AAMC SB CPF

Question 1

k cat

Answer 1

describes the rate limiting step of catalysis under saturating conditions of substrate

Question 2

michaelis menten kinetics

Answer 2

describes a hyperbolic dependence on Vo on substrate conditions

vs linear when 1/Vo (y axis) and 1/[S] (x axis)

know the equation
V = (Vmax * [S] ) / ( [S] +Km)

Question 3

ion exchange columns

+ elution

Answer 3

Ion-exchange columns will bind the matching ion; strength of binding depends on overall charge of the peptide → eg. an anion exchange column will bind anions

Even if they are able to bind, small net charges will be more easily eluted than those with larger net charges → eg. a -1 net charge peptide will be eluted from an anion exchange column before a -5 net charge peptide is

Question 4

visible light wavelength

- what colors absorb what

Answer 4

Visible light wavelength is about 350nm to 750nm (reverse ROYGBV)
– Red has the longest wavelength at about 750nm while purple / violet has the shortest at about 350nm

Thus, colors will absorb their complement.

• • Determine complements by drawing a circle, cutting it into six slices, and going around labelling them w one letter each from ROYGBV.
• • Complement colors will be across from each other.

Eg. If your compound is yellow, then the complementary color purple will be absorbed the most; purple is at the end of the spectrum w the smallest wavelength so about ~350nm.

Question 5

describe the hydrolysis of a glycosidic linkage

Answer 5

The cleavage reaction described is a hydrolysis of the glycoside linkage in a disaccharide. The deprotonated water attacks the galactose and so this sugar will be labeled with O-18. The glucose is protonated and acts a leaving group without reacting with an oxygen atom provided by water.

Question 6

affinity chromatography

+ example of tagging

Answer 6

separates biomolecules based on a specific binding interaction between a ligand and a binding partner

isolation of a particular protein of interest

eg. insert histidine tag with gene of interest, thus producing protein of interest that is tagged – histidine tag interacts with nickel column, thus is not eluted and can be washed out after

Question 7

SDS PAGE
native
reducing
nonreducing

Answer 7

native = doesn’t change the protein in anyway

reducing = breaks the quaternary structure (aka denatures) and the disulfide bonds

non-reducing (aka denaturing) = only breaks the quaternary structure
– affects dimers / trimers / etc but does not affect disulfide bonds

Question 8

what does the stability of both DNA and RNA depend on

Answer 8

largely dependent on the number of GC base pairs contained with the folded structure

thus would want to replace as many AT or AU pairings as possible with GC

this is bc GC base pairs interact w more hydrogen bonds (3) than AU base pairs (2)
– more H bonding = more stability in folded structure

Question 9

Tm

Answer 9

temperature at which 50% of the molecules are denatured or the fraction folded is 0.5

Question 10

catalytic efficiency

Answer 10

kcat/Km

Question 11

ketose vs aldose

Answer 11

An aldose sugar contains an aldehyde functional group in its structure; ketose sugars contain ketone functional groups.

Aldose sugars are reducing; ketose are non-reducing.

eg. glucose is a six carbon aldose but fructose is a six carbon ketose

Question 12

reducing vs nonreducing sugars

Answer 12

If the anomeric carbon has on -OH attached to it, it is considered a reducing sugar. If it doesn’t, it’s considered a nonreducing.

Aldose sugars are reducing; ketose are non-reducing.

Question 13

hydrogen bond acceptors / donors in base pairs

Answer 13

acceptors = N and O
donors = H's on N/O

Adenine: 1 donor and 1 acceptor

Thymine: 1 donor and 1 acceptor

Guanine: 2 donors and 1 acceptor

Cytosine: 1 donor and 2 acceptors

Question 14

Thermal denaturation experiments can be used to follow the transition of double-stranded DNA into single-stranded DNA. What affects the Tm of dsDNA in this experiment and how? (3)

Answer 14

pH of solution → drops in pH can lead to protonation of interacting base pairs, thus reducing their hydrogen bonding interactions

Ionic strength of soln → presence of cations can stabilize the negative phosphate groups on DNA by shielding the effects of electron repulsion

Longer DNA strands → more base pairs mean more bonds to break, requiring more energy

Question 15

The side chain of which amino acid can form a bond that is similar to a peptide bond?

Answer 15

lysine side chain can form isopeptide bonds by reacting with a carboxylic acid group, which is the same way that peptide bonds are formed

Question 16

the unfolding of proteins is ____

Answer 16

cooperative; graph is marked by sigmoidal curves

Question 17

what factors of blood determine the force of viscosity

Answer 17

reduced viscosity force in smaller vessel diameters which increases in larger diameter vessels bc the coefficient of viscosity of blood is directly proportional to the frequency of interactions of erythrocytes with the vessel walls

Question 18

magnetic force equation Fm

Answer 18

Fm = q * v * B where q is the charge, v is the velocity, and B is the magnetic field

Question 19

Volume flow rate (Q)

Answer 19

Q = volume / time = (area * distance) / time = area * velocity

For flow through pipes or arteries, area can be found as pir2 or 0.25pid2

Question 20

magnetic force acts on a moving charge in a direction that is _____

Answer 20

perpendicular to both the velocity of the charge and the direction of the magnetic field

This is a basic law of the interaction of electric currents and magnetic fields.

Question 21

after a block begins to slide, how does its speed varies w time?

Answer 21

coeff of kinetic friction is less than that of static, thus there is a NET ACCELERATING FORCE on the block once it starts to slide

F = ma, thus the velocity of the block increases linearly w time

Question 22

time of something thrown in the air; round trip

velocity something hits the ground with when dropped from rest

how far something has been dropped

max height of something thrown straight in the air

Answer 22

t = 2v/g

v = a*t

h = 0.5(g* t squared)

h max = - (v squared) / (2a)

Question 23

why does sound get muffled when it moves through a wall

Answer 23

Sound wave are reflected and absorbed when incident on materials just as light waves are. In doing so the waves are reduced in their forward intensity (units of J/m2).

When a wall is placed between a source of sound and the listener, some of the sound energy is transmitted to the listener, but some is reflected and sent backward toward the source or absorbed in the material. The listener hears less sound, but at the same frequency and wavelength as the unimpeded sound.

Question 24

torque

Answer 24

torque = mgdsin(theta)

Question 25

nodes and wavelengths

Answer 25

half wavelength has a node at each end; the spacing btwn nodes is wavelength / 2

Question 26

Standing wave pattern; superposition of two traveling waves

• amplitudes
• directions

Answer 26

equal amplitudes

opposite directions

Question 27

resistance

Answer 27

resistivity * (length / area)