C/P TEST topics and questions

E/Z isomerism

Z - highest priority groups are on the same side

effective nuclear charge equation

Zeff = Z - S, where Z is the number of protons and S is shielding of the core (non-valence electrons)

glycoside

a carbohydrate in which the -OH of the anomeric carbon is replaced by -OR, bind anomeric carbon to another molecule notation .....side

what leads to formation of a chiral product

a chiral enzyme

what is a free radical?

a molecule with an unpaired valence electron

what type of functional group is a glycosidic bond?

acetal

Acyl Halide and its reaction with alcohol

acyl halide + alcohol produces an ester

name for 1st group on periodic table

alkali metals

oxidation states of groups

alkali metals: +1 alkalien earth metal: +2 chalcogens: -2 (nonmetals) or +6 (metals) halogens: -1

name for 2nd group on periodic table

alkaline earth metals as you go down the periodic table, the reactivity increases as the atomic number increases

Bonds in glycogen

alpha 1,6 and alpha 1,4

type of bond in glycogen

alpha 1-4 glycosidic linkage

amino end and carboxyl end in protein formation

amino end (nuc with lone pairs) attacks CA end (electrophile)

how are peptides named?

amino end to carboxyl end

substrates in strecker synthesis

ammonia, cyanide, and aldehyde or ketone

electron affinity

amount of energy released when a gaseous species gains an electron in its valence shell

in mirrors the angle of incidence is equivalent to the

angle of reflection

what does the angle of incidence equal to

angle of reflection

for an electrolytic cell the

anode and cathode are reversed, the thing with lower (more negative/smaller) reduction potential becomes the cathode

Anode vs Cathode

anode is always where oxidation is taking place and cathode is always where reduction is taking place

one function of enzymes at active site

arrange reactants in ideal spatial orientation in a reaction

relationship between size of diffraction grating and resolution

as diffraction grating decreases in size, diffraction becomes more pronounced and resolution worses

relationship between temperature and resistance

as one increases temperature the resistance increases, linear (proportionate relationship)

temperatures impact on ksp

as temperature increases ksp also increases

when is entropy maximized?

at equilibrium

total pressure

atm pressure + gauge pressure

atomic number vs. mass number

atomic number is the number of protons while mass number is neutrons + protons

Is sodium bicarbonate an acid or a base?

base

how do beta particles and gamma particles differ

beta particles will be deflected in magnetic field while gamma particles will not gamma particles are high energy photons

delta H reaction

bond broken- bonds formed breaking bonds requires energy forming bonds releases energy, exothermic

at ph=7 what happens to hydrogens on phosphate groups and carboxylic acids

both lost

what is required for a stereocenter

bound to 4 different substituents

lyase

breaks molecules without water

Rate limiting step of Sn1

carbocation formation unimolecular

furanose

carbohydrate with a 5 membered ring

how does high acetyl-coA affect gluconeogenesis

causes shift of pyruvate into gluconeogenesis pathway acetyl-CoA activates pyruvate carboxylase and inhibits pyruvate dehydrogenase

faraday

charge of 1 mole of electrons

requirement to rotate polarized light

chiral carbon

difference between a coenzyme and a cofactor

coenzymes are generally organic molecules, while cofactors are usually small, charged metal ions

Geiger counter

compares relative magnitude of 2 nuclear waste depositories

what is solubility

comparison between intermolecular forces that hold a solid together and forces that solvent can exert on solute molecules

hydrogen atoms that are pumped by complex

complex I: 4H+ complex III: 4H+ complex IV: 2H+

gases are

compressible

factors that impact reaction rate

concentration of reactants (Except for zero order reactions- only can be changed by adding a catalyst or raising temperature), temperature that the reaction takes place at, surface area, adding a catalyst, also the medium that the reaction takes place in is important

what types of systems absorb UV light?

conjugated systems absorb UV light

what thing allows a system to absorb light?

conjugation

keq

constant at a constant temperature in addition only gases and aqueous solutions appear liquids and solids do not appear

type of bond metal coordination complexes

coordinate covalent ligand acts as a lewis base (electron donor) central atom acts as a lewis acid (electron acceptor)

what type of bonds are found in metal complexes?

