Lecture 2 Bio Sci 93

Atom

the smallest unit of matter that still retains the properties of an element; composed of protons, neutrons, and electrons

Element

a substance that cannot be broken down into other substances by a chemical reaction; composed of only one type of atom

Molecule

two or more atoms (of the same or different elements) held together by covalent bonds

Compound

a substance made of two or more different elements combined in a fized ratio (e.g., NaCl is one sodium atom for every chlorine atom)

Covalent bond

a strong chemical bond formed by the sharing of a pair of valence electrons between two atoms

Ionic bond

a strong bond resulting from the attraction between two oppositely charged ions, which formed when one atom transferred electron(s) to another

Hydrogen bond

a weak bond formed when a hydrogen atom, already covalently bonded to one electronegative atom, is also weakly attracted to an electronegative atom in another (or the same) molecule

Hydration shell

the sphere of water molecules that surrounds each dissolved ion (or polar molecule) when an ionic or polar compound dissolves in water

Hydrophobic

described nonpolar, nonionic substances that repel water because they cannot form hydrogen bonds with it (e.g., oils and lipids)

Hydrophilic

describes substances with polar or ionic bonds that ahve affinity for water and can form hydrogen bonds with it

Solvent

the substance (often water in biology) in which another substance dissolves

Solute

a substance that is dissolved in a solvent (e.g., salt dissolved in water)

Solution

the resulting mizture formed when a solute is fully dissolved in a solvent

pH

the negative logarithm of the hydrogen ion concentration of a solution (pH = -log[H+]); it describes how acidic or basic/alkaline a solution is on a scale of 0-14

Hydrogen ion (hydronium ion)

H+ also called H3)+ in aqueous solution: a proton released whena. hydrogen atom loses its electron and transfers it to another water molecule during water’s dissociation; acids increase its concentration in solution

Hydroxide ion

OH- the negatively charged ion left behind when a water molecule loses a proton (H+) during dissociation; bases increase its concentration in solution

Dissociation (of water)

the process by which a hydrogen atom shifts from one water molecule to another, leaving its electron behind. This creates a hydronium ion (H3O+, the molecule that gained the proton) and a hydroxide ion (OH-, the molecule that lost it): H2O ⇌ H+ + OH-

Buffer

a substance that resists change in a solution’s pH by donating H+ when the solution loses H+ (acting as an acid) and accepting H+ when there’s an excess (acting as a base)

Van der Waals

very weak, short-range attractions between molecules or parts of molecules, arising from transient (constantly shifting) local partial charges - important in protein folding

Nonpolar (covalent bond)

a bond in which electrons are shared equally between two atoms, typically because the atoms have the same or very similar electronegativity (e.g., C-C or C-H bonds)

Polar (covalent bond)

a bond in which electrons are shared unequally because on atom is more electronegative than the other, creating a partial negative charge (δ-) on one side and a partial positive charge (δ+) on the other (e.g., O-H bonds in water)

Cohesion

the tendency of water molecules to stick to each other via hydrogen bonds, which contributes to surface tension and helpds water move as a continuous column (e.g., up a plant stem)

Adhesion

the tendency of water (a polar molecule) to stick to other polar or charged surfaces, such as the walls of a plant’s xylem - it works together with cohesion to pull water upward against gravity

Surface tension

a measure of how difficult it is to stretch or break the surface of a liquid, caused in water by cohesive hydrogen bonding between surface molecules - strong enough to support small organisms like water striders

Low pH

indicates a high concentration of free H+ ions relative to OH-, meaning the solution is acidic (pH values below 7, like battery acid or gastric juice)

High pH

indicates a low concentration of free H+ ions relative to OH-, meaning the solution is basic (pH values above 7, like household ammonia or bleach)

Carbonic acid

H2CO3; the H+ DONOR (acid) half of blood’s main buffer pair. It forms from CO2 + H2O, and it’s produced (“response to a rise in pH”) when the blood needs to release more H+ to counter rising pH

Bicarbonate

HCO3-; the H+ ACCEPTOR (base) half of blood’s main buffer pair. It’s produced (“response to a drop in pH”) when carbonic acid donates H+, soaking up excess acid to keep blood pH stable

How does the carbonic acid/bicarbonate buffer respond to pH changes?

CO2 + H2O ⇌ H2CO3 (carbonic acid, the acid/H+ donor) ⇌ HCO3- (bicarbonate, the base/H+ acceptor) + H+. If pH rises (too basic), the reaction shifts right, releasing H+ from carbonic acid to lower pH. If pH drops (too acidic), it shifts left, as bicarbonate mops up excess H+ to raise pH back toward 7.4

High specific heat capacity

the amount of heat needed to raise water's temperature is high, because heat first breaks hydrogen bonds instead of speeding up molecules. Lets water resist rapid temperature change

High heat of vaporization

the amount of heat needed to evaporate water is high, since hydrogen bonds must break for molecules to escape as gas. This is why evaporation (e.g., sweating) cools a surface