Chemical and Physical Foundations Section Flashcards
Chromatography
the separation of a mixture by passing it in solution or suspension or as a vapor (as in gas chromatography) through a medium in which the components move at different rates.
- The solute concentration will affect the size of the spots on the paper chromatogram, not the average migration rate.
- Thickness of the paper affects the amount that each component can be fully separated, not the relative migration rates of components.
- stationary phase will be an immobilized surface, not a solution.
- migration rate may depend on hydrogen bonding
amino acids
a group of organic molecules (organic is primarily made of carbon molecules) that consist of a basic amino group (NH2-), an acidic carboxyl group (-COOH) and an organic R group (side chain that Is unique to each amino acid). Each amino acid contains a central (alpha) carbon.
non polar amino acids
They are hydrophobic, in water, they will bury their side chains on the inside. (polarity is based on the side chain)
Nonpolar= alanine, valine, leucine, glycine, isoleucine, methionine, tryptophan, phenylalanine, proline
polar, uncharged amino acids
serine, cysteine, asparagine, glutamine, threonine, tyrosine.
must have at least one atom (N, S, O) with electron pairs available for hydrogen bonding to water and other molecules.
acidic amino acids
Aspartic and glutamic acid
Each has a carboxylic acid on it side chain which gives it electron donating properties. At a physiological pH, these amino acids will ionize, giving them a charge of -1. The ionic forms are aspartate and glutamate.
basic amino acids
arginine, histidine, and lysine. Each side chain is basic- meaning it can accept a proton
in dehydration reaction
-OH is lost from the carboxyl group and an H is lost from the amino group. This will take a molecule of H2O and leave an amide linking two amino acids.
Carbocation intermediate
SN1, E1, and alkene addition reactions will have a carbocation intermediate.
carbocation intermediate from Alkene addition
adding strong acid to an alkene gets us a carbocation
strong acid
any acid that ionizes completely in a solution. That means, a great number of hydrogen ions or protons will dissociate. Strong acids are able to conduct electricity.
HClO3, HBr, HCl, HI, HNO3, HCLO4, H2SO4
Good nucleophile
A good base is usually a good nucleophile. So, strong bases — substances with negatively charged O, N, and C atoms — are strong nucleophiles. Examples are: RO⁻, OH⁻, RLi, RC≡C:⁻, and NH₂⁻. Some strong bases are poor nucleophiles because of steric hindrance.
SN1 reaction
The SN1 reaction is a substitution reaction in organic chemistry. “SN” stands for “nucleophilic substitution”, and the “1” says that the rate-determining step is unimolecular. Thus, the rate equation is often shown as having first-order dependence on electrophile and zero-order dependence on nucleophile
The SN1 reaction mechanism involves an intermediate carbocation that is formed by loss of the leaving group. A nucleophile can react with the planar carbocation from either side, leading to the inversion or retention of the configuration at the site of the substitution.
Electrophile
In chemistry, an electrophile is a chemical species that forms bonds with nucleophiles by accepting an electron pair. Because electrophiles accept electrons, they are Lewis acids.
Good Electrophiles
Good electrophiles typically contain weak polar or polarizable bonds. This means that electrons can favor one side of a bond over the other, creating dipoles.
carbon-centric
Organic chemistry is carbon-centric. Carbon is the key atom in these reactions and carbon atoms do some very predictable things- like many four bonds.
Cis and Trans Isomers
cis isomer has two groups on the same side. Trans isomer has two groups on opposite sides.
Non polar molecule identification
Non polar molecules will be made up of one element. For example, N2, O2, Cl2, and noble gases are non polar. Containing only carbon and hydrogen is non polar. Does the molecule have symmetry?
CO2 is non polar, for example. I-Br is also non polar because the electronegativity difference between the atoms is not great along the bond.
Polar molecule identification
If hydrogen is directly attached to N, O, F, it is polar. Ex, water, CH3OH (presence of alcohol), CH3COOH, if molecule lacks symmetry and the bond is polar then it will be a polar molecule.
stereospecific
A reaction in which the stereochemistry of the reactants controls the outcome of the reaction. In general, one stereoisomer of certain reactant produces one stereoisomer of a certain product, whereas a different stereoisomer of the same reactant produces a different stereoisomer of the same product. You wouldn’t end up with a mixture of cis and trans alkenes in the product.
aldehyde
Carbon atom shares a double bond with oxygen, a single bond with H, and a single bond with R. Derived from alcohols.
H-C-R
=O (the equal sign should be vertical). That is the carbonyl group.
