Intro to Organic Chemistry & BioChem (full semester combo for final)

carbonate ion

(CO3)2-

electrophile

(aka electron lover, seeking the negative): an electron-poor, NEUTRAL or POSITIVE species that can accept a pair of electrons to form a new covalent bond. Any molecule, ion or atom that is electron deficient in some way can behave as an electrophile. Electron deficiency would include a formal positive charge (methyl carbocation), a partial positive charge (d+), usually in conjunction with a polar bond (such as H-Cl) or an open octet (borane). "E" or "E+" are common abbreviations for generic electrophiles.

nucleophile

(aka nucleus lover, seeking the positive): an electron-rich, NEGATIVE species that can donate a pair of electrons to form a new covalent bond. The most common indications that electrons are available to be shared are formal negative charge (iodide ion), a partial negative charge (d-), usually in conjunction with a polar bond (methyl magnesium bromide), a p bond (isobutylene) or lone pairs (ammonia). "Nuc" or "Nu" are common abbreviations for generic nucleophile

predicting equilibrium shift

(balance the pendulum) add to reactants = shift right add to product = shift left subtract from reactant = shift left subtract from product = shift right introduce base = consume strongest acid (H3O+) → shift toward the consumed portion of equation to make more increase pH = decreasing H3O+ → shift right to make more

calculate pH of buffer

(pKa value of weak acid) + log (base 10) of [M of the conjugate base]/[M of the acid]

carboxyl group

-COOH

carboxyl group

-COOH aka -CO₂H aka C(=O)-OH

hydroxyl group

-OH

calculate pH of strong acids

-log (base 10) of original Molarity of the acid reactant

pKa

-log Ka value

pH

-log [H3O+] aka: the negative log of the concentration of hydronium ions

pOH

-log [OH-] aka: the negative log of the concentration of hydroxide ions

Hückel's rule

1-must have the magic number (4n+2) of electrons in the delocalized, conjugated p-orbital cloud; 2-the molecule must be cyclic (a ring); and, 3-every atom in the ring must be able to participate in delocalizing the electrons by having a p-orbital or an unshared pair of electrons (there must be alternation between single-double or single-unpaired electron).

carboxylic acid reaction: decarboxylation

1. heat mechanism: RCOOH →high heat→ R-H + CO2 (loss of CO2 by a -COOH at high temperatures) 2. beta-keto enolation R(C=O)CH2(C=O)-OH → R(C=O)CH3 + CO2 (beta-keto acids decarboxylate at medium heat easily and the anion is stabilized as an enolate; the middle CH2 is the alpha-carbon, 1st C=O is beta-carbon aka beta-ketone)

carboxylic acid reaction: neutralization

1. with a strong base: RCOOH + NaOH → RCOO⁻Na⁺ + H2O (a carboxylic salt) 2. intramolecular neutralization: RCH(NH2)COOH → RCH(NH3⁺)COO⁻

ideal bond-angle tetrahedral

109.5°

ideal bond-angle trigonal pyramidal

109.5°

ideal bond-angle bent

120°

ideal bond-angle trigonal planar

120°

ideal bond-angle linear

180°

alpha

1st letter of Greek alphabet

calculate pH of weak acids

1st: sqrt(Ka value of weak acid x M of weak acid) = x 2nd: -log (x)

alcohol reaction: acid-catalyzed dehydration

1° alcohol needs H2SO4 + 180°C 2° alcohol needs H2SO4 + 140°C 3° alcohol needs H2SO4 + 50°C

benzene combustion

2C6H6 + 15O2 → 12CO2 + 6H2O

thiol reaction: oxidation-reduction

2HOCH2CH2SH ←O2→ HOCH2CH2S-SCH2CH2OH

beta

2nd letter of Greek alphabet

2ⁿ rule

2ⁿ isomers possible for each 'n' stereocenter; 2 stereoisomers = 1 pair of enantiomers.

gamma

3rd letter of Greek alphabet

delta

4th letter of Greek alphabet

epsilon

5th letter of Greek alphabet

natural gas

90% methane + lesser amounts of ethane and lower-molecular-weight hydrocarbons

head group

A bulky part of a molecule, often containing one or more functional groups, attached to a relatively long aliphatic tail or backbone

phosphoric ester

A phosphoric acid molecule that has formed a monoalkyl, a dialkyl, or a trialkyl ester by reaction with one, two, or three molecules of an alcohol

carboxylate

A salt or ester of an organic acid, containing the radical COO⁻

esterification

AKA Fischer esterification: the process of forming an ester by refluxing a carboxylic acid and an alcohol in the presence of an acid catalyst, commonly H2SO4

maltose

AKA Glcα(1→4)Glc a disaccharide of two molecules of alpha-D-glucose joined by a 1,4-glycosidic bond; becomes the repeating units of starch

cellobiose

AKA Glcβ(1→4)Glc disaccharide that becomes the repeating units of cellulose

superposable

AKA achiral: the mirror image and the original represent the same molecule

Ka

AKA acid ionization constant AKA acid dissociation constant: the equilibrium constant for a chemical reaction known as dissociation in the context of acid-base reactions. In aqueous solution, HA is a generic acid that dissociates into A−, known as the conjugate base of the acid and a hydrogen ion which combines with a water molecule to make an hydronium ion (H3O+).

geometric isomerism

AKA cis-trans isomerism: two or more compounds that differ from each other in the arrangement of groups with respect to a double bond, ring, or other rigid structure

ΔG⁰

AKA delta G naught: free activation energy reaction rate and activation energy inversely proportional: if ΔG⁰↑, then reaction rate slow; if ΔG⁰↓, then reaction rate fast

carboxylic ester

AKA ester: derivative of a carboxylic acid in which a carbon group replaces the H of the carboxyl group

fatty acids reaction: saponification

AKA fatty acid neutralization: the hydrolysis of an ester in aqueous NaOH or KOH to an alcohol and the sodium or potassium salt of a carboxylic acid.

monosaccharide reaction: formation of glycosides

AKA formation of acetals AKA condensation: a reversible reaction with an alcohol in which the anomeric carbon becomes fixed as an acetal to the -R from the alcohol and H2O is a byproduct. Reverse reaction is hydrolysis.

cis-trans isomerism

AKA geometric isomerism and E/Z isomerism: compounds with the same molecular formula, the same connectivity of their atoms, but a different arrangement of their atoms in space because of restricted rotation about the carbon-carbon bonds of a ring or a double bond.

glycoside bond

AKA glycosidic linkage: the bond from the anomeric carbon of a glycoside to an -OR group

thiols: physical properties

AKA mercaptans: an -SH (sulfhydryl) group bonded to a tetrahedral C atom -non-polar -stinky -slightly acidic -lower b.p. & less soluble than alcohols

lactose

AKA milk sugar AKA Galβ(1→4)Glc a disaccharide consisting of beta-D-galactose joined to D-glucose (either alpha or beta) by a beta-1,4-glycosidic bond

glycerophospholipid

AKA phosphoglycerides: diglycerides with some kind of phosphate group at position 3. Name by using locant and fatty acyl names for the groups at positions 1 and 2 replacing suffix -ic with suffix -oyl, add phosphatidyl for the phosphate group + name of head group attached to the phosphate (such as choline, serine, ethanolamine, etc.); e.g. 1,2-distearoylphosphatidylcholine Key component in cell membranes

peptide

AKA polyamide: a polymer of amino acids linked by peptide (amide) bonds AND/OR relatively short peptide (13 - 50 linked amino acids)

Tollens' reagent

AKA silver-mirror test: a colorless, basic, aqueous solution containing silver ions coordinated to ammonia [Ag(NH3)2+]. a qualitative laboratory test used to distinguish between an aldehyde and a ketone, exploiting the fact that aldehydes are readily oxidized , whereas ketones are not.

constitutional isomerism

AKA structural isomerism: compounds that have the same molecular formula and different connectivity

sucrose

AKA table sugar AKA Glcα(1→2)Fruβ a disaccharide consisting of alpha-D-glucose joined to beta-D-fructose by an alpha-1,2-glycosidic bond

N-terminus

AKA the amino-terminus, NH2-terminus, N-terminal end or amine-terminus: refers to the start of a protein or polypeptide terminated by an amino acid with a free amine group (-NH2) pKa = 9

C-terminus

AKA the carboxyl-terminus, carboxy-terminus, C-terminal tail, C-terminal end, or COOH-terminus: refers to the end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH) pKa = 2

monosaccharide reaction: formation of hemiacetals

AKA transition to ring-form: a five-carbon straight-chain formation becomes a five-membered ring (aka furanose); a six-carbon straight-chain formation becomes a six-membered ring (aka pyranose)

triglyceride

AKA triacylglycerol: triester of glycerol and long-chain carboxylic acids (aka fatty acids)

keto-enol tautomerism

Acidic alpha hydrogen removed, leaving double bond (-ene) on most substituted carbonyl carbon and creating -OH from carbonyl oxygen. End result is a chemical equilibrium (not resonance) between a keto form (a ketone or an aldehyde) and an enol (an alcohol). The enol and keto forms are said to be tautomers of each other.

carboxylic acid: chemistry

Acidity = weak, but easily influenced by substituents Neutralization reactions = carboxylic salt w/ strong base or intramolecular Amidation (-COOH + amine w/ heat = amide) Reduction (takes LiAlH4 to affect the -COOH group) Esterification Decarboxylation (at very high temps or if a ketone C=O is in beta position to -COOH @ alpha)

amine

An organic compound in which one, two or three hydrogens of ammonia are replaced by carbon groups: RNH₂, R₂NH or R₃N

terpene

Any of a class of hydrocarbons consisting of two or more isoprene (C5H8) units joined together. Simple terpenes are found in the essential oils and resins of plants such as conifers. Turpentine, for example, is such an oil.

