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249 Cards in this Set

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Characteristics of Alcohols
R-OH

-functional group is -OH
- H-bonding results in both elevated boiling point and better solubility.
- Weakly acidic
R(=O)H
Aldehyde
R(=O)R
Ketone
R-O-R
Ether
(CH3)3 - C
t-butyl
(CH3)3-CH2-C
neopentyl
(CH3)2-CH
isopropyl
R(=O)-OH
Carboxylic Acid
R(=O)-OR
Ester
R(=O)-X
Acyl Halide
R(=O)-NH2
Amide
CH3-CH2-CH(CH3)
sec-butyl
RC(triple bond)N
cyanide/nitrile
CH2-CH(CH3)-CH2
isobutyl
Alkanes
Cn H2n+2

Fully saturated hydrocarbons consisting of hydrogen/carbon joined by single bonds.

C1-C4: gases, C5-C15: liquids, longer: waxes and harder solids.

increase in chain length = increase in bp, mp, and density.

increase in branching = decrease in all three above.
Alkenes
Cn H2n (double bond) "olefins"

May described as cis, trans, E, or Z

Can be separated by fractional distillation.

Trans-alkenes: have high MP than cis, because of symmetry.

Cis-alkenes: have high BP than trans due to their polarity.
Alkynes
Cn H2n-2 (triple bond)

Physical properties are similar to alkenes and alkanes.

Shorter = gases, boiling at high T than alkenes.
Nomenclature
1. Multiple bonds should be on backbone.
2. -OH is high priority (placed above multiple bond)
3. Haloalkanes, ethers, and ketones are often given common names (e.g. methyl chloride, diethyl ketone)
4. Aldehydes/carboxylic acids are terminal functional groups
5. Specify isomer, if relevant (such as cis/trans, R or S, etc).
Isomers
Chemical compounds that have same molecular formula, but differ in structure.

May be extremely similar or extremely different.
Structural Isomers
Share only their molecular formula, but their atomic connectivity is different.

Therefore, they may have very different chemical and physical properties.
Stereoisomers
Have same atomic connections, but the atoms are arranged differently in space.

Examples:
Geometric isomers, Enantiomers, Diastereomers, Meso Compounds, and Conformational.
Chirality
Carbon atoms have four different substituents.
Geometric Isomers
Differ in position of substituents attached to a double bond.

Cis (Z) - Substituents on same side (based on high atomic number)

Trans (E) - Substituents are on opposite sides.
Enantiomers
Chiral objects that are non-superimposable mirror images.

Specific type of stereoisomers.
Absolute Configuration
(R) and (S) notation.

- Think of a steering wheel.
- Lowest priority substituent is in fourth position and should point away from you, down the column.
- While #1, 2, and 3 lie on the wheel itself.
- R is clockwise, and S is counterclockwise.
Fischer Projection
Horizontal lines indicate bonds that project from plane of page, while vertical lines behind plane of page.
Racemic mixture
Mixture of equal concentrations of both the (+) and (-) enantiomers.

Rotations cancel each other out, thus NO optical activity.
Diastereomers
Differ in chirality, but are NOT mirror images.

For any molecule with n chiral centers, there are 2^n possible stereoisomers.

e.g. Compound with 2 chiral centers = 4 stereoisomers.
Meso Compounds
Have a mirror image that is superimposable.

Thus, NOT optically active.

Have a mirror plane of symmetry
Conformational Isomers
Differ only by rotation about one or more single bonds.

Analogous to a person sitting or standing.

Can be seen in Newman projection.
Newman Projection
Line of sight extends along a carbon carbon bond axis. (Gauge, anti, eclipsed versions)
Straight-Chain Conformations
gauche < eclipsed < totally eclipsed

anti isomers have lowest energy
totally eclipsed have highest energy

At RT these easily interconvert
Cyclic Conformations
Strain Energy is due to ring strain, angle strain, torsional strain, and nonbonded strain (van der waals)

Chair and boat conformations are most important forms of cyclohexane. Chair is most stable and lowest energy.
Axial Substituents
Axial substituents are on Vertical Axis, like axial skeleton.

Axial is NOT favored.
Equatorial Substituents
Equatorial substituents go around the middle, like earth's equator.

Equatorial is favored over axial.

A bulky substituent can prevent the ring from adapting certain conformations.
Hybridization
Concept of mixing atomic orbitals to form new hybrid orbitals.

Useful in explanation of shape of molecular orbitals.
Bonding Summary (single, double, and triple bonds)
Single bonds: sigma, sp^3, 109.5 degrees

Double bonds: sigma/pi, sp^2, 120 degrees

Triple bonds: sigma/pi/pi, sp, 180 degrees
Free Radical Halogenation
One or more H atoms are replaced by halogen atoms (Cl, Br, or I) via free radical substitution. Occurs in Alkanes.

Three steps:
1. Initiation
2. Propagation
3. Termination

Bromine is slow and picky and attacks most substituted.
Chlorine is rapid and attacks primary H with abundance.
Combustion
Occurs in Alkanes.

Reaction of alkanes with molecular oxygen.

Forms CO2, Water, and Heat (desired product)
Pyrolysis
Occurs in Alkanes.

Also called "cracking".

