Cumulative Review 3.txt

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Cumulative Review 3.txt
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  1. Celsius – Kelvin conversion
    • 0˚ C = 273.15 K
    • -273.15˚ C = 0 K
    • Absolute zero = 0 K
  2. Kinetic Energy of Gasses (formula)
    • KE = 3/2kT
    • k = Boltzman's constant (1.3806503 e 23 m2 kg s-2 K-1)
  3. Enthalpy
    • (∆H)
    • The energy contained within chemical bonds or HEAT
  4. Entropy
    • (∆S)
    • A measure of the randomness or disorder in a system
  5. Standard State
    • Standard State is 25˚ C (298K) and ∆H = 0
    • *For thermodynamics problems
  6. STP
    • STP (standard temperature and pressure) is 0˚ Celsius (273K) and 1 atm
    • *For gas problems
  7. + ∆S =
    Increased randomness, energy released and available to do work
  8. – ∆S =
    Decreased randomness, energy is required to "create" increased order and that energy is thus unavailable to do work
  9. Entropy (∆S) increases with: (5 things)
    • 1. Increased number of items/particles/etc. (Gas trumps # of moles or particles. This means that if two moles of reactants makes one mole of product and that product is a gas, it is still +∆S)
    • 2. Increased volume
    • 3. Increased temperature
    • 4. Increased disorder
    • 5. Decreased pressure (the higher the pressure the more packing and order of molecules)
  10. Gibbs Free Energy (∆G)
    ∆G = the amount of "free" or "useful" energy available to do work.

    • -∆G = Spontaneous; exothermic
    • +∆G = Non-spontaneous; endothermic
  11. Rate Order Graphs
    • 0 order: [A] vs. time is linear with slope -k
    • 1st order: ln[A] vs. time is linear with slope -k
    • 2nd order: 1/[A] vs. time is linear with slope k
    • 3rd order: 1/2[A]2 vs. time is linear with slope k
  12. Fundamental Thermodynamic Relation formula
    ∆G = ∆H - T∆S

    • ∆G - Gibbs
    • ∆H - Enthalpy
    • ∆S - Entropy
    • T - Temp K
  13. Entropy signs
    • (+) means more disorder or increased entropy.
    • (–) means more order or decreased entropy.
  14. Extraction (reaction mixture polarities)
    • Option 1: Aqueous (polar)
    • Option 2: Organic (non-polar)

    Both will have an extraction solvent with an opposite polarity added to their mixture.
  15. Extraction mixture effectiveness
    The reaction mixture will only work with an oppositely charged extraction solvent if the product is more soluble n the extraction solvent than it is in its current solvent.

    This can be remedied by protonating or deprotonating the product, resulting in a charge.
  16. Top vs. Bottom
    When an aqueous solvent is mixed with almost any non-polar organic solvent the water will be the bottom layer. This is unless the organic solvent is more dense than water, which means density will be given in the q-stem.
  17. Strong acid
    Protonates any base
  18. Weak acid
    Protonates strong bases only
  19. Weak base
    Deprotonates strong acids only
  20. Strong base
    Deprotonates any acid
  21. Gravity filtration
    Physical separation of a solid through filtration paper.
  22. Crystallization
    Mixture containing the desired product is cooled very slowly, because pure substances crystallize.
  23. Chromatography general rule
    The first substance "out" will be the LEAST polar.
  24. Rf (retention factor) of Paper Chromatography
    Distance traveled by component / Distance traveled by solvent
  25. Rf values and polarity
    Inversely proportional to one another. Rf values range between 0-1. 0.9 would be non-polar and .1 would be extremely polar.
  26. Column Chromatography
    The mixture to be separated is passed through a column packed with charged glass beads or another polar matrix. The targeted material is stuck in the beads and the rest passes through.
  27. Gas Chromatography
    Mixture is dissolved in an inert substance and heated to form a gas. It passes through a tube of something polar or non polar depending on the desired product. The gasses will separate according to their retention to the substance and the substances will exit at different times.
  28. Carbonyl, C=O (IR absorbance)
    1700 sharp, deep
  29. Alcohol, OH (IR absorbance)
    3300 broad, separate from CH
  30. Saturated Alkane, CH (IR absorbance)
    2800 sharp, deep
  31. Carboxylic Acid, OH (IR absorbance)
    3000 broad, overlaps CH
  32. Amine, NH (IR absorbance)
    3300 broad, shallow
  33. Amide, NH (IR absorbance)
    3300 broad, deep
  34. Nitriles, CN (IR absorbance)
    2250 sharp, deep
  35. NMR
    An atom must have either an odd atomic number or an odd mass number to register on an NMR (or an MRI; for the MCAT, think of MRIs as a large-scale NMR of the human body).
  36. Mass Spec
    • e- bombardment of a molecule to:
    • 1. Break apart into smaller pieces
    • 2. To ionize
  37. Parent peak (Mass Spec)
    Represents the original molecule missing one electron.
  38. Base peak (Mass Spec)
    Is the most common fragment and equals 100% relative abundance.
  39. Peak heights (Mass Spec)
    The height of each peak gives the relative abundance of each individual fragment with a unique m/z.
  40. Clusters of splitting peaks in HNMR represent...
    n + 1 sub-peaks, where n is the number of non-equivalent hydrogen neighbors.
  41. Order of UV absorbance from least to greatest in UV Spec
    • Sigma only show little to none
    • Double and triple bonds absorb strongly
    • Conjugated systems absorb UV even more strongly than do isolated double or triple bonds