Ba(OH)2

Barium hydroxide, a strong base

decane

C10H22

sesquiterpene

C15 molecule derived from 3 isoprene units.

diterpene

C20 molecule derived from 4 isoprene units.

sesterterpene

C25 molecule derived from 5 isoprene units.

ethane

C2H6

triterpene

C30 molecule derived from 6 isoprene units.

propane

C3H8

butane

C4H10

pentane

C5H12

hexane

C6H14

phenyl group

C6H5-the aryl group derived from removing a hydrogen atom from benzene. What a benzene ring is named when it becomes the substituent to a parent chain. Represented by symbol Ph-

formula for benzene

C6H6

heptane

C7H16

octane

C8H18

nonane

C9H20

carbonyl group

C=O

ethene (aka ethylene)

CH2=CH2

amine reaction: neutralization

CH3(CH2)2-NH2 + HCl → CH3(CH2)2-NH3⁺ Cl⁻ (amine + acid = salt)

butane (condensed structural formula)

CH3(CH2)2CH3

pentane (condensed structural formula)

CH3(CH2)3CH3

hexane (condensed structural formula)

CH3(CH2)4CH3

heptane (condensed structural formula)

CH3(CH2)5CH3

octane (condensed structural formula)

CH3(CH2)6CH3

nonane (condensed structural formula)

CH3(CH2)7CH3

decane (condensed structural formula)

CH3(CH2)8CH3

2-Methylpropene (aka isobutylene)

CH3-C(CH3)=CH2

ketone reaction: addition

CH3C=OCH3 + CH3-OH → CH3C(OH)-OCH3 (a hemiketal) alcohol splits at OH bond, an ether joins the carbonyl carbon, the H protonates the O CH3C(OH)-OCH3 (a hemiketal) →H⁺→ CH3C(OCH3)2(a ketal) in presence of acid, reaction continues

propane (condensed structural formula)

CH3CH2CH3

thiol reaction: neutralization

CH3CH2SH + NaOH →(H2O)→ CH3CH2S- Na⁺ + H2O (a tholiate salt)

ethane (condensed structural formula)

CH3CH3

propene (aka propylene)

CH3CH=CH2

aldehyde reaction: addition

CH3CH=O + CH3-OH → CH3CH(OH)-OCH3 (a hemiacetal) alcohol splits at OH bond, an ether joins the carbonyl carbon, the H protonates the O CH3CH(OH)-OCH3 (a hemiacetal) →H⁺→ CH3CH(OCH3)-OCH3 (an acetal) in presence of acid, reaction continues

methane (condensed structural formula)

CH4

methane

CH₄

priorities mnemonic (2 middle eastern dudes)

Caan Estamalke Altham alk-alk Etalnialk

Ca(OH)2

Calcium hydroxide, a strong base

CsOH

Cesium hydroxide, a strong base

HClO3

Chloric acid, a strong acid

formula for cycloalkenes

CnH(2n-2)

formula for cycloalkynes

CnH(2n-4)

formula for alkenes

CnH2n

formula for cycloalkanes

CnH2n

formula for alkanes

CnH2n+2

formula for alkynes

CnH2n-2

lactone

Cyclic esters = lactones; name simple lactones by replacing -ic acid from the carboxylic acid name with -olactone

Acetylene (aka ethyne)

C₂H₂

Ethylene (aka ethene)

C₂H₄

Ethane

C₂H₆

anhydride: physical properties

EXTREMELY reactive and rarely found in nature. POLAR participate in h-bonding high m.w. have strong LDF high m.p., high b.p. (similar to carboxylic acids, but not quite an acid because missing -OH group(s))

straight-chain formation

Fischer projection of carbohydrate structure

zwitterion

German for "hybrid ion": ions that are electrically neutral overall but contain nonadjacent regions of positive and negative charges

chitin

Glc NAc β(1-4) Glc NAc glucan made from N-acetylglucosamine; structural support in exoskeletons

amylose

Glcα(1-4)Glc monomer (i.e. alpha-glucose linked to alpha-glucose in a α(1-4) glycosidic bond) plant-based storage carbohydrate; simplest starch, a linear glucan with α(1-4) linkages

cellulose

Glcβ(1-4)Glc monomer (i.e. beta-glucose linked to beta-glucose in a β(1-4) glycosidic bond) glucan made from cellobiose monomers; structural support for plants

sulfuric acid (aka sulphuric acid)

H2SO4

Hydronium ion

H3O+

the magnificent seven (strong acids)

HCl, HBr, HI, HNO3, H2SO4, HClO3, HClO4

HBr

Hydrobromic acid, a strong acid

HCl

Hydrochloric acid, a strong acid

HI

Hydroiodic acid, a strong acid

conjugate acid

In the Bronsted-Lowry theory, a substance formed when a base accepts a proton. Add a proton (H⁺) to a base in order to configure its conjugate acid, calculate new net charge

ICE chart

Initial (values), Change, at Equilibrium table constructed to calculate pH of weak acids; Henderson-Hasselbalch equation used instead for simplicity

IUPAC

International Union of Pure and Applied Chemistry

large Ka or Keq

Ka = greater than one (1), Right-ward reaction favored, i.e. product formation

small Ka or Keq

Ka = less than one (1), Left-ward reaction favored, i.e. reactants formation

ion product of water

Kw: 1.0 x 10^-14; pKw = 14.00

the 8 of base (strong bases)

LiOH, NaOH, KOH, Ba(OH)2, Ca(OH)2, Sr(OH)2, RbOH, CsOH

LiOH

Lithium hyroxide, a strong base

alcohol reaction: nucleophilic substitution

Mechanism #1: carbon attached to -OH acts as electrophile, attracts attack by nucleophile, pops off -OH which joins abandoned H and leaves as water: CH3-OH + HCl → CH3-Cl + H2O Mechanism #2: -OH group acts as nucleophile, breaks atom or groups attached to partial positive carbon, sheds H and joins two compounds as O in the middle of an ether: CH3(CH2)4-Br + CH3CH2-OH → CH3(CH2)4-O-H2CH3C

ketones: chemistry

NO oxidation reduction (2 mechanisms to become 2° alcohol) addition (+ -OH becomes alcohol + ether aka hemiacetal AKA hemiketal)

HNO3

Nitric acid, a strong acid

carbohydrates: chemistry

Nucleophilic substitution (Sn2) Oxidation: Aldoses: when in straight-chain form, aldehydes are easily oxidized to carboxylic acid, ∴ aldoses function as reducing agent, ∴ aldoses are called reducing sugars (as long as the sugar can open to straight-chain form) Ketoses: lack aldehyde, however keto-enol tautomerism permits conversion of the ketone to an aldehyde ∴ ketoses are also reducing sugars Glycolysation (form esters/addition rxn): the addition of an alcohol to a hemiacetal or hemiketal to form an acetal or ketal. (NOTE: if the anomeric -OH group is replaced with -OR (i.e. an ether & now you have an acetal or ketal), the ring cannot open to the straight-chain form and that sugar cannot be easily oxidized and is ∴ called a non-reducing sugar)

amide: physical properties

POLAR participate in h-bonding high m.w. have strong LDF high m.p., high b.p. (similar to carboxylic acids)

ester: physical properties

POLAR participate in h-bonding high m.w. have strong LDF high m.p., high b.p. (similar to carboxylic acids)

HClO4

Perchloric acid, a strong acid

KOH

Potassium hydroxide, a strong base

R/S system

R = rectus (right), S = sinister (left): a set of rules for specifying the configuration about a stereocenter; attached group/section prioritized by atomic number, double bonds count double

ketal

R2C(OR)2; a functional group bearing two alkyl groups and two alkoxy groups on one carbon atom; produced in the acid-catalyzed alcoholysis of a ketone or a hemiketal

hemiketal

RC(R')(OH)OR", a product of the addition of an alcohol to a ketone. In the ketose sugars, the hemiketal formation is from an attack by an internal OH on the ketone carbonyl leading to intramolecular cyclization (furanose or pyranose); the hemiketal forms of the sugars are involved in polysaccharide formation, as glycosyls or glycosides

carboxylic acid reaction: reduction

RCOOH + LiAlH4 → RCH2-OH + H2O (resist previously seen reduction methods, i.e. H2/Pd or NaBH4, but will reduce to a 1° alcohol under influence of lithium aluminum hydride)

carboxylic acid reaction: esterification

RCOOH + R-OH →H2SO4→ RC(=O)-O-R + H2O (the acid-catalyzed reaction of a carboxylic acid and an alcohol)

electron domains

RONCs aka "regions of negative charge", dependent upon the number of electrons in the atom's valence shell and the maximum or preferred number of connections possible

ester reaction: hydrolysis

Reverse Fischer esterification; H2O nucleophilically attacks one acyl group and an alcohol leaves. SLOW reaction unless acid/base catalyzed: acid: CH3C(=O)CH2CH3 + H2O →H2SO4→ CH3C(=O)-OH + CH3CH2OH (acid required in catalytic amounts; reverseible) base: CH3C(=O)CH2CH3 + NaOH →H2O→ CH3C(=O)-O⁻Na⁺ + CH3CH2OH (AKA saponification; base required in stoichiometric amounts; irreversible)

RbOH

Rubidium hydroxide, a strong base

sulfonic acid (aka sulphonic acid)

S(=O)2-OH

NaOH

Sodium hydroxide, a strong base

Sr(OH)2

Strontium hydroxide, a strong base

H2SO4

Sulfuric acid, a strong acid

carbohydrates: physical properties

VERY POLAR (strong dipole forces and lots of opportunities for h-bonding) high b.p. (solids at room temp) water soluble (lots of h-bonding w/ H2O possible) heavier molecules, therefore strong LDF too

carboxylic acid: physical properties

VERY, VERY POLAR m.p. & b.p. higher than corresponding hydrocarbons, alcohols, aldehyds, ketones and amines Water soluble (C1-C4 acids infinitely soluble, C5+ acids decrease in solubility as MW increases) Sharp odors (goat-y, thus the capr- prefix) Sour taste Acidic (weak acids, so have pKa values: unsubstituted acids have pKa ~4.5, substitution with an electronegative group lowers the pKa)

polysubstituted benzene

When three or more of the positions on the ring has been substituted with another atom or group of atoms

disubstituted benzene

When two of the positions on an aromatic ring have been substituted with another atom or group of atoms

ions with suffix -ate

__ic acid (e.g.: sulfate ion (SO4)2- becomes sulfuric acid)

ions with suffix -ite

__ous acid (e.g.: sulfite ion (SO3)2- becomes sulfurous acid

weak base

a base that is only partially ionized in aqueous solution

orbital diagram

a box representing each orbital and a half arrow representing each electron Example: the orbital diagram for sodium (atomic number 11) reflects the electron configuration of 1s2 2s2 2p6 3s1

pentose

a carbohydrate containing five carbons; e.g. ribose

tetrose

a carbohydrate containing four carbons

oligosaccharide

a carbohydrate containing from six to ten monosaccharide units, each joined to the next by a glycosidic bond

hexose

a carbohydrate containing six carbons; e.g. glucose

triose

a carbohydrate containing three carbons; e.g. glyceraldehyde

keto-enol tautomerism

a chemical equilibrium between a keto form (a ketone or an aldehyde) and an enol (an alcohol). The enol and keto forms are said to be tautomers of each other.