Molecule is broken down by HEAT. Used to reduce average MW of heavy oils and increase production of more desirable volatile compounds.
Nucleophilic Substitutions
Occurs in Alkanes.

Nucleophiles are electron rich species that attracted to positively polarized atoms.

Basicity: Stronger the base, stronger the nucleophile.

Size/polarizability: dependson solvent. Protic = larger atoms. Aprotic = more basic atoms are better.
Best Leaving Groups
I > Br > Cl > F

Weak bases make good leaving groups.

Can accept electron pair and dissociate to form stable species.
Sn1 Reactions
Rate is dependent on ONE species.

Rate determining step is the carbocation.

Favored in POLAR protic solvents (water or acetone)

rate = k[RX]

Want stable carbocations: 3 > 2 > 1 > CH3 (favored with use of bulky nucleophiles)

Produces Racemic products (lose optical activity)

Leaving group = weak bases are best.
Sn2 Reactions
ONE step (no carbocation)

rate = k[Nu][RX] (substrate and nucleophile)

Usually attacks from the backside.

Best Reactant: 1 > 2 > 3

Favored in polar APROTIC solvents.

Optically active and inverted products.

Need strong nucleophile and transition state.
Elimination Reactions
Used in synthesis of alkenes.

Elimination reactions of either alcohols or alkyl halides.

In these reactions, the carbon skeleton loses HX (X = halide) or a molecule of water, to form double bond.

Two types E1 and E2
Unimolecular Elimination (E1)
TWO step process, proceeding through a carbocation intermediate.

k = [RX] (substrate)

Elimination of leaving group plus proton = double bond.

1. Leaving group departs, producing carbocation.
2. Proton is removed by a base.

E1 is favored by same factors as SN1: highly polar solvents, Weak Nu, highly branched carbon chains (3), and good leaving groups.

However, HIGH temps favor E1.
Bimolecular Elimination (E2)
ONE step process.

k = [RX][Base]

Strong base such as ethoxide ion (C2H5O-) removes a proton, while halide ion anti to proton leaves = double bond.

Often two possible products, but more substituted preferred.

Steric hindrance does NOT affect E2.

Strong base favors E2 over SN2.

SN2 favored over by E2 by weak Lewis bases. (Strong Nu)
Catalytic Hydrogenation
Reductive process of adding hydrogen to a double bond with aid of a metal catalyst. (platinum, palladium, and nickel)

Product: Alkane with syn addition of H.

Reaction takes place on metal surface, thus H atoms are added to same face (syn addition).
Addition of HX
An electrophilic addition that occurs in alkenes.

Electron of double bond acts as Lewis base and reacts with electrophilic HX molecules.

1. Yields carbocation after double bond reacts with H+
2. Halide ion combines with carbocation to give alkyl halide.

Follows Markovnikov rule (add to the most substituted carbon)

Product: Alkyl halide
Addition of X2
Addition of halogens to double bond.

Rapid process.

Nucleophile is the double bond, which attacks an X2 molecule, displacing X-.

Forms intermediate cyclic halonium ion, which is then attacked by X- to make a dihalo compound.

Anti-addition (attacks SN2).

Product: dihalo alkane
Addition of H20
Water can be added to alkenes under acidic conditions.

Protonated according to markovnikov.

Performed at LOW temperatures.

Product = alcohol
Free radical Additions
Alternate mechanism for addition of HX to double bond.

Occurs when PEROXIDES, O2, or other impurities are present.

Disobeys Markovnikov rule.

Product: terminal alkyl halides.
Hydroboration
Diborane (B2H6) adds readily to double bonds.

1. Boron atoms is the Lewis Acd and attaches to less sterically hindered C atom.

2. Oxidation-hydrolysis with PEROXIDE/Aq. base produces alcohol with ANTI-markovnikov, syn orientation.

Product: Alcohol with anti-Markovnikov.
Potassium Permangate (KMnO4)
Involved in Oxidation.

1. Cold, dilute KMnO4 produces 1, 2 diols (vicinal) with syn orientation.

2. Hot, basic KMnO4 plus acid produces:

- Nonterminal alkenes = 2M COOH
- Terminal - 1M COOH and 1 CO2 (if disubsituted it makes a ketone).
Ozonolysis
Involved in Oxidation.

Treatment of alkenes with OZONE, followed by reduction with Zn/H20 results in CLEAVAGE of double bond.

Product: Aldehyde.

If reduced with NaBH4 instead of Zn/H2) will result in Alcohols.
Peroxycarboxylic Acids
Alkenes can be oxidized with peroxycarboxylic acids.

e.g. Peroxyacetic acid (CH3CO3H) OR m-chloroperoxybenzoic acid (mcpba).

Products = Epoxides or Oxiranes.
Polymerization
Creation of long, MW chains composed of repeating subunits in alkenes.

Occurs through radical mechanism, requires HIGH TEMP and PRESSURE.
Synthesis of Alkynes
1. Elimination of HX from geminal and vicinal dihalides with HEAT and BASE.

2. Add existing Triple bond to Nucleophile by removing acidic proton with STRONG BASE.
Reduction of Alkynes
Can be hydrogenated with a catalyst.

