Chemistry/Physics Flashcards
Chromatography “Separation and Purification methods” OCR: p. 112
- the primary reason for chemical separation during a chromatographic separation on cellulose is that the relative amount of hydrogen bonding to the stationary phase will determine the relative rate of migration of the various components in the sample
The variety of opsins “How light and sound interact with matter”
enable the detection of different colors
Retinal Binding Site
BR p. 48
hydrophobic environment (retinal is mainly carbon and hydrogen)
Rf Values with developed chromatography plates “Separation and purification methods.”
- Rf is the ratio of the distance travelled by the analyte relative to the solvent front during a chromatographic separation. - equation: distance of substance investigated / distance of solvent front
Stereospecific/ Stereospecific Reaction “Nature of molecules and intermolecular interactions.” OCR p. 45
- meaning rxn produces only one form of product - a rxn in which the stereochemistry of the reactant completely determines the stereochemistry of the product without any other option.
Rhodopsin “Principles of chemical thermodynamics and kinetics.”
ATP (required for kinase activity): source of phosphate groups added to the molecule
Hybridization States
- “Nature of molecules and intermolecular interactions.”
Steric Number = # bonded Atoms + Lone pairs
4 = sp^3
3 = sp^2 2= sp
amine group “functional group” “Structure, function, and reactivity of biologically-relevant molecules.”
the functional group that forms during peptide bond formation is known as an amide group.
Aldehyde functional group
Carbonyl
Ketone
Acetal
Hemiacetal
Imine
Enamine
Aldol
Alcohol
Carboxylic Acid
Amide
Ester
Lipase
BR: p. 48
hydrolyzes fatty acids
Anhydride
Phenol
What affects rate of subsitution in a reaction?
OCR:
The rate of substitution of protonated alcohols is subject to steric hindrance. This inhibits the ability of nucleophiles to collide with the reacting electrophilic center and slows the rate of reaction.
pH
BCR p. 51
pH = -log[H+]
[H+] = 10^-pH
pOH = -log[OH-]
pH + pOH = 14
difference of 3 pH units = 1000-fold difference in proton concentration
If Reaction 2 (Figure 4) is repeated with HCl and the compound shown next to the reaction, which of the following compounds is NOT a direct product (without rearrangement)?
the structure shown in this response requires an additional shift of hydride atoms prior to elimination and is therefore NOT a direct product.
In a gas-liquid chromatograph, the first peak observed in the gc trace is attributable to which compound?
OCR p.123
Whichever compound will exhibit the lowest molecular weight and also the weakest intermolecular forces of attraction will therefore migrate the fastest and be the first peak in the gas chromatograph (gc) trace.
Acid Dissociation
BCR p. 69
- higher Ka (acid dissociation)/ lower pka: stronger acid
- acid dissociation: net positive charge vs net negative charge acid - the net negative charge will be weaker acid / dissociate to a smaller extent
Glycogen/Glycogenesis
BCR: p. 123
- Most glucose units in glycogen are linked by α-1,4-glycosidic bonds
-branching with glycogen: α-1,6-glycosidic bond
- Glycogen: polymer of glucose in muscle/liver cells
- Glycogenesis: glu-6-p→ isomerized in reversible rxn to glu-1-P w/ phosphoglucomutase → glu-1-p is activated w/ UTP to form UDP-glucose→ added to glycogen polymer by glycogen synthase
What is the product of the reaction of Compound 1 (nxt to rxn) with HBr by the pathway shown in Figure 3?
OCR
(S)-1-bromo-1-deuteriopentane
because the incoming nucleophile displaces the leaving group form the opposite side of the reacting center during an SN2 reaction.
UDP
- deals with glycogen synthase
- contains uridine (nucleic acid used in RNA)
- structure of RNA contains ribose
- KNOW STRUCTURE OF RIBOSE
Phosphatase
- removes phosphate group from a protein
- removal of phosphate prior to gel electrophoresis –> decrease in band intensity
thin lens equation
an object O is at a distance of three focal lengths from the center of a convex lens. What is the ratio of the height of the image to the height of the object?
- (1/o) + (1/i) = (1/f)
- magnification: -i/o
- if asked for ratio of height of image to height of object (given height of object): solve for i and then plug into magnification formula
- Object distance = 3f, focal length = f, image distance = i.
