AP Biology Unit 1: Chemistry of Life

• AP Biology Unit 1 covers essential chemistry for biology, focusing on water properties, hydrogen bonding, elements of life, and biomolecules.
• The four biomolecule families crucial to living things: carbohydrates, lipids, proteins, and nucleic acids (DNA and RNA).
• A study checklist is available at AP bios to aid in test preparation for Unit 1 and the AP Bio exam.

Water and Hydrogen Bonding

• Water is a polar molecule due to unequal electron sharing between oxygen (partial negative charge) and hydrogen (partial positive charge).
• Hydrogen bonds are intermolecular bonds, forming between molecules, unlike covalent or ionic bonds which are intramolecular.
• Hydrogen bonds form between the partially negative oxygen of one water molecule and the partially positive hydrogen of another.
• Hydrogen bonds are weaker than covalent and ionic bonds.
• Hydrogen bonds are crucial in biology, not just within water.
• Hydrogen bonds are key to the structure of DNA, RNA, and proteins.
• In DNA, hydrogen bonds form between nitrogenous bases like adenine and thymine, holding the DNA strands together.
• Cohesion is the attraction between water molecules due to hydrogen bonds.
• Cohesion gives water a high heat of vaporization, high specific heat, and high surface tension.
• Adhesion is water's attraction to other substances.
• In plants, adhesion helps water stick to the cellulose walls of xylem, aiding transpiration (water moving up the plant).
• Surface tension is the force exerted by water molecules at the surface, creating a "net" that allows small objects to rest on it.
• Acidic solutions have more hydrogen ions (H+) than hydroxide ions (OH-), resulting in a pH below 7.
• Basic solutions have more hydroxide ions (OH-) than hydrogen ions (H+), resulting in a pH above 7.
• While direct pH questions might not be common on the AP exam, understanding pH as an underlying concept is crucial.

Elements of Life

• Key elements in living organisms (CHNOPS): carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur.
• Carbon is central to all molecules in living things.
• Hydrogen is used for energy exchange in molecules like NAD+/NADH, crucial for ATP synthesis and acidity/alkalinity.
• Phosphorus is found in phosphate groups, like those in ATP.
• Interconnected knowledge (e.g., phosphorus in ATP and DNA) is essential for success in AP Biology.

Monomers and Polymers/Functional Groups

• Biomolecules (carbohydrates, proteins, nucleic acids) are built from smaller monomers.
• Living things build macromolecules (proteins, nucleic acids, polysaccharides) with specific 3D shapes, determining function.
• Monomers are like Legos; they combine to create larger polymer structures.
• Each unspecified vertex in a structural formula represents a carbon atom.
• Dehydration synthesis: Enzymes remove a water molecule (H2O) to join monomers, creating a bond.
• Hydrolysis: Enzymes insert a water molecule to break the bond between monomers in a polymer.
• The suffix "-lyse" in biology indicates breaking.
• Functional groups are unlikely to directly appear on the AP Bio exam.
• Functional Groups are important for understanding molecules in biology.
• Phosphate groups (in ATP) are key for energy exchange and energize DNA monomers.
• Methyl groups silence DNA and make molecules nonpolar/hydrophobic.
• Hydroxyl and carbonyl groups make molecules hydrophilic/water-soluble.
• Carboxyl and amino groups are essential in amino acids.
• Sulfhydryl groups stabilize protein structure with bonds for specific 3D shapes.
• Acetyl groups activate DNA through acetylation.