Two Ways:
1. Lindlar's catalyst (H2, Pd/BaSO4, Quinoline)

Product: Alkane (cis)

2. Na, NH3 (liquid) -33 degrees C.

Product: Trans alkene.
Electrophilic addition of alkynes.
Electrophilic addition to alkynes occurs in same manner as it does alkenes. (X2 added)

Occurs according to Markovnikov.

Can be stopped at alkene or proceed further.

Product: Dihalo alkene or alkane
Free Radical Addition of Alkynes
Radicals add to triple bonds as with double bonds with ANTI-markovnikov (X-).

Product: trans isomer.

Because intermediate vinyl radical can isomerize to its more stable form.
Hydroboration Addition of Alkynes
Addition to triple bonds is same as double bonds.

Addition is syn and BORON adds first.

Boron can be replaced with proton from acetic acid = cis alkene.

Product: syn alkene.
Oxidation Addition
Alkynes can be oxidatively cleaved with either basic KMnO4 followed by acidification or Ozone.

KMnO4 Product: 2 M COOH

Ozone Product: 2 M COOH
Huckel's Rule
4n + 2 pi electrons

Important indicator of aromaticity.

n = any nonnegative integer; thus can be 2, 6, 10, 14, 18, etc.
Aromatic Compounds
Aryl compounds or arenes (Ar)

1,2 substituted = Ortho- or 0-
1,3 subst = meta or m-
1,4 subst = para or p-

Physical properties are similar to hydrocarbons.

All 6C atoms are sp2 hybridized.

has delocalized pi electron system.
Electrophilic Aromatic Substitution
Most important reaction of aromatic compounds.

Reaction: electrophile replaces a proton on ring, producing substituted aromatic compound.

Common e.g.:
1. Halogenation
2. Sulfonation
3. Nitration
4. Acylation
Halogenation of Aromatic Compounds
An electrophilic aromatic substitution

Aromatic ring reacts with Br2 or Cl2 in presence of FeCl3, FeBr3, or AlCl3 to produce a monosubstituted product.

Product: aromatic ring with X.
Aromatic Rings
+
Br2 or Cl2
+
FeBr3, FeCl3, or AlCl3

(name product)
Electrophilic Aromatic Substitution of Br or Cl to aromatic ring.
Sulfonation of Aromatics
An electrophilic aromatic substitution.

Aromatic reacts with fuming H2SO4 (mixture of SO3 and H2SO4) to form sulfonic acids.
Aromatic Rings + Fuming H2SO4 (SO3/H2SO4)

(name product)
An electrophilic aromatic substitution.

Formation of Sulfonic acids.

Aromatic ring + SO3H
Nitration of Aromatic Rings
An electrophilic substitution.

Mixture of nitric and sulfuric acids is used to create the nitronium ion, NO2+ (strong electrophile).

This reacts with Ar. rings to produce nitro compounds.
Aromatic Rings
+
Nitric (HNO3)/Sulfuric acids

(name product)
Product: Nitro Compounds
Friedel-Crafts Acylation
A carbocation electrophile, usually an acyl group is incorporated into Aromatic.

Usually catalyzed by Lewis Acids such as AlCl3.

Product = Ar-Acyl group
CH3C(=O)Cl + Aromatic + AlCl3 --> ?
Product: Aromatic Ring-Acyl group + HCl
Substituent Effects
1. Activating, ORTHO/PARA-directing substituents: (electron donating) NH2, NR2, OH, NHCOR, OR, OCOR, R

2. Deactivating, ORTHO/PARA-directing subs (weakly electron withdrawing): F, Cl, Br, I

3. Deactivating, META-directing substituents (electron withdrawing): NO2, SO3H, Carbonyl compounds (COOH, COOR, COR, CHO)
NO2, SO3H, Carbonyl compounds (COOH, COOR, COR, CHO)
Deactivating, META-directing substituents (electron withdrawing)
Catalytic Reduction of Aromatics
Benzene rings can be reduced under vigourous conditions (elevated Temperature and Pressure) to yield cyclohexane.

Ruthenium and Rhodium are most common catalysts.

Product: cyclohexane
Aromatic ring + H2/Rh/C and high T/P --> ?
Benzene --> cyclohexane
Br2, Hv
electrophilic addition

occurs according to Markovnikov "most substituted"
1) CH3MgBr
2) H3O+
Converts carbonyl compounds to alcohol

Addition reaction by Markovnikov.
Hydrogen bonds can form with..."
"F-O-N"

Fluorine, Oxygen, Nitrogen.
1) NaBH4
2) H3O+
A reducing agent.

It is more selective and easier to handle, but will NOT reduce carboxylic acids and esters.

Will reduce aldehydes and ketones.
1) Lithium Aluminum Hydride
(LiAlH4 or LAH)

2) H3O+
A reducing agent.

Strong and powerful.

More difficult to work with.

Will reduce all aldehydes, ketones, carboxylic acids, and esters.
1) BH3
2) H2O2, OH-
Hydroboration

BH3 adds readily to double bonds.

Second step is oxidation-hydrolysis in an ANTI-markovnikov, syn orientation.

In presence of peroxides will convert to alcohol.
Cold, dilute KMnO4
An oxidizing agent.

Produces 1,2 diols (vicinal diols). a.k.a. glycols with syn orientation.
Alkene + Br2/CCL4 --> ?
Addition of halogens to double bonds is rapid.
Double bond is nucleophile and attacks X2.

