Kaplan content videos Flashcards
The ___ model was first to show the atom as being mostly empty space
rutherford
Plancks formula
E (energy radiated off by atom)= frequency of that radiation (f) times constant (h) 6.626 x 10 - 34. Important to note that energy is proportional to frequency.
Energy level is defined by
principle quantum number
Two equations Bohr defined
L= nh/2pi, where L is angular momentum, n is principle quantum number, and h is plancks constant.
2. E = -Rh/n^2. Rh is 2.18x 10-18 J/electron.
True or false, electrons can be excited by more than one energy level from a single absorption of energy
true
Release of energy is in form of photon
calculate with E= hc/ lambda (wavelength). wavelength is inversely proportional to energy of that photon
The three most common electronic energy series
Lyman (UV light). Balmer series (visible spectrum) Paschen series (IR spectra)
When lithiums valence electron jumps to energy level n=4, it absorbs light at 486 nm. What wavelength of light would be absorbed if the electron jumped to energy level n=3 instead?
E= hc/ lambda E= -Rh (1/ni^2 - 1/nf^2)
answer is 656 nm. The principle quantum number is inversely proportional to the wavelength of the photon.
What will happen to the total energy of an electron as it drops from n=4 to ground state
the total energy would decrease by a factor of 4. A difference of two energy levels is a difference of 4x the energy. In the ground state lithium is n=2
Planck
First quantum theory, E=hf
Bohr
E= -Rh/ n^2
Emission and Absorption
E= hc// lambda = -Rh (1/ni^2 - 1/nf^2)
General characteristics of enzymes
biological catalysts to drive life processes. key characteristic is they are unchanged after rxn. ribozymes are biological catalysts composed of RNA instead of polypeptides
Primary structure
sequence of aa in a polypeptide chain. held together by covalent bonds
secondary structure
a and b
tertiary structure
protein domains on a chain , subunit conformation, held together by hydrogen bonds and disulfide bridges
quaternary structure
number and type of chains, arrangement of subunits and held together by h bonds and disulfide bridges
Activation energy : Ea
Input of energy needed to overcome barriers to reaction
Enzymes
decrease Ea so molecular collisions exceeding it occur more often
Do enzymes affect the thermodynamics of a rxn?
no
Oxidoreductases
facilitate redox reactions. reducing a molecule, fewer bonds to oxygen and more to hydrogen. common cofactors include NAD+ and Heme. Examples: oxidases, reductases, peroxidases, dehydrogenases , etc
Transferases
Move functional groups between molecules, often employ coenzyme donors eg coenzyme A. Named as trans[functional group ] ases, [functional group] transferase. Kinases are phosphotransferases, usually with ATP as donor. Anoter exception is polymerases. they are nucleotidyltransferases
Hydrolases
Add water into a reaction. Pepsin is a hydrolase. Named as [substrate]hydrolase; [substrate]ase. Examples : peptidases, nucleases, lipases. Reverse reaction of this is dehydration synthesis
Lyases
Cleave portions from molecules without addition of water. they often form rings or multiple bonds to reform octets. Example is adenylate cyclase. Names as : [substrate]lyase OR [product] synthase. They can put molecules together.
Isomerase
Alter the arrangement of atoms within a molecule. Interconvert between constitutional isomers and stereoisomers. Example is triose phosphate isomerase. Names [substrate] isomerase [substrate ase]. They are often involved in moving electrons or breaking bonds, therefore they may also be oxidoreductases, lyases or transferases
Ligases
Use ATP to join large biological molecules, usually of the same type. Typically encountered in the contxt of DNA synthesis/ repair. Example is DNA ligase. They are the only class that absolutely need ATP to function. Named as : [substrate] synthase; [substrate] synthetase. Synthetase must be a ligase.
