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AAMC section bank chem/physics

Terms in this set (67)

formula for electric field
E= V/d
know the structure of hydroquinone and benzoquinone
...
frequency/ wavelength
they are inversely proportional to each other...meaning that if the frequency is double the wavelength will be halved
determining perfect laser/photon energy
Looking at the diagram, you can see that the basic flow of energy goes from laser (photon energy) --> cell excitation on the lens (releases heat, causing sound waves) --> microphone --> and is ultimately picked up by the energy meter in some form.

When the laser/photon energy is just right, that means no excess heat is released from bond breakages inside the cell, and therefore no sound waves are produced. Thus the energy meter will read 0!
what must be true to break a bond?

1. energy emitted must have higher frequency that that of bond
2. it must emit fewer photon
3. longer wavelength
in order to break a bond, the radiation frequency must be above the threshold aka high. frequency is directly proportional to photons emitted.
kinetic energy
KE= hf- work function
Energy in term of h, n, f
E=hf=hc/y

n=c/ny
which is best way to extraction (extraction technique)
if the reaction product contains mostly acids, you want to add bases to hydrolyze --you will be left with neutral layer that you can then extract.
Which extraction procedure will completely separate an amide from the by-product of the reaction between an amine and excess carboxylic acid anhydride?
Add 0.1M NaOH (aq) to quench unreacted anhydride. Then add diethyl ether and separate the layers. The amide can be obtained from the ether layer by evaporating the solvent.

this basically takes advantage of the fact that when you mix COOH anhydride+amine= you will get amide and Carboxylic acid. since excess carboxylic acid anhydride is being used, all the reaction will be converted to amide.
--quenching something means to make it unreactive.
if intensity max is 80 dB and intensity min is 30 dB, what is the ratio of max/min?
1x10^5

Imax= Iox 1x10^8

I min = Io x 1x10^3

I max/I min= 1x10^8/1x10^2
what does it mean when the voltmeter is equal to 0?
if voltmeter reads 0 then there is 0 potential difference between the two points in the circuit. this means that current is still flowing, if the voltage source was unplugged then no current would be flowing---which is not the case rn
---if voltage drop at R was 5V R1 would also be 5v or somewhere close to this value.

--if the voltmeter was not same, then voltage in R1 and R would not be the same.

refer to Q 17 in your notebook
what is pyrophosphate
it is two phosphates joined together
(Pi)
phosphonic acids
phosphates with OR, OH group
phosphatides
type of fatty acid/phospholipid
why do liposome fluoresce during size-exclusion chromatography?
bc the fluorescent was trapped inside. this is a good way to detect liposome presence

-liposomes are difficult to detect bc they do not absorb visible light; they only absorb UV light

Fluorescent dyes are non-protein molecules that absorb light and re-emit it at a longer wavelength.
identifying kinetic vs thermodynamic
kinetic produces largely irreversible reaction. new product is formed most quickly

thermodynamic: lower free energy aka more stable product; major product in the solution; it can be reversed to form more stable product
cobalt (II) electron configuration
loss of 4s electrons

[Ar]3d7
measure of catalytic efficiency
ratio of Kcat to Km
why would one want to deprotonate a water molecule
to make it more nucleophilic such as by glutamate so it can attack the electrophilic carbonyl
follow the step of this reaction: a deprotonated water and carbonyl (peptide hydrolysis mechanism)
water is deprotonate, becomes more nucleophilic and attacks the spa electrophilic carbon. the double bond break and now we have sp3 structure. The c=o is too unstable so it forms right back up and becomes sp2 again.
hydrolysis mechanism described in passage 5
It does this by adding water to the carbonyl carbon of the terminal peptide bond. So, the mechanism says that the glutamate residue deprotonates water molecule to create a hydroxide (good nucleophile), which then attacks the carbonyl carbon in a nucleophilic addition reaction. So the carbonyl carbon is now a tetrahedral intermediate with four substituents bonded to it. So it went from sp2 to sp3. To complete hydrolysis, the double bond between the oxygen and carbon reforms and the C-N bonds breaks. So the hybridization of the carbon atom changes back to sp2.
what is the best way to minimize interaction between the side chain and the active site of the enzyme?
the best way to do so is by adding an amino acid that minimally alters the structure of the enzyme but also eliminates the interaction of each side chain with the active site. ex: replacing E with A.