Addition is anti, because X- attacks cyclic halonium ion in SN2 displacement.
AlCl3 + X2 or acyl group --?
AlCl3 is a lewis acid.

X2 in presence of lewis acid (FeCl3, FeBr3, AlCl3) produces monosubstituted products in good yield.

AlCl3 + acyl groups = Friedel-Crafts Acylation. will incorporate acyl group.
Zwitterion
An ion with both a positive and negative charge.
Alcohol + Carboxylic acid --> ?
Makes an ester
Henderson-Hasselbalch Equation
pH = pKa - log ([conjugate base]/[conjugate acid])
Nonpolar Amino Acids
Valine, Alanine, Isoleucine, Leucine, Proline, Phenylalanine, Glycine, and Tryptophan.

non - "TV PIG PAL"


Have R-groups that are saturated hydrocarbons. R-groups are hydrophobic and decrease solubility of amino acid.

Often found at core of globular proteins or in transmembrane regions of proteins.
Polar Amino Acids
Methionine, Serine, Threonine, Cysteine, Tyrosine, Asparagine, and Glutamine.

Have polar, uncharged R-groups that are HYDROPHILIC, increasing the solubility of the amino acid in water.

Usually found on protein surfaces.
Acidic Amino Acids
Aspartic Acid, Glutamic Acid

R-group contains carboxyl groups. They have net negative charge at physiological pH and exist in salt form in the body. Play important role in substrate-binding sites of enzymes.

Have three distinct pKa's
Basic Amino Acids
Arginine, Lysine, Histidine

Amino acids whose R-group contains an amino group and carry a net positive charge at physiological pH.
pH vs pI
If pH < pI, think positive charge.

If pH > pI think negative charge.
Peptide bonds
Link amino acid subunits between the carboxyl group of one amino acid and the amino group of another.

Formed via condensation reaction (water is lost).
Primary Structure
Refers to sequence of amino acids listed from N- to C- terminus, linked by COVALENT bonds btw neighboring chains.
Secondary Structure
Local structure of neighboring amino acids, governed mostly by HYDROGEN bond interactions.

Most common types are alpha-helix and beta-pleated sheet.
Alpha-Helix
Rod-like structure in which the peptide chain coils clockwise about a central axis.

e.g. keratin
Tertiary Structure
Three-dimensional shape of the protein
Quaternary Structure
Arrangement of polypeptide units
Conjugated proteins
Have prosthetic groups.
Denaturation
Loss of three-dimensional structure.
Carbohydrates
Aldehydes and ketons with many hydroxyl groups
Monosaccharides
Simplest units and are classified by the number of carbons.
D and L designations
Based on stereochemistry of glyceraldehude.

If Lowest -OH is on the LEFT, the molecule is L.

If the -OH is on the RIGHT, its D.
Epimers
Differ in configuration at only one carbon.
Ketose
Fructose
Aldose
Glucose, Galactose, and Mannose
Pyranose
Six-membered rings
Furanose
five-membered rings
Key reactions of monosaccharides"
1. ester formation
2. oxidation
3. glycosidic reactions
Glycosidic Reactions
hemiacetal + alcohol --> acetal
Spectroscopy
Process of measuring the energy differences between the possible states of a molecular system by determining the frequencies of electromagnetic radiation absorbed by the molecules.
Infrared Spectroscopy
Measures molecular vibrations, which include bond stretching, bending, and rotation.

Best used for identification of functional groups.

Alcohols are BROAD peaks
Acids are BROADEST peaks
Ketones and Amines are SHARP peaks.
Nuclear Magnetic Resonance (NMR)
One of the most widely used spectroscopic tools in organic chemistry. NMR is based on the fact that certain nuclei have magnetic moments that are normally oriented at random.

Most commonly used to study H nuclei (protons) and 13C nuclei, but any atom possessing a nuclear spin can be studied.
1H NMR
1H nuclei come into resonance between 0 and 10 delta downfield from TMS.

Each peak represents a single proton or a group of equivalent protons. (the number of peaks represent the number of groups of nonequivalent protons).

The relative area of each peak reflects the ratio of the protons producing each peak.

The position of the peak (upfield or downfield) due to shielding or deshielding effects reflects the chemical environment of the protons.

Proton NMR is good for:
1. Determining the relative number of protons and their relative chemical environments.

2. Showing how many adjacent protons there are by splittting patterns.

3. Showing certain functional groups.
TMS
provides a reference peak. The signal for its H atoms is assigned a delta = 0.
Downfield
Deshielded
Carbon NMR
Can show:
1. The number of different carbons with their relative chemical environments.
2. Their number of hydrogens (spin coupled NMR only)
UV Spectroscopy
Most useful for studying compounds containing double bonds, and/or hetero atoms with lone pairs.

Can be applied quantitatively by using Beer's law.
Beer's law
A = epsilon(b)(c)

A = absorbance (measured by UV)
(epsilon) = a constant for the substance at a given wavelenght.
b = path length (usually equal to one)
c = concentration
Mass Spectrometry
Differs in that it is not true spectroscopy.

No absorption of electromagnetic radiation is involved.

Does not allow for reuse of sample.