Carbohydrates and Lipids

• Four major types of macromolecules: carbohydrates, lipids, proteins, and nucleic acids.
• Carbohydrates:
  • Monosaccharides are simple sugars like glucose (fuel of life).
  • Disaccharides (e.g., lactose) consist of two linked monosaccharides.
  • Polysaccharides store energy (starch in plants, glycogen in animals) or provide structure (cellulose in plant cell walls).
• Humans cannot digest cellulose for food energy due to the lack of enzymes to break the bonds between glucose monomers.
• Termites and ruminants have symbiotic relationships with microorganisms that can break the bonds in cellulose.
• Lactose Tolerance:
  • Lactose is the sugar in milk.
  • Lactase is the enzyme that hydrolyzes lactose into monosaccharides.
  • Most mammals only produce lactase during infancy.
  • Some human groups (pastoralists) evolved mutations to continue lactase production into adulthood.
  • Lactase persistence is widespread in specific areas, not globally, with large populations remaining lactose intolerant as adults.
  • Lactate products containing lactase is used as additives to food and helps break lactose down into lactose and glucose..
• Lipids:
  • Lipids are nonpolar/hydrophobic.
  • Lipids are not composed of repeating monomers but may have subunits.
  • Functions include: energy storage (fats/triglycerides), waterproofing (waxes), cell membranes (phospholipids), and signaling (steroid hormones).
• Phospholipids:
  • Hydrophobic tails and hydrophilic heads connected by glycerol.
  • Spontaneously form bilayers in water, with heads interacting with water and tails avoiding it.
  • Phospholipid bilayers form the structural framework of cell membranes.

Proteins

• Monomer is an amino acid with a central carbon.
• The central carbon is connected to an amine group (basic), a carboxyl group (acidic), a hydrogen atom, and an R-group (variable).
• There are 20 common amino acids in all life, with different R-groups.
• Four levels of protein structure: primary, secondary, tertiary, and quaternary.
• Primary: linear sequence of amino acids determined genetically.
• Secondary: interactions involving the polypeptide backbone.
  • Hydrogen bonds between carboxyl and amine groups stabilize shapes like alpha helices (corkscrew) and beta pleated sheets (parallel or anti-parallel).
• Tertiary: interactions between R-groups/side chains.
  • Hydrogen bonds, ionic bonds, covalent bonds (disulfide bridges between sulfhydryl groups), and hydrophobic clustering.
  • Myoglobin is an example of a tertiary protein that exists within muscle tissue
  • Hydrophobic bonds causes the formation of fibres within cells and causes spike to form.
• Quaternary: interactions between multiple folded tertiary peptides.
  • Spike protein on SARS-CoV-2 is a quaternary protein.
• Hemoglobin Structure and Function/Sickle Cell Anemia:
  • Hemoglobin is a quaternary protein.
  • Hemoglobin helps transport oxygen in red blood cells.
  • Sickle cell disease is caused by genetics
  • A mutation of the gene causes veine to substitute glutamic acid.
  • Valine is nonpolar; glutamic acid is acidic.
  • Mutation causes hydrophobic bonds to form between hemoglobin molecules when blood is deoxygenated.
  • Fibers develop, cells become sickle-shaped, clump in arteries, cause pain, and damage tissues.
  • Sickle cell disease can now be managed with good medical care.
  • Gene therapy is being researched.
  • Sickle cell trait (one copy of the gene) provides resistance to malaria.

Nucleic Acids

• DNA and RNA:
• Nucleic Acids are molecules of genetic information.
  • DNA is the molecule of heredity passed from generation to generation.
  • RNA is the hereditary molecule in some viruses.
    • RNA's key role is information transfer (messenger RNA). - Cell processes: DNA (repository of information) -> RNA (transcription) -> Protein (translation and ribosome activity).
• RNA is a very versatile molecule, that can take many forms and act as an enzyme catalyzing reactions.
• ATP is a nucleotide monomer, also one of the monomers in RNA.
• Nucleotide Structure (monomers):
  • Consist of a five-carbon sugar, a phosphate group, and a nitrogenous base
  • The phosphate group is connected to a number 5 carbon.
  • The nitrogenous bases is connected to a number 1 carbon.
• DNA vs. RNA Sugars: - DNA uses deoxyribose as its sugar. - RNA uses ribose as its sugar.
• Nitrogenous bases in DNA: adenine (A), thymine (T), cytosine (C), guanine (G).
• Nitrogenous bases in RNA: uracil (U), cytosine (C), guanine (G).
• DNA Structure:
  • Two nucleotide strands connected by sugar-phosphate bonds within each strand.
  • The strands connect to one another by hydrogen bonds
  • Hydrogen bonds connect strands: A with T, C with G (memorize the rules).
  • Strands are anti-parallel.
• DNA Directionality:
  • Enzymes (DNA polymerase) can only add new nucleotides at the 3' end of a growing strand.
  • Nucleic acids are built in the 5' to 3' direction.