coordinate covalent bonding

octahedral

coordinated by 6 atoms

S

counterclockwise

bond in HCL

covalent

disulfides are what type of bond?

covalent bond

when solutes are added what happens to melting point

decreases

spontaneous reaction characterized by ?

delta G < 0 and Keq>Q

keq>1

delta G is negative

Q=keq

delta G=0 at equilibrium

delta G

delta H - T delta S

delta G

delta g not + RTlnQ

light waves travel more slowly in

denser mediums, indicated by the index of refraction

examples of non-polar solvents

diethyl ether, hexane, acetone, and dichloromethane

enantiomers

differ at all chiral carbons

Anomers

differ in configuration at the anomeric carbon therefore alpha and beta anomers have opposite absolute configuration

enantiomers

different conformation at every chiral carbon

Rf

distance of solute (compound)/distance of solvent

reflux chemistry

distillation technique in which solution is heated

FADH2

donates 1 or 2 electrons

electrolyic cells

drive a non-spontaneous reaction so they drive an endergonic (delta G>O) reaction and also they include decomposition

what are D and L glucose

enantiomers

most dissolutions are

endothermic

thermodynamically favorable/ kinetically unfavorable means

energy of the products is less than the reactants and there is a high activation energy

heat

energy transfer due to difference in temperature

doppler shift equation

f'=f((vs+/-vl)/(vs+/-vs))

reaction order of M-M

first part of graph when [S]>km, the reaction is first order because dependent on [S], but then at high [S] the reaction is zeroth order

power equation

force x velocity

enolate

formed when enol undergoes deprotonation

delta G greater than zero

forward reaction is not spontaneous, reverse reaction is spontaneous so reaction proceeeds in reverse direction

name for electrochemical cell

galvanic and voltaic E>0 so it is spontaneous

dipole-dipole interactions are negligible during what phase?

gas phase due to the distance between the molecules

different enzymes for gluconeogenesis

glucose 6 phosphatase fructose-1,6-bisphophatase pyruvate carboxylase

Sucrose (alpha or beta?)

glucose is alpha fructose is beta alpha 1,2

rate limiting step pentose phosphate pathway

glucose-6-phosphate dehydrogenase

glycerol can be converted to

glyceraldehyde 3 phosphate (enters gluconeogenesis)

NADH cannot cross the mitochondrial membrane. Therefore it needs these two shuttles.

glycerol 3 -phosphate shuttle malate-aspartate shuttle

what is the only amino acid without a B carbon

glycine

rate limiting step glycogenesis

glycogen synthase

link between nitrogenous base and ribose is what type of linkage

glycosidic linkage

electrons farther away from the nucleus have greater or less energy

greater energy, therefore there emission spectra produces lower wavelength lines

gram - bacteria

has an outer and inner membrane membrane thin peptidoglycan cell wall OM contains porins that regulates passage in and out OM contains LPS

alpha nucleus is the same as a

helium nucleus

what stimulates pyruvate kinase

insulin

where are hydrophobic side chains located in a protein

interior of the protein

is the boiling point due to intramolecular or intermolecular forces?

intermolecular forces more intramolecular forces a molecule has, less intermolecular forces it has and therefore, results in a lower melting point

period

inverse of frequency or seconds/cycle

image distance +

inverted and real

anomeric carbon

invertible epimer

Fo

ion channel

hill coefficient

is a measure of cooperation n>1 cooperative n<1 non-cooperative

anomeric carbon of a sugar

is an invertible epimer

rate limiting step of krebs

isocitrate dehydrogenase (iso→a-ketoglutarate +CO2+NADH)

what does adding a resistor in parallel do to the overall resistance?

it decreases the overall resistance

what does magnetic quantum number designate?

it defines the orientation of a subshell

what is stereochemistry across a double bond determined by?

it is determined by each carbon separately?