Helps in distinguishing certain compounds.
Extraction
Separates dissolved substances based on differential solubility in aqueous versus organic solvents (oil and water).

hydrogen bonding: alcohols/acids --> aqueous

dipole-dipole: less likely to move to aqueous

van der Waals: compounds are least likely to move into aqueous layer.
Filtration
Separates solids from liquids
Recrystallization
Separates solids based on differential solubility; temperature is important here.
Sublimation
Separates solids based on their ability to sublime.

Must raise the temp at a low enough pressure, or lower the pressure at a very cold temperature.
Centrifugation
Separates large things (like cells, organelles, and macromolecules) based on mass and density.
Distillation
Separates liquids based on boiling point, which in turn depends on intermolecular forces.
Chromatography
Uses a stationary phase and a mobile phase to separate compounds based on how tightly they adhere (generally due to polarity but sometimes size as well).
Electrophoresis
Used to separate biological macromolecules (such as proteins or nucleic acids) based on size and sometimes charge.
Amines
Boiling points of amines are between those of alkanes and alcohols.

Are bases and readily accept protons to form ammonium ions.

Function as weak acids.
Alkylation of Ammonia (Direct)
Alkyl halides + ammonia (NH3) --> alkylammonium halide salts.

Ammonia functions as a nucleophile and displaces the halide atom. When the salt is treated with a base, the alkylamine product is formed.

A SN2 reaction: halides are good leaving groups and ammonia is a good nucleophile
Gabriel synthesis
Converts a primary alkyl halide to a primary amine.

Also a SN2 reaction.
Amines can be formed by:
1. SN2 reactions: ammonia reacting with alkyl halides or gabriel synthesis.

2. Reduction of: amides, aniline and its derivatives, nitriles, and imines.

Amines can be destroyed (converted to alkenes) by exhaustive methylation.
Nitro Compounds + (Fe or Zn) + diluted HCl --> ?
Product: Nitro replaced with Amine.

Useful for aromatic compounds, because nitration of aromatic rings is facile.

Fe or Zn + HCl: common reducing agent.
Nitriles + (Hydrogen/catalyst or with LAH) --> ?
Product: Primary amines
Reductive amination
Process whereby an aldehyde or ketone is reacted with ammonia, a primary amine, or a secondary amine to form a primary, secondary, or tertiary amine, respectively.
Amine + (Aldehyde or Ketone) -->
Product: Imine

Additional reduction with hydrogen in presence of a catalyst (Raney Nickel) = amine.
Imine + (H2/Nickel) -->
Product: Amine
Imine
Nitrogen double bonded to a carbon and has about the same polarity as a carbonyl functionality.
DMSO
Good Polar Aprotic Solvent.

Therefore, good in SN2 reactions.
CN-
Strong nucleophile.

Good in SN2 reactions.
I-
Weak base, therefore good leaving group for SN2 reaction.
Definition of aromtaticity
(4n + 2) pi

So, can be 2, 6, 10, etc...
Cl2 + FeCl3 + Aromatic -->
Cl is Ortho, Para-directing, so will attach Cl to para or ortho positions depending on substituents.
KMnO4
Oxidizing agent

Change toluene to COOH.
HNO3/H2SO4 + toluene --> ?
R-groups are Ortho-, para- directing, so nitro will add to ortho or para position.
Wolff-Kishner Reduction
Aldehydes and ketones can be completely reduced to alkanes by this metho. The carbonyl is first converted to a hydrazone, which releases molecular nitrogen when heated and forms an alkane. Only useful under basic conditions.

(use H2NNH2/Base/heat)
Clemmensem Reduction
Where an aldehyde or ketone is heated with amalgamated zinc in hydrochloric acid.
Grignard Addition
Grignard reagents (RMgX) add to the carbonyl groups of ESTERS to form KETONES; however, the ketones are more reactive than the initial esters and are readily attacked with more grignard reagent to make TERTIARY ALCOHOLS.
Claisen Condensation
Important reaction of ESTERS.

Simplest case: two moles of ethyl acentate react under basic conditions to produce a beta-keto ester. Also called teh acetoacetic ester condensation.

Enolate ion of one ester acts as a nucleophile, attacking another ester.
Grignard reagent
RMgX (equivalent to R- nucleophile)
Transesterification
When a different alcohol attacks the ester, the ester is TRANSformed, and TRANSesterification results.

(ester into another ester)
NH3 + ester --> ?
Answer: amide + alcohol

Nitrogen bases such as ammonia will attack the electron-deficient carbon atom, displacing alkoxide, to yield an amide and an alcohol side product.
Hofmann Rearrangement
Converts amides to primary amines with the LOSS of the carbonyl carbon.

Involves the formation of a nitrene (nitrogen analog of carbene).
Reduction of Amides --> ?
Amides can be reduced with LAH to the corresponding AMINE, but NO carbon is lost.
KMnO4 + H2O2/OH-
Oxidation reagent. Will reduce to carboxylic acids.
Br2/hv
Free radical halogenation. Will add to most substituted carbon.

Bromine is picky, but chlorine will more rapid and depends not only on the stability of intermediate, but on the number of hydrogens present.
Which compound will undergo an oxidation reaction without the cleavage of any covalent bond between two carbons?

a. t-butyl alcohol
b. ethyl methyl ketone
c. acetaldehyde
d. acetate
e. all of the above
c. acetaldehyde

Hydrogen is accessible at the end to oxidizing agent.
Reagents used for oxidation of aldehydes
KMnO4, CrO3, Ag2O, H2O2. The product of oxidation is a CARBOXYLIC ACID.
Carboxylic Acid + Alcohols --> ?
Esters.