    *The greater the degree of conjugation, the farther to the right (longer wavelength in nm) the species will absorb.
  42. Characteristics of a base
    Receives protons and is electron dense.
  43. Characteristics of a nucleophile
    Nu attack carbon or other central atoms like nitrogen.
  44. Characteristics of an electrophile
    E+ are electron poor species with a full or partial positive charge.
  45. E1 number of steps
    2
  46. E1 order of reaction
    First order
  47. E1 C+ formed?
    Yes
  48. E1 methyl or hydride shifts?
    Yes
  49. E1 product stereochemistry
    Planar
  50. E1 favored by...
    Weak bases; 3˚ carbons only; polar protic solvents
  51. SN1 number of steps
    2
  52. SN1 order of reaction
    First order
  53. SN1 C+ formed?
    Yes
  54. SN1 methyl or hydride shifts?
    Yes
  55. SN1 product stereochemistry
    Racemic mixture
  56. SN1 favored by...
    Poor nucleophiles; 3˚ carbons only; polar protic solvents
  57. E2 number of steps
    1
  58. E2 order of reaction
    Second order
  59. E2 C+ formed?
    No
  60. E2 methyl or hydride shifts?
    No
  61. E2 product stereochemistry
    Planar
  62. E2 favored by...
    Strong bases
  63. SN2 number of steps
    1
  64. SN2 order of reaction
    Second order
  65. SN2 C+ formed?
    No
  66. SN2 methyl or hydride shifts?
    No
  67. SN2 product stereochemistry
    Inversion of relative configuration
  68. SN2 favored by...
    Good nucleophiles; methyl, 1˚ or 2˚ carbons
  69. Alkanes physical properties
    • Insoluble in water
    • Very low density
    • Non-polar
    • Most are oils/gases
  70. General mp and bp trends
    • Bp increases with increasing chain length and molecular weight.
    • Branching signifcantly lowers bp.
    • Mp increases with increasing chain length and molecular weight.
    • Mp decreases with branching.
  71. Alkane combustion definition
    A violent, radical, chain reaction with oxygen, requiring a very high energy of activation.

    Ex: CH4 + 2O2 -> CO2 + H2O + Heat
  72. Radical halogenation of an alkane
    Alkanes react with Flourine, Chlorine or Bromine (Not Iodine) in the presence of heat or ligh via a radical chain reaction.

    *The major product-forming step is propogation, NOT termination.
  73. Radical halogenation of an alkane
  74. Radical Stability
    Tertiary > Secondary > Primary

    • Reactivity: F > Cl > Br
    • Selectivity: Br > Cl > F
  75. The most stable place for bond formation between an alkane and a halogen
    The most substituted carbon
  76. Synthesis of an Alkane from an Alkene
    Reduce an alkene with H2 in the presence of a metal catalyst. This is syn addition.
  77. Alkene properties
    • Nucleophiles
    • Slightly more polar than alkanes, less dense than water, only slightly soluble.
    • More acidic than alkanes, but still unlikely to give up a hydrogen.
    • Like alkanes, bp andmp increase with mw and decrease with branching.
  78. Alkene stability
    Tetrasubstituted > trisubstituted > disubstituted > monosubstituted > unsubstituted

    *R-groups inrease alkene stability
  79. Alkene physical properties
    • Slightly more polar than alkanes, less dense than water, only slightly soluble.
    • More acidic than alkanes, but still unlikely to give up a hydrogen.
    • Like alkanes, bp and mp increase with mw and decrease with branching.
  80. Alcohols physical properties
    • Boiling point goes up with increasing mw and down with increased branching.
    • Melting point goes up with increasing mw.

    Alcohols have high bp and mp due to h-bonding.
  81. Alcohol acidity
    Alcohols are less acidic than water.

    Alcohols increase in acidity from tertiary to primary.
  82. Acid base definitions
    • Arrhenius: Acids produce [H+] ions in solution and bases produce [OH] ions in solution
    • Bronstead-Lowry: Acids donate protons [H+]; bases accept protons [H+].
    • Lewis: Acids accept a pair of electrons; bases donate a pair of electrons.

    Amphoteric substances can act as either an acid or a base. (e.g. H2O)
  83. pH scale
    • pH = –log[H+]
    • pOH = –log[OH]
    • pH + pOH = 14
  84. Strong Acids
    • HI
    • HBr
    • HCl
    • HNO3
    • HClO4
    • HClO3
    • H2SO4

    Polyprotic acids: acids with more than one acidic proton like sulfuric acid. The second proton is always significantly less acidic.
  85. Strong Bases
    • Group IA hydroxides (NaOH, KOH, etc.)
    • NH2
    • H
    • Ca(OH)2
    • Na2O
    • CaO
  86. Antibonding orbitals
    Higher in energy than bonding orbitals; contains electrons "out of phase" that are said to be "repulsive".
  87. Bonding Orbitals
    Lower in energy than anti-bonding orbitals; contain electrons that are "in phase" that are said to be "attractive".
  88. Good electrolytes
    Covalent compounds that dissociate 100% in water (strong acids and strong bases) and ionic compounds are always good electrolytes.
  89. Condosity
    The condosity of a solution is defined as the molar concentration of sodium chloride that has the same specific electrical conductance as the solution.

    (ex. 3M LiCl has a condosity of less than 3M because Na has more metallic character than Li so a lower concentration of Na Cl would be sufficient to conduct electricity just as well)
  90. Bond Energy
    The energy stored in a bond. This is the amoung of energy that will be required to break the bond. Therefore, stable compounds have the highest bond energies, and unstable compounds have low bond energies.

    According to the MCAT this is also known as "bond dissociation energy".
  91. Heat of Combustion
    The higher the energy of the molecule (i.e. less stable) the higher the heat of combustion.
  92. Empirical vs Molecular formulas
    The empirical formula is the simplest formula for a compound. A molecular formula is the same as or a multiple of the empirical formula, and is based on the actual number of atoms of each type in the compound. For example, if the empirical formula of a compound is C3H8 , its molecular formula may be C3H8 , C6H16 , etc.
  93. Percent mass
    The percent mass of one element in the formula/total mass of all elements in the formula.
  94. Deriving a formula from percent mass
    • 1) Change the percent for each species into grams.
    • 2) Convert the grams of each species into moles by dividing by molar mass.
    • 3) Look at the element with the lowest number of moles. Calculate approximately how many times it will divide into each of the other molar amounts for each of the other elements -- this number is the subscript for each element in the empirical formula. If the subscripts are not at there lowest common denominator, reduce to get the empirical formula.

