bio 141: ch 2 the nature of molecules and properties of water

matter

has mass and takes up space

atoms

all matter is composed of…

atom structure

understanding this is critical to understanding the nature of biological molecules

within the nucleus of an atom

protons +1 charge, neutrons 0 charge

protons

atoms with the same number of these are all the same chemical element regardless of the number of neutrons or electrons

surrounding the nucleus

electrons -1 charge

protons

define an atom as a unique element

experimental evidence for the nucleus

rutherford, geiger, marsden’s gold foil experiment 1913

isotopes

atoms of one element (same number of protons) but with variable numbers of neutrons

decay

describes radioactivity of isotopes as they change into different elements at a known rate

neutrons

do not affect the number of electrons, so the chemical properties of the element are largely unchanged

half life

the time taken for the radioactivity of a specified isotope to fall to half its original value

uranium 235

the decay of this element suggests the earth is 4.5 billion years old

octet rule

except for hydrogen and helium, many elements, especially the most common in biology (carbon, oxygen, nitrogen) want to have eight electrons surrounding their nuclei in their outermost shell

covalent bond

sharing of electrons in the outermost (valent) layer of electrons; strongest form of bonding

salts

ionic bonds form these substances

ionic bonds

transferring of electrons from one element to another; the two atoms are then drawn together via electronegativity (Na+Cl-, Li+PO4-); second strongest bond

ion

any substance, an atom or a molecule, with a positive or a negative charge

hydrogen bond

weakest form of bonding

covalent bonds

complex possible arrangement of atoms in its molecules

covalent bonds

stable in solvents, like water

covalent bonds

can be solid, liquid, or gas

covalent bonds

identified by one, two, or three lines connecting atoms

ionic bonds

relatively few possible arrangement of atoms in salts

ionic bonds

can easily be broken in water

ionic bonds

solid in pure form

ionic bonds

electrostatic attraction

water

life is inextricably tied to…

hydrogen bonds

single most outstanding chemical property of water is its ability to form…

hydrogen bonds

weak chemical associations that form between the partially negative oxygen atoms and the partially positive hydrogen atoms of two water molecules

electronegativity

atom’s affinity for electrons

nonpolar covalent bonds

equal sharing of electrons

polar covalent bonds

unequal sharing of electrons

electronegativity

differences dictate how electrons are distributed in covalent bonds

nonpolar bond

electronegativity (E-) difference of 0.0 to 0.5

polar bond

electronegativity (E-) difference of 0.5 to 1.5

electronegativity difference

determines if the covalent bond between two atoms is polar or nonpolar

nonpolar

any molecule made of all carbon and hydrogen atoms are called hydrocarbons and are always…

water

highly polar due to the bonds between oxygen and hydrogen

water

partial electrical charges develop within…

polar covalent bonds

result in slight separation of charge; important in biological systems; may result in formation of hydrogen bonds

hydrogen bonds

weak bonds form when a hydrogen atom in polar molecule is attracted to electronegative atom in same or another polar molecule

hydrogen bonds

may be short-lived, but numerous bonds add strength like velcro

polarity

of water dictates that water molecules be attracted to one another

hydrogen bonds

each individual bond is weak and transitory

hydrogen bonds

responsible for many of water’s important physical properties

high specific heat

a large amount of energy is required to change the temperature of water due to hydrogen bonds

high heat of vaporization

the evaporation of water from a surface causes cooling of that surface

less dense

compared to liquid water, solid water is…

top down

bodies of water freeze from the…

good solvent

water dissolves polar molecules and ions, making it a…

water

organizes nonpolar molecules

water

causes hydrophobic molecules to aggregate or assume specific shapes

hydrophilic

water-loving

hydrophobic

water-fearing

ions

water can form…

pure water

considered to be neutral; neither basic or acidic; [H+] of 10^-7 M

pH

a negative logarithm or hydrogen ion concentration of a solution

formula for pH

-log[H+]

acid

any substance that dissociates in water to increase [H+] and lower the pH; the stronger it is, the more hydrogen ions it produces and the lower its pH

base

substance that combines H+ dissolved in water and thus lowers the [H+]

powers of 10

pH scale is based on…

buffers

substance that resists change in pH

buffers act by…

releasing hydrogen ions when a base is added, absorbing hydrogen ions when acid is added

buffers

have an overall effect of keeping hydrogen ion concentration relatively constant

biological buffers

most consist of a pair of molecules: one acid and one base