Mixtures of COOH and -OH will condense into esters, liberating water, under acidic conditions.
Conformational isomers
Compounds that differ only by rotation about one or more single bonds.

(Different positions of a compound)
Geometric Isomers
Compounds that differ in the position of substituents attached to a double bond. (e.g. cis/trans and Z/E)
Acetone
(CH3)2C(=O)
Heats of hydrogenation
Heats of hydrogenation can be used to measure the relative stability of isomeric alkenes.

Heats of hydrogenation correlate with structure just like heats of combustion do.

The greater the heat of hydrogenation, the less stable the alkene.
Which of the following could be the formula for an ester?

a. C6H12O
b. C7H12O2
c. C7H14O
d. C7H16O2
e. C7H16O
b. C7H12O2
William Ether Synthesis
Produces ethers from the reaction of metal alkoxides with primary alkyl halides or tosylates.

Alkoxides behave as nucleophiles, displacing halide or tosylate via an SN2 reaction, producing an ether.
What is the product of the following reaction:

CH3Cl + CH3O-Na+ --> ?
CH3OCH3

William ether synthesis reaction.
With molecular formular CH4, how many structural isomers can be formed? C2H6? C3H8? C4H10? C5H12? C6H14? C7H16? C8H18? C9H20? C10H22?
CH4 = 1
C2H6 = 1
C3H8 = 1
C4H10 = 2
C5H12 = 3
C6H14 = 5
C7H16 = 9
C8H18 = 18
C9H20 = 35
C10H22 = 75
Aromatic (with C2H5) attached + KMnO4 --> + SOCl2 --> + HCN --> + H2O --> ?

what is final product of these reactions?
aromatic + C(=O)COOH
Thionyl Chloride
SOCl2

Used to convert carboxylic acids to acyl chlorides.

Also alcohols to corresponding alkyl chlorides.
acetal
Molecule with two single bonded oxygens attached to the same carbon atom.
Ketal
Functional group or molecule containing the functional group of a carbon bonded to two -OR groups.
Purine
Purine is a heterocyclic aromatic organic compound, consisting of a pyrimidine ring fused to an imidazole ring.

(4 nitrogens: 2 in hexane ring, 2 in pentane. They are attached)
Pyrmidine
Pyrimidine is a heterocyclic aromatic organic compound similar to benzene and pyridine, containing two nitrogen atoms at positions 1 and 3 of the six-member ring.
To prepare a primary alcohol with a grignard reagent, the grignard reagent must react only with

a. CH3COCH3
b. CH2CHO
C. HCHO
d. HCOOH
e. CO2
c. HCHO

converts ketones and esters to alcohols.
D2O
Heavy water. or H2O.
CH3MgBr + D2O --> ?
DCH3
Ch3MgBr + CO2 --> ?
CH3COO-
The base-catalyzed condensation products of two acetaldehyde molecules is...
a beta-hydroxylaldehyde
HCN + aldehydes or ketones --> ??
Aldehydes and ketones react with HCN to produce stable compounds called cyanohydrins. (CN and OH attached to same carbon group)
Aldehyde + Aldehyde + base --> ??

e.g. two acetaldehyde molecules + base --> ??
Aldol Condensation reaction:

Aldehyde acts as both nucleophile and target. This will create an aldol = aldehyde + alchohol.

Product: a beta-hydroxyaldehyde
Define spin splitting in HNMR?
If two magnetically different protons are within three bonds of each other a phenomenon known as coupling, or splitting occurs.
Note on E2 reactions regarding base used
Bulkyness of base affects the hydrogen attacked on species. Will attack less substituted if base is bulky.

If base is not bulky, then it will attack most substituted.
Concerted reaction
Chemical reaction in which all bond breaking and bond making occurs in a SINGLE step.
Which of the following would be the best solvent for an SN2 reaction?

a. H2O
b. CH3OH
c. CH3SOCH3
d. heptane
e. tosylate
c. CH3SOCH3 (dimethyl sulfoxide) gives best results if a polar aprotic solvent is used.

a and b are wrong because these are both polar.
D is a heptane and is incorect because it is a nonpolar solvent.
c. tosylate is a good leaving group not a solvent.
Combustion
Reaction of alkanes with molecular oxygen to form Carbon dioxide, water, and heat.
CH3COOH + CH3MgBr --> ??
CH3COO-

Grignard reagents normally convert esters and ketones to alcohols.
Williamson Ether Synthesis is an example of what type of reaction?

a. E2 or SN2
b. E2
c. SN2
d. E1 or SN1
e. two of the above
c. SN2

William Ether synthesis produces ethers from reaction of metal alkoxides with primary alkyl halides or tosylates. Via an SN2 reaction.
RCOOH + NaOH --> ??
RCOO-Na+ (a soap) + H2O
Peroxycarboxylic acids (mcpba or m-chloroperoxybenzoic acid)
Alkenes can be oxidized with mcpba. The products are formed are OXIRANES.
True or false: Phenol can exist as a very temporary and less stable keto form via tautomerizing?
True
Ozonolysis
Reduction mechanism. Results in aldehydes or ketones depending on treatment.
Alkyne + O3 -->
Alkynes can be oxidatively cleaved with ozone to make 2M COOH.
Which reagent will give a CIS-product when reacted with an alkyne?
1. H2, Pd/BaSO4, Quinoline (lindlar's catalyst)

2. a)BH3 b)CH3COOH

both produce cis products.
Epimers
Stereoisomer of another compound that has different configuration at only ONE of several sterogenic centers.
Oligodendrocytes
Produce myelin in the central nervous system
Schwann Cells
Produce myelin in the peripheral nervous system
Nodes of Ranvier
Gaps between segments of myelin
Resting potential
At rest a neuron is POLARIZED at -70 millivots.

