Biochemistry Pearson Textbook: Sections 2.1 - 2.5 (no 2.4)

Date: October 4, 2023

Topic: Chapters 2.1 - 2.3 Notes Pearson Textbook

Recall:

Notes

• Element: cannot be broken down to other substances by chemical reactions.

• More than 90 naturally-occurring elements.

• Compound: two or more elements in a ratio that is fixed (NaCl: Na and Cl in a 1:1 ratio.)

• Emergent properties: The properties a compound has, as it has different properties than its constituent elements.

• Humans: 25 necessary elements, plants — 17.

• Trace elements: required in very minute quantities, and some are only required by certain species.

• Human body elements:

  • Oxygen (O), 65.0% of body mass w/water.

  • Carbon (C), 18.5%

  • Hydrogen (H), 9.5%

  • Nitrogen (N), 3.3%

  • Calcium (Ca), 1.5%

  • Phosphorus (P), 1.0%

  • Potassium (K), 0.4%

  • Sulfur (S), 0.3%

  • Sodium (Na), 0.2%

  • Chlorine (Cl), 0.2%

  • Magnesium (Mg), 0.1%.

• Trace elements in human body: Boron, Chromium, Cobalt, Copper, Fluorine, Iodine, Iron, Manganese, Molybdenum, Selenium, Silicon, Tin, Vanadium, Zinc

• Species evolve/adapt to environments containing toxic elements, such as lead, zinc and heavy metals.

• Every element has a slightly different structure; element symbol stands for both the element itself and a single atom of the element.

• Parts which compose an atom: subatomic parts. 3 relevant ones: proton, neutron, electron. Proton is positively charged, electron is negatively charged, and a neutron is electrically neutral.

• Protons and neutrons are in the nucleus, which is positively charged. Electrons make a negative charge cloud around the nucleus and the attraction between the 2 charges is what holds the atoms together.

• Neutron and proton have a similar mass, 1.7 * 10^-24 grams. This is not useful, and so in science the mass is expressed as 1 dalton or 1 atomic mass unit (amu). Neutrons and protons weight 1 amu roughly, while electrons are about 1/2000 of that, so they are ignored when taking atom mass.

• Atomic number: unique to each element, number of protons. Written as a subscript to the left of element symbol.

• Unless you are told otherwise, all atoms are electrically neutral (protons and electrons balance), and so atomic number also tells amount of electrons in a neutral atom.

• Neutrons is taken from atomic mass, atomic mass - number of protons = neutrons. Mass is written as superscript to the left of the symbol.

• Almost all atomic mass is concentrated in the nucleus

• Isotopes: More neutrons (diff mass)

• Stable - do not tend to decay

• Radioactive/unstable: decays spontaneously and gives off energy/particles

• Nucleus: extremely small compared to atom itself

• Electrons: farther from nucleus, more potential energy, mostly fixed increments

• Space-filling model (coinciding circles): most accurate in showing molecule shapes

• Ionic bond: electron is “stolen” leaving multiple ions

• Cation: positive, anion: negative

• Ionic compounds: salts

• Chemical formulas for ionic bonds: just a ratio, not a molecule in and of itself

• Covalent inside of an ionic bond can be one of the ions

• Weak interactions:

  • Hydrogen bonds

  • Van der Waals: ever changing electron distribution that allows sticking (gecko to wall)

• Molecular shape: crucial. Linear, tetrahedron, etc.

  • Similar shapes: mimicking

• Water’s bonds: Polar covalent

• V-shape = polar molecule (uneven charges)

  • Oxygen: 2 negatives, 2 positive hydrogens

• Positive hydrogen attracted to nearby other water: negative oxygen

• Hydrogen bonds (above): not very strong, last trillionths of a second, constantly new ones.

• Cohesion: main water force against gravity in plants, touching water-conducting cells.

  • Adhesion, smaller effect to counter gravity (sticking to plant veins)

• Surface tension: how difficult it is to stretch/break a substance.

  • Water: unusually high surface tension due to the air interface

• Temperature: average kinetic energy, while thermal energy is total (therefore depends on volume)

• Thermal energy in transfer between substances is defined as heat.

• Calorie: amount of heat needed to raise 1g of water by 1 degree C, also amount released in opposite direction.

• Kilocalorie: 1000 calories, or heat to warm 1kg of water 1 degree C.

  • Food packet calories: Kcals

  • Joule = 0.239 cal, cal = 4.184 J

• Specific heat: amount of heat needed to raise any 1g of any substance 1 degree C.

• Water specific heat: calorie, particularly high.

• Higher specific heat = it heats slower (iron spec. heat = 1/10 of water’s, pot heats much faster than the water.)

• Water has high specific heat because much of the heat is used to break water’s hydrogen bonds.

• Water is a good coolant because of the high specific heat: when water cools down many hydrogen bonds form and much energy is released.

• Heat of vaporization: heat a liquid must absorb for 1g to go from liquid to gaseous state.

• Water at 25C: 580 cal, twice alcohol.

• Evaporative cooling: “hottest” molecules in a substance being heated will escape as gas, leaving cooler ones behind.

• Ice floats on liquid water: water expands when freezing because the energy is needed in the hydrogen bonds, keeping molecules “arm’s length” away, expanding the water by about 10%.

  • Water greatest density: 4 degrees C.

• Ice not sinking prevents all the bodies of water on the Earth from freezing up and making living impossible.

• Aqueous solution: water is the solvent

• Water’s solvent properties: owed to the polarity. It is attracted to the substances in it and forms a hydration shell.

  • Large molecules will not dissolve in the same way.

  • Cellulose forms hydrogen bonds with water, which creates adhesion. Therefore cellulose does not dissolve in the same way either.

• Molecular mass: sum of all the atom masses in a molecule.

• Mole represents Avogadro’s number of a certain substance (6.02 × 10²³.) Avogadro daltons in a gram. To get 1 mole of sucrose, measure 342 grams. (Molecular mass in grams = mole)

• Molarity: Concentrations in aqueous solutions: moles of solute per water liter.

• Double arrows: Reversible change, constant equilibrium

• At 25 degrees C, product of [H+] and [OH-] = 10^-14. This is a neutral solution.

  • Acid: adds hydrogen and removes hydroxide. Base: opposite. Represented by pH scale.

  • pH scale is based on [H+] concentration. pH decreases as [H+] increases.

• A buffer minimizes changes in concentrations of these in a solution

• CO2 dissolves in water to form carbonic acid, reducing ocean pH. This harms life in the ocean. (Acidification)