Alanine participates in alpha and beta sheets extensively, which is useful for keeping the structure intact.
"assuming something.."
when STEM states this, they are asking you to assume something so you can eliminate confounders and look for answer directly in the passage through a given data point or something.
"substrate binding"
look at the rate of Km
catalytic turnover
look at Kcat data

(also termed kcat) is defined as the maximum number of chemical conversions of substrate molecules per second that a single catalytic site will execute for a given enzyme concentration .
HEW lysozyme (1.0 mL, 0.1 mM) was titrated with 25 injections of NAG3 (10 µL, 2.5 mM) in the presence of various amounts of NAG and the heat associated with each injection was measured.
What quantity of NAG3 was required to reach the equivalence point in the titration?
the key word in this question is various amount of NAG...we are given a set amount of HEW. we use this set amount to find a mol based on the M given (1.0mLx.1mM)= 100nmol!!

the ratio presented in passage is 1:1 mol of both HEW and NAG3, which means that we need 100nmol to neutralize NAG and vice versa

***

usually "X is titrated with Y" means that X is the unknown concentration and Y is the titrant.
To get to the equivalence point, you need to match the amount of moles of NAG with the amount of moles of HEW lysozyme. Therefore, you calculate the number of moles of HEW lysozyme with the information already given.
Ka
affinity constant, the higher the Ka, the lower the Kd and Km. Kd and Km are interchangeable on the MCAT

Ka= [ES]/[E][S]
Km and Kd is inverse of Ka: [E][S]/[ES]

if Ka is high, then more product can be made (think equilibrium constant)
addition of second substrate on the rate or affinity constant
addition of second constant means that the enzyme is interacting with ONE another substrate now and the affinity changes (affinity increases -competitive inhibitors). so if you wish to decrease the affinity constant between 1st substrate and the enzyme--you would just add more of the second substrate.
when performing experiments to measure the Kcat of an enzyme, the substrate concentration should be:
saturating

Kcat is used to describe the rate limiting step of catalysis under the saturating conditions of substrate.
what is the shape of Vo versus substrate concentration of tradition MM kinetics?
the answer is hyperbolic dependence on [S].

I originally thought it was sigmoidal but apparently it's not!
uncompetitive inhibitor
results in lower apparent Km and Vmax
At pH 7, which of the following peptides will bind to an anion column and require the lowest concentration of NaCl for elution?
this question is basically asking "Which negative charge peptide has the least negative charge."

If it asked for largest amount of NaCl to elute, then you would look for most amount of negative charge present.

Anion exchange column pulls down anion. you also want the least amount of salt to elute out..the salt functions to compete with the stuff that is bound to stationary phase aka anionic peptide in this case. The more negative it is, the higher the connectration of salt you will need to outcompete the peptide.
anion vs cation column chromatography
they are both type of ion exchange chromatography

Anion exchange chromatography is a type of ion-exchange chromatography. Anion exchange columns are packed with resins that contain positive charge which pulls down negatively charged peptides. Conversely, cation exchange columns are packed with resins that contain negative charge which pulls down positively charged peptides. I like to remember the names as what they pull down - anion exchange takes out anions and vice versa.

HIPAGEATEKALRGD

go over the side chain pKa and the charges that protein carry at physiological pH.
which experimental technique was most likely used by the students to determine the rate of reaction--given that that substrate was chosen based on the fact that it produced a yellow colored product?

A. monitor increase in absorbance of the solution at 200nm
B. monitor increase in absorbance of the solution at 360 nm
C. monitor decrease in absorbance of the solution at 360 nm
the answer is B. you want to monitor the complementary color absorbance aka purple, which is complementary to yellow. (at 360 nm)
if you label water with 18-O tag and follow a reaction of lactase catalyzed hydrolysis of lactose, which produces galactose and glucose, where will the tag show up?
https://upload.wikimedia.org/wikipedia/commons/thumb/c/cd/LactaseMechanism2.png/500px-LactaseMechanism2.png

this is a hydrolysis reaction, where the lactose is broken down into galactose and glucose. Glucose leaves as a leaving group. The tagged water is deprotonate by glutamate--which acts as a nucleophile and attacks the galactose--so this sugar will be labeled with O-18 tag.

the glucose is protonated and acts as a leaving group without reacting with oxygen atom provided by water
purpose of deprotonation vs protonation in terms of nucleophile and electrophile?
deprotonation step occurs to make something a better nucleophile where protonation of an atom is done to make something a good leaving group.
linearweaver burk, calculation of Km/Vmax
Y intercept : 1/ Vmax
X intercept: -1/Km(negative side indicates that its on the -side of graph)
Slope: Km/Vmax

Given [S]= .05, what is Km?
1/.05= 20 mM

suppose that the Vmax line crosses at .4 at Y axis, calculate Vmax.

Y= 1/vmax= .4
1/.4= 2.5 is the Vmax.

Vmax is determined as the inverse of the Y- intercept in the graph shown
imagine you dilute 25 mL buffer with .10 mL solution. initially you had mixed 1 mL enzyme with 1mL substrate, what is the concentration of enzyme in this?
25 mL dilute with .1 ml is 25/.1= 250.
and since you mixed 1+1= 2 ml of further dilution
250 x 2= 500
effect of biotin on DNA
it stabilizes the DNA structure by binding to it tightly just like methyl does
"relative to rate under condition 3"
means that the condition 3 is used as control
avidin
binds to biotic with high affinity and is useful for tracking desired outcome in experiment like fluorescence tags.

if avidin was immobalized then then it would not travel. If it did not bind to some type of substrate then it would be invisible to us, bc we wont be able to track that substrate
homodimer
a protein dimer is a macromolecular complex formed by two protein monomers, or single proteins, which are usually non-covalently bound.
in non reducing form
proteins act like monomers
how would this protein travel as under SDS PAGE non reducing condition: disulfide linked homodimers comprised of 19kDa monomers?