- 1/o + 1/i = 1/f –> 1/3f + 1/i = 1/f. R
- 1/i = 1/f - 1/3f ==> 1/i = 2/3f ==> i = 1.5f.
Plug this into the magnification formula m = -i/o and you get 1.5f/3f = (1/2)
Gamma decay
occurs when nucleus emits photons
spontaneous vs nonspontaneous reactions
- spontaneous: negative ΔG, positive ΔS°, negative ΔH ( - reaction that create gaseous products from solids and liquids = positive ΔS°)
- nonspontaneous: positive ΔG, negative ΔS°, positive ΔH
net sum of chemical reactions
catalysts
If a homogeneous catalyst cannot be separated from the products at the end of a reaction: products will be contaminated with the catalyst
If solid catalyst is finely ground before it is added to the reaction mixture:
- Faster rxn rate: a greater surface area of catalyst will be exposed.
- grinding a heterogeneous catalyst increases the amount of catalyst available to the reaction and therefore increases its rate
V = IR
oxidation-reduction reactions / metal strips in solutions
GCR p. 268
this link is very helpful:
https: //chem.libretexts.org/Bookshelves/Analytical_Chemistry/Supplemental_Modules_(Analytical_Chemistry)/Electrochemistry/Redox_Chemistry/Balancing_Redox_reactions
- putting a metal strip in a solution: if it results in a solid –> metal strip is oxidized and the other ion has higher reduction potential…make two half-reactions and balance # e- (if solution is oxidized: e- go on right side) –> add together to get new equation
- spontaneous reaction: E° is greater than zero; 1) make half-reaction equation and take values (reverse signs based on which ion is oxidized in solution)
common ion effect with solubility
GCR: p. 216
If you have a solution and solute in equilibrium, adding a common ion (an ion that is common with the dissolving solid) decreases the solubility of the solute. This is because Le Chatelier’s principle states the reaction will shift toward the left (toward the reactants) to relieve the stress of the excess product. When equilibrium is shifted toward the reactants, the solute precipitates.
molarity (M)
mol/V
M = molar concentration
n = moles solute
v = liters solution
Units of Power (P)
watt, defined as J/s = ft•lb/s = kg•m2/s3
Amino acid substitution / pKa
-naming: original amino acid, position, new amino acid
- pH is less than pKa of acidic group = acidic group is in protonated form
- pH is greater than pKa of acidic group = deprotonated form
- Acids with low pKa deprotonate easily
radioactive decay
GCR p. 53
alpha decay: large nucleus wants to become more stable by reducing # protons and neutrons (atomic # -2; atomic mass -4)
beta decay: when unstable nucleus contains too many neutrons –> convert neutron to proton and electron (atomic # +1)
gamma decay: after the nucleus has undergone alpha or beta decay, it can “relax” to its ground state by emitting photons (atomic # stays same)
- Oxidizing and Reducing Agents
Ex question from mock MCAT 1 bio q. 53: When a strip of Zn is placed in a beaker containing 0.1 M HCl, H2(g) evolves. If a strip of Al is placed in a beaker containing 0.1 M HCl, does H2(g) evolve?
- Because Zn has higher reduction potential, since H2 gas evolves when in the presence of Zn(s), and Al(s) has an even higher oxidation potential than Zn(s), we know that H2 gas must evolve - or in other words, H+ must be reduced - when in the presence of Al(s).
(If Zn can reduce H+, then Al definitely can because it’s stronger than Zn.)
Note:
The more negative the reaction potential –> stronger reducing agent
nuclear localization signal
BR p. 176
- larger proteins cannot pass freely through nuclear pores and are excluded from nuclear interior unless they contain sequence of basic amino acids
- if they have sequence = translated on cytoplasmic ribosomes and then imported into the nucleus by specific transport mechanisms
- basically a signal that guides a protein molecule to the nucleus; useful to up/down regulate certain cellular processes and products
- permits proteins to enter the nucleus (not likely for transmembrane protein)
signal sequence
- what allows proteins to enter the rough ER (proteins that are either going to be secreted from the cell or perform their function within the cell membrane)
- transmembrane proteins: located in cell membrane (enter the endomembrane system by docking at the rough ER w/ signal sequence)
- definition: short sequence of AA (usually found at N-terminus) of a protein being translated, that directs the ribosome and its associated mRNA to the membranes of rough ER where translation will be completed; found on membrane-bound proteins, secreted proteins, and proteins destined for other organelles
mature mRNA
- has been spliced and processed; ready for translation
- not likely to contain introns or promoter sequences!
