Atoms, Ions, and Molecules: Comprehensive Notes

Matter, Atoms, and Elements

• The human body is made of matter in three forms:

  • Solid (like bone)

  • Liquid (like blood)

  • Gas (like oxygen)

• Matter is made of atoms, which are the smallest parts that show what an element is like.

Periodic Table

• Elements are organized in the periodic table by:

  • Chemical symbol: A short way to write the element's name (like C for carbon).

  • Atomic number: The number of protons in an atom, found above the element symbol. Elements are arranged by this number in rows.

  • Average atomic mass: The weight of protons and neutrons, shown below the element symbol.

Subatomic Particles

• Atoms have three smaller parts:

  • Protons: Have a positive charge (+1).

  • Neutrons: Have no charge.

  • Electrons: Have a negative charge (-1), and are in orbitals at different distances from the center of the atom.

Determining Subatomic Particle Numbers

• Number of protons = atomic number

• Number of neutrons ≈ number of protons

• Number of electrons = number of protons

Isotopes

• Isotopes: Different types of the same element with:

  • Same number of protons and electrons

  • Different numbers of neutrons

  • Almost the same chemical properties

Examples

• Carbon isotopes:

  • Carbon-12 (6 protons, 6 neutrons, 6 electrons) - most common

  • Carbon-13 (6 protons, 7 neutrons, 6 electrons)

  • Carbon-14 (6 protons, 8 neutrons, 6 electrons)

Radioisotopes

• Radioisotopes: Unstable isotopes with extra neutrons.

• They give off high-energy radiation (alpha particles, beta particles, gamma rays).

• Biological half-life (T1⁄2): The time it takes for half of the radioactive material to leave the body.

  • $T \frac{1}{2} (C^{14}) = 5730$ years

  • $T \frac{1}{2} (N^{16}) = 7.13$ seconds

  • $T \frac{1}{2} (Ba^{124}) = 10.6$ minutes

Medical Applications of Radioisotopes

• Radioisotopes are used for medical scans and treatments.

• Cells use radioisotopes like they use nonradioisotopes.

• They help follow how the body uses chemicals.

• Example: Using iodine radioisotopes to look at the thyroid gland.

Isomers

• Isomers: Molecules that have the same formula but are arranged differently.

• Isomers can have different chemical properties.

Examples

• Glucose, galactose, and fructose: All have the formula $C<em>6H</em>{12}O_6$.

Chemical Compounds and Bonds

• Chemical compounds: When two or more elements join together in a set way.

• Types of chemical bonds:

  • Ionic

  • Covalent

  • Hydrogen

Ions and Ionic Compounds

• Ions: Atoms that have a positive or negative charge because they have lost or gained electrons.

• Commonly used in the body for important jobs.

  • Example: $Na^+$ for sending electrical signals in nerves.

  • Example: $Ca^{2+}$ for blood clotting and muscle use.

  • Example: $Cl^−$ in stomach acid.

Common Cations & Their Physiological Significance

• Sodium Ion ($Na^+$)

  • Most common cation outside of cells.

  • Helps nerves send signals.

  • Helps water move in the body.

  • Helps move other things around.

• Potassium Ion ($K^+$)

  • Most common cation inside of cells.

  • Helps nerves send signals.

  • Helps store sugar in the liver and muscles.

  • Helps keep the body's pH balanced.

• Calcium Ion ($Ca^{2+}$)

  • Makes bones and teeth strong.

  • Helps muscles contract.

  • Helps cells release things.

  • Helps blood clot.

  • Acts as a messenger for hormones.

• Magnesium Ion ($Mg^{2+}$)

  • Needed to make ATP (energy).

• Hydrogen Ion ($H^+$)

  • Decides the pH of blood and body fluids.

Common Anions & Their Physiological Significance

• Chloride Ion ($Cl^−$)

  • Changes how nerves react.

  • Is part of stomach acid (HCl).

  • Helps red blood cells.

• Bicarbonate Ion ($HCO_3^−$)

  • Changes $CO<em>2$ into $HCO</em>3^−$ to move it in the blood.

  • Helps keep the blood's pH steady.

• Phosphate Ion ($PO_4^{3−}$)

  • Makes bones and teeth hard as $Ca<em>3(PO</em>4)_2$.

  • Is part of phospholipids.

  • Is part of nucleotides, like ATP, DNA, and RNA.

Ionic Bonds

• Ionic bonds happen when atoms give or take electrons, making ions that are attracted to each other.

  • Example: Making NaCl (table salt) from sodium (Na) and chlorine (Cl).

Covalent Bonding

• Covalent bond: Happens when atoms share electrons.

  • Happens when atoms need electrons.

  • Common in atoms with 4-7 electrons in their outer shell.

• Common elements in the body that make covalent bonds:

  • Oxygen (O)

  • Carbon (C)

  • Hydrogen (H)

  • Nitrogen (N)

Types of Covalent Bonds

• Single bond: Sharing one pair of electrons (like hydrogen gas, $H_2$).

• Double bond: Sharing two pairs of electrons (like oxygen gas, $O_2$).

• Triple bond: Sharing three pairs of electrons (like nitrogen gas, $N_2$).

• Example: Carbon dioxide ($CO_2$) molecules.

Nonpolar and Polar Covalent Bonds

• Nonpolar covalent bonds: Electrons are shared equally.

• Polar covalent bonds: Electrons are shared unequally, making partial charges ($\delta +$ and $\delta −$).

• Amphipathic molecules: Molecules with both polar and nonpolar parts (like phospholipids).