    AN EMPIRICAL FORMULA IS ALL YOU CAN GET FROM PERCENT MASS ALONE. TO GET THE MOLECULAR FORMULA, YOU MUST BE GIVEN THE MW OF THE UNKOWN COMPOUND. Then simply divide that MW by the MW of the empirical formula. You should get a whole number. Multiply each subscript by that number to get the molecular formula.
  95. Combination Reaction
    A+BAB
  96. Decomposition Reaction
    ABA + B
  97. Single Displacement Reaction
    AB + CAC + B
  98. Double Displacement Reaction (Metathesis Reaction)
    AB + CDAC + BD
  99. How to name general Ionic compounds
    Name the cation first, then the anion (e.g., CaSo₄ is Calcium Sulfate)
  100. How to name Transition Metals
    When written in words, compounds including transition elements must have a roman numeral showing the oxidation state of the metal (i.e., Iron(II)Sulfate vs. Iron(III)sulfate).
  101. How to name Monatomic ions
    Named by replacing the last syllable with "ide" (i.e., Sulfide, Hydride, Chloride, etc.)
  102. How to name Acids
    "ate" becomes "ic" (Sulfuric/Nitric acid)"ite" becomes "ous" (Nitrous acid)"ide" becomes "hydro/ic" (hydroiodic/hydroflouric acid)
  103. Steps in balancing reactions
    • 1) Balance Carbons
    • 2) Balance Hydrogens
    • 3) Balance oxygens
    • 4) Balance others
    • 5) Finally, multiply all species by the number in the denominator of any fraction to remove the fractions
  104. How to find limiting reagent
    • 1) Convert to moles
    • 2) Balance the equations
    • 3) compare the number of moles you have to the number of moles required to run one cycle of the reaction.

    The reactant you run out of first is the limiting reagent. This may not always be the reactant you have the least of (grams or moles).
  105. Trick for finding which compound requires more oxygen to combust
    Add 1 point for each carbon there is and subtract 1/2 for each oxygen there is in the compound...the compound with the highest point value requires the greatest number of oxygens
  106. Yields
    Theoretical Yield: products formed when all the limiting reagent is used.

    Actual Yield: product obtained from reaction - always less then theoretical yield.

    Percent Yield: actual/theoretical X 100%
  107. Chemical Equilibrium
    • Keq = [products]x / [reactants]y
    • Keq is written with every term raised to an exponent equal to its coefficient in the balanced equation (remember, however, that you do NOT do this when writing rate laws). Pure liquids (l) and pure solids (s) are never included!
  108. The Reaction Quotient (Q)
    The equilibrium constant can ONLY by calculated at equilibrium. IF you make the exact same calculation using concentration values taken at any point other than equilibrium the result is called the REACTION QUOTIENT, Q.

    • If Q > K, run will proceed to the left
    • If Q < K, run will proceed to the right.
  109. How does increasing temperature in an exothermic reaction change Keq?
    Increases it which shifts the equilibrium to the left making more reactants.
  110. (Le Chatelier) Add Reactants
    Right shift
  111. (Le Chatelier) Add Products
    Left shift
  112. (Le Chatelier) Increase Pressure
    Shift to side with the less gas molecules
  113. (Le Chatelier) Increase temperature
    Shift toward side that heat species is not on.
  114. Polar molecule characteristics
    Highest electronegativity and smallest radius.
  115. Coordinate Covalent
    One atom provides both electrons to the bond and the other has an empty valence shell.

    Almost always includes a transition metal.

    NH3 is very very commonly used.
  116. Phase state of ionic compounds
    Solids at room temp.
  117. 1 cm3 is equivalent to...
    1 mL
  118. Accompanies most all radioactive decay
    Gamma ray emission.
  119. Keq definition
    Ration of products over reactants raised to their coefficients in the balanced equation.

    Strong acids dissociate 100% and therefore are all product over almost no reactant.
  120. Metals always form _______.
    Cations
  121. Non-metals always form _______.
    Anions
  122. Cations are _______ than their neutral counterparts.
    Smaller
  123. Anions are _______ than their neutral counterparts.
    Larger
  124. Metals
    Very large atoms with loosely held electrons...Form cations, are lustrous, ductile, malleable, and excellent conductors of both heat and electricity...they are usually only involved in ionic bonds.
  125. Non-metals
    Smaller atoms with loosely held electrons...Form anions, have much lower melting points than metals, and with very few exceptions, only nonmetals form covalent bonds.
  126. Large atom characteristics
    Larger atoms are better at stabilizing charges, form weaker pi bonds, and have d orbitals where they can "stash" extra electrons.
  127. Alkali metals
    Group 1, 1 electron in outer level, very reactive, soft, silver, shiny, low density; Lithium, Sodium, Potassium, Rubidium, Cesium, Francium
  128. Alkaline earth metals
    Metallic elements in group 2 of the periodic table which are harder than the alkali metals and are also less reactive.
  129. Lanthanides
    The first of the two rows below the main part of periodic table. usually used in alloys, soft, malleable, shiny and good electrical conductors.
  130. Actinides
    In the 2nd row of transition metals, radioactive, unstable, do not occur in nature.
  131. Periodic table blocks
  132. Electron Affinity
    • The amount of energy released when an electron is added to a neutral atom or molecule to form a negative ion.
    • X + e− → X−



    It increases from left to right and from bottom to top
  133. Electronegativity
    The ability of an atom to attract electrons when the atom is in a compound.



    It increases from left to right and from bottom to top
  134. Ionization Energy
    The energy required to remove 1 mole of electrons from 1 mole of gaseous atoms or ions. Large atoms or molecules have a low ionization energy, while small molecules tend to have higher ionization energies.



    It increases from left to right and from bottom to top
  135. Atomic Radius Trends


    Atomic radius gets larger from right to left and top to bottom.
  136. Metallic Character Trends


    Increases from right to left and top to bottom
  137. Metallic characteristics
    BIG and low low ionization energy
  138. First Quantum Number
    "n" (the principle quantum number)

    Gives the Shell (i.e., Valence electrons are in the outermost "shell") and is approximately equal to the relative energy of electrons in that shell.
  139. Second Quantum Number
    "" (the azimuthal quantum number)

    • Gives the subshell: has values of 0,1,2,3 and from this were know the shape:
    • 0=S ; 1=P ; 2=d ; 3=f
  140. Third Quantum Number
    "m" (the magnetic quantum number)"the magnetic quantum number"

    Gives the orbital; has a value of - to (from the azimuthal quantum number)

    The orbital is the portion of the subshell where an electron is most likely to be found (i.e., which "dumbbell" of a p subshell)
  141. Fourth Quantum Number
    "ms" (the electron spin quantum number)

    Gives the spin which is either +1/2 or -1/2 (Positive is up arrow or negative is down arrow)
  142. Heisenberg uncertainty principle
    States a fundamental limit on the accuracy with which certain pairs of physical properties of a particle, such as position and momentum, can be simultaneously known.

