AAMC SB CPF Flashcards
k cat
describes the rate limiting step of catalysis under saturating conditions of substrate
michaelis menten kinetics
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)
ion exchange columns
+ elution
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
visible light wavelength
- what colors absorb what
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.
describe the hydrolysis of a glycosidic linkage
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.
affinity chromatography
+ example of tagging
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
SDS PAGE
native
reducing
nonreducing
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
what does the stability of both DNA and RNA depend on
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
Tm
temperature at which 50% of the molecules are denatured or the fraction folded is 0.5
catalytic efficiency
kcat/Km
ketose vs aldose
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
reducing vs nonreducing sugars
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.
hydrogen bond acceptors / donors in base pairs
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
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)
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
The side chain of which amino acid can form a bond that is similar to a peptide bond?
lysine side chain can form isopeptide bonds by reacting with a carboxylic acid group, which is the same way that peptide bonds are formed
the unfolding of proteins is ____
cooperative; graph is marked by sigmoidal curves
what factors of blood determine the force of viscosity
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
magnetic force equation Fm
Fm = q * v * B where q is the charge, v is the velocity, and B is the magnetic field
Volume flow rate (Q)
Q = volume / time = (area * distance) / time = area * velocity
For flow through pipes or arteries, area can be found as pir2 or 0.25pid2
magnetic force acts on a moving charge in a direction that is _____
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.
after a block begins to slide, how does its speed varies w time?
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
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
t = 2v/g
v = a*t
h = 0.5(g* t squared)
h max = - (v squared) / (2a)
why does sound get muffled when it moves through a wall
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.
torque
torque = mgdsin(theta)
nodes and wavelengths
half wavelength has a node at each end; the spacing btwn nodes is wavelength / 2
Standing wave pattern; superposition of two traveling waves
- amplitudes
- directions
equal amplitudes
opposite directions
resistance
resistivity * (length / area)