2. homotrimer comprised of 25 kDa monomer
they would travel as 19+19= 38 kDa bc since it is a non reducing situation, the disulfide links would not be broken to separate the protein

2. each of them would travel as their own monomer, aka they will have 1 kDa mass each
how many mol of NADH is needed to reduce 4 disulfide bond?
each can reduce 4 bonds, so we need 4 molecules.
which protien would have the highest net negative charge at pH 7?

a. protein that would bind to anionic-exchange column and require a high concentration of NaCl for elution
B. protien that binds to catio-exchange column and requires a high concentration of NaCl for elution
protein that would bind to anionic-exchange column and require a high concentration of NaCl for elution
does a more compact or less compact structure migrate further?
more compact

Smaller molecules and more compact molecules will move farther in gel electrophoresis. Compact means higher density essentially. So like the same number of nucleotides, but clumped together more. (think euchromatin vs heterochromatin). Smaller size, but same weight and number of nucleotides.

note: folded structure usually tend to not travel in gel electrophoresis
Tm
the temperature at which 50% of the molecules are denatured and 50% is folded.
interaction with backbone
amino acids that can't h-bond such as glycine
which has highest catalytic efficiency, looking at kcat and Km?
look for one with highest Kcat and lowest Km value
low Vmax, what does this say about km?
it means that less of the substrate will be needed to reach Vmax, so km will be low.
"enzyme is unfolded"
if this was the case then the enzyme would stop showing any type of activity aka no value to Km/kcat etc.
the amount of H -bond donor and acceptor in DNA bases?
adenine contanis 1 donor and 1 acceptor, thymine contains 1 donor and 1 acceptor, Guanine contains 2 donors and 1 acceptor, cytosine contains 1 donor and 2 acceptor.
thermal denaturation experiments can be used to follow the transition of double stranded DNA into single stranded DNA, which would affect the Tm of ds DNA?

I. pH of solution
II. Ionic strength of solution
III. length of DNA strands
all of them! they would all effect the thermodynamic stability of the DNA double helix.

drop in pH= protonation of H-bond acceptors, leading to loss in base-pairing interactions

presence of + ions in solution, especially Mg2+ leads to stabilization of DNA via fold shielding of the repulsion between phosphate group within the DNA backbone.

length of DNA strand plays a tole as well, more energy would be required to denature the dsDNA the longer they get bc they are held together by more H-bonds
which nucleoside has the largest MW?

A. adenosine
B. guanosine
C. deoxyadenosine
D. deoxyguanosine
answer is B. RNA bases/nucleoside have large MW than DNA due to presence of extra OH on 2'. and guanosine is larger than adenosine due to presence of carboxyl.
amino acids likely to increase pI
basic amino acids

HKR
maltose
reducing disacc in which only one of the anomeric carbon in onvolved in the glycosidic bond
specific activity
measure of solution purity
acitivity unit

total protein concentration: 3000
spicific activity initally : .1 units/mg

final step: total p conc: 3
specific activity: 20

what is the purification yield?
provide the best measurement of yield

3000x.1= 300
20x 3= 60

60/300= .2 or 20%


total protein/ specific activity
phosphate in h-bond?
phosphate can be stabilized by H-bonding bc the P is negatively charged which is stabilized by partially + charged Hydrogen .
salt-bridge interaction vs h-bond
X−H⋅⋅⋅⋅Y-- H bond tend to be between 3 atoms and are directional interaction.

Salt bridge interaction is a type of electrostatic interaction and occurs between the centre of positive and a negative charge.
how many band are observed in Native and SDS-PAGE considering the molecule is homodimer?

what if they were heterodimer?
So in SDS PAGE, a detergent and reducing agent are used to break the quarternary structure of the protein, while Native PAGE does not break the quartenary structure. Since the Native PAGE does not separate into subunits, if your sample is pure, you should expect one band representing the entire protein.

Breaking the protein into subunits can result in multiple bands. Identical subunits will result in the same band since SDS separates material by mass. In this case, a homodimer (protein with two subunits, both identical) will only show one band in SDS because the subunits are identical. If it is a heterodimer (two subunits, not identical) two bands will show in SDS since the two subunits have different masses. Tetramers and beyond can potentially show more bands, depending on whether or not there are repeating subunits.
be familiar with the structure of glycerol
it contains Oh, which can H bond umm look it up lol
phosphorylation of a certain compound
structural change
ordered vs random mechanism
ordered: all the substrates are first bound to the enzyme in a defined order or sequence. The products, too, are released after catalysis in a defined order or sequence.

random: the substrates and products are bound and then released in no preferred order, or "random" order.
presence of cysteine in a code of amino acids
means that a covalently linked dimer would be formed
viscosity force in a small diameter
decreased/reduced; increases in larger diameter vessel

--less viscosity = travels faster such as in small diameter where the velocity increases.
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