    The more precisely one property is measured, the less precisely the other can be controlled, determined, or known. You can know it's momentum, or where it's at, but you can't know both at the same time.
  143. Pauli exclusion principle
    No two electrons in a single atom can have the same four quantum numbers; if n, , and m are the same, ms must be different such that the electrons have opposite spins, and so on.
  144. The Work Function
    If you bombard certain metals with energy, you can cause the ejection of an electron from their outermost shell (i.e., valence electron). The amount of energy required to do this is called the "work functions."

    This is not the same as the Ionization energy because that refers to only lone atoms in a gaseous state. The work function refers to the valence electrons being ejected from the surface of a metal.
  145. Work Function formula
    KE = E –

    • - work function variable
    • KE - of the ejected electron
    • E - amount of energy added

    -or-

    E = hf

    • E - energy of a photon
    • h - Planck's constant
    • f - frequency
  146. Alpha Decay
    A He nucleus (2 neutrons and 2 protons) are ejected
  147. Beta Decay
    Neutron is changed into a proton (with the ejection of an electron)
  148. Electron Capture
    A proton is changed into a neutron via capture of an electrion
  149. Positron Emission (beta+ decay)
    A proton is changed into a neutron (with expulsion of a positron)
  150. Calculating Percent Mass
    Mass of one element divided by the total mass.
  151. Deriving a formula from percent mass
    • 1. Change the percent for each species into grams
    • 2. Convert the grams of each species into moles by dividing by molar mass.
    • 3. Look at the element with the lowest number of moles. Calculate approximately how many times it will divide into each of the other molar amounts for each of the other elements--this number is the subscript for each element in the empirical formula. If the subscripts are not at their lowest common denominator, reduce to get the empirical formula.
  152. How to determine moles from mL
    m = V * P

    mass (g) = volume (cm3 or mL) * density (g/cm3)

    Then divide mass by molecular weight to get moles.
  153. Incomplete Penetrance
    Occurs when the individual has the allele but is not expressed in the phenotype.
  154. Co-dominance
    Two of the same gene and both are dominant and both are expressed.

    ex- Blood type...IaIb gives you AB blood, IaIo gives you type A, IbIo gives you type B, and IoIo gives you type O...spotted horses and cows..in parts of the animal's skin one allele is expressed to give one color and in other areas the other allele is expressed to give the other color
  155. Incomplete Dominance
    One allele is not completely dominant over the other, thus you get a mixed phenotype.
  156. According to the MCAT, when do you have genetic linkage?
    When there is any deviation from Mendelian ratios.
  157. Gene pool
    The complete set of unique alleles in a population...small gene pool= not a lot of genetic diversity and large gene pool= lots of diversity.
  158. Evolution
    Any change to the heritable characteristics (DNA) of a species across several generations or over time.
  159. Polymorphism
    A completely unique phenotypic trait that is expressed in different members of the same species...ex- black man vs a white woman.
  160. Niche
    The way an animal lives.

    Fundamental niche - an organism in a particular environment could grow any way it wanted and feed off whatever it felt like if there was no competition.

    Realized niche - Because all species do live in competitive environments and do have more superior competitors competing with them for resources a species may have to adapt to a particular niche (way of life) to which it is most highly adapted.
  161. Natural Selection
    Non-random process by which certain alleles (traits) become either more or less common in a population due to the effects of those traits on the fitness of the individual with emphasis on those alleles that contribute to reproductive success in particular. It is a mechanism of evolution but is not evolution itself.
  162. Speciation
    When one species in different environments evolves into two different species.
  163. Adaptive radiation
    Same species with different adaptations.

    Ex. Galapogos Island finches.
  164. Evolutionary Bottleneck
    Some random event kills off a large portion of a population indiscriminately...the most fit individuals do NOT necessarily survive...these events INCREASE genetic drift bc with a much smaller gene pool random matings and assortment of gametes will have a much larger outcome on the gene pool of the population.
  165. Genetic Drift
    The random fluctuations in the allele frequencies in a population.
  166. Carrying capacity
    The population size that the local environment can support.
  167. R-selected population
    Rapid growth, numerous offspring, offspring mature rapidly and don't require a lot, if any, post-natal care. dies quickly. predominates in unstable/unpredictable environments. usually have small body size. i.e. bacteria.
  168. K-selection
    Pop size is close to carrying capacity. roughtly constant pop size. low reproduction rate, offspring large and require more post-natal care. Predominates in stable/predictable enviroments. i.e. humans.
  169. Hardy-Weinberg Assumptions
    • 1) Large population
    • 2) No mutation
    • 3) No immigration or emigration
    • 4) Random mating
    • 5) No natural selection
  170. Hardy-Weinberg Equations
    • p2 + 2pq + q2 = 1
    • p + q = 1

    • p - dominant allele frequency in a population
    • q - recessive allele frequency in a population
    • p2 - percentage of individuals with homozygous dominant genotype
    • 2pq - percentage of individuals with heterozygous genotype
  171. Taxonomy
    (Domain), Kingdom, Phylum, Class, Order, Family, Genus, Species
  172. Human Taxonomy
    Eukarya, Animalia, Chordata (vertebrae and skull), Mammalia, Primates, Hominidae, Homo, Sapiens
  173. Symbiosis
    The "living together of unlike organisms".
  174. Mutualism
    Any relationship between members of different species in which each member derives a benefit from the relationship.
  175. Commensalism
    A relationship in which one individual benefits and the other individual is not significantly harmed OR helped.
  176. Parasitic
    One member of the relationship benefits while the other is harmed.
  177. Virus
    A small infectious agent that can ONLY replicate inside the cells of another living organism.
  178. Latent period
    The virus is dormant inside the cell of another organism...means that it is there and capable of functioning but it has not started to divide and replicate.
  179. Virulence
    A measure of how likely an infection (via the virus) is to occur and how severe the symptoms are in the organism it infects after infection.
  180. Which of the following is a virus likely to be classified as?A) Highly virulent
    B) Optimally virulent
    C) Low virulent
    Optimally virulent..if the parasite/virus infects the host and causes symptoms so severe that the host dies before the virus has time to infect another host then the virus dies and thus its genetic material is less fit...this is just as bad for the virus as a virus with a low virulence that has a hard time infecting hosts.
  181. Provirus
    The viral genome that is integrated into the host's DNA.
  182. Reverse Transcriptase
    Retroviruses have RNA as their genetic material so they have a reverse transcriptase that converts their RNA into DNA which can then be inserted into the host's genome transcribed by the host cell's transcription machinery to replicate the virus.
  183. Retrovirus
    RNA virus that uses reverse transcriptase to turn its RNA into DNA.
  184. Gram Positive Characteristics
    • Stain purple (high amount of peptidoglycan retains dye)
    • Very thick cell walls
    • Form endospores
    • Single cell membrane
  185. Gram Negative Characteristics
    • Stain pink (bc the relatively low amount of peptidoglycan)
    • Relatively thin cell wall
    • Do NOT form endospores
    • Contain two cell membranes (inside and outside of the cell wall)
  186. Bacteria characteristics
    ALL bacteria are prokaryotes...they all have at least one cell membrane, a cell wall, and secrete some sort of capsule...they don't have any complex membrane-bound organelles...they have a single circular DNA chromosome and several small circular DNA molecules called plasmids.
  187. Three types of bacteria
    • Bacilli - rod-shaped
    • Cocci - round-shaped
    • Spirilla - spiral-shaped
  188. Conjugation
    The building of a sex pilus between two bacteria cells. The donor cell has to be F+ while the recepient must be F- (lacking F plasmid).
  189. Transformation
    Pick up DNA from environment
  190. Transduction
    Viruses accidentally incorporate host genetic material into their nucleic acids.
  191. Prokaryotes vs. Eukaryotes
    Prokaryotes: bacteria only , cell wall present, no nucleus but nucleoid, no membrane bound organelle, unicellular, smaller ribosomes