Transmembrane domains
similar to signal sequence, but they are located in middle of protein, not removed after translation, and occur on integral membrane proteins
Metric Units
There are 6 MCAT-relevant base units
Prefixes
6 prefixes, symbol, and “multiple”
Angstrom
unit of length = 10^-10 m
used with atomic radii and bond lengths
Know the general “look” of these polyatmoic ions
half-life
GCR p 59
Rules for Assigning Oxidation States
Exception to rule 6: in peroxides (H2O2 or Na2 O2), O2 is in a -1 oxidation state
In determining which reactant loses the –OH group, which of the following isotopic substitutions would be most useful?
Replace the hydroxyl oxygen of ethanol with O-18.
this experiment involves labeling a group which does not exchange with other groups present prior to reaction and will therefore give information about the true identity of the groups, which are exchanged during the reaction.
whether or not that O18 is in the final compound will give us the information we want. If it is in the compound, we know that the ethanol kept its -OH group and therefore acetic acid lost its -OH. If the O18 isn’t in the compound, that means ethanol lost its -OH instead.
The graph below shows the relationship between the predominant form of iron as a function of solution pH and applied potential. Based on the graph, which of the following statements is true?
GCR
At a potential of –0.44 V, the equilibrium between Fe and Fe2+ is independent of solution pH below pH 6.
At an applied potential of −0.44V and pH below 6, there is an equilibrium between Fe(s) and Fe2+(aq), as shown by the line of demarcation. The fact that this line moves horizontally with increasing pH up until pH = 6 means that this equilibrium is unaffected by changing the pH.
Trends
elements in same group show similar reactivity (all have same # e- in outermost shell)
metalloids: possess qualities of metals and nonmetals
Periodic Trends - radius
as we go across a period, e- are added, but new shells are not –> e- feel greater effective nuclear charge –> radius decreases
as we go down a group, as new shells are added –> v e- experience increased shielding (smaller effective nuclear charge)–> RADIUS decreases
if we form an ion, the radius will decrease as e- are removed (the ones that are left are drawn in more closely to the nucleus); radius will increase as e- are added
shielding effect
bond between two sugar molecules:
α-glycosidic linkage
The bond between the two sugars in the diagram is an α-glycosidic linkage, because the anomeric carbon of glucose is pointing down
When β-glycosidic linkages are formed the linkage “locks” the carbohydrate in the β position, where the OH and CH2OH groups are on the same side of the ring
Phosphodiester bonds
covalent bonds formed between a phosphate group and pentose sugar that utilize two ester linkages; used to form backbone of nucleic acids
oxidative decarboxylation
C-3 hydroxyl group in 6-phosphogluconate is oxidized to a ketone, promoting the loss of the carboxyl group at C-1, which is lost as CO2.
thermodynamic equilibrium with unfolding and folding protein structure (q. 52 from mock MCAT course test 2)
A thermodynamic equilibrium between folded and unfolded scr SH3 can be achieved through the application of shearing forces.
- the thermodynamics of unfolding are slightly endergonic in the absence of force, but with the application of force, the final value of the free energy decreases, as shown in Figure 1b. Somewhere in this process ΔG will be 0 and the system will be at thermodynamic equilibrium.
urea w/ protein unfolding
Urea acts to stabilize the denatured state of scr SH3 by associating with backbone polar groups and charged side chains.
- unfolding will cause entropy to increase, not decrease, due to the disordering effect of unfolding
- Based on its structure, urea, CO(NH2)2, will interact with the polar moieties of a protein via hydrogen bonding, which include the peptide backbone and polar residues (charged or uncharged). By disabling intramolecular hydrogen bonding urea is capable of stabilizing the denatured state of a protein
- urea is not a reducing agent and will not affect disulfide bonds!
- note: Proteins can be denatured by urea through several processes. One method involves direct interaction whereby urea hydrogen bonds to polarized areas of charge, such as peptide groups. This mutual influence weakens the intermolecular bonds and interactions, weakening the overall secondary and tertiary structure. Once gradual protein unfolding occurs, water and urea can access more easily the hydrophobic inner core of the protein in question, speeding up the denaturation process.