substitution reaction

a chemical reaction during which one functional group in a chemical compound is replaced by another functional group

addition reaction

a chemical reaction in which one molecule combines with another to form a larger molecule with no other products

cycloalkyne

a closed ring of carbon atoms containing one or more triple bonds. Because of the linear nature of the C-CΞC-C alkyne unit, cycloalkynes can be highly strained and can only exist when the number of carbon atoms in the ring is great enough to provide the flexibility necessary to accommodate this geometry (cyclooctyne being the smallest stable compound).

mercaptan

a common name for any molecule containing an -SH group

hydrocarbon

a compound composed of only carbon and hydrogen

carboxylic acid

a compound containing a -COOH group

ketone

a compound containing a carbonyl group (C=O) bonded to two carbon groups

aldehyde

a compound containing a carbonyl group bonded to a hydrogen (-CHO)

alcohol

a compound containing a hydroxyl group (-OH) bonded to a tetrahedral carbon atom

aromatic aldehyde

a compound containing an aldehyde and an aromatic (benzene) ring, simplest being benzaldehyde

ester

a compound in which a carbonyl group is linked to an ether; derived from a carboxylic acid and an alcohol. Most common origin is as a product of Fischer esterification: carboxylic acid is reacted with an alcohol in the presence of an acid catylist.

anhydride

a compound in which two acid groups (acyl groups) are linked via an oxygen atom (i.e. carbonyl-O-carbonyl); may be symmetrical (R=R₁) or mixed (R≠R₁). Carboxylic acid derivative formed when a lone pair on the -OH group of attacks the carbonyl carbon of another molecule, leaving the two molecules connected at an -O- and shedding an H2O molecule.

sphingolipids

a compound that consists of a lipid and a sphingosine; found in high concentrations in the brain and nervous system

triol

a compound with three -OH (hydroxyl) groups

diol

a compound with two -OH (hydroxyl) groups

cycloalkene

a cyclic hydrocarbon in which at least one of the carbon-carbon bonds is double

lewis structure

a drawing of a molecule that illustrates the connectivity of the compound, as well as identifying the lone pairs of electrons available for bonding with other molecules. Lines between atoms represent covalent bonds and lone pair electrons are drawn as a pair of dot

zinc finger

a fingerlike loop of peptides enclosing a bound zinc ion at one end, typically part of a larger protein molecule (in particular one regulating transcription)

furanose

a five-membered cyclic hemiacetal form of a monosaccharide

alkyl group

a group derived by removing a hydrogen from an alkane; given the symbol R- denoting a substituent comprised of an aliphatic hydrocarbon (made attachable by removal of a hydrogen atom)

cyclic hydrocarbon

a hydrocarbon that contains carbon atoms bonded to form a ring

unsaturated

a hydrocarbon that contains one or more carbon-carbon double bonds, triple bonds or benzene rings

petroleum

a liquid mixture of thousands of different hydrocarbons

racemic mixture

a mixture of equal amounts of two entantiomers

resonance hybrid

a molecule best described as a hybrid of two or more Lewis contributing structures

hemiacetal

a molecule containing a terminal carbon bonded to one -OH group and one -OR group; the product of adding one molecule of alcohol to the carbonyl group of an aldehyde

enol

a molecule containing an -OH group bonded to a carbon of a carbon-carbon double bond (i.e. an -ene)

hemiketal

a molecule containing an internal carbon bonded to one -OH group and one -OR group; the product of adding one molecule of alcohol to the carbonyl group of a ketone

dipole

a molecule in which a concentration of positive electric charge is separated from a concentration of negative charge

nonpolar

a molecule which has no separation of charge, so no positive or negative poles are formed

L-monosaccharide

a monosaccharide that, when written as a Fischer projection, has the -OH group on its penultimate carbon to the left

D-monosaccharide

a monosaccharide that, when written as a Fischer projection, has the -OH group on its penultimate carbon to the right

passive transport

a movement of biochemicals and other atomic or molecular substances across cell membranes without need of energy input

amino group

a nitrogen atom bonded to one, two or three R groups (RNH₂, R₂NH or R₃N) where the symbol R represents a carbon group

nucleoside

a nucleobase in glycosidic linkage with a sugar, usually a ribose or 2-deoxyribose

electron configuration

a number for the shell and a letter (s,p, d or f, etc.) for the occupied subshell with a superscript indicating the number of electrons in that subshell. Example: the electron configuration for sodium (atomic number 11) is 1s2 2s2 2p6 3s1

locant

a number to indicate the position of a functional group (or feature i.e. double bond or chiral center) within a molecule

conjugate acid-base pair

a pair of molecules or ions that are related to one another by the gain or loss of a proton

monosaccharides

a polyhydroxylated aldehyde or ketone or derivative thereof (but not a polymer, just ONE); most common general formula CnH2nOn; carbohydrates that cannot be hydrolyzed to a simpler compound

oligopeptide

a polymer consisting of several (< 12) amino acids (e.g. dipeptide = 2 amino acids linked, tripeptide = 3 amino acids linked, tetrapeptide, etc.)

monopolymer

a polymer derived from just one simple monomer, e.g. polystyrene

axial orientation

a position on a chair conformation of a cyclohexane ring that extends from the ring parallel to the imaginary axis of the ring

equatorial orientation

a position on a chair conformation of a cyclohexane ring that extends from the ring perpendicular to the imaginary axis of the ring

penta-

a prefix added to indicate five of that type substitutent. e.g. pentaphenyl

tetra-

a prefix added to indicate four of that type substitutent. e.g. tetramethyl

tri-

a prefix added to indicate three of that type substitutent. e.g. trichloro

di-

a prefix added to indicate two of that type substitutent. e.g. diethyl

aromaticity

a property of conjugated cycloalkenes in which the stabilization of the molecule is enhanced due to the ability of the electrons in the π orbitals to delocalize; determined by applying Huckel's rule

regioselectivity

a reaction in which one direction of bond forming or bond breaking occurs in preference to all other directions. Experimentally demonstrated by major and minor products of reactions: if more than one reaction could occur between a set of reactants under the same conditions giving products that are constitutional isomers and if one product forms in greater amounts than the others, the overall reaction is said to be regioselective.

van der Waals interactions

a result of electrostatic attraction between temporary dipoles and induced dipoles caused by movement of electrons in atoms and molecules

cycloalkane

a saturated hydrocarbon that contains carbon atoms bonded to form a ring (i.e. a cyclic hydrocarbon if all the carbon-carbon bonds are single)

pyranose

a six-membered cyclic hemiacetal form of a monosaccharide

buffer

a solution that resists change in pH when limited amounts of an acid or a base are added to it; the most common example is an aqueous solution containing a weak acid and its conjugate base

carbocation

a species containing a carbon atom with only three bonds to it and bearing a positive charge

soap micelles

a spherical aggregate of ampipathic molecules in which portions of like polarity associate surrounding non-polar dirts or oils and thereby make soluble/transportable; wedge shape of fatty acid salts foster formation of a spherical aggregate

reaction mechanism

a step-by-step description of how a chemical reaction occurs

amphiprotic

a substance that can act as either an acid or a base

benzene halogenation

a substitution reaction: C6H6 + Cl2 →(+FeCl3)→ C6H5Cl + HCl requires the presence of an iron catalyst containing the same halogen and generates a hydrogen halide as minor product. d. Halogenation of an alkene is an addition reaction; halogenation of an arene is a substitution reaction

benzene sulfonation

a substitution reaction: C6H6 + H2SO4 →(heat)→ C6H5SO3H + H2O requires the aromatic compound be heated with concentrated sulfuric acid

benzene nitration

a substitution reaction: C6H6 + HNO3→(+H2SO4)→ C6H5NO2 + H2O requires the presence of sulfuric acid and generates water as a minor product (of particular value, the nitro group can be reduced further to a primary amino group by catalytic reaction in the presence of a transition metal)

alkane halogenation

a substitution reaction: CH3CH3+ Br2 →(+heat/light)→ CH3CH2-Br + HCl

polyesters

a synthetic resin in which the polymer units are linked by ester groups, used chiefly to make synthetic textile fiber

polycarbonate

a synthetic resin in which the polymer units are linked through carbonate groups, including many molding materials and films

conjugated

a system of connected p-orbitals with delocalized electrons in molecules with alternating single and multiple bonds, which in general may lower the overall energy of the molecule and increase stability

stereocenter

a tetrahedral carbon atom that has four different groups bonded to it. Stereocenter not possible where two of the attachments are identical or there are multiple bonds

Fischer projection

a two-dimensional representation of a three-dimensional organic molecule. (understood to have vertical plane signifying recession into the plane of the paper, the horizontal plane representing projection out from the plane of the paper and the intersections representing chiral centers on the plane of the paper)

neutralization

a type of chemical reaction in which a strong acid and strong base react with each other to form water and salt

polar bond

a type of covalent bond between two atoms in which electrons are shared unequally, resulting in a bond in which one atom has a slightly negative charge and the other a slightly positive charge.

