Biochemistry and Thermodynamics Quiz

Molecular Biophysics

• Molecular biophysics is a field that applies physics principles to understand biological systems at the molecular level.

Basic Components of Life

• Atom: The basic unit of matter. Living and non-living systems are composed of atoms.
• Molecule: Bonded atoms. Molecules are the building blocks of larger structures.
• Macromolecule: Larger complex molecules, such as proteins, nucleic acids, carbohydrates. and lipids.
• Organelle: Organelles are parts of the cell, carrying out specific cellular functions.
• Cell: The basic unit of life, perform all the functions of life and form tissues.
• Tissue: Cells working together for similar function.
• Organ: Groups of tissues working for a specific purpose.
• Organ system: Several organs working together.
• Organism: Any living creature.
• Living things have highly organized molecular structures based on interactions of atoms, intramolecular and intermolecular interactions.

Atomic and Molecular Content of Livings

• Essential elements in the human body (99.3%): Hydrogen, Oxygen, Carbon, Nitrogen.
• Other elements (0.7%): Calcium, Phosphorus, Potassium, Sulfur, Sodium, Chlorine, Magnesium, etc.
• Trace elements (0.01%): Iron, Iodine, Copper, Zinc, Selenium, Cobalt, Chromium, Fluorine.
• The properties of molecules depend on their atomic structures.

Types of Bonds

• Metallic bonds: Electrostatic attraction between positively charged ions and free-moving valence electrons. These bonds form a lattice and exhibit high melting points, electrical conductivity, and malleability(e.g. metals like iron or gold.)
• Ionic bonds: Formed by transferring electrons from one atom to another, resulting in oppositely charged ions. The electrostatic attraction between these ions forms the bond (e.g. sodium chloride or table salt).
• Covalent bonds: Formed by sharing electrons between atoms. Can be polar (unequal sharing) or non-polar (equal sharing) (e.g. water molecules).
• Hydrogen bonds: A special type of dipole-dipole attraction, where a hydrogen atom bonded to a highly electronegative atom (like oxygen, nitrogen, or fluorine) is attracted to another electronegative atom in a different molecule (e.g. water molecules, DNA base interactions).

Intermolecular Interactions

• Intermolecular forces are weaker than intramolecular forces.
• Van der Waals forces: Weak attractive forces between all atoms and molecules due to temporary fluctuations in electron distribution, resulting in temporary dipoles and inducing dipoles in neighboring atoms/molecules (e.g. London forces, dipole-dipole, dipole-induced dipole).
• Hydrogen bonding: A special case of dipole-dipole force that occurs between molecules containing hydrogen bonded to a highly electronegative atoms, leading to strong intermolecular interactions (e.g. water or biological molecules.)
• Ion-dipole forces: Attractive forces between an ion and a polar molecule. These interactions occur when an ion interacts with a polar solvent, like water (e.g., dissolving salt).
• The physical properties of compound and molecules are controlled by intermolecular interactions

Water and Its Importance for Livings

• Water is essential to all living things, making up a substantial portion of many organisms.
• A polar molecule, meaning it has an uneven distribution of charge due to its bent shape.
• Water molecules exhibit strong cohesive forces due to their ability to form hydrogen bonds with each other, resulting in high surface tension.
• Water's high surface tension is responsible for several important phenomena in nature and in living organisms (e.g., insects walking on water).
• Water exhibits high specific heat and high heat of vaporization, helping moderate temperature fluctuations in organisms and their environments.
• Water exhibits a lower density as a solid (ice) compared to its liquid state, enabling ice to float and providing insulation for aquatic life in cold environments.
• Water is an excellent solvent due to its polarity, ability to form hydrogen bonds, and engaging in electrostatic interactions with other polar molecules and ions.

Molecular Dynamics

• Rate of the reaction: The speed at which a chemical reaction takes place and how fast the products form.
• Equilibrium: The state in which the rates of the forward and reverse reactions are equal, and the concentrations of reactants and products remain constant.
• Reversibility in Chemical Reactions The ability to turn back a process such that both system and the surroundings return to their original states.
• Irreversibility in Chemical Reactions Processes will not come back to their initial state.

Summary of Intermolecular Interactions

• A flow chart is presented that helps predict the type of intermolecular force for any given molecule.