    Eukaryotes: protists, fungi, plants, animals, cell wall only in fungi and plants, contains a nucleus and membrane bound organelle, smaller ribosomes.
  192. Difference between mitosis and binary fission
    Mitosis occurs in eukaryotes and involves spindle fibers; does not allow for exponential growth. Binary fission occurs only in prokaryotes; no spindle fibers; allows for exponential growth.

    Both result in daughter cells that recieve full copies of parental chromosome. However, with binary fission, daughter cells may get unequal distribution of plasmids.
  193. Chemotroph vs Phototroph
    Chemotrophs gain their energy via the oxidation of chemical compounds that they get from their env't...Phototrophs get their energy by harnessing the energy of photons (light).
  194. Autotroph vs. Heterotroph
    • Autotrophs - the organism can rely on CO2 as a carbon source.
    • Heterotrophs - must consume organic materials for their carbon.
  195. Why do telomeres get shorter with each cell replication?
    Because the enzymes that copy the DNA cannot proceed to the very end of the strand. Telomeres, long repeating sections of DNA that do not contain genes, protect the chromosome from degradation. The telomeres are shortened after each replication instead of losing important gene-bearing sections of the strand.
  196. Diazotrophs
    Bacteria that can convert N2 in the atmosphere into NH3 and NH3 into NO3
  197. Fungi characteristics
    • 1) Chemoheterotrophic (they do NOT have chloroplasts)...all fungi are saprophytic (they live off dead organisms)
    • 2) They digest their food BEFORE they ingest it
    • 3) Fungi have cell walls made of CHITIN (as opposed to the cellulose that make up cell walls of plants)
  198. Fungal Reproduction
    • Fungi spend most of their life as haploid (this is their growth phase which is also called hyphae - haploid.
    • Yeasts primarily reproduce by a process called budding which is basically the same as binary fission except that it is an unequal division (one of the new cells is much larger than the other).
    • Most fungi can reproduce sexually and asexually
  199. Fungal sexual vs asexual reproduction
    When life is hard due to stress, bad environment, little food, etc fungi reproduce sexually because this increases the chances of new phenotypic traits that will be more favorable due to increased genetic variability. However, when life is good fungi reproduce asexually.
  200. Cofactor
    Any species required by an enzyme to function.
  201. Competitive Inhibitor
    • Binds at the active site
    • Overcome by increasing substrate
  202. Non-competitive inhibitor
    • Binds away from the active site and changes the enzyme's shape
    • Decreases efficiency
  203. Irreversible inhibitor
    Binds covalently to the enzyme and permanently disables it
  204. Positive feedback
    When the product of an enzymatic reaction series returns to activate the enzyme again; occurs less often than negative feedback.

    Childbirth
  205. Negative feedback
    A shutdown mechanism for a series of enzymatic reactions; when a series produces a sufficient amount of product it sends a signal back to stop it.

    Blood glucose regulation
  206. Zymogen
    Inactive enzyme precursor. Keeps the enzyme inactive until it has finished folding/being transported to the right place
  207. Allosteric Regulation
    Regulation away from the active site. Feedback inhibitors do not resemble substrate of enzyme being inhibited, they bind and cause a conformational change. There are both allosteric inhibitors and activators.
  208. Kinase function
    Transfers PO₄³�?� to a substrate - phosphorylates others
  209. Phosphatase function
    Removes PO₄³�?� from a substrate - dephosphorylates others
  210. Metabolism
    The sum of all chemical reactions in the body.
  211. Respiration
    The breakdown of macromolecules into smaller species to harvest energy.
  212. Facultative aerobes/anaerobes
    An organism that can live in either an aerobic or an anaerobic environment (some types of bacteria; yeasts; individual human cells).
  213. Obligate aerobe
    Organism that REQUIRES oxygen to grow (humans)
  214. Obligate anaerobes
    An organism that MUST live in an anaerobic environment.
  215. Substrate Level Phosphorylation
    Formation of ATP from direct transfer of a phosphate group from a phosphorylated intermediate onto ADP.
  216. Oxidative Phosphorylation
    Oxidation energy is used to create a concentration gradient and use the stored energy from the concentration gradient to create ATP...although oxidation is coupled to phosphorylation in glycolysis, this is NOT an example of oxidative phosphorylation.
  217. Fermentation
    Sole route for many bacteria...used by animals ONLY during oxygen debt.
  218. Ethanol Fermentation
    Ethanol is produced and is the final electron acceptor.
  219. Lactic Acid Fermentation
    Lactate is produced and is the final electron acceptor.
  220. Lipid Metabolism
    Occurs in the Mitochondria; and to a limited degree in the peroxisomes.