Carboxyl group
Same as Aldehyde except for there is an O where the H would’ve been. A carboxyl group can react with an amine to form a peptide bond.
amine group
Contain basic nitrogen atom with a lone pair. These form peptide bonds. The conjugate base of an amine is also called an amide (like the bond that is made when a peptide is formed).
amine group
Contain basic nitrogen atom with a lone pair. These form peptide bonds. The conjugate base of an amine is also called an amide (like the bond that is made when a peptide is formed).
alkyl
contains only carbon and hydrogen atoms in a chain. Ex: CH3.
backside attack SN2
results in an inversion of configuration where the product’s configuration is opposite of the substrate’s. Inversion at the carbon that bears the leaving group.
steric hindrance
At a secondary carbon, there is more crowding from the adjacent carbon chains, which makes nucleophilic substitution slower.
1,2 hydride shift
carbocation rearrangement which a hydrogen atom in a carbocation migrates to the carbon atom bearing the formal charge of +1 (carbon 2) from an adjacent carbon (carbon 1)
least to most stable carbocations
primary= least stable, secondary, tertiary- most stable.
A primary carbocation is attached to one other carbon, a secondary to two, and a tertiary to 3 other carbons.
how does a carbocation form
A carbocation is an organic molecule, an intermediate, that forms as a result of the loss of two valence electrons, normally shared electrons, from a carbon atom that already has four bonds.
This is a carbon atom bearing a positive charge where it’s fourth bond should be. It wants to have four bonds but if it has 3, it could be a carbocation. Positively charged species would mean that they are electron-poor.
in gas to liquid chromatography:
the first peak to emerge will be from the least polar, most volatile compound. 2-Methyl-2-butene is nonpolar and the most volatile because it only has London forces for intermolecular attraction. (no dipole will mean no force of attraction).
Larger and heavier molecules typically have stronger dispersion forces than smaller, lighter ones.
Look for the non polar option to be the most volatile, and the first peak- those that interact the fastest.
S v R stereochemistry
When determining from heaviest to lightest and excluding the H, left is S (think of how you would begin drawing it) and right is R (think of r and R)
When determining organic chem products
Count the carbons, look for configuration (look at what atoms were replaced when determining configuration).
which reactant loses the -OH group?
an oxygen atom on ethanol must be radiolabeled. 100% of the alcohol will be retained in the ester. Acetic acid only supplies OH that is lost to form water.
Eye lens is a converging lens.
The negative sign of lens strength is indicative of a diverging lens. When solving these problems, for example, 0.02^-1, but 1/0.02^1, I multiplied each and got 0.5 which is like 50.
If you want to slow the ionization of a compound in a solution…
you could add a strong acid because it will increase the amount of H+ in a solution and therefore decrease the amount of other compound that is ionizing.
diluting a solution would…
increase the amount of ionization occurring. From Le Chatelier’s Principle, adding water to the equilibrium would cause the equilibrium to shift to the right. A shift to the right implies that more acid would be in dissociated form, and thus the percent ionization increases accordingly.
Ohm’s law
according to Ohm’s law, current is equal to voltage divided by resistance. If current increases and resistance is constant, then voltage increases as well.
V=IR
I=V/R
current through a conductor between two points is directly proportional to the voltage across the two points.
Math tip: division of numbers that aren’t whole
The MCAT will give options that look wrong, looks right, and are right- for example. 3/2.1
answer options:
0.7, 2.1, 3.0, 1.4. Think to yourself: how many times does 2.1 go into 3? If you think of it that way, you can easily rule out options.
Intensity of radiation emitted:
The energy of electromagnetic radiation equals to the number of photons, and the intensity of electromagnetic radiation, and is defined as energy emitted per unit time.
Intensity of radiation is not related to propagation speed, wavelength, or polarization state- but to the number of photons emitted per unit of time and their respective frequency.
1 THz (tetrahertz) =
1012 hertz
so 610 THz= 610 (1012) hz
practice math problem
610 THZ) (6.6x10^-34)= ? (4.0 x10^19
- multiply 610 by 1012 to get in Hz= 6.1 x10^12
- multiply the whole numbers first… like 6x6 is 36 (and look for answer with a little more)
- Then, focus on exponentials… -34 + 12 is 19, 20… close to that is 19
MCAT doesn’t give calculators so be creative and think your way around these math problems like you always do.
substituting equations
Ex problem: Substitute Pp = Ps – Pd into equation PMPA = Pd + (Ps – Pd)/3.
