CELL1010 Chapter 2 - Dr. V Tulane University

orbit

path by electron around nucleus

orbital

space around nucleus where there's highest probability of finding an electron. regions surrounding the nucleus where electrons travel. S, P, etc

energy level (shell)

state where particles are confined b/c of amount of energy. every element other than hydrogen & helium follow the octet rule

radioactive isotopes

nucleus is unstable & break up into elements w/ lower atomic numbers while emitting energy during this decay

compound

atoms of different elements come together

molecule

atoms of the same elements come together

Covalent Bond

electrons are equally shared. strongest of all chemical bonds.

Polar Covalent Bond

2 atoms w/ diff electronegativity. electrons are closer to 1 atom=unequal sharing of electrons; partial positive and partial negative

Hydrogen Bond

force of weak electrical attraction between molecules w/ polar covalent bonds. can collectively form strong bonds (holds DNA strands together). but individual are weak & break easily (substrate & enzyme bonding)

Ionic Bonds

bonds between a cation and an anion; a weak force of attraction

cation

net positive charge

anion

net negative charge

Covalent Bond

Bond Responsible for recognition between enzyme and substrate

Free Radical

Molecule with an atom that has 1 unpaired electron in its outer shell, formed by radiation and toxins, made as an adaptive response to stress

catalyase

breaks down free radicals to water

antioxidants

supply electrons to free radicals without being transformed into a free radical themselves

hydrogen peroxide

chemical that attacks the membrane of bacteria

HOOH

Chemical Reaction

breakage of old bonds and formation of new ones. requires energy source. require an aqueous environment

Cataylsts

increase rate of reaction by stressing and stretching bonds in reaction

biochemical pathway

products of 1st reaction enter into next step

water

solvent needed for most reactions; universal solvent; all of its properties are due to POLARITY; polar covalent bonds will dissolve in water
-can act as a weak buffer- has the capacity to ionize

cohesion, adhesion, high specific heat, high heat of vaporization, low density of ice, solubility

6 Properties of Water

cohesion

molecules of same type attract and bind to eachother (water bugs on surface)

adhesion

allows water to lubricate internal organs (lungs). water adhering to other molecules

high specific heat

allows water to mainain temp; amount of energy required to heat 1g by 1*C

high heat of vaporization

liquid to gas. 586 cal/ 1g water, at its boiling point the amount of energy required to change 1 mol of water to vapor

hydrophilic

"water loving" ions and molecules with polar covalent bonds dissolve in water

hydrophobic

"water-fearing" nonpolar molecules (like hydrocarbons) don't dissolve in water

amphipathic molecule

has polar and ionized regions at 1+sites and nonpolar regions at other sites. may form micelles in water. (ex. phospholipid bilayer) ; hydrophilic & hydrophonic regions present

amount solute/volume solution

weight of solution (concentration)

moles/L water

molarity (concentration).

add solute

decrease water freezing pt. & increase water boiling point

anabolism

acts through condensation reactions (dehydration synthesis). water molecules are lost as smaller molecules are put together into larger units

catabolism

large molecules are broken down into smaller units (hydrolytic cleavage)

turgor pressure

responsible for hydrostatic skeleton causing plants to stand up. water accumulates in plant vacuoles and provides strength and pressure to plants

10^(-14) M

pure water charge of H+ and OH- ions

pH

log base 10 of [H+]

roles of pH

affects shape and function of molecules, rate of chemical reactions, ability for 2 molecules to bind, ability for ions/molecules to dissolve in water

buffers

can add acidity or basic nature to equilize pH. allow organisms to tolerate small changes in pH

atoms

nature's building material

matter

anything that has mass and occupies space

Niels Bohr

depicted atom as a cloud

hydrogen atom

1 proton + 1 electron

S orbitals

spherical orbitals

P orbitals

propeller or dumbbell shaped orbitals

2 electrons

each orbital can hold __ electrons

1st shell

1 spherical orbital (1s); holds 2 electrons

2nd shell

1 spherical orbital (2s) and 3 dumbbell shaped orbitals (2p); holds 4 pairs of electrons

valence electrons

electrons in the outer shell that are available to combine with other atoms

atomic number

# of protons in an atom

inert atoms

have outer shell level filled

hydrogen

outer shell filled w/ 2 electrons

atomic mass

# of protons + neutrons in an atom. average of the weights of different isotopes of an element

carbon 12

most common form of carbon

hydrogen (atomic mass=1)

atom w/ 1/12 the mass of carbon

dalton

unit of measurement for atomic mass. equals 1/12 the mass of a carbon atom.

mole

contains 6.022*10^(23) atoms= avogadro's #.

isotopes

forms of an element w/ diff # neutrons but same chemical properties.

hydrogen, oxygen, carbon, & nitrogen

elements that typically make up about 95% of the atoms in living organisms

hydrogen and oxygen

occur primarily in water

nitrogen

element found in proteins

carbon

the building block of all living matter

mineral elements

make up less than 1%

trace elements

make up less than 0.01%. essential for normal growth and function

molecule

2+ atoms bonded together

molecular formula

has chemical symbols for elements found in a molecule w/ who many (subscripts)

compound

molecule w/ 2+ elements

covalent/polar covalent, hydrogen, ionic

3 types of bonds

electrons in outer shell of the atom of higher electronegativity

polar covalent bond. distribution of electrons creates polarity/diff in electrical charge. electrons are closer to which atom

water, oxygen

example of polar covalent bond ___, electrons tend to be more electronegative in the __ atom,

hydrogen bonds

weak attractions between molecules with polar covalent bonds, dashed/dotted lines, holds DNA strands together, weakly holds substrate & enzyme bonding; POLARITY gives rise to these bonds

flexibility of covalent bonds

molecules may change shape due to __

-O2, -OH, NO

3 examples of free radicals

radiation & toxins

free radicals form __

rupture of cell membrane, genotoxin (damages DNA)

effects of free radicals

destroy infective agents (H2O2)

beneficial aspects of free radicals

killing healthy cells, absorb food containing antioxidants

harmfull effect of free radicals

chemical reactions

1 substance changed into new substance; breaking old bonds & forming new ones

properties of chemical reactions

require source of energy, often require catalyst (enzymes), tend to proceed in particular direction but will often reach equilibrium, occur in liquid environment (water)

solvent & solute

solution is made up of these 2 components

water

solvent for aqueous solutions

ions and molecules containing polar covalent bonds

things that will dissolve in water

micelles

amphipathic molecules w/ polar region at surface and nonpolar ends oriented towards center of micelle

water

the cradle of life

concentration of dissolved solute

colligative properties depend on ___ not the specific type of particle

produce antifreeze molecules to dissolve their body fluids

how animals lower the freezing pt. of their fluids to prevent their blood and cells from freezing in extreme cold

participates in chemical reactions, provides force & support, removes toxic waste components, evaporative cooling, cohesion & adhesion, can ionize H+ and OH- ions (to small extent)

water's many important properties (7)

release H+ ions

how acids cause acidic solutions

release OH- ions/ binding to H+

how bases lower H+ concentration

6 or below

pH of acidic solutions

8 or above

pH of basic/alkaline solutions

reverse reaction

equilibrium is reached when forward reaction = backward reaction

maintaining homeostasis

High specific heat & high heat of vaporization

high heat of fusion

amount of energy released by a liquid to form a solid

colligative properties of water

ability to modify melting/boiling point