lower IMF's does what to boiling point

it lowers the boiling point

what does that acid catalysis of a hydroxide do to that hydroxide

it makes the alcohol a better leaving group

what does acid do in esterification reactions

it plays only a catalytic role

keq equals (rates)

k (forward) / k (reverse)

if delta G is less than 0, then

keq>1

alpha-keto acid

ketone on alpha carbon of carboxylic acid

1 newton

kg m/s^2

difference between kinase and phosphorylase

kinase use ATP as substrate while phosphorylase use inorganic phosphate

kinetic vs. thermodynamic products

kinetic products form faster (b.c lower activation energy), but the products have greater free energy thermodynamic produces form slower (b/c of elevated activation energy), but the products have lower free energy

most amino acids are

l amino acids

what makes a sugar non-reducing?

lack of hemiacetal groups, cannot undergo mutorotation and ring openining example of non-reducing (sucrose) reducing sugars get oxidized

spherical abberation

lenses produce images @ several focal points

decrease in entropy (negative entropy) represented by

less moles

where is glucokinase found

liver and pancreas

1st order reaction

ln[A] v. time

are sound waves longitudinal or transverse

longitudinal

lewis structure of ozone

looking at structure of ozone it is clear that it has a permanent dipole

beta decay

loss of an electron

pH of anode and cathode

low pH for anode and high pH for cathode

Increase IMF = _______ vapor pressure

lower, increased boiling point

metric units

m = mili 10^-3 ----- K = kilo 10^3 u = micro 10^-6 -----M=Mega 10^6 n=nano 10^-9 -------G=Giga 10^9 p=pico 10^-12 -------T=Tera 10^12

heat capacity

m*c

what do tosylates do?

make alcohols better electrophiles

entropy at equilibrium

maximized

ionic bonds occur between

metals and nonmetals

molecule in which carbon is in its lowest oxidation state

methane (-4)

All _______ are reducing sugars

monosaccharides

higher Rf value indicates

more nonpolar stationary phase (silica beads) is polar

Ka of a weak acid

much less than 1

4 quantum numbers

n - average energy of a shell l - describes shape of a shell ml - orientational ms - spin orientation

total internal reflection

n1>n2 angle of incidence is greater than the critical angle

index of refraction

n=c/v

pka of indicator

near pH of the equivalence point

what is the Delta G for any reaction that occurs in the body

negative

what type of charge moves from low potential to high potential

negative charge

what is the charge of ADP

negatively charged because of phosphates

effective nuclear charge

net positive charge of the nucleus experiences by electrons in the valence shell increases as you go across a period, but little change as you go down a group

are catalysts used up during a reaction?

no

does frequency change between different mediums?

no

are alpha and beta glucose enantiomers?

no they are anomers, differ at one chiral carbon. enantiomers have similar physical properties and differ at all chiral centers.

what makes a fluid ideal?

no viscosity, incompressible, laminar flow (velocity at all points is constant)

is glycine opitcally active

no, because it lacks a chiral center

atoms least likely to participate in ionic bonds

noble gases because full valence shell includes (He) -> noble gas

is allosteric regulation covalent or non-covalent

non-covalent

what type of bonding between antibodies and antigens?

non-covalent bonding interactions (electrostatic interactions and hydrogen bonding)

is dichloromethane polar or nonpolar

nonpolar

lipids have

nonpolar tails and polar heads

no chiral carbons

not enantiomers

Are esters water soluble?

not generally if have long fatty acid chain

Zeroth Law of Thermodynamics

objects are in thermal equilibrium when they are at the same temperature

specific rotation equation

observed rotation / [solution] x tube length (dm)

what is a stereospecific reaction?

only produces one conformation

can cyclic and linear form of glucose undergo oxidation

only the linear form of glucose can undergo oxidation

what can one use to characterize enantiomers?

optical rotation

enzymes involved in redox reactions

oxidases, reductases, dehydrogenase, mono-oxygenase

where do oxidation and reduction always occur?