- Substitute Pp into the parentheses because they are equal.
- write as PMPA= Pd + Pp/3.
- To match up with correct answer option, I could multiply each part by 3. For example. 3PMPA= 3pD + Pp, then rearrange to Pp= 3PMPA- 3pD. That’s simple algebra- think back to 8th grade! You got this.
When you looked at this one, you talked your way through it. You’re smart… you know what you’re doing. Pull off of old material I’ve learned. If you think you have an idea of the answer, you probably do.
Work (w)=
J/s, so calculated answer will be in joules… change to appropriate unit. For example, if options show kJ, take away 3 decimal places.
disulfide bridges S-S
intermolecular covalent bonding
intramolecular v intermolecular
intramolecular hold atoms together within molecules while intermolecular hold molecules together within a compound.
aliphatic
carbons form open chains, not aromatic rings
Cross-linking region is different from the
cell adhesion region
For amino acids that make electrostatic interactions/ aid in cell adhesion/ stability, look for:
polar/acidic- not non polar (side chains that can participate in electrostatic interactions)
Phosphorylation occurs at
free hydroxyls (Ser, Thr, Phe) in that order.
pH dependence of aggregation depends on
side chains whose net charges respond to pH. Not hydrogen bonding, long alkyl tails (ldfs), covalent linkages, etc.
Velocity of blood flow depends on
total cross-sectional area- not elasticity. If larger area, less velocity. So, arteries have higher velocity due to smaller cross-sectional area.
oxidation is
losing an electron. For example, Fe2+ to Fe3+. Lose negatively charged electron means become a more positive charge.
orbitals for octahedral compounds
d2, sp3
What assumption is made about ideal gases?
individual molecular volume and intermolecular forces are negligible
a variety of opsonins function to
enable the detection of different colors
Retinal binding site would be hydrophobic because…
it is PRIMARILY composed of hydrogen, carbon- making it largely hydrophobic.
A positively charged binding domain is well suited for positioning substrates that
have areas of negative charge.
What are the hybridization states of the carbon atoms involved in the conversion of trans to cis retinal?
sp2
In rate laws, m + n equal ___ for second order
2
To determine how much Pb2+ will precipitate, you must know its
solubility (Ksp= solubility product constant)
Indicators will change color over a specific pH range. For example, HI- will change to ___ past this range.
I-; therefore you must know the pKA of HI to determine when a pH color change would occur.
Formal Charge Calculation
FC= Valence Electrons (VE)- (bonds + dots) attached to the element
carbocation
carbon atom with a positive formal charge. C+
radical
formal charge= 0
Radicals tend to be neutral
aldehyde vs. ketone
carbonyl (c=o) bonded to hydrogen (at the end of the chain is aldehyde) in the middle= ketone
ether
oxygen atom between two carbon atoms
ester
two oxygen atoms and a carbonyl group
carboxylic acid
COOH- when you combine a carbonyl and hydroxyl group
Group 1 periodic table
+1 charge, alkaline metals
Group 2 periodic table
alkaline earth metals, +2, 2 valence electrons that they typically give away
Group 3 (to the right)
form +3 charges
Group 4
form +2 charges mostly
Group 5
tend to form negative charges -3, N, P especially
Group 6
Like to form -2 charges
Group 7 Halogens
form -1 charges (7 valence electrons). They are extremely reactive
Group 8 Noble Gases
Typically don’t interact- very stable
Common Transition Metals
Ti, Cr, Mn, Fe, Co, Ni, Cu, Zn, Ag, Au, Cd, Hg
Acids typically have ____
and H in front of them: HCl, HF, HC2H3O2. Typically attached to a nonmetal. If Hydrogen has a positive charge, it’s an acid. If it has a negative charge, it’s a case. Usually positively charged. Acids usually release H+ ions into the substance. Bonded to water so it exists as H3O+.
Bases typically…
Have hydrogen next to a metal, Like NaOH, NaH, KOH. Hydrogen has a negative charge. Releases OH ions into solutions.
Bronsted-Lowry
Acids are proton donors, bases are proton acceptors. Acid turns into the CB and the base turns into the CA. For example, HCl + H20= Cl-(CB) and H3O+ (CA)
pH + pOH = 14
pH= -log [H3O+], pOH= -log [OH-]. To find concentrations, it is a calculation of 10^-pH. They are all interconnected. I remember this from chemistry in the summer.
