chemistry

periods

rows of periodic table

groups

columns of periodic table

metals

good electrical conductors, solid under standard conditions, shiny, ductile, and malleable (left side of the periodic table)

nonmetals

not lustrous, poor conductors, (right side of the periodic table)

metalloids

share traits of nonmentals and metals, brittle, poor to decent conductors

metalloid elements

B, Si, Ge, As, Sb, Te, Pb (staircase between transition metals and nonmentals)

alkali metals

group 1, have 1 valence electron, highly reactive, readily form cations

alkaline earth metals

group 2, have 2 valence electrons, metallic and reactive

transition metals

groups 3-12, hard durable, conduct electricity, take vivid colors from electron transitions from unfilled d orbital

group 13

contains metalloid B, rest are metals, 3 valence electrons

group 14

carbon family, 4 valence electrons, capable of forming oxides

group 15

nitrogen family, 5 valence electrons, N and P most common

group 16

chalcogens, contains O and S

group 17

halogens, nonmetal, highly reactive, found in diatomic covalently bonded molecules

noble gases

group 18, non-metallic, unreactive bc full valence electron shell, exist as gas under standard conditions

effective nuclear charge (Zeff)

attractove force of positively charged nucleus on atom’s valence electrons

Zeff periodic trends

* Zeff increases along a row bc adding protons to nucleus
* Zeff decreases down group bc valence electrons farther from nucleus

atomic radius

if Zeff stronger, then radius is smaller

if Zeff weaker, then radius is larger

ionic radius

radius of ions/charged species

* increase radius if ions add more electrons (electrostatic repulsion)
* losing electrons makes radius smaller

ionization energy

energy needed to remove 1 valence electron from neutral atom in gaseous state

* positive bc energy needed to pull electron away
* first ionization energy is lower than second, difficult to remove electrons from stable molecules

proton

hydrogen ions if stripped of its only electron (H+)

functional group

specific group of atoms that contribute in predictable way to behavior of a molecule

polar covalent bond

partial negative forms on more electronegative atom, positive charge forms on less electronegative atom

amphipathic

molecule that has regions of polarity and nonpolarity

residues that attract one another

negative + positive, nonpolar + nonpolar, polar + polar

alipathic

straight chain hydrocarbon side groups (hydrophobic)

cysteine

R configuration

glycine

only achiral amino acid

proline

side chain loops back onto amine group that is part of amino acid skeleton

* interferes with secondary structure of proteins
* proline kinks breaks up helical and sheet motifs

nonpolar amino acids

glycine (G), alanine (A), valine (V), leucine (L), isoleucine (I), methionine (M), proline (P)

aromatic amino acids (nonpolar)

phenylalanine (F), tyrosine (Y), tryptophan (W)

polar uncharged amino acids (alcohols + thiols)

serine (S), threonine (T), cysteine (C)

polar uncharged amino acids (amides)

asparagine (N), glutamine (Q)

basic amino acids

lysine (K), arginine (R), histidine (H)

Bronsted Lowry

acids = proton donors, bases = proton acceptors

acidic amino acids

asparatic acid (D), glutamic acid (E)

* both have carboxylic acids

atomic theory

* all matter consists of invisible atoms
* atoms of same element are identical
* compounds consist of atoms of more than one element together
* chemical reactions are result of atoms recombining

molecule

any structure composed of multiple atoms

ions

when atom/element gains or loses electron

binary compound

compound made of 2 elements

ionic compound

contain metal and nonmetal

molecular compound

contain 2 nonmetals

* molecular compound in order of electronegativity
* suffix “-ide” added to end of name of second element

nonpolar covalent bond

elements with similar or same electronegativity bonded together

polar covalent bond

atoms with difference in electronegativity bonded together

electronegativity in bonds

* < 0.5 = nonpolar covalent bond
* 0.5 - 1.7 = polar
* > 1.7 = ionic

ionic bonds

complete transfer of valence electron, full charges on resulting ions

metallic bonds

metal atoms join together where electrons are delocalized, sea of electrons free to move

intramolecular forces

forces that hold atoms together in molecules

intermolecular forces

interactions between molecules

* weaker than intramolecular forces
* stronger intermolecular force = higher melting and boiling points

forces in increasing strength

London dispersion < dipole-dipole < H-bonds < ion-dipole < ionic interaction

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london dispersion forces

weakest force, can occur between any molecule (even nonpolar)