oxidation always occurs at the anode, while reduction always occurs at the cathode

equivalence point for a strong acid + strong base

pH = 7

impact of dilutions on pH

pH increases because lower [H+]

diamagnetic

paired electrons (even # of electrons), repelled by magnetic field

head group of sphingolipid could have

phosphoethanolamine group monosaccharide oligosaccharide

rate limiting step of glycolysis

phosphofructokinase

example of covalent modification

phosphorylation

Polarity of the Silica Gel

polar

lipids

polar heads, nonpolar tails

electric field lines go from _____ charge to _______ charge

positive negative

Q>Ksp

precipitate forms

Pascal's Principle

pressure applied to a fluid is transmitted throughout the fluid P1=P2....F1/A1=F2/A2

equation for intensity

pressure per unit area = P/A

what happens to esters and CA's when treated with LiALH4?

primary alcohols

can amines be a hydrogen bond donor or acceptor?

primary amines can do both

keq>1

products are favored

1 volt

J/C

1 W

J/s

catalytic efficiency

Kcat/Km ability of the enzyme to work at low substrate conditions it is the linear beginning part of the M-M graph, the initial slope of the M-M graph

NMR peaks between 0-3 ppm

protons attached to alkane carbons

D v. L notation

put the most oxidized group on top, then note the positions of the OH group OH group on left (L) OH group on right (D)

units for rate laws

M/s

1 Joule

N*m

1 tesla

N/A*m

nitrogen gas

N2, inert, un-reactive because of the strength of the N=N triple bond

ionization energies of N and O

N>O because of half filled d subshell

Can acetyl CoA be used to make glucose?

NO!

equation for entropy

S=Q/T

second law of thermodynamics

S>0

inversion of stereochemistry

Sn2

reverse phase HPLC

Stationary phase is nonpolar, so more polar will move further

2nd order reaction

rate= k [A]^2; graph of 1/A is straight line

Keq < 1 means

reactants are favored the forward rate constant is smaller than reverse rate constant keq= k forward / k reverse

conformation isomers

rearrangement around a single bond

what is the color of oxygenated blood?

red

orbital

region of space around the nucleus defined by the probability of finding an electron in that region of space

polarity of cholesterol

relatively non-polar

diamagnetic

repelled by an external magnetic field

what does the azimuthal number (L) indicate?

shape and number of subshells

what does primary quantum number give info about?

size (radius) + energy level

slope for zeroth order, first order, and second order reactions

slope zeroth order = -k first order = -k second order = k

covalent bonds are composed of elements with a ______ EN difference

small

does sound travel faster in solids or gases?

solids

what time of wave travels faster in more dense medium?

sound waves travel faster in more dense medium, but light waves more slower in more dense medium

hybridization of amide bond

sp2, because planar. conjugation and resonance partial double bond character

trigonal bipyramidal

sp3d and 5 groups

anion-exchange chromatography

stationary phase contains + chages

km

substrate concentration at 1/2 Vmax

critical point

temperature and pressure at which liquid and gas state are indistinguishable

Tm

temperature at which a solution of DNA molecules is 50% melted

what remains constant in a phase transition?

temperature is constant in a phase transition

what remains constant in a phase transition?

temperature remains constant, all heat is put into breaking bonds and does not contribute to KE or temperature of the substance

what protein structure do R groups contribute to?

tertiary structure

at the boiling point what are the KE's of the liquid and the gas?

the KE's are the same since the gas and liquid have the same temperature

when naming an ester what is named first

the alcohol side chain

When pH=pKa, then...

the concentration of the acid and the conjugate base are equivalent

mass defect

the difference between the mass of an atom and the sum of the masses of its protons, neutrons, and electrons

what increases with differences in electronegativity?

the dipole moment

current is what?

the direction that positive charge flows

focal length

the distance from the center of a lens to the focal point

how does the distance from the nucleus impact the energy of the electron

the farther an electron is from the nucleus the greater its energy

image distance and object distance in plane mirrors

the image distance and the object distance are equivalent in plane mirros

in competitive inhibition what happens

the inhibitor binds to the active site

what is inertia dependent upon?

the mass of the object

critical point

the temperature and pressure at which the gas and liquid states of a substance become identical and form one phase

what happens to the vapor pressure as one increases the temperature

the vapor pressure increases

if an acid has multiple acidic protons?

then the acid can act as a buffer over several pH ranges

does H bonding occur when substance is in the gaseous state?