Haworth projection

a way to view furanose and pyranose forms of monosaccharides; the ring is drawn flat and viewed through its edge, with the anomeric carbon on the right, the oxygen atom to the rear and the -OH groups bonded to the ring projecting above or below the plane of the ring (one fewer -OH projection than in middle of Fischer diagram). Carbonyl carbon becomes anomeric carbon, oxygen from -OH group on the penultimate carbon becomes a member of the ring and cedes H to carbonyl oxygen, tail carbon-OH group becomes ring-tail. Ring-tail points up for D-sugars, down for L-sugars

hydrogen bond

a weak bond between two molecules resulting from an electrostatic attraction between a proton in one molecule and an electronegative atom in the othe

line-angle formula

abbreviated way to draw structural formulas in which each vertex and line terminus represents a carbon atom and each line represents a bond

CH3COOH

acetic acid (a weak acid)

ester reaction: rxn with alcohol

acid-catalyzed also known as transesterification; equilibrium reaction that can be driven in either direction: CH3CH2C(=O)-O-CH3 + HO-CH2CH2CH3 →HCl← HC=CHC(=O)-O-CH2CH2CH2CH3 + CH3-OH

alcohols: chemistry

acid-catalyzed dehydration (easier 1° - 2° - 3°) oxidation (1° & 2° only) nucleophilic substitution

Lewis theory definition

acids are electron-pair acceptors; bases are electron pair donors (definition preferred by organic chemists)

monoprotic acids

acids that can give up only one proton (H⁺)

triprotic acids

acids that can give up three protons (H⁺)

diprotic acids

acids that can give up two protons (H⁺)

hydration

addition of water

purine base

adenine & guanine

ATP

adenine triphosphate

purine nucleoside

adenosine & guanosine

alkyl halide

aka halogenoalkanes or haloalkanes: a group of chemical compounds derived from alkanes containing one or more halogens

monoterpene

aka terpene (prefix not needed) C10 molecule derived from 2 isoprene units.

mannose

aldohexose with L-L-R-R configuration

galactose

aldohexose with R-L-L-R configuration

glucose

aldohexose with R-L-R-R configuration

ribose

aldopentose with R-R-R configuration

soaps

alkali salts of fatty acids

alkane combustion

alkane + O2 → CO2 + H2O (then balance the equation)

alkene combustion

alkene + O2 → CO2 + H2O (then balance the equation)

sec-butyl

alkyl attachment = (CH3)CH(CH2CH3)

tert-butyl

alkyl attachment = -C(CH3)3

isopropyl

alkyl attachment = -CH(CH3)2

isobutyl

alkyl attachment = -CH2-CH(CH3)2

butyl

alkyl attachment = -CH2CH2CH2CH3

propyl

alkyl attachment = -CH2CH2CH3

ethyl

alkyl attachment = -CH2CH3

methyl

alkyl attachment = -CH3

alkyne reactions

alkynes undergo the same reactions as alkenes: combustion (like any other hydrocarbons, alkynes will burn in a plentiful supply of oxygen to produce carbon dioxide and water), hydrohalogenation, acid-catalyzed hydration, halogenation, hydrogenation. On top of their own transformations, through partial reduction, alkynes can also be transformed to alkenes (which themselves have a host of reactions) or even alkanes (which can then be transformed to alkyl halides, which also have a host of reactions). Two factors influence the relative reactivity of alkynes compared to alkenes: increased nucleophilicity of the starting p system (C≡C vs C=C), and stability of any intermediates (for example carbocations)

amide reaction: rxn with alcohol

amides do not react with alcohols

amide reaction: rxn with ammonia /amines

amides do not react with ammonia or with 1° or 2° amines

Alanine

amino acid 1-letter code: A 3-letter code: Ala pKa = N/A (non-polar)

Cysteine

amino acid 1-letter code: C 3-letter code: Cys pKa = 8 ACIDIC only AA to form disulfide bonds

Aspartic Acid

amino acid 1-letter code: D 3-letter code: Asp pKa = 4 VERY acidic

Glutamic Acid

amino acid 1-letter code: E 3-letter code: Glu pKa = 4 VERY acidic

Phenylalanine

amino acid 1-letter code: F 3-letter code: Phe pKa = N/A (non-polar)

Glycine

amino acid 1-letter code: G 3-letter code: Gly pKa = N/A (non-polar)

Histidine

amino acid 1-letter code: H 3-letter code: His pKa = 6 ACIDIC

Isoleucine

amino acid 1-letter code: I 3-letter code: Ile pKa = N/A (non-polar)

Lysine

amino acid 1-letter code: K 3-letter code: Lys pKa = 10.5 BASIC

Leucine

amino acid 1-letter code: L 3-letter code: Leu pKa = N/A (non-polar)

Methionine

amino acid 1-letter code: M 3-letter code: Met pKa = N/A (non-polar)

Asparagine

amino acid 1-letter code: N 3-letter code: Asn pKa = N/A (non-polar) NEUTRAL

Proline

amino acid 1-letter code: P 3-letter code: Pro pKa = N/A (non-polar) NEUTRAL

Glutamine

amino acid 1-letter code: Q 3-letter code: Gln pKa = N/A (non-polar) NEUTRAL

Arginine

amino acid 1-letter code: R 3-letter code: Arg pKa = 12.5 BASIC

Serine

amino acid 1-letter code: S 3-letter code: Ser pKa = N/A (non-polar) NEUTRAL

Threonine

amino acid 1-letter code: T 3-letter code: Thr pKa = N/A (non-polar) NEUTRAL

Valine

amino acid 1-letter code: V 3-letter code: Val pKa = N/A (non-polar)

Tryptophan

amino acid 1-letter code: W 3-letter code: Trp pKa = N/A (non-polar)

Tyrosine

amino acid 1-letter code: Y 3-letter code: Tyr pKa = 10.5 ACIDIC

NAC

amino acid repeating structure: amino group (NH2) - alpha-carbon w/ R-group attachment (AKA amino group sidecar) - carbonyl carbon (C=O)

NH4+

ammonium ion

steroids

amphipathic molecules with a characteristic fused four-ring skeleton; a family of lipid molecules that includes cholesterol, steroid hormones, and bile salts

glycerophospholipids: physical properties

ampipathic: polar head group, non-polar tails cylindrical shape: forms lipid bilayer saturation/unsaturation: saturated acyl groups pack well = stiff membrane unsaturated = kinky = more fluid membrane

alcohols: physical properties

an -OH (hydroxyl) group bonded to a tetrahedral C atom -POLAR -approximately same pH as water -higher b.p. than alkanes, alkenes & alkynes of similar MW due to polarity, hydrogen bonding & LDF -infinite water solubility at lower MW, less so at 6C+

sphingosine

an 18-carbon amino (NH2) alcohol with an unsaturated hydrocarbon tail; forms a primary part of sphingolipids

Bronsted-Lowry definition

an acid is a proton donor; a base is a proton acceptor; an acid-base reaction is a proton-transfer reaction. (Allows for the expansion of the acid/base definitions beyond water)

Arrhenius definition

an acid is a substance that produces H+ ions in aqueous solution; a base is a substance that produces OH- ions in aqueous solution

strong acid

an acid that ionizes completely in aqueous solution

weak acid

an acid that is only partially ionized in aqueous solution

alkene hydration

an addition reaction: CH2=CH2 + H2O →(+H2SO4)→ CH2(H)-CH2(OH) requires the presence of an acid-catalyst

alkene hydrohalogenation

an addition reaction: CH2=CH2 + HCl → CH2(H)-CH2(Cl)

alkene hydrogenation (aka catalytic reduction (aka catalytic hydrogenation)

an addition reaction: CH3CH=CHCH3 + H2 →(+Pd/25°, 3atm)→ CH3CH2CH2CH3 requires the presence of a transition metal catalyst, typically palladium, platinum or nickel. alkene is reduced to a carbon-carbon single bond compound in the presence of H2 + catalyst

alkyne hydrogenation

an addition reaction: CH3C≡CCH3 + H2 →(Pd)→ CH3CH=CHCH3 alkene is reduced to a carbon-carbon double bond compound in the presence of H2 + catalyst (usually Pd-palladium or Pt-platinum), then eventually to an alkyl halide

alkyne hydration

an addition reaction: CH3C≡CCH3 + H2O →(H2SO4)→ CH3CH=C(OH)CH3 ↔ CH3CH-C(=O)CH3 requires the presence of an acid-catalyst, most commonly sufuric acid (H2SO4) & a catalyst (typically with mercury salt (Hg2+)). Will go from the alkyne to an intermediate alkene (enol), then to an alkane (ketone).

alkyne hydrohalogenation

an addition reaction: CH3C≡CCH3 + HX → CH3CH=CH-X where X stands for Cl, Br or I. Regioselectivity predicted by Markovnikov's rule with the H adding to the C with the most H already present

alkene halogenation

an addition reaction: CH2=CH2 + BR2 →(+CH2Br2)→ CH3-CH(Br)-CH(Br)-CH3 requires the presence of a reagent containing the same halogen -or- CH2=CH2 →(Br2)→ CH2(Br)-CH2(Br) reaction can be carried out by mixing the pure reagents together

1° alcohol

an alcohol in which the carbon bearing the -OH group is bonded to only one carbon

3° alcohol

an alcohol in which the carbon bearing the -OH group is bonded to three carbons

2° alcohol

an alcohol in which the carbon bearing the -OH group is bonded to two carbons

trisubstituted alkene

an alkene in which the doubly bonded carbons are bonded to a total of three carbon atoms excluding each other. generates an E/Z isomerism

disubstituted alkene

an alkene in which the doubly bonded carbons are bonded to a total of two carbon atoms. opens the possibility of a cis/trans or E/Z isomeric relationships

monosubstituted alkene

an alkene in which the doubly bonded carbons are bonded to only one carbon excluding each other. opens the possibility of a cis/trans isomeric relationships

polyene

an alkene that contains 5+ (or simply several) double bonds.