Which means that the inside is MORE NEGATIVE than the outside.

Due to ionic permeability of the neuronal cell membrane and is maintained by active transport by Na+/K+ pump.
Concentration of K+: Is it higher or lower inside the neuron?
HIGHER than outside.
Concentration of Na+: higher or lower in the inside of the neuron?
LOWER inside the neuron, therefore HIGHER outside.

Neurons are IMPERMEABLE to Na, so the cell remains polarized.
Na+/K+ pump
Gradients are restored by this pump. It uses ATP energy and transports 3 Na+ out for every 2 K+ it transports into the cell.
Action Potential
If the cell becomes sufficiently excited or depolarized (inside becomes LESS NEGATIVE), an action potential is generated.

Minimum THRESHOLD membrane potential (usually around -50 mV) is level it is initiated.
When does an action potential begin?
When voltage-gated Na+ channels open in response to depolarization, allowing Na+ to rush down its electrochemical gradient INTO the cell, causing rapid depolarization of the segment of the cell.
What causes a neuron to be repolarized?
Voltage gated Na+ channels then close and voltage gated K+ channels open, allowing K+ to rush OUTSIDE down its electrochemical gradient.
Hyperpolarization
When a neuron shoots past the resting potential and becomes even MORE NEGATIVE than normal.
Refractory Period
Immediately after an action potential , it my be difficult or impossible to initiate another action potential.
Afferent neurons
Sensory neurons: carry sensory info about external or internal environment TO brain and spinal cord.
Efferent neurons
MOTOR neurons: they carry them FROM the brain or spinal cord to various parts of body.
Central Nervous system
Consists of Brain and Spinal Cord.
Brain
Mass of neurons that resides in the skull.

Consists of OUTER portion called GRAY matter (cell bodies) and INNER WHITE matter (mylelinated axons).

Brain can be divided into FOREBRAIN, MIDBRAIN, and HINDBRAIN
Parts of Forebrain
Also called PROSENCEPHALON

Consists of:
Telencephalon and Diencephalon
Parts of Telencephalon
1. Cerebral cortex
- Highly convoluted gray matter that can be seen on the surface of the brain. It processes and integrates sensory input and motor responses and is important in MEMORY and CREATIVE thought.

2. Olfactory Bulb
- Center for reception and integration of olfactory input.
Parts of Diencephalon
1. Thalamus
- RELAY and INTEGRATION center for spinal cord and cerebral cortex.
2. Hypothalamus
- Controls VISCERAL function such as HUNGER, THIRST, SEX DRIVE, WATER balance, BLOOD pressure, and TEMPERATURE regulation. Also plays an important role in endocrine system.
Parts of Midbrain
RELAY center for VISUAL and AUDITORY impulses. Plas an important role in motor control.

Is also called MESENCEPHALON
Parts of Hindbrain
Also called RHOMBENCEPHALON. It is posterior part of brain.

1. Cerebellum
- Helps modulate MOTOR impulses initiated by cerebral cortex.
- important in maintenance of BALANCE, HAND-EYE coordination, and the timing of RAPID movements.

2. Pons
- Act as a RELAY center to allow the cortex to COMMUNICATE with CEREBELLUM.

3. Medulla Oblangata
- Controls vital functions such as BREATHING, HEART RATE, and GI activity.
What is Brainstem?
Midbrain, pons and medulla oblangata
Spinal Cord
Elongated extension of the brain.

OUTER WHITE matter: contains motor and sensory axons AND
INNER GRAY matter containing cell bodies.
Dorsal Horn
sensory info enters the spinal cord through this.

The cell bodies of these sensory neurons are located in the dorsal root ganglia.
Ventral Horn
All motor information exits the spinal cord.
Sympathetic Nervous System
"Flight or Fight"
Increases blood flow to skeletal muscels, and decreases gut motility.

Dilates bronchioles and uses NOREPINEPHRINE as primary neurotransmitter.
Parasympathetic Nervous System
"Rest and Digest"

Acts to CONSERVE ENERGY and RESTORE the body to resting activity levels.

- Lowers heart rate
- increases gut motility
- One important parasympathetic nerve is VAGUS nerve.

ACETYLCHOLINE is primary neurotransmitter.
Sexual Reproduction in PLANTS
- life cycles of plants are characterized by ALTERNATION of DIPLOID sporophyte and the HAPLOID gametophyte generation.

Evolutionary trend has been towards INCREASED dominance of the SPOROPHYTE generation.
Gametophyte Generation
HAPLOID gametophyte generation produces GAMETES by MITOSIS.