    Super long fatty acids are broken into smaller lipids in peroxisomes and these pieces are sent back to the mitochondria where they undergo ß-oxidation.
  221. Beta oxidation
    Fatty acid continues to cycle through beta oxidation getting 2 carbons shorter each time until fatty acid is totaly gone.
  222. Protein Metabolism
    Amino acids are broken down into acetyl CoA and fed into the Kreb's cycle.
  223. Order of Metabolism
    Healthy individuals burn carbohydrates first, then fats, then proteins.
  224. Bidirectional Replication
    Replication occurs on both the leading strand and the lagging strand at the same time.
  225. Semi-conservative replication
    Each strand of the original DNA becomes the template strand for the new DNA strand.
  226. Semi-discontinuous
    Leading Strand is replicated continuously whereas the lagging strand is replicated in segments called Okazaki fragments.
  227. DNA polymerase
    Reads the template strand 3'->5' but synthesizes the NEW strand 5'->3' (new nucleotides are added on to the 3' end of the sugar preceding it).
  228. Describe the process of DNA replication
    Starts at the origin of replication...it opens up into a replication bubble...replication is occurring in 4 separate areas inside this bubble at the same time! Why?...DNA polymerase III requires an RNA primer to be already annealed to the DNA strand in order to begin synthesizing...helicase goes in front of DNA polymerase III and unwinds the DNA to allow room for replication...DNA polymerase I has 5' -> 3' exonuclease activity so it comes in at the end and plows off all the primers (plus maybe a few more nucleotides) and replaces them with DNA nucleotides...and then ligase comes in a binds the okazaki fragments together...throughout this whole process, the strain on DNA caused by the unwinding DNA is released by topoisomerases and gyrases.
  229. Telomerase
    Has its own RNA template that it uses to do reverse transcriptase and create DNA nucleotides to add on to the end of a DNA polymer to protect it from degradation.
  230. RNA vs DNA
    • RNA has a 2' hydroxyl group and DNA doesn't
    • RNA is usually single-stranded and DNA is usually double-stranded
    • Uracil (RNA) vs. Thymine (DNA)
    • RNA exists in 3 forms vs. DNA which is in 1 form
    • RNA exits the nucleus but DNA does not
  231. Transcription process
    • 1. RNA polymerase attaches to the promotor region of the DNA template strand.
    • 2. DNA is unwound to form a replication bubble. 3. RNA polymerase starts synthesizing the pre-mRNA via RNA complementary base pairing.
    • 3. The replication bubble continues down the DNA with the DNA behind it binding back together.
    • 4. Once the RNA polymerase gets to the termination sequence, it releases from the template strand as well as the pre-mRNA.
    • 5. Splicesome splices out introns in pre-MRA.
    • 6. Poly-A-tail attached to 3' end.
    • 7. 5' cap added. 8. mRNA is finally ready to be shipped out of the nucleus.
  232. Names for the strand of DNA being TRANSCRIBED
    • Anti-sense strand
    • Anti-coding strand
    • Template strand
  233. Names for the strand of DNA NOT being TRANSCRIBED
    • Coding Strand
    • Sense Strand
    • these are EXACTLY the same as the RNA strand but with thymine instead of Uracil.
    • Watch out for the 5'3' convention of writing RNA!
  234. 3 ways to regulate Transcription
    1) Rate of transcription-> RNA has a short half-life so genes must be constantly transcribed in order to continue protein production

    2) Activators and Repressors-> certain substances upregulate transciption and others downregulate it...(Classify the following as activators or repressors for the Lac operon...lactose, glucose, Lac I protein, cAMP, CAP)

    3) Permanent or Semi-permanent Repression-> methylation or other covalent modification that prevents transcription (When a promoter region of DNA is methylated it often silences the genes)
  235. Special aspects about the genetic code
    1) Degenerative= more than one codon for a single amino acid (the 3' nucleotide in the codon and the 5' nucleotide in the anticodon do NOT always need to match perfectly...wobble base pairs)

    2) Unambiguous= there is never more than one amino acid coded for by a particular codon
  236. 1 start codon and 3 stop codons
    • Start: AUG (methionine)
    • Stop: UAA, UAG, UGA
  237. Codons vs. Anticodons
    Codons are the 3-nucleotide segments on the mRNA strand (they are read in the 5'->3' direction)...anti-codons are the 3-nucleotide segments that are on the complementary tRNA that brings in the appropriate nucleotide (they are also read in the 5'->3' direction but remember that they are complementary and pair up with codons in the anti-parallel direction).
  238. Translation process
    Ribosome binds upstream of the initial codon and reads the mRNA strand in the 5'->3' direction(the region btwn the ribosome binding site and the intial codon is called the 5' UTR)...when it reaches the Start codon it begins bringing in tRNA's with the appropriate amino acids and catalyzes the polymerization of a polypeptide.
  239. Location of translation
    Cytoplasm

    (mRNA protein)
  240. Germ cells vs. Somatic cells
    Germ cells produce gametes (meiosis) whereas Somatic cells produce normal cells (mitosis) throughout the body.

    Germ (sex) cells much worse because they can be transmitted to offspring while somatic (body) cells don't get transmitted.
  241. 6 types of DNA mutations
    • 1) Point= a single nucleotide is changed
    • 2) Missense mutation= a single nucleotide is changed that causes a new codon in the mRNA strand that codes for a different amino acid
    • 3) Nonsense mutation= a single nucleotide is changed that causes a premature stop codon
    • 4) Neutral Mutation= the mutation has NO effect on the individual's fitness (the amino acid might still be the same or it might be different but still have none to very little effect on protein function and structure and thus little effect on the organism's fitness)
    • 5) Silent mutation= a mutation that has NO effect on the amino acids of the protein...it might be a mutation that creates a new codon that codes for the same protein or it might be a mutation in an intron
    • 6) Frameshift mutation= an insertion or deletion causes a shift in the reading frame so that everything after it is new or distorted codons
  242. Metastasis
    Spread of diseased cells from one area of the body to another.
  243. Proto-oncogene
    Proto-oncogenes are genes that help regulate cell growth.
  244. Oncogene
    A gene that has been mutated so that its products, in one way or another, cause cancer
  245. True breeding
    Homozygous for a given trait (may be either dominant or recessive).
  246. P1, F1, F2 generations
    • P1 = you
    • F1 = your kids
    • F2 = your grandkids
  247. Alleles
    Alternate forms of the same gene.
  248. Mutagen vs Carcinogen
    Both cause mutations but carcinogens always cause cancer while mutagens may be benign. All carcinogens are mutagens but not all mutagens are carcinogens.
  249. Law of Segregation
    Alleles segregate independently of one another when forming gametes.