Hydrogen Bonds

• Hydrogen bond: A weak attraction between a slightly positive hydrogen atom and a slightly negative atom (like oxygen or nitrogen).

• Weak alone but strong together.

• Helps molecules have a 3D shape.

Interpreting the pH Scale

• pH scale goes from 0 to 14.

• Neutral solutions: Have the same amount of $H^+$ and $OH^−$, pH = 7.

• Acidic solutions: Have more $H^+$ than $OH^−$, pH < 7.

• Basic solutions: Have more $OH^−$ than $H^+$, pH > 7.

pH Values of Common Substances

• Acidic: Lemon juice (2-3), Tomato juice (4.7)

• Neutral: Pure water (7)

• Basic: Human blood (7.4), Seawater (8), Household ammonia (10.5-11), Sodium hydroxide (14)

• $[H^+]$ = hydrogen ion amount

• H^+ > OH^−: Acidic

• H^+ < OH^−: Basic

Buffers

• Neutralization: Making an acidic or basic solution neutral.

  • Acids are made neutral by bases.

  • Bases are made neutral by acids.

• Buffers: Help keep pH steady by taking $H^+$ from extra acid or giving $H^+$ to balance base.

  • Example: Carbonic acid (weak acid) and bicarbonate (weak base) buffer blood pH.

Biochemistry

• Organic compounds:

  • Have lots of carbon and hydrogen, joined by sharing electrons, often big.

• Inorganic compounds:

  • Don't have much carbon (usually just one).

  • Examples: Water, salts, acids, and bases

Organic Compounds

• Organic molecules have carbon.

• Biological macromolecules: Big organic molecules needed for life.

• Four main types:

  • Lipids

  • Carbohydrates

  • Nucleic acids

  • Proteins

Functional Groups

• Hydroxyl (-OH): Polar, dissolves in water better; in carbohydrates.

• Carbonyl (C=O): Polar, makes hydrogen bonds, dissolves in water better; in proteins, nucleic acids, lipids, and carbohydrates.

• Carboxyl (-COOH): Polar, acts like an acid; in proteins and lipids.

• Amine ($NH_2$): Polar, makes hydrogen bonds, dissolves in water better, acts like a base; in proteins and nucleic acids.

• Phosphate ($PO_4^{3−}$): Makes phosphodiester bonds; in nucleic acids, phospholipids, and ATP.

Carbohydrates

• Have carbon, hydrogen, and oxygen.

• Main job: Source of food for cells.

• Examples:

  • Monosaccharides (simple sugars)

  • Disaccharides (double sugars)

  • Polysaccharides (many simple sugars joined)

• Starch in potato cells

• Glucose

• Glycogen in muscle tissue

• Cellulose in plant cell walls

Lipids

• Different types of fatty compounds that don't dissolve in water.

• Not made of monomers.

• Jobs: Storing nutrients, making cell membranes, hormones.

• Four main types:

  • Triglycerides

  • Phospholipids

  • Steroids

  • Eicosanoids

Neutral Fats (Triglycerides)

• Made of three fatty acids joined to a glycerol molecule.

Phospholipids

• Like triglycerides but with two fatty acids and a phosphorus group.

• Have a polar "head" and a nonpolar "tail"

Steroids

• Ring-shaped, some are hormones.

• Made of hydrocarbons in a ring shape.

• Different because of the side chains on their rings.

• Examples: Cholesterol, steroid hormones (like testosterone), and bile salts.

• Cholesterol is in membranes and helps make other steroids.

Fatty Acids

• Saturated fats: Mostly animal fats; solid at room temperature.

• Unsaturated fats: Mostly vegetable fats; liquid at room temperature; usually healthier.

• Hydrogenation: Making unsaturated fats into saturated fats.

• Trans fats: Made by partially hydrogenating fats; can cause heart problems.

Nucleic Acids

• Nucleotide:

  • Sugar (five-carbon pentose)

  • Phosphate group

  • Nitrogenous base

Nitrogenous Bases

• Purines: Adenine (A) and Guanine (G)

• Pyrimidines: Cytosine (C), Thymine (T) (only in DNA), and Uracil (U) (only in RNA)

Types of Nucleic Acids

• Deoxyribonucleic acid (DNA):

  • Double-stranded.

  • In chromosomes in the nucleus and in mitochondria.

  • Has deoxyribose sugar, phosphate, and bases A, G, C, T.

  • Held together by hydrogen bonds (T with A, G with C).

• Ribonucleic acid (RNA):

  • Single-stranded.

  • In the nucleus and cytoplasm.

  • Has ribose sugar, phosphate, and bases A, G, C, U.

  • Three types: messenger RNA, transfer RNA, and ribosomal RNA

Adenosine Triphosphate (ATP)

• Made of adenine, ribose, and three phosphate groups.

• The cell's energy.

Proteins

• Made of amino acids.

• 20 different amino acids.

• Amino acids have an amine group and a carboxylic acid group.

Amino Acid Structure

• A carbon atom joined to:

  • Amine group ($NH_2$)

  • Carboxylic acid group (COOH)

  • Hydrogen (H)

  • R group (different for each amino acid)

• Peptide bonds join amino acids

  • N-terminal: the start of the chain

  • C-terminal: the end of the chain

Types of Amino Acids Based on R-Groups

• Nonpolar: Glycine, Valine, Isoleucine, Leucine, Phenylalanine, Tryptophan, Alanine, Methionine, Proline

• Polar: Serine, Threonine, Cysteine, Tyrosine, Glutamine, Asparagine

• Charged (Ionic):

  • Acidic (- charge): Aspartic acid and Glutamic acid

  • Basic (+ charge): Lysine, Arginine, Histidine