tetraene

an alkene that contains four double bonds. signified by the prefix tetra- added to the parent suffix

triene

an alkene that contains three double bonds. signified by the prefix tri- added to to the parent suffix

diene

an alkene that contains two double bonds. signified by the prefix di- added to to the parent suffix

aliphatic amine

an amine in which all the carbons bonded to nitrogen are derived from alkyl groups

aromatic amine

an amine in which one or more of the groups bonded to nitrogen are aryl groups

heterocyclic amine

an amine in which the nitrogen atom is part of a ring

heterocyclic aliphatic amine

an amine in which the nitrogen atom is part of a saturated ring

heterocyclic aromatic amine

an amine in which the nitrogen atom is part of an aromatic ring

arene

an aromatic hydrocarbon, benzene being the simplest

substituent

an atom or group of atoms substituted in place of a hydrogen atom on the parent chain of a hydrocarbon

functional group

an atom or group of atoms within a molecule that shows a characteristic set of predictable physical and chemical behaviors

valence electron

an electron in one of the outer shells of an atom that can participate in forming chemical bonds with other atoms

oxonium ion

an ion in which oxygen is bonded to three other atoms and bears a positive charge

ethers: physical properties

an oxygen (-O-) bonded to two C atoms -Polar with oxygen bearing partial negative and causing attached carbons to bear partial positive -higher b.p. than alkanes, alkenes & alkynes of similar MW due to polarity & LDF, but significantly lower b.p. than alcohols for lack of h-bonding -more soluble than similar MW hydrocarbons, but far less soluble than isomeric alcohols

trans fatty acids

an unsaturated fatty acid of a type occurring in margarine and manufactured cooking oils as a result of the hydrogenation process, having a trans arrangement of the carbon atoms adjacent to its double bonds

cycloalkenes

an unsaturated hydrocarbon that contains carbon atoms bonded to form a ring. the carbon atoms of the ring double bond are numbered 1 and 2 in the direction that gives the first substituent encountered the lowest number

titration

analytical procedure whereby a known volume of solution of known concentration is reacted with a known volume of a solution of unknown concentration; equivalence point allows determination of unknown concentration

glycogen

animal-based storage carbohydrate; similar to, but more highly branched than amylopectin; stored in the liver

acetal

any compound with the general formula R2C(OR)2 or RCH(OR)2, in which R indicates an alkyl or aryl group

R group

any hydrogen or carbon chain that is bonded to the alpha carbon; substituent group to the parent chain

alkaloid

any of a class of nitrogenous organic compounds of plant origin that have pronounced physiological actions on humans. They include many drugs (morphine, quinine) and poisons (atropine, strychnine).

glycoside

any of numerous sugar derivatives that contain a nonsugar group attached to a sugar through an oxygen or nitrogen bond and that upon hydrolysis will yield a sugar (as glucose) a cyclic acetal derived from a monsaccharide in which the -OH group on its anomeric carbon is replaced with an -OR group;

hemiacetal

any of the class of organic chemical compounds having the terminal, general formula RCH(OH)OR, where R is an organic group

reducing sugar

any sugar that is capable of acting as a reducing agent because it has a free aldehyde group or a free ketone group. All monosaccharides are reducing sugars, along with some disaccharides, oligosaccharides, and polysaccharides a carbohydrate that reacts with a mild oxidizing agent under basic conditions to give an aldonic acid; the carbohydrate reduces the oxidizing agent;

conformations

any three dimensional arrangements of atoms in a molecule that result from rotation about a single bond

leukotrienes

arachidonic acid derivatives with no fused-ring attachment; mainly found in white blood cells, producing long-lasting muscle contractions

strong bases

bases that ionize completely in aqueous solution

common aldehydes

benzaldehyde formaldehyde

aromatic compound

benzene or one of its derivatives

toluene

benzene ring with a methyl attachment. carbon count begins at namesake substituent

benzaldehyde

benzene ring with an aldehyde group (-CHO) attachment. carbon count begins at namesake substituent

aniline

benzene ring with an amino group (NH2) attachment. carbon count begins at namesake substituent

benzoic acid

benzene ring with an carboxyl group (-COOH) attachment. carbon count begins at namesake substituent

ethylbenzene

benzene ring with an ethyl attachment. carbon count begins at namesake substituent

phenol

benzene ring with an hydroxyl group attachment. carbon count begins at namesake substituent

anisole

benzene ring with an methoxy group (-OCH3) attachment. carbon count begins at namesake substituent

styrene

benzene ring with an vinyl group attachment. carbon count begins at namesake substituent

HCO3-

bicarbonate ion

NAHD / NAD+

biological reagent that signifies reduction (coenzyme that will act as a hydride donor in biological systems, functions like NaBH4 in aldehyde/ketone reductions)

H3BO3

boric acid (a weak acid)

-1 x log of Molarity

calculate pH for strong acids

disaccharides

carbohydrates containing two monosaccharide units joined by a glycosidic bond; e.g. sucrose, lactose & maltose

H2CO3

carbonic acid (a weak acid)

ketones: physical properties

carbonyl (C=O) group in-between two carbons -electronegative O creates partial positive on C and makes it a target for nucleophiles, partial negative O is target for protonation -polar, but no h-bonding -m.p. and b.p. higher than corresponding hydrocarbons, but less than alcohols or amines -water soluble at low MW, less polar & less water soluble as MW increases (5-6C+)

priorities of functional groups

carboxylic acid anhydride ester amide aldehyde ketone alcohol thiol amine alkyne / alkene ether alkyl halide nitro alkane

enzyme

catalyst; proteinaceous substances in plants and animals that speed biochemical reactions

organic chemistry

chemistry of the compounds of carbon (excluding CO, CO₂ + carbonates)

1° protein structure

classification according to AA sequence + disulfide bonds: the connectivity of atoms in a protein, including any disulfide bonds

2° protein structure

classification according to localized 3-D structure: the shape(s) of the strand (e.g. alpha-helix, beta-sheet anti-parallel, beta-sheet parallel, loops, etc.)

4° protein structure

classification according to the conformation of multiple, separate structures in proximity / interaction

3° protein structure

classification according to the overall shape of the protein: all alpha-helices, all beta-sheets, mixed

ceramide

combination of a fatty acid and a sphingosine

addition

combination reactions in which parts of one reactant are distributed across the two atoms of a double bond: 1. hydration: addition of a water across a double bond to yield an alcohol 2. hydrohalogenation: addition of a hydrogen halide across a double bond to yield a haloalkane 3. halogenation: addition of a halogen across a double bond to yield a haloalkane 4. hydrogenation: addition of diatomic hydrogen across a double bond (used for alkenes) to yield an alkane 5. reaction of aldehyde or ketone with an alcohol to form a hemiacetal/hemiketal

amino acid chirality

common amino acids all have the penultimate amino group pointing left (aka L-amino acids) according to Fischer projection

butyric acid

common name for carboxylic acid: butanoic acid

acetic acid

common name for carboxylic acid: ethanoic acid

formic acid

common name for carboxylic acid: methanoic acid

propionic acid

common name for carboxylic acid: propanoic acid

glycolipids

complex lipids containing a carbohydrate group, commonly glucose or galactose

amylopectin

complex plant-based storage carbohydrate; a linear glucan with branches at α(1-6)

glycol

compound containing hydroxyl groups on adjacent carbons

amide

compound in which a carbonyl group is bonded to a nitrogen atom (of ammonia or an amine); derived from carboxylic acid + ammonia or amine.

stereoisomers: chemistry

compounds behave identically except for optical isomers when reacting with something that is also chiral (i.e. enzymes)

optical isomerism

compounds that are identical in molecular weight and most chemical and physical properties but differ in their effect on the rotation of polarized light.

stereoisomersim

compounds that have the same connectivity of their atoms but a different orientation of their atoms in space. Geometric isomerism is one form

constitutional isomer

compounds that have the same molecular formula but a different order of attachment (connectivity) of their atoms. AKA structural isomers

geometric isomerism

compounds that have the same molecular formula, but a different arrangement of groups with respect to a double bond, ring, or other rigid structure. Same connections, different shape

tautomerism

constitutional isomers of organic compounds that readily interconvert by a chemical reaction called tautomerization. This reaction commonly results in the formal migration of a hydrogen atom or proton, accompanied by a switch of a single bond and adjacent double bond.

tautomers

constitutional isomers that differ in the location of a hydrogen atom and a double bond

saturated carbon

contain only carbon-carbon single bonds and each carbon has the maximum number of hydrogens bonded to it

fatty acid hydrogenation

conversion of an unsatruated liquid oil to solid by reducing carbon-carbon double bonds via reaction with hydrogen and catalyst

lactam

cyclic amides = lactams; named by adding the word lactam to the correct IUPAC name of the parent amino acid.

aryl group: formula

denoting a substituent comprised of an aromatic hydrocarbon (made attachable by removal of a hydrogen atom) a group derived from an arene by removal of an H atom from an arene and given the symbol Ar- (comparable to the R- groups of alkanes)

enolate

deprotonated enol; salts of enols (or of the tautomeric aldehydes or ketones), in which the anionic charge is delocalized over oxygen and carbon

amide

derivative of a carboxylic acid in which an amino group replaces the -OH of the carboxyl group (aka the carbonyl group is bonded to a nitrogen atom)

bile salts

derivative products of cholesterols reacted with a carboxylic, sulfuric or amino acid (such as glycine or taurine); ampipathic molecules essential for breaking down dietary lipids into fine emulsions, thereby facilitating digestion

amines: physical properties

derivatives of ammonia in which one, two or three hydrogens are replaced by alkyl or aryl groups -BASIC (but weak bases like ammonia) -polar (but less so than alcohols), h- bonding for 1° and 2° amines only -water soluble at lower MW, less so or insoluble at higher MW (6C+) -higher b.p. than alkanes, alkenes & alkynes of similar MW due to polarity, some h-bonding & LDF, but significantly lower b.p. than alcohols on account of weak N-H bond -stinky -classified as 1°, 2°, 3° or 4° -can have smaller bonding groups attached which are then given the locant(s) 'N'

eiconasoids

derivatives of arachidonic acid (e.g. prostaglandins, thromboxanes, leukotrienes); act as local messenger molecules (like hormones, but don't travel throughout whole body)

fluid mosaic model

description of the interactions between lipids and proteins in membranes: lateral motion, diffusion of nonpolar compounds, diverse topography of proteins dispersed throughout