* occur when temporary dipoles arise by chance
* larger structure = greater LDF

dipole-dipole interaction

attractive force occurs between positive dipole of one polar molecule and negative dipole of another molecule

hydrogen bonds

occurs when H attached to N, O, or F is attracted to lone pair of N, O, F

ion-dipole forces

occur between ions and molecules with a dipole and molecules with full charge

elution

process of extracting one material from another by washing with solvent

* weakest interaction with stationary phase will elute first
* H bonds strength will make it take longer to elute

exergonic

releases energy, product lower energy than reactants

endergonic

product higher energy than reactants

enzyme-substrate interaction

catalytic site is where rxn is catalyzed, binding site is where intermolecular interactions occur

specificity

substrate specific to enzyme

Lock and Key theory

active site of enzyme and substrates fit together like puzzle (not accurate)

induced fit theory

enzyme and substrate binding induces conformational shifts, allows closer binding and more efficient catalysis

enzyme regulation

orthosteric regulatory interacts at active site, allosteric regulatory interacts at other site (binds noncovalently)

upstream

describes earlier steps in pathway

downstream

later steps in pathway

negative feedback

when downstream product makes previous step less likely to happen or less efficient (downregulating)

* maintains homeostasis

positive feedback

downstream product makes upstream effects better

feed-forward regulation

compound A makes enzyme 2 better at converting B to C, upstream product of pathway alters activity of enzyme function downstream

cooperativity

binding one ligand to an active site makes it easier for second ligand to bind

hemoglobin

transport protein that carries oxygen throughtout blood/body

Hill coefficient

degree of cooperativity

* Hill > 1 = positive cooperativity (sharper S curve)
* Hill = 1 = no cooperativity
* Hill < 1 = negative cooperativity (binding ligand lowers affinity for other)

cofactors

enzymes require another chemical compound to be present in order for enzyme to function

* inorganic: metal ions (Mg2+, Zn2+, Cu2+)
* organic: coenzymes

coenzymes

contribute to function of enzymes by carrying functional groups from one place to another in a rxn

* often vitamins or vitamin derivatives

prosthetic groups

coenzymes that are tightly/covalently bonded to their enzymes

holoenzyme

enzyme together with however many cofactors and coenzymes it needs (whole)

apoenzyme

enzymes without cofactors needed to function properly

saturated

all enzyme molecules are occupied

vmax

maximum rate of reaction

Km

concentration of substrate that corresponds to half of vmax

* high Km = low affinity, low Km = high affinity
* decreasing enzyme concentration will decrease Km

Lineweaver-Burk plots

double reciprocal transformation of Michaelis-Menten plot

* x-intercept = -1/Km, y-intercept = 1/vmax
* increasing vmax makes y-intercept closer to origin (decrease)
* increasing Km makes x-intercept closer to 0 (increase)

competitive inhibitor

compete with substrate for active site, no affect on vmax

* affects Km
* makes slope steeper for Lineweaver

noncompetitive inhibitor

interact with enzyme allosterically, effect similar to reducing amount of enzyme present

* reduces vmax
* doesn’t affect Km (Km is same)

uncompetitive inhibitor

prevents enzyme from converting substrate to product

* reduces rate of catalyzed reaction = reduces vmax
* decreases Km = increases affinity bc of stabilization

mixed inhibitor

affect Km differently depending on binding presence/preference of inhibitor

* always decrease vmax
* if prefer to bind with free enzyme, Km increases (like competitive)
* if prefer to bind with enzyme-substrate complex, Km decreases (like uncompetitive
* Menton plot will shift downward
* Lineweaver plot if y-intercept high and x-intercept closer to 0

atomic weight

avg mass of all isotopes of an atom calculated using mass and relative abundance of isotopes

Bohr model

* lower to higher = absorbing photon
* higher to lower = emitting photon

Pauli exclusion principle

no 2 electrons can have same 4 quantum numbers

principal quantum number (n)

specifies energy level of electron

angular momentum number (l)

specifies shape of orbital

* n-1 → ex n = 4 → l = 0, 1, 2, 3

magnetic quantum number (ml)

specifies spatial orientation (-l to +l)

spin quantum number (ms)

electrons have opposite spins (-1/2 and 1/2)

electron configuration

electrons fill orbitals in order of lowest to highest energy

* transition metals electrons removed from subshell with highest quantum energy (4s^2, 3d^4 → 4s^1, 3d^10)

Heisenberg uncertainty principle

can’t know exact position and momentum of electron

free radicals

highly reactive bc compounds have odd number of valence electrons

sigma bond

single bond

pi bond

interaction between 2 p orbitals

tetrahedral molecular shape

4 single bonds, no double/triple bonds (109.5)

trigonal pyramidal

3 single bonds + 1 lone pair (107)

bent

2 bonded atoms + 2 lp (104)

trigonal planar

3 bonded atoms (120)

linear

2 bonded atoms (180)