Common Strong Acids
HCl, HBr, HI, HNO3, H2SO4, HClO4
common weak acids- don’t ionize completely
HF, NH4+, acetic acid (HC2H3O2), HCN, HNO2, H2SO3
more oxygens means more acidic
why? Trend only works for comparing those with oxygens.
when writing equations, double arrow is used for reversible equations that contain
weak acids that don’t ionize completely
strong bases v weak bases
strong= ionize completely (KOH, NaOH, Ba(OH)2). weak= doesn’t ionize much (Al(OH)3), F-, NO2-, C2H3O2-, N-
Ka value
acid dissociation constant. Equation= [concentration of the products]/[concentration of reactants]. As Ka increases, the acid is stronger, but the pKa decreases. pKa= [-logKa]
Water (H2O) can act as both
an acid and base- depending on the other reactant. It is known as amphoteric- it can accept a proton or donate a proton. Another example= H2PO4-
Kw= 1x10^14
auto ionization constant for water. Same equation as for Ka and Kb. [concentration of the products]/[concentration of the reactants]. Kw is dependent on temp. As temp increases, Kw increases and more ionization occurs.
For most chem problems, if no temp, assume to be
25 cel or 298 K (temp + 273)
pKa + pKb=
14
Ka x Kb =
Kw
A strong acid will have a pKa _______
less than zero
MATH TIP EXAMPLE Q
How many moles of Cl- ions are found in 4.93 (round up to 5) L of 0.096 (round to 0.1) molar solution? Round numbers and guesstimate from there. Multiple numbers.
On the MCAT, close enough is…
…good enough. When it comes to math rounding, for example.
F=ma
Force (N)= mass x acceleration
converting g to m/s^2
For force equation, convert g to kg because Force= kg/m/s^2
1kg=
1000g
Another example math question:
0.089 x 213
1. round each number
0.09 x 200
2. multiply one by 100, and divide the other by 100.
9x2= 18
23 x (4.67/4.67)=
23
In math problems, use Leah4Sci method of making the smaller number bigger, and the bigger number smaller. Usually to get rid of decimals because they are confusing. As long as you don’t change the full identity of the question. For example:
0.05 x 400
multiply smaller by 100
divide bigger by 100
5x4= 20
Exponent addition example:
- 3x10^-3 + 5.6x10^-3
1. If the exponents are the same, just add the coefficients.
Exponent addition example:
When exponents are different: 5x10^-6 + 4x10^-5 1. Choose one number multiply or divide exponent by 10, and make sure you do the opposite to the coefficient of that number to justify it. 2. Now it is 50x10^-5 + 4x10^-5. For proper scientific notation: 3. 54x10^-5 should be 5.4x10^-4
Finding Molarity
M= mol/L
When multiplying numbers with exponents…
multiply the coefficients and add their exponents.
For dividing numbers with exponents…
divide the coefficients then subtract your exponents.
10^3 divided by 10=
10^2
For molarity questions (example finding hydronium ion concentration given the Ka)
Ka= x^2/Mi
1. H+ concentration= x
Example math question:
0.05 x 1.8x10^-5
1. multiply left side by 100 and divide right side by 100.
(for exponents, they drop by 1 for each division by a factor of 10).
the square root of 1x10^-6=
1x10^-3 (divide by 2 if the exponent that’s being squared is an even number)
the square root of x is x raised to the half power x^1/2. So, to solve
When an exponent is raised using another exponent, just multiply the exponents.
Vf^2= Vi^2 + 2a delta x
Standard kinematic equation used in physics to track the motion of an object, neglecting friction. In this equation, x stands for position. Essentially the change between final and initial position of object. If dealing with height and gravitational acceleration, we can change the a to -g (for gravitational acceleration), and the x to y for height. When an object reaches its maximum height, the velocity at the top will be zero.
On the mcat, you can use the value ___ for gravitational acceleration.
10
Solving for moles
Set up dimensional analysis using given times ratio
1. 1 mole of something = its molar mass. If a compound, add molar masses of all elements. (round molar masses on mcat)
Gravitational Force Equation
F= gmm/r^2. One m is the mass of a planet and the other m is mass of an object
SOHCAHTOA
Used to find Sin, Cos, and Tan from a triangle. Sin typically refers to your y value (son) you cos typically refers to your x value (cosx). Tan is usually y/x
To find force in the x direction for a problem
multiply the force by the cos of angle value we got. Think of shortcut table from Leah4Sci
finding the -log of a value
log base 10
1. Ask, “10 to what power is equal to this number?”
2. Example. -log(0.1)= 1 is
1x10^-1, think of scientific notation= 0.1