The ATP synthase found in mitochondria is a(n)
lyase because it involves two small, different molecules
Free energy of rxn is or is not altered by enzyme
not altered
Reduction of activation energy mechanisms
1Transition state stabilization (dissipation of torsional strain and favorable bond formation, inductive effects of the active site residues). 2microenvironment adjustments (through exlusion of water, adjustment of local environments pH) 3. Adjusting substrate proximity to increase collisions. 4. transient covalent bonding- substrates briefly contact active site residues sequentially (as opposed to just once, substrate is susceptible to nucleophilic attack)
Reactant destabilization
by creating torsional strain or hydrophobic - hydrophilic reactions (this is another reduction of activation energy mechanism)
Enzyme- Substrate complex
fundamental to enzyme activity. E+ S ES > E +P.
Lock and Key
Less accepted. Proposes the active site is complementary to the substrate, any enzymatic change for reaction must occur after binding substrate. Weakened by the model of competitive inhibition and promiscuous reactivity, also because of reverse catalysis
Induced Fit Model
Active site is complementary only after binding initiates. Continual changes in conformation can occur during binding,, catalysis and release. Experimental evidence includes: competitive inhibition, X ray crystallography (shows literal proteins changing formation w/o substrate binding to it first)
Coenzymes
extrinsic organic molecules necessary for protein function. many are adenine derived or vitamin derived
fat soluble vitamins
adek
water soluble
b c
Prosthetic groups
tightly and often covalently bond coenzymes
Cofactors
Inorganic molecules necessary for protein function. Usually free metal iions, but can be polyatomic. dietary mineral requirements.
Holoenzyme
necessary cofactors and coenzymes present
Apoenzymes
necessary cofactors and coenzymes are not present
The site where a protein binds essential cofactors bind is most likely to be
negatively charged
Km- Michaelis constant
Km is [s] such that v= 1/2 vmax. Basically this describes enzyme affinity for substrate. If on the graph you find the Km is closer to 0 on the x axis, that means that it has a “lower “ km value but actually it indicates that the enzyme has a higher affinity for the substrate. The opposite is true if the Km extrapolated on the x axis is further to the right. This would give us a “higher” km value, but actually it has a lower affinity.
Michaelis Menten Relationship
v= vmax[s]/ Km + [s]
Calculate Km
K2 + k3/ (k1)
Purpose of finding the michaelis constant
to compare the enzyme substrate affinity of two or more enzymes
Lineweaver - Burke slope increase indicates
the enzyme has a larger Km value
cooperative binding
sigmoidal shape, hemoglobin
graph shape that accurately depicts the relationship between substrate concentration and monomeric enzyme velocity
hyperbolic
Calculate vmax from Lineweaver burk plot
take value of y intercept, set it equal to 1/vmax and solve for vmax.
Calculate km from lineweaver burk plot
take value of x intercept , set it equal to -1/km to solve for km.
The four subunits of hemoglobin exhibit cooperative binding. As Po2 of blood changes entering the pulmonary veins, the Km of hemoglobin towards this substrate
remains unchanged, the km is not affected by substrate concentration
Glucose is bound by both glucokinase (KM= 5mM) and hexokinase (KM=0.1mM) after a meal, a diners blood glucose level rises from 1mM to 5mM. At this point, what can you infer
Hexokinase binds more glucose at all times
KM relationships
High values of KM represent low affinity for es complex. Lower Km value will bind more .
Enzyme activity, velocity and rate
measure of the amount of active enzyme present- or enzyme that is available to transform substrates into products per unit time
Temperature impact on enzyme
positive impact: every 10 degree increase up to 37 degrees c doubles the rate of reaction. negative: once enzymes reach a certain temp the enzyme will denature and lose function. some enzymes can regain function once cooled.
pH on enzyme
blood pH at 7.4. Altering pH can protonate or deprotonate the enzyme, alters active site and entire structure. Stomach pH = 2.0 (pepsin). Small intestine = pH 8.5
Salinity on enzyme
not of physiological significance. Hydrogen and ionic bonds may be disrupted which can change the conformation of an enzyme. this is not observed in humans but in the lab
pH that would best support and enzyme involved in the initial steps of chemical protein digestion
around 2, because this occurs in the stomach.