H2PO4-

dihydrogen phosphate ion

contributing structure

each individual Lewis structure that is possible for a particular molecular formula

optical isomers

each of two or more forms of a compound that have the same structure but are mirror images of each other and typically differ in optical activity

carboxylic acid reaction: acidity

electronegative atoms on the carbon adjacent to the carbonyl group increase acidity by pulling electron density away from the OH bond, thereby facilitating ionization of the carboxyl group and making it a stronger acid. If pH of the solution is 2.0 or lower, carboxylic acid is present almost entirely as -RCOOH. If the pH of the solution is 7.0 or higher, -RCOO⁻. In pH 4.0-5.0 range (value for most unsubstituted carboxylic acids), acid and conjugate base exist in equilibrium.

dehydration

elimination reaction wherein reactant loses a molecule of water

optically active

enantiomers that rotate the plane of light differently

monosaccharide reaction: oxidation

enzyme catalyzed reaction with two outcomes: 1. CHO group oxidizes to -COOH = aldonic acid, replace suffix -ose with -onic acid 2. tail group (CH2OH) oxidizes to -COOH = uronic acid, replace suffix -ose with -uronic acid any carbohydrate that reacts with a mild oxidizing agent to form an aldonic acid is classified as a reducing sugar

monosaccharide reaction: phosphorylation

enzyme catalyzed substitution reaction

isomerases

enzymes that catalyze: all types of isomerization: cis/trans, epimerization (R/S), intramolecular ox-reduction (e.g. Glu→Fru) and/or rearrangements (e.g. intramolecular transfers) general rxn: A → B (one reactant to one product)

lyases

enzymes that catalyze: bond cleavage with concomitant multiple bond formation OR ring formation (or the reverse) (i.e. elimination OR addition reactions) general rxn: A → C + D OR C + D → A (one reactant makes two products OR two reactants join to make one product; AKA one reactant has a new multiple bond or one reactant loses a multiple bond or ring form; reversible)

ligases

enzymes that catalyze: bond formation with concomitant generation of ATP hydrolysis products (e.g. ATP → ADP + Pi or ATP → AMP + PPi) general rxn: A + B → (ATP→ADP+Pi) → A-B (two products + ATP create new molecule and split the ATP into smaller pieces)

hydrolases

enzymes that catalyze: hydrolysis general rxn: A-B + H2O → A-H + B-OH (a bond is breaking and water is reactant; two products formed)

transferases

enzymes that catalyze: movement of functional groups from one reactant to another (i.e. substitution reactions) general rxn: A-X + B → A + B-X common name(s): kinase, glucosyltransferase, acyltransferase

oxidoreductases

enzymes that catalyze: redox reactions general rxn: 2 reactants → 2 products (the main substrate will undergo either oxidation or reduction while another molecule, usually a coenzyme, undergoes reduction or oxidation) common name(s): dehydrogenase, oxidoreductase

wax

esters of long chain alcohols & fatty acids; very non-polar

Hund's rule

every orbital in a subshell is singly occupied with one electron before any one orbital is doubly occupied, and all electrons in singly occupied orbitals have the same spin

phospholipids

example of a complex lipid containing an alcohol, two fatty acids and a phosphate group; essential component of cell membranes

prostaglandins

fatty-acid-like substances constructed from arachidonic acid fused to a five-membered ring; known to stimulate and/or relax smooth muscle, assisting in labor contraction, lowering blood pressure, reducing inflammation, etc.

thromboxanes

fatty-acid-like substances constructed from arachidonic acid fused to a six-membered ring; induces platelet aggregation / blood clotting

neutralization equilibrium

favors the side with the weaker products, i.e. strong acids/bases --> make more weak conjugate acid/base Ex: HCN + Cl- ↔ HCl + CN- (acid-w) (base-w) (acid-str) (base-rel.str) strong is on right, therefore LEFT is favored

intermolecular forces

forces of attraction or repulsion which act between neighboring particles (atoms, molecules or ions). Weak compared to the intramolecular forces, the forces which keep a molecule together

HCOOH

formic acid (a weak acid)

amidation

forming an amide, two mechanisms of creation: 1. reaction of a carboxylic acid with an amine + heat creates an ammonium salt which will yield an amide + H2O 2. reaction of an anhydride with an amine creates an amide and carboxylic acid byproduct (which then further neutralizes to an ammonium salt in the presence of a second mole of amine ).

aldehyde: formula

formula: -C(=O)-H (see picture) substituent name: oxo suffix: -al

amide: formula

formula: -C(=O)-NH2 (see picture) substituent name: N/A suffix: -amide

anhydride: formula

formula: -C(=O)-O-C(=O) (see picture) substituent name: N/A suffix: acid name + anhydride

ester: formula

formula: -C(=O)-O-R (see picture) substituent name: N/A suffix: alkyl (space) + -ate OR alkyl + "ester"

carboxylic acid: formula

formula: -COOH substituent name: carboxy suffix: -ic acid

nitro: formula

formula: -NO2 substituent name: nitro suffix: N/A (does not change parent name ending)

ketone: formula

formula: C-C(=O)-C (see picture) substituent name: oxo suffix: -one common name scheme: name alkyl groups on either side, followed by 'ketone'

amine (formula)

formula: C-NH2 substituent name: amino suffix: -amine

ether: formula

formula: C-O-C substituent name: alkoxy suffix: N/A (does not change parent name ending OR is named for each hydrocarbon attached + ether)

alcohol: formula

formula: C-OH substituent name: hydroxyl suffix: -ol

thiol: formula

formula: C-SH substituent name: mercapto suffix: -thiol

alkyl halide: formula

formula: C-X substituent name: halo suffix: N/A (does not change parent name ending)

alkene: formula

formula: C=C substituent name: alken/alkenyl suffix: -ene

alkyne: formula

formula: C≡C substituent name: alkynyl suffix: -yne

alkane: formula

formula: saturated hydrocarbon chain substituent name: alkyl suffix: -ane

ribose (ring form)

furanose with D-D configuration on Haworth project (picture shows beta-ring form)

fructose (ring form)

furanose with U-D configuration

cerebroside

generalized term for complex lipids combining a ceramide and a sugar; present in the sheaths of nerve fibers, primarily in the brain

entgegen

german: opposite. used to denote the relative positions of the highest priority groups attached on either side of an alkene double bond

zussamen

german: same. used to denote the relative positions of the highest priority groups attached on either side of an alkene double bond

β(1→4)

glycosidic linkage indicating connection from a β- positioned anomeric carbon (C1=aldose) to the C4 position on another sugar; typically NOT easily digestible, e.g. cellulose

α(1→4)

glycosidic linkage indicating connection from an α- positioned anomeric carbon (C1=aldose) to the C4 position on another sugar; typically easily digestible, e.g. starch

meta

greek: after. indication of locants with an empty spot between them on a benzene ring

para

greek: beyond. indication of locants positioned across from each other on a benzene ring

ortho

greek: straight. indication of locants right next to each other on a benzene ring

amino acid stabilizing factors

h-bonding (between amide H on one strand and the carbonyl O on another R-groups (sidecars) point above or below the plane of the sheet so as to minimize steric hindrance and optimize interactions with other R-groups on other portions of the structure pi stacking (i.e. magnetic attractions between the NASCAR tracks of aromatic R-groups; requires R-groups in question to be between 3-4 residues apart in order to properly align the rings) ion-ion interactions (AKA salt bridges): attractions between oppositely charged R-groups

imidazole

heterocyclic aromatic amine

indole

heterocyclic aromatic amine

pyrazine

heterocyclic aromatic amine

pyridine

heterocyclic aromatic amine

pyrole

heterocyclic aromatic amine

benzene physical properties

higher m.p. compared to alkanes or alkenes with similar molecular weights b.p. predominant factor is size (whereas for the melting point trend, shape plays a much more important role.) planar (and therefore cis-trans isomerism not possible), delocalized, a resonance hybrid of two equally contributing Lewis structures. Like any other hydrocarbons, benzene will also burn. Aromatic compounds DO NOT undergo addition reactions because that would involve breaking the delocalisation and losing that stability.

priorities of functional groups

highest priority: -COOH (carboxylic acid) (C=O)-O-(C=O) (anhydride) -(C=O)-O-R (ester) -(C=O)-NH2 (amide) -(C=O)H (aldehyde) C(C=O)C (ketone) C-OH (alcohol) C-SH (thiol) C-NH2 (amine) C≡C (alkyne) C=C (alkene) C-O-C (ether) C-X (alkyl halide) -NO2 (nitro) C-C (alkane ) lowest priorty

glycan

homopolymer of sugars; e.g. glucan = polymer of only glucose molecules, mannan = polymer of only mannose, etc.

H-

hydride ion

ions with suffix -ide

hydro __ic acid (e.g.: chloride ion (Cl-) becomes hydrochloric acid (HCl))

polynuclear aromatic hydrocarbons (aka PAHs)

hydrocarbons containing two or more adjacent benzene rings

HCN

hydrocyanic acid (a weak acid)

H+

hydrogen ion

(HPO4)2-

hydrogen phosphate ion

OH-

hydroxide ion

-OH

hydroxyl functional group

stereoisomers: physical properties

identical physical properties (m.p., b.p., solubility and chemistry except for how they rotate plane-polarized light)

Markovnikov's Rule (aka "the rich get richer")

in an addition reaction, the negative portion of the compound added (i.e. the bromine in hydrogen bromide) becomes attached to the least hydrogenated end of the carbon-carbon double bond (aka the most substituted end aka the carbon with the most substituents aka 'the heavy'). In other words, when an unsymmetrical alkene undergoes addition with E-Nu, then the electrophile, E(+), adds to the carbon of the alkene that has the greater number of hydrogen substituents, and the nucleophile, Nu(-), to the heavy side (the carbon of the alkene with the fewer number of hydrogen substituents).