    Homologous pairs divide (1 to each gamete) during meiosis.
  250. Law of Independent Assortment
    Genes located on different chromosomes assort independently.

    When homologous pairs line up on the metaphase plate they arrange themselves in a random fashion.
  251. Important MCAT genetics convention
    Whenever the genotype of an individual is not stated you should assume that it is HOMOZYGOUS DOMINANT!!!!...if the individual is a carrier or is affected (homozygous recessive usually) they will tell you.
  252. Penetrance
    The number of individuals in the population carrying the allele who actually express the phenotype.
  253. Expressivity
    The varying expression of disease symptoms despite identical genotypes.
  254. Polygenic
    A characteristic/trait for which the phenotype depends on many genes to help dictate it.
  255. Pleiotrophy
    A single allele that affects many traits.
  256. Mosaicim
    When cells within the same person have different genetic make-up.
  257. Genetic imprinting
    When expression of a gene depends on the parent of origin. Sometimes both copies of a gene are not expressed and the "active" gene is dependent on who the gene came from.
  258. Tissue types
    • Epithelial
    • Nervous
    • Connective
    • Muscle
  259. Tissue Organization
    Organ systems > Organs > Tissues > Cells
  260. Communication characteristics of the endocrine system
    Slow, general, long-lasting
  261. Communication characteristics of the nervous system
    Fast, specific, short-lived
  262. Communication characteristics of the paracrine system
    Local mediator hormones only
  263. Diploid number
    Having a pair of each type of chromosome, so that the basic chromosome number is doubled. 46 in humans.
  264. Haploid number
    The haploid number is the number of chromosomes in a gamete of an individual. This is distinct from the monoploid number (x), which is the number of unique chromosomes in a single complete set. Gametes (sperm, and ova) are haploid cells.
  265. Mitosis yields:
    Two genetically identical, diploid daughter cells.
  266. Meiosis yields:
    Four genetically distinct, haploid daughter cells.
  267. Lipid definition
    Any biomolecule soluble in non-polar solvents and insoluble in polar solvents.
  268. Triacylglycerol (triglyceride) structure
  269. Description of basic steroid structure
    All are four-ringed structures.
  270. Definition of amphipathic
    An amphipathic substance is one that is polar at one end of the molecule (hydrophilic) and nonpolar (hydrophobic) at the other.
  271. Essential vs Non-Essential
    Essential means that your body cannot synthesize it and therefor must get it from its environment- sun, food, etc.
  272. 6 things responsible for the tertiary structure of proteins
    • Disulfide bonds (covalent)
    • Ionic bonds (salt bridge)
    • Hydrophobic interactions
    • Hydroden bonding
    • Proline turns
    • Van der Waals' forces
  273. Determines the protein folding structure
    1˚ structure (amino acid sequence)
  274. Different protein denaturing agents and what they affect
    • Acid- electrostatic bonds
    • Heat- all forces
    • Urea- hydrogen bonds
    • Mercaptoethanol- disulfide bonds

    To refold simply remove the denaturing agent
  275. Between which parts of how many AAs are the hydrogen bonds forming an alpha helix?
    Between the CO group of an AA and the NH group of the AA four (4) residues ahead of it; the helix is right-handed.
  276. D-Fructose
  277. D-Glucose
  278. Digestible to humans α vs β
    • α - animals
    • β - bacteria
  279. Three components of nucleotides
    • 1) Nitrogenous Base
    • 2) 5-C sugar
    • 3) Phosphate Group

    Hydroxyl group always at 3' carbon. base at 1' carbon. phosphate at 5' carbon.
  280. Examples of Nucleotides
    NADH, ATP, DNA, RNA, etc.
  281. Vitamins
    Organic compoundmade in plants and animals vulnerable to heat.
  282. Examples of Vitamins
    • Riboflavin
    • Thiamine
    • Cobalamin
  283. Minerals
    • Inorganic compounds (often metals).
    • Found in soil and water not vulnerable to heat.
  284. -tase vs. -ase?
    • -ase = enzyme
    • -tase = ATP-requiring enzyme
  285. Two important classifications of vitamins
    • Water-soluble
    • Fat-soluble
  286. Induced fit theory
    Theory of enzyme specificity. substrate plays role in final shape of enzyme and that enzyme is partially flexible.
  287. Lock and key theory
    Only the correct key will activate the lock. very specific.
  288. Coenzyme
    Non-protein species NOT permanently attached to the enzyme but required by the enzyme to function.
  289. Prosthetic group
    Non-protein species permanently attached to the enzyme and required by the enzyme to function.
  290. Bidirectional Replication
    Replication occurs on both the leading strand and the lagging strand at the same time.
  291. Semi-conservative replication
    Each strand of the original DNA becomes the template strand for the new DNA strand.
  292. Semi-discontinuous
    Leading Strand is replicated continuously whereas the lagging strand is replicated in segments called Okazaki fragments.
  293. DNA polymerase
    Reads the template strand 3'->5' but synthesizes the NEW strand 5'->3' (new nucleotides are added on to the 3' end of the sugar preceding it).
  294. Describe the process of DNA replication
    Starts at the origin of replication...it opens up into a replication bubble...replication is occurring in 4 separate areas inside this bubble at the same time! Why?...DNA polymerase III requires an RNA primer to be already annealed to the DNA strand in order to begin synthesizing...helicase goes in front of DNA polymerase III and unwinds the DNA to allow room for replication...DNA polymerase I has 5' -> 3' exonuclease activity so it comes in at the end and plows off all the primers (plus maybe a few more nucleotides) and replaces them with DNA nucleotides...and then ligase comes in a binds the okazaki fragments together...throughout this whole process, the strain on DNA caused by the unwinding DNA is released by topoisomerases and gyrases.
  295. Telomerase
    Has its own RNA template that it uses to do reverse transcriptase and create DNA nucleotides to add on to the end of a DNA polymer to protect it from degradation.
  296. RNA vs DNA
    • RNA has a 2' hydroxyl group and DNA doesn't
    • RNA is usually single-stranded and DNA is usually double-stranded
    • Uracil (RNA) vs. Thymine (DNA)
    • RNA exists in 3 forms vs. DNA which is in 1 form
    • RNA exits the nucleus but DNA does not
  297. Transcription process
    • 1. RNA polymerase attaches to the promotor region of the DNA template strand.
    • 2. DNA is unwound to form a replication bubble. 3. RNA polymerase starts synthesizing the pre-mRNA via RNA complementary base pairing.
    • 3. The replication bubble continues down the DNA with the DNA behind it binding back together.
    • 4. Once the RNA polymerase gets to the termination sequence, it releases from the template strand as well as the pre-mRNA.
    • 5. Splicesome splices out introns in pre-MRA.
    • 6. Poly-A-tail attached to 3' end.
    • 7. 5' cap added. 8. mRNA is finally ready to be shipped out of the nucleus.
  298. Names for the strand of DNA being TRANSCRIBED
    • Anti-sense strand
    • Anti-coding strand
    • Template strand
  299. Names for the strand of DNA NOT being TRANSCRIBED
    • Coding Strand
    • Sense Strand
    • these are EXACTLY the same as the RNA strand but with thymine instead of Uracil.
    • Watch out for the 5'3' convention of writing RNA!
  300. 3 ways to regulate Transcription
    1) Rate of transcription-> RNA has a short half-life so genes must be constantly transcribed in order to continue protein production