there is no H bonding when a substance is in the gaseous state

for W=Fdcos(theta) what does theta refer to?

theta is the angle between the displacement vector and the force

are resistors conductors or insulators?

they are conductors as they still allow the passage of electrons through the circuit.

nonpolar molecules contain polar or nonpolar bonds

they can contain both

hydrophobic molecules on surface of protein do what to the entropy of water molecules surrounding the protein?

they decrease the entropy of the water molecules because the molecules must take positions that minimize interactions with the hydrophobic proteins and maximize with other water molecules

what are spectator ions?

they do not participate in a reaction, never incorporated into a compound or a complex

what do tosylates to?

they make alcohols better electrophiles

effect of enzymes on a reaction

they speed up reactions, but do not change the equilibrium of reactions

what is heat?

transfer of energy that results from temperature differences

heat

transfer of energy that results from the differences of temperature between two substances

kcat

turnover number= Vmax/[E] plateau part of Michaelis-Menten graph ES-> E + P at high [S], kcat=Vmax

in transition metals color is associated with

unfilled d orbitals, electrons get promoted into higher energy orbital states.

paramagnetic

unpaired electrons (odd # of electrons), attracted to magnetic field

paramagnetic

unpaired electrons and attracted by an electric field

image distance -

upright and virtual

oxidation state equation

valence - bonded - nonbonded

product of combustion reactions

water and C02

what constitutes a buffer?

weak acid/base and its salt

the conjugate base of a weak acid is a

weak base

do weight and normal force form action reaction pair

weight and normal force do not form an action reaction pair

what is the best buffering region?

when the acid concentration is equivalent to the concentration of base

what makes an ideal buffer

when the pH=pKa

Newtown's Third Law

with every force there must be an equal and opposite reaction force acting on two diff bodies... example body exerts force on earth and exerts a force on body

power is equivalent to

work/time

Is helium a noble gas?

yes

are cultured cells considered a reasonable approximation for in-vivo cells?

yes

does histidine have an aromatic ring?

yes histidine has an aromatic ring with nitrogen

is ring closing thermodynamically favorable

yes, especially if the ring that is formed is a 6 membered right, a 6 membered ring is more thermodynamically favorable than a 4,5 , or 7 membered ring.

neutral solution most amino acids exist as

zwitterions

Diffraction

The bending of a wave as it moves around an obstacle or passes through a narrow opening

Q>keq

Then the forward reaction has exceeded equilibrium: 1) There is a greater concentration of products than at equilibrium. 2) The reverse reaction is increased to restore equilibrium. Delta G (forward reaction) is greater than zero

Q<keq

Then the forward reaction has not yet reached equilibrium. 1) There is a greater concentration of reactants than at equilibrium 2) The forward rate of the reaction is increased to restore equilibrium delta G (forward reaction) is less than zero

equation relating moles of gas and volume

V1/n1=V2/n2

When does entropy increase?

When dillution occurs, when ions are dispersed, when there are more moles of product than reactants, phase change entropy increases when a solute dissolves in solvent

When does refraction occur?

When the wave enters a new medium with a different index of refraction however, the light needs to enter at an angle relative to the normal

what determines shape in VSEPR?

# of lone pairs

factors that impact entropy

# of moles of reactants and products... if less moles in products then decrease in entropy phase change: entropy increases from solid-> liquid-> gas entropy increases if something is dissolved in solution

what determines geometry?

# of of groups

D notation

(+), cw rotation dextrorotary

L notation

(-), ccw rotation levorotary

epimer

*subtype of diatereomers *differ in configuration at exactly one chiral carbon

properties of enantiomers

- Same boiling point, melting point, and density - Same refractive index - Rotate the plane of polarized light in the same magnitude, but opposite directions - Different interaction with other chiral molecules

zero-order reactions

- have a constant rate that does not depend on the concentration of reactant - rate can only be affected by changing the temperature or adding a catalyst

oxidation number of nitrogen

-3

Delta G equation

-RTlnKeq

delta G not

-RTlnKeq

Delta G not

-nFEnotcell

what is the potential difference around any closed loop

0

E cell not

0.0592/n*log(k)

