Chemistry & Biomolecules Lecture 3

Lecture 3: Chemistry & Biomolecules

• Lecture 3 covered chemistry and biomolecules.
• Additional resources were provided for further study: Martini, Nath, and Bartholomew (2017), Fundamentals of Anatomy and Physiology, pages 27-40, and various OpenStax resources.
• Review of Lecture 3 and Assignment #2 (Chemistry) were assigned for the next class.
• Lab 2 (Bones of the Skeletal system) and Lab 3 (Joints) readings were also assigned.

Learning Objectives (Lecture 2)

• Review key chemical terms: atom, element, molecule, macromolecule, organic/inorganic compound, ionic bond, covalent bond, polar covalent, ion, acid, base, buffer, pH, and salt.
• Define terms: anabolism, synthesis, catabolism, and decomposition.
• Explain water's importance:
  • Describe water's structure.
  • Explain why water is a polar molecule (include a diagram).
  • Define and diagram a hydrogen bond.
  • List and explain the functions of water supporting life.
• Define monomer, polymer, and macromolecule.
  • Describe dehydration synthesis reactions using examples.
  • Describe hydrolysis reactions using examples.

Basic Particles of Matter

• Atoms: The smallest unit of matter retaining element properties. Made of protons, neutrons, and electrons.
• Elements: Pure substances of one atom type identified by atomic number (protons), found on the periodic table with chemical symbols (e.g., Oxygen, Hydrogen, Nitrogen).
• Molecules: Two or more atoms bonded together.
• Compounds: Formed when two or more different elements bond, all compounds are molecules but not all molecules are compounds (e.g., water, carbon dioxide).
• Matter: Anything that occupies space and has mass.

The Atom

• Bohr model resembles a solar system, with negatively charged electrons orbiting a dense nucleus.
• Nucleus contains positively charged protons and neutral neutrons.
• Quantum mechanics expanded understanding of atoms with orbital theory; existence of electron clouds.
• Atoms are mostly empty space.
• Mass of a proton and neutron is 1 atomic mass unit (amu).
• Electrons have no mass (0 amu).
• Atomic number = number of protons. This determines the atom's identity and arrangement on the periodic table.
• Atomic mass = sum of protons and neutrons.

Isotopes

• Isotopes are versions of atoms of the same element but have different numbers of neutrons.
• Different isotopes have different atomic masses.
• Some isotopes are stable, while others are radioactive and unstable.
• Radioactive isotopes have biological applications, like carbon dating for fossils, nuclear medicine, radioactive tracers, and radiotherapy.

Chemical Bonds

• Chemical bond: an attraction between atoms that holds them together
• Types of bonds:
  • Ionic bonds: complete electron transfer between atoms, forming ions.
  • Covalent bonds: atoms share electrons (polar and nonpolar- in polar covalent, electrons are shared unevenly).
  • Hydrogen bonds: weak attractions between a partially positive hydrogen atom and a partially negative atom (Oxygen or Nitrogen) in another molecule.
• Electronegativity: the ability of an atom to attract electrons. Higher electronegativity = greater ability to attract electrons.

Chemical Reactions

• Chemical reaction: atoms in compounds rearranging to form new substances with new properties.
• Evidence of a chemical reaction: Heat production, color changes, precipitate formation, gas production.
• Types of reactions:
  • Exergonic: releases energy/ spontaneous (e.g., cellular respiration).
  • Endergonic: requires energy (e.g., muscle growth).
• Metabolism: The sum of all chemical processes in organisms including both catabolic and anabolic pathways (catabolism: breaking down and anabolism: building up)
• ATP: The primary energy currency used in cells (Adenosine triphosphate), involved in energy coupling.

Importance of Water

• Water is polar, allowing hydrogen bonding between water molecules. This unique characteristic gives water many special properties (such as cohesion, adhesion, a good solvent, reactivity, high specific heat, lubrication).
• Hydrophilic compounds dissolve in water.
• Hydrophobic compounds do not dissolve in water.
• Water's cohesion and adhesion are important for many biological processes.
• Water’s high specific heat helps to regulate temperature in organisms.

Acids & Bases

• Water dissociation: Water spontaneously breaks down into H⁺ and OH⁻ ions in a solution.
• Acids: Substances that release H⁺ ions when in water.
• Bases: Substances that accept H⁺ ions when in water.
• pH Scale: 0 to 14 scale measuring the concentration of H⁺ and OH⁻ ions in a solution (0-7 acidic, 7 neutral, 7-14 basic)
• Buffers: Solutions that resist changes in pH.

Introduction to Biomolecules

• Major macromolecules:
  • Lipids: create cell membranes and store long-term energy.
  • Nucleic acids: encode and transmit genetic information.
  • Carbohydrates: provide energy.
  • Proteins: have many functions including pores/pumps for transport and enzymes that speed up reactions.
• Monomers are the single units from which polymers are constructed.

Assignment #2: Atoms, Chemical Bonds, and Reactions

• Questions regarding identifying compounds, calculating the number of subatomic particles for various elements, drawing models of water interacting with hydrogen bonds, and identifying likely polar covalent compounds from structural formulas.