    2) Activators and Repressors-> certain substances upregulate transciption and others downregulate it...(Classify the following as activators or repressors for the Lac operon...lactose, glucose, Lac I protein, cAMP, CAP)

    3) Permanent or Semi-permanent Repression-> methylation or other covalent modification that prevents transcription (When a promoter region of DNA is methylated it often silences the genes)
  301. Special aspects about the genetic code
    1) Degenerative= more than one codon for a single amino acid (the 3' nucleotide in the codon and the 5' nucleotide in the anticodon do NOT always need to match perfectly...wobble base pairs)

    2) Unambiguous= there is never more than one amino acid coded for by a particular codon
  302. 1 start codon and 3 stop codons
    • Start: AUG (methionine)
    • Stop: UAA, UAG, UGA
  303. Codons vs. Anticodons
    Codons are the 3-nucleotide segments on the mRNA strand (they are read in the 5'->3' direction)...anti-codons are the 3-nucleotide segments that are on the complementary tRNA that brings in the appropriate nucleotide (they are also read in the 5'->3' direction but remember that they are complementary and pair up with codons in the anti-parallel direction).
  304. Translation process
    Ribosome binds upstream of the initial codon and reads the mRNA strand in the 5'->3' direction(the region btwn the ribosome binding site and the intial codon is called the 5' UTR)...when it reaches the Start codon it begins bringing in tRNA's with the appropriate amino acids and catalyzes the polymerization of a polypeptide.
  305. Location of translation
    Cytoplasm

    (mRNA protein)
  306. Germ cells vs. Somatic cells
    Germ cells produce gametes (meiosis) whereas Somatic cells produce normal cells (mitosis) throughout the body.

    Germ (sex) cells much worse because they can be transmitted to offspring while somatic (body) cells don't get transmitted.
  307. 6 types of DNA mutations
    • 1) Point= a single nucleotide is changed
    • 2) Missense mutation= a single nucleotide is changed that causes a new codon in the mRNA strand that codes for a different amino acid
    • 3) Nonsense mutation= a single nucleotide is changed that causes a premature stop codon
    • 4) Neutral Mutation= the mutation has NO effect on the individual's fitness (the amino acid might still be the same or it might be different but still have none to very little effect on protein function and structure and thus little effect on the organism's fitness)
    • 5) Silent mutation= a mutation that has NO effect on the amino acids of the protein...it might be a mutation that creates a new codon that codes for the same protein or it might be a mutation in an intron
    • 6) Frameshift mutation= an insertion or deletion causes a shift in the reading frame so that everything after it is new or distorted codons
  308. Metastasis
    Spread of diseased cells from one area of the body to another.
  309. Proto-oncogene
    Proto-oncogenes are genes that help regulate cell growth.
  310. Oncogene
    A gene that has been mutated so that its products, in one way or another, cause cancer
  311. True breeding
    Homozygous for a given trait (may be either dominant or recessive).
  312. P1, F1, F2 generations
    • P1 = you
    • F1 = your kids
    • F2 = your grandkids
  313. Alleles
    Alternate forms of the same gene.
  314. Mutagen vs Carcinogen
    Both cause mutations but carcinogens always cause cancer while mutagens may be benign. All carcinogens are mutagens but not all mutagens are carcinogens.
  315. Law of Segregation
    Alleles segregate independently of one another when forming gametes.

    Homologous pairs divide (1 to each gamete) during meiosis.
  316. Law of Independent Assortment
    Genes located on different chromosomes assort independently.

    When homologous pairs line up on the metaphase plate they arrange themselves in a random fashion.
  317. Important MCAT genetics convention
    Whenever the genotype of an individual is not stated you should assume that it is HOMOZYGOUS DOMINANT!!!!...if the individual is a carrier or is affected (homozygous recessive usually) they will tell you.
  318. Penetrance
    The number of individuals in the population carrying the allele who actually express the phenotype.
  319. Expressivity
    The varying expression of disease symptoms despite identical genotypes.
  320. Polygenic
    A characteristic/trait for which the phenotype depends on many genes to help dictate it.
  321. Pleiotrophy
    A single allele that affects many traits.
  322. Mosaicim
    When cells within the same person have different genetic make-up.
  323. Genetic imprinting
    When expression of a gene depends on the parent of origin. Sometimes both copies of a gene are not expressed and the "active" gene is dependent on who the gene came from.
  324. Tissue types
    • Epithelial
    • Nervous
    • Connective
    • Muscle
  325. Tissue Organization
    Organ systems > Organs > Tissues > Cells
  326. Communication characteristics of the endocrine system
    Slow, general, long-lasting
  327. Communication characteristics of the nervous system
    Fast, specific, short-lived
  328. Communication characteristics of the paracrine system
    Local mediator hormones only
  329. Diploid number
    Having a pair of each type of chromosome, so that the basic chromosome number is doubled. 46 in humans.
  330. Haploid number
    The haploid number is the number of chromosomes in a gamete of an individual. This is distinct from the monoploid number (x), which is the number of unique chromosomes in a single complete set. Gametes (sperm, and ova) are haploid cells.
  331. Mitosis yields:
    Two genetically identical, diploid daughter cells.
  332. Meiosis yields:
    Four genetically distinct, haploid daughter cells.
  333. Lipid definition
    Any biomolecule soluble in non-polar solvents and insoluble in polar solvents.

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