how many electrons does cytochrome c transfer

1 at a time, Fe2+ -> Fe3+

how many electrons are moved with cytochrome c

1 electron at a time

for a given temperature the specific rotation has only

1 value

newton's laws

1) an object at rest will stay at rest and an object in motion will stay in motion unless acted on by an outside force 2) F=m*a 3) every action has an equal and opposite reaction

frequency

1/s or number of cycles/s

NADH

2 electron transfers, does not react with O2

number of stereoisomers

2^n where n is the number of chiral centers

trigonal pyramidal

3 bonds, 1 lone pair

How many residues per turn in an alpha helix?

3.6 residues per turn

Average KE of a Gas

3/2*KT

how many rings in a steroid

4 (3 that are 6 membered, 1 that is 5 membered)

square planar

4 bonds, 2 lone pairs

pI of cysteine

5.07

pyranose

6 membered ring

octahedral

6-0 and sp3d2

1 Coulomb

A*s

F1

ATP synthase

Solubility Rules

Acetate (C2H3O2-) Group 1 SO4(2-)** Ammonium (NH4+) Group 17* SO4s will not be soluble if they are paired with a PMS (Pb, Mercury, Silver) or CASTRO BEAR (Ca, Sr, Ba). Group 17s will not be soluble if they are paired up with PMS.

Reactivity of carboxylic acid derivatives

Anhydrides > Esters/Carboxylic Acids > Amides

atomic weight

Average of the mass numbers of all isotopes

1 farad

C/V

first law of thermodynamics

Delta U=Q-W

Stuctural Isomers

Different covalent arrangement of their atoms

Energy of a photon equation

E=hf=hc/lambda E=hf equation gives the energy of a photon

potential of galvanic cell

E>0 which is spontaneous

Ecell

Ecathode + Eanode

Nerst Equation

Ecell=Ecell0-.0592/n*logQ or Ecell=Ecell0-RT/nF*LnQ

formal charge equation

Formal charge= valence-Nnonbonding-.5Nbonding

rate limiting step gluconeogenesis

Fructose-1,6-bisphosphatase

what activates phosphofructokinase

Fructose-2,6-bisphosphate (produced by phosphofructokinase 2 - activated by insulin and inhibited by glucagon) + AMP

GLUT 2 v GLUT 4 transporter

GLUT 4 -> normal cells (Adipose and muscle) GLUT 2 -> liver and pancreas

what do alkaline earth metals form when they react with water

H2 gas

list of strong acids

HCl, HBr, HI, H2SO4, HNO3, HClO4

where are hydrophobic side chains located in a protein

inside the protein

mutorotation

In solution, the hemiacetal ring of glucose will break open spontaneously and re-form to rotate between C-1 and C-2 to produce either the a or B anomer. This reaction would be named the __________ of glucose.

Irreversible steps of glycolysis

hexokinase, phosphofructokinase, pyruvate kinase

Irreversible steps of glycolysis

hexokinase, phosphofructokinase, pyruvate kinase large negative delta G exothermic

what is a gamma particle?

high energy photon, ionizing

Do ionic solids have high or low melting points?

high melting points

FE-S

holds 1 electron at a time

FE-S

holds 1 electron at a time, in complex's 1 and 3

Ubiquinone

holds 2 electrons, moves 1 electron at a time

FMNH2

holds 2 electrons, transfers 1 electron at a time found in complex 1

Apoenzyme + cofactor =

holoenzyme

fischer projection

horizontal lines (out of page) vertical lines into page

what determines if a material is electrically conducting?

if it has free electrons

if radius decreases what happens to pressure of a fluid?

if radius decreases the velocity increases. if the velocity increases then pressure decreases

how to tell difference between D and L sugars?

in linear form: highest oxidized group on top D: OH on the right L: OH on the left in cyclic form: go to the 5th carbon, highest priority chiral carbon in ring. R conformation -> D S conformation -> L

when counting carbons in a fatty acid

include carbon that is a part of the carboxylic acid

aromatic amino acids

include histidine

what does an enzyme do

increases the rate of a reaction, but does not change the chemical equilibrium