Union of female and male gametes at fertilization restores the diploid sporophyte.

Gametophytes reproduce SEXUALLY while the sporophyte reproduces asexually.

Mosses (bracheophyta): gametophyte is the dominant generation.
Sporophyte Generation
DIPLOID sporophyte produces haploid spore by MEIOSIS.

Spores divide by mitosis to produce the haploid or gametophyte generation.

e.g. Ferns: Sporophyte is dominant.
Angiosperms: Woody plant seen is sporophyte stage.
How is blood type determined?
By three alleles, Ia, Ib, and i.

Only two alleles are present in any single individual, but the population contains all three alleles.
Homozygous DOMINANT red snapdragons crossed with Homozygous white snapdragons RECESSIVE gives what in F1 progeny? F2?

What type of dominance is this?
F1 generation will give 100% pink flowers, since generation will give Rr.

F2 will give 1:2:1 progeny in this ratio.
(red, pink, white)

Pink color is result of the combined effects of the red and white genes in heterozygotes.

The type of dominance is called INCOMPLETE dominance because of the pink.
Dihybrid Cross
Parents differ in TWO traits.
Crossing over
Genes on the same chromosome will stay together unless crossing over occurs.

Exchanges information between chromosomes and may break the linkage of certain patterns. = Mendel's Law of Indenpendent Assortment
TTPP x ttpp = ?
Genotype for all is TtPp and iwll be phenotypically dominant for both traits.
TtPp x TtPp = ?
Produces four different phenotypes:

tall purple, tall white, dwarf purple, dwarf white, in the ratio of 9:3:3:1, respectively.

Typical pattern of mendelian inheritance in a dihybrid cross between heterozygotes with independently assorting traits.
Curare
Blocks the POST-synaptic ACETYLCHOLINE receptors so that acetylcholine is unable to interact with the receptor.

Leads to PARALYSIS by blocking nerve impulses to muscles.
Gibberellins
Stimulate rapid STEM ELONGATION, particularly in plants that normally do not grow tall.

INHIBIT the FORMATION of new ROOTS.

STIMULATE the production of NEW PHLOEM cells by CAMBIUM.

TERMINATE DORMANCY of seeds and buds.
Auxins
STIMULATE the production of NEW XYLEM cells.

Important class of plant hormones associated with several growth patterns:
1. Phototropism
- (growth towards light; Indole acetic acid is one of the auxins associated with phototropism) - MORE auxins = DECREASED growth.

2. Geotropism:
(Growth TOWARDS or AWAY from gravity)
- NEGATIVE geotropism = Causes shoot to grow UPWARD, AWAY from acceleration of gravity. (INCREASE in auxin = incerase growth)

- POSITIVE geotropism = Causes roots to grow TOWARDS the pull of gravity. (HIGH concentration of auxin = inhibit growth)
Peptide Hormones
SURFACE receptors
Generally act VIA secondary messengers
Steroid Hormones
INTRACELLULLAR receptors
Hormone/receptor binding to DNA promotes transcription of specific genes.

e.g. estrogen and aldosterone
Gastrointestinal Hormones
1. Gastrin - stimulates secretion of HCl
2. Secretin - released by small intestine and stimulates secreation of bicarbonate to neutralize acidity.
3. Cholescystokinin - released from small intestine in response to presence of fats and causes contraction of gallbladder and release of bile.
4. Bile - involved in digestion of FATS.
Calcitonin is released from what gland? what does it do?
Thyroid, decreases calcium concentration in plasma by inhibiting release of Ca2+ from bone.
Inducible Systems
REPRESSOR binds to OPERATOR, forming a barrier that PREVENTS RNA polymerase from transcribing the structural genes.

For transcription to occur, the INDUCER must bind to the REPRESSOR forming an inducer-repressor complex. This cannot bind to operator.
Repressible Systems
REPRESSOR is INACTIVE until it combines with the COREPRESSOR.

Repressor can bind to operator and PREVENT transcription only when it has formed a repressor-corepressor complex.

Corepressor is END-product since it is being synthesized.
Types of Gene Regulation in Prokaryotes
1. Inducible Systems
2. Repressible Systems

Based on accessibility of RNA polymerase.

Directed by OPERON, which consists of structural, operator, and promoter genes.
Nondisjunction
Either the failure of homologous chromosomes to separate properly during MEIOSIS I, or the failture of sister chromatids to separate properly during MEIOSIS II.

Can result in trisomy (2N +1) or Monosomy (2N -1).

e.g. trisomy is down syndrome (chr. 21)
Sickle-Cell anemia
Disease in which red blood cells become crescent-shaped because defective hemoglobin.

Carries less oxygen.

Caused by SUBSTITUTION of VALINE (GUA or GUG) for GLUTAMIC ACID (GAA or GAG).
Reagents used to effect Markovnikov addition to an alkene
H2O/Cl2
Hg(OAc)2/H2O then NaBH4
H2O/H2SO4
Antiaromatic
A cyclic, conjugated polyene that possesses 4n electrons.
Permutations
p = q! (q - r)!

When working with problems in which items are taken from a larger set in SPECIFIC ORDER.

q = represent a set of items
r = objects taken r at a time in specific order.
Combinations
qCr = q! / [r!(q - r)!]

Possible number of combinations = qCr