glycoside: nomenclature

in sugar + alcohol glycolysation, list the alkyl or aryl group bonded to oxygen followed by the full name of the carbohydrate in which the -e ending is replaced with -ide; e.g. ethyl beta-D-glucopyranoside in sugar+sugar glycolysation (i.e. disaccharides, oligosaccharides, etc.), all sugars but the terminal sugar adopt suffix -yl. List the full name of the sugar including position (alpha or beta) of anomeric carbon and type of ring, -yl suffix, dash, parenthesize locants of linkage, dash, next sugar same as the first until terminal sugar ends in -ose; e.g. beta-D-galactopyranosyl-(1-4)-alpha-D-glucopyranose AKA lactose locant numbers start at anomeric carbon

conjugate base

in the Bronsted-Lowry theory, a substance formed when an acid donates a proton to another molecule or ion. Remove a proton (H⁺) from an acid in order to configure its conjugate base, calculate new net charge

ring formation

intramolecular addition reaction between -OH group of a sugar and the sugar's C=O group to yield a hemiacetal or a hemiketal. l.p. on the penultimate carbon -OH group will attack the partial positive on the carbonyl carbon & form a ring. -OH group can attack the carbonyl carbon from top or bottom (50/50 chance). Attack from the top pushes the carbonyl carbon's resultant -OH group down to yield alpha-anomer; attack from the bottom pushes the carbonyl carbon's resultant -OH group up to yield beta-anomer. (α fishies are down in the sea, βirdies are up in the sky) If D-sugar -OH group initiates attack, tail points up; if L-sugar -OH group initiates attack, tail points down. When the attack occurs, the trigonal planar formation about the anomeric carbon become tetrahedral. Ring forms are in equilibrium with straight-chain form

amino acids: chemistry

intramolecular neutralization: l.p. on amino group can snatch electron off of carboxylic group creating full positive (NH3+) and full negative (COO-) and therefore a VERY polar molecule sidecar special: R-groups can confer special chemical properties (e.g. mercapto group on Cys can form disulfide bonds, acid/base reactions for polarized R-groups, substitution reactions from nucleophilic R-groups) amidation AKA peptide bond: amide linkage between two amino acids (i.e. linkage between carbonyl carbon of one AA and the amino group of another AA)

stereoisomers

isomeric molecules that have the same molecular formula and sequence of bonded atoms (constitution), but differ in the three-dimensional orientations of their atoms in space

cis-trans isomers

isomers that have the same connectivity of their atoms but a different arrangement of their atoms in space. Specifically, cis/trans stereoisomers result from the presence of either a ring or a carbon-carbon double bond

geometric isomers

isomers where groups are oriented differently in space

iso-

italicized prefix (from "equal") used to designate any alkyl group (of six carbons or less) that has a single one-carbon branch on the next-to-last carbon of a chain and has the point of attachment at the opposite end of the chain. i.e. the snake tongue

sec-

italicized prefix (from "secondary") used to indicate two additional side chains connected to the first side-chain carbon.

tert-

italicized prefix (from "tertiary") used to indicate three additional side chains connected to the first side-chain carbon

fructose

ketohexose with L-R-R configuration

amine reaction: nucleophilic substitution

l.p. (lone pair) on N enables amine to act as nucleophile, attacking positive portion, kicking off negative portion & shedding a proton (H⁺). To create major product: redraw original structure, subtract an H, insert second structure without the negative element.

CH3CH(OH)COOH

lactic acid

plane-polarized light

light with waves vibrating only in parallel planes

carbohydrate

literally: hydrate of carbon polyhydroxyaldehydes or polyhydroxyketones or substances that give these compounds upon hydrolysis; categorized by highest priority functional group: aldose, ketose, aldonic acid, uronic acid

polysaccharides

long molecule chains derived from 1 carbohydrate molecule (called the monomer) linked to multiple copies of itself in a long chain. e.g. cellulose, starch (amylose & amylopectin), glycogen, chitin.

fatty acids

long, unbranched-chain carboxylic acids, most commonly with 12 to 20 carbons; derived from hydrolysis of animal fats, vegetable oils or the phospholipids of biological membranes; saturated or unsaturated. Predominate formation for unsaturated fatty acids: cis isomer

polypeptide

longer peptide chain (> 50 amino acids); somewhat interchangeable with the term 'protein' as it represents VERY long polypeptide chains

reverse turn

loop formed by directional changes in an anti-parallel beta sheet; often seen after Gly or Pro AA

cysteine noose

loop formed by disulfide connections between beta-sheet pleats

LEO the lion says GER

lose electron = oxidation gain electron = reduction

alkane physical properties

lower than almost any other compound with the same molecular weight (MW). b.p. and m.p. increase with increasing MW b.p. decreases with increasing branching (as surface area decreases. LDF decrease, attraction btw molecules decrease, b.p. decreases). Like any other hydrocarbons, alkenes will burn.

ketone reaction: reduction

mechanism #1: hydrogenation CH3C(=O)CH3 + H2 →Pd→ CH3CH(-OH)CH3 mechanism #2: selective reduction reagent = NaBH4 / H+ (aq) CH2=CH(CH2)2C(=O)CH3 →NaBH4→ CH2=CH(CH2)2CH(-OH)CH3

aldehyde reaction: reduction

mechanism #1: hydrogenation CH3CH=O + H2 →Pd→ CH3CH2-OH mechanism #2: selective reduction reagent = NaBH4 / H+ (aq) CH2=CHCH=O →NaBH4→ CH2=CHCH2-OH

step-growth polymerization

mechanism in which molecules containing two functional groups (monomers) react to form first dimers, then trimers, longer oligomers and eventually long chain polymers

E/Z designations

method for labeling geometric isomerism in alkenes: 1-determine if geometric isomerism exists: if the carbon on either side of the double bond bears two identical substituents (i.e. H off the top, H off the bottom), then no geometric isomerism exists. If each sp2 hybridized carbon bears two different groups, then geometric isomerism is possible 2-bisect the double bond and prioritize each quadrant of attachment 3-relating each quadrant to an imaginary line parallel to the double bond, determine the if the highest priority group from each side are opposite (entgegen) or on the same side (zussamen)

anhydride reaction: rxn with ammonia or 1°/2° amines

method of amide formation, requires 2 moles of amine: one to form amide, one to neutralize carboxylic acid by-product CH3C(=O)-O-C(=O)CH3 + NH3 → CH3C(=O)NH2 + CH3C(=O)-OH then CH3C(=O)-OH + NH3 → CH3C(=O)O⁻NH4⁺ net reaction: CH3C(=O)-O-C(=O)CH3 + 2 NH3 → CH3C(=O)NH2 + CH3C(=O)O⁻NH4⁺

fats

mixtures of triglycerides containing a high proportion of long-chain, saturated fatty acids

oils

mixtures of triglycerides containing a high proportion of long-chain, unsaturated fatty acids or short-chain, saturated fatty acids

downright up-lefting

mnemonic for positioning carbohydrate ring -OH groups

Caan Estamalke & Altham alk-alk Ethalnialk

mnemonic for remembering prioritization: Carboxylic acid Anhydride Ester Amide Aldehyde Ketone Alcohol Thiol Amine Alkyne/Alkene Ether Alkyl halide Nitro group Alkane

condensed structural formula

molecular formula broken down into each carbon and the atoms bonded to it. e.g. CH₃CH₂CH₃ for Propane

ketal

molecules containing two -OR groups bonded to the same (internal) carbon

acetal

molecules containing two -OR groups bonded to the same (terminal) carbon

amino sugar

monosaccharide in which an -OH group is replaced with an -NH2 group; most common = D-glucosamine, D-mannosamine

ketoses

monosaccharides containing a ketone group; anomeric carbon of ketose = C2

aldoses

monosaccharides containing an aldehyde group; anomeric carbon of aldose = C1

anomers

monosaccharides that differ in configuration only at their anomeric carbons

ester: nomenclature

name alkyl group bonded to oxygen first, space, followed by the name of the acid replacing suffix -ic acid with -ate.

amide: nomenclature

name parent carboxylic acid, then replace suffix "-oic acid" with "-amide". If the nitrogen atom of the amide is bonded to an alkyl or aryl group, the group is named and its location on nitrogen indicated by locant 'N'. Two alkyl groups are indicated by 'N,N'; two identical alkyl groups are indicated by 'N,N-di-...' Amides don't build in a space (like esters), therefore stereochemistry can be indicated at beginning of string

anhydride: nomenclature

name the carboxylic acid and replace word 'acid' with word 'anhydride'; e.g. ethanoic acid becomes ethanoic anhydride (aka acetic acid becomes acetic anhydride)

carboxylic acid: nomenclature

name the longest carbon chain containing the carboxyl group, drop the final -e from the parent alkane and replace with -oic acid. Numbering for substituents starts at the carbonyl carbon (commonly use greek letters as locants). Numbers of the carboxyl carbons not needed as the can only be at the ends of the parent chain. When carboxyl group present at both ends, add suffix -dioic acid.

alkane nomenclature

name the parent by tracing the longest chain of carbon atoms and adding the suffix -ane to the number prefix, assign locants to the carbons starting with the end closest to the first substituent, name substituents by identifying locant(s) and adding -yl to number prefix (adding di, tri, etc. as necessary for multiples), alphabetize substituents and finish with parent name.

alkene nomenclature

name the parent by tracing the longest chain of carbon atoms that includes all double bonds and adding the suffix -ene to the number prefix, assign locants to the carbons starting with the end closest to the first double bond, name substituents by identifying locant(s) and adding -yl to number prefix (adding di, tri, etc. as necessary for multiples), alphabetize substituents and finish with parent name.

amines: chemistry

neutralization nucleophilic substitution

fatty acids: chemistry

neutralization (saponification) esterification

thiols: chemistry

neutralization to form thiolate salts oxidation to form disulfides reduction (disulfides) to form thiols

anomeric carbon

new carbon stereocenter created in forming the cyclic structure of a carbohydrate; the hemiacetal carbon of the cyclic form of a monosaccharide

alkyne physical properties

nonpolar compounds, only LDF attractions between molecules. b.p. and m.p. increase with increasing MW VERY linear compounds, so LDF attractions have greater surface area upon which to act. b.p. and m.p. higher than alkanes or alkenes

alkene physical properties

nonpolar compounds, only LDF attractions between molecules. b.p. and m.p. increase with increasing MW b.p. decreases with increasing branching (as surface area decreases. LDF decrease, attraction btw molecules decrease, b.p. decreases). Like any other hydrocarbons, alkenes will burn.

alkane solubility

nonpolar compounds, therefore not soluble in water, but soluble with eachother

nucleotide

nucleosides linked to one or more phosphates

cyclic ethers

one of the atoms in a ring is oxygen

nucleobase

one of two types of heterocyclic amine, usually aromatic, found in nucleic acid: purine (adenine, guanine) or pyrimidine (uracil, thimine, cytosine)

carboxylic acid

organic compound in which the highest functional group is a carboxyl group

amino acid net charge

overall charge of the protein dependent upon the pH of the environment and the pKa values of the R-groups (sidecars) present

aldehydes: chemical properties

oxidation (becomes carboxylic acid) reduction (2 mechanisms to become 1° alcohol) addition (+ -OH becomes alcohol + ether aka hemiacetal)

facilitated transport

passage through a membrane via interaction between transport channel and transported molecule

C6H5OH

phenol

resorcinol (aka 1,3-benzenediol)

phenol + additional hydroxyl group at the meta position

catechol (aka 1,2-benzenediol)

phenol + additional hydroxyl group at the ortho position

hydroquinone

phenol + additional hydroxyl group at the para position

cresol

phenol + methyl group

H3PO4

phosphoric acid (strongest of the weak acids)

"like dissolves like"

polar compounds will dissolve in polar solvents, nonpolar compounds will dissolve in nonpolar solvents

heteropolymer

polymer derived from 2 or more alternating monomers (called copolymers), e.g. poly (styrene-co-ethylene)

protein

polymer of amino acids

acidic polysaccharides

polysaccharides with uronic acid or sulfated sugars as part of the structure (containing carboxyl groups and/or sulfuric ester groups), anionic at pH 7 (i.e. ionized to -COO⁻ and/or -SO3⁻ at the pH of bodily fluids). These polysaccharides have net negative charges. Important component of connective tissues, e.g. glycosaminoglycans

keto-

prefix indicating a ketone

aldo-

prefix indicating an aldehyde

trans

prefix indication that the substituents are on opposite sides of the plane of a ring or double bond

cis

prefix indication that the substituents are on the same side of an imaginary line drawn parallel to a double bond

meth-

prefix to indicate 1 carbon in the hydrocarbon chain

dec-

prefix to indicate 10 carbons in the hydrocarbon chain

eth-

prefix to indicate 2 carbons in the hydrocarbon chain

prop-

prefix to indicate 3 carbons in the hydrocarbon chain

but-

prefix to indicate 4 carbons in the hydrocarbon chain

pent-

prefix to indicate 5 carbons in the hydrocarbon chain

hex-

prefix to indicate 6 carbons in the hydrocarbon chain

hept-

prefix to indicate 7 carbons in the hydrocarbon chain

oct-

prefix to indicate 8 carbons in the hydrocarbon chain

non-

prefix to indicate 9 carbons in the hydrocarbon chain

1° amine

primary amine: the nitrogen atom is bonded to one carbon

reduction

process by which a substance gains electrons; products contain fewer multiple bonds and/or oxygen atoms (e.g. aldehyde or carboxylic acid becomes a primary alcohol)

carbohydrates reaction: oxidation

process by which a substance loses electrons; products contain additional multiple bonds and/or additional oxygen atoms e.g. aldehydes are easily oxidized to carboxylic acid when in straight-chain form; ketoses lack end carbonyl group, however keto-enol tautomerism permits conversion of the ketone to an aldehyde then they can also be reducing sugars

oxidation

process by which a substance loses electrons; products contain additional multiple bonds and/or additional oxygen atoms (e.g. alcohol becomes aldehyde or carboxylic acid) (i.e. a chemical reaction in which an atom or ion loses electrons, thus undergoing an increase in valence. Removing an electron from an iron atom having a valence of +2 changes the valence to +3)

salt

product from an acid + metal (or metal hydroxide, metal oxide, carbonate, bicarbonate, ammonia or amine)

polyamides

product from reaction between dicarboxylic acids and diamines

common ketones

propanone aka dimethyl ketone aka acetone

glucose (ring form)

pyranose with D-U-D configuration (picture shows beta-D conformation)

galactose (ring form)

pyranose with D-U-U configuration

mannose (ring form)

pyranose with U-U-D configuration

4° amine

quaternary amine: the nitrogen atom is bonded to four carbons (and has positive charge)

equal Ka or Keq

rarely ratio is one (1), means both reactants and products equally favored

anhydride reaction: hydrolysis

react readily with water to give two carboxylic acids. H2O nucleophilically attacks carbonyl carbon of one acyl group and carboxylate ion leaves, joins with H+ from H2O to make two identical products CH3C(=O)-O-C(=O)CH3 + H2O → 2 CH3C(=O)-OH

hydrolysis

reaction in which a bond is broken and the two atoms that were part of the bond are joined to parts of water, thus water plus the organic reactant yields two products (Ayer's e.g. saponification)

ester reaction: rxn with ammonia or 1°/2° amines

reaction yields an amide and an alcohol; best method of amide formation: -R-C(=O)-OR + NH3 → -R-C(=O)-HN2 + HO-R

substitution

reactions in which an atom or group on a reactant is replaced with a different atom or group; nucleophilic attack is involved: 1. Sn2 (nucleophilic substitution): replacement of an atom or group with another on a tetrahedral carbon 2. esterification: replacement of -OH (or -OR) on carboxy group (or anhydride) with an ether 3. amidation: replacement of -OH (or -OR) on carboxy group (or anhydride) with an ammonia or an amine 4. halogenation of alkanes in presence of light/heat to yield a haloalkane

elimination

reactions in which one reactant loses groups on adjacent carbons to yield two products, one of which contains a multiple bond. Typically the products are an alkene and a small molecule: 1. dehydration: loss of water from a molecule to yield a multiple bond, usually C=C 2. dehydrohalogenation: loss of a hydrogen halide to yield a multiple bond, usually C=C

H2SO4 or H3PO4/ heat

reagent / conditions that signify dehydration

K2Cr2O7 / H2SO4

reagent / conditions that signify oxidation

NaBH4/H+ (aq)

reagent / conditions that signify reduction

alcohol reaction: oxidation

reagent = K2Cr2O7 1° alcohol becomes aldehyde (with distillation) or proceeds to carboxylic acid 2° alcohol becomes ketone 3° do not oxidize

aldehyde reaction: oxidation

reagent = K2Cr2O7 / H2SO4 CH3CH2CH=O →K2Cr2O7 / H2SO4→ CH3CH2C(=O)OH

monosaccharide reaction: reduction

reduction of the carbonyl group of an aldose or ketose to a hydroxyl group yields a polyhydroxyl compound called an alditol

configuration

refers to the arrangement of atoms about a stereocenter, i.e. to the relative arrangement of parts ofa molecule in space

aliphatic hydrocarbons

relating to or denoting organic compounds in which carbon atoms form open chains (as in the alkanes), not aromatic rings

alkane reactions

relatively nonreactive. will ONLY experience: combustion (alkane oxidized to CO2 + H2O) and halogenation (requires heat or light, then produces haloalkane + hydrogen halide: a halogen is substituted for a hydrogen creating the haloalkane and the displaced hydrogen hooks up with the remaining halogen to form the hydrogen halide)

fatty acids reaction: esterification

replacement of an -OH (or -OR) group with an ether

amide reaction: hydrolysis

requires vigorous persuasion (heat + H2O + acid OR heat + H2O + base): CH3CH2CH2C(=O)-NH2 + H2O + HCl →H2O/heat→ CH3CH2CH2C(=O)-OH + NH4⁺Cl⁻ (acid-catalyzed reaction yields carboxylic acid and ammonium ion; requires one mole of acid per one mole of amide) CH3C(=O)-NH2 + NaOH →H2O/heat→ CH3C(=O)-O⁻Na⁺ + NH2 (base-catalyzed reaction yields carboxylic acid salt + ammonia or amine; requires one mole of baes per one mole of amide)

ethers: chemistry

resist reactions, do not oxidize or reduce. frequent product, infrequent reactant

palmitic acid

saturated fatty acid with formula 16:0

stearic acid

saturated fatty acid with formula 18:0

2° amine

secondary amine: the nitrogen atom is bonded to two carbons

alkane

simplest type of organic compounds

neutral

solution with pH equal to 7.00

basic

solution with pH greater than 7.00

acidic

solution with pH less than 7.00

hybrid orbital for molecular geometry: linear

sp

hybrid orbital for molecular geometry: trigonal planar

sp2

hybrid orbital for molecular geometry: bent

sp2 or sp3

hybrid orbital for molecular geometry: tetrahedral

sp3

hybrid orbital for molecular geometry: trigonal pyramidal

sp3

predominant species

species of chemical (acid or conjugate base) most present at a given pH (when pH = pKa, concentration of acid [HA] = concentration of conjugate base [A-]; ratio is 50:50 when pH < pKa, (i.e. solution is more acidic), then the acid form predominates when pH > pKa, (i.e. solution is more basic), then the conjugate base form predominates) Ex: acetic acid pKa = 4.74 at pH 4.74, acetic acid : acetate = 50:50 at pH 3.0, acetic acid predominates at pH 12, acetate predominates

glucocerebroside

specific term for a GLUCOSE sugar + ceramide (AKA glucosylceramide)

micelles

spherical arrangements of molecules in aqueous solution such that their hydrophobic (water-hating) parts are shielded from the aqueous environment and their hydrophilic (water-loving) parts are on the surface of the sphere and in contact with the aqueous environment; formed when constituent phospholipids molecules have wedge shape

lipoprotein

spherically shaped clusters containing both lipid molecules and protein molecules; transporters for cholesterol

sphingomyelin

sphingosine + phosphate group a substance that occurs widely in brain and nervous tissue, consisting of complex phosphoryl derivatives of sphingosine and choline

enantiomer

stereoisomers that are nonsuperimposable mirror images; refers to a relationship between pairs of objects

diastereomers

stereoisomers that are not mirror images: A-B are enantiomers and C-D are enantiomers, but A-C and B-D are diastereomers

epimers

stereoisomers that differ in stