.
Carbon’s tetravalence allows it to form long chains or backbones by bonding with itself and other elements, enabling the vast diversity of biomolecules.
Carbohydrates
General formula: empirical ratio H: C: O ≈ 2:1:1; for example, glucose: ext{C}6 ext{H}{12} ext{O}_6
Carbohydrates have a two-to-one ratio of hydrogen to carbon and oxygen when expressed as H:C:O ≈ 2:1:1.
Functions: important energy sources for cells.
Proteins
Built from amino acids; each amino acid has:
A central carbon atom (the α-carbon)
A hydrogen atom
An amino group (–NH₂)
A carboxyl group (–COOH)
A radical (side) group (R) that differentiates each amino acid
Amino acids join to form peptides; longer chains form polypeptides; groups of polypeptides form proteins.
Proteins have complex folded structures that determine their function.
Functions include:
Structural support
Regulation of body processes
Transport of molecules
Catalysis of chemical reactions
Defense against invaders
Muscle contraction
Cell-to-cell binding
Lipids
Organic molecules composed mainly of carbon, hydrogen, and oxygen.
Fatty acids: carboxyl group, hydrocarbon chain, and a methyl group.
Triglycerides: three fatty acids bonded to a glycerol molecule.
Roles: energy storage and thermal insulation in body fat.
Lipids are generally hydrophobic due to long hydrocarbon chains.
Nucleic acids
Comprised of repeating units called nucleotides.
Each nucleotide has three components:
A monosaccharide (sugar)
A nitrogen-containing ring (nitrogenous base)
One or more phosphate groups
Nucleic acids (e.g., DNA) are important for the storage and transmission of genetic information.
Simple biochemical interactions in solution
An electrolyte is a substance that, when dissolved in water, yields a solution capable of conducting electricity.
The light bulb example illustrates that a solution containing many ions conducts electricity well (strong electrolyte).
In solvation, polar water molecules orient around ions:
Positive ends of water (hydrogen sides) attract negative ions (e.g., Cl⁻).
Negative ends of water (oxygen side) attract positive ions (e.g., Na⁺).
Dissociation of salts:
For sodium chloride in water:
ext{NaCl}{(s)} ightarrow ext{Na}^+{(aq)} + ext{Cl}^-_{(aq)}
This ionization leads to a large number of free ions and strong electrical conduction.
Carbon dioxide in water and carbonic acid
Carbon dioxide dissolves in water to form carbonic acid:
ext{CO}2 + ext{H}2 ext{O}
ightleftharpoons ext{H}2 ext{CO}3Carbonic acid (H₂CO₃) is a weak acid that only partially ionizes in water, making it a weak electrolyte.
At equilibrium, the solution contains mostly nonionized H₂CO₃ and small amounts of ions:
ext{H}2 ext{CO}3
ightleftharpoons ext{H}^+ + ext{HCO}_3^-
Glucose in water
Glucose does not dissociate into ions in water; it is a nonelectrolyte.
Glucose contains many polar –OH groups; the oxygen bears partial negative charges and hydrogens bear partial positive charges, forming a molecular dipole.
Water (also polar) interacts with glucose via dipole–dipole attractions and hydrogen bonding:
These interactions help break glucose–glucose attractions and allow glucose to dissolve, while covalent glucose molecules remain intact.
By comparison, ionic compounds like NaCl dissociate into ions in solution.
Hydrogen bonding and dipole interactions
Dipole-dipole attractions occur between polar molecules (e.g., water–glucose).
Hydrogen bonds are a specific, strong type of dipole–dipole interaction between a hydrogen atom bonded to a highly electronegative atom (e.g., O, N) and a lone pair on another electronegative atom (often O in water or glucose).
These interactions contribute to solubility and the physical properties of water, glucose, and other polar molecules.
Enzymes: biological catalysts
Enzymes are proteins that speed up chemical reactions in the cell.
The active site is a special region whose shape fits specific substrate molecules.
Mechanism:
Substrates bind at the active site to form an enzyme–substrate (ES) complex:
E + S
ightleftharpoons ES
The enzyme stabilizes the transition state, stresses or weakens certain chemical bonds, and promotes a chemical transformation to form a product:
ES
ightarrow E + P
The enzyme returns to its original shape after the reaction and can catalyze additional reactions.
Some enzymes can catalyze two products from a single substrate, illustrating versatility in catalytic outcomes.
Connections to broader concepts
Atomic structure underpins chemical bonding, reactivity, and the formation of molecules essential for life.
The octet rule (valence electrons) governs the stability of atoms and the types of bonds formed.
Water’s polarity and hydrogen-bonding capability are central to solubility, acid-base behavior (e.g., carbonic acid), and biochemical interactions.
The four major biomolecule classes (carbohydrates, proteins, lipids, nucleic acids) form the basis of cellular structure and function.
Enzymes exemplify how protein structure determines function and how biochemical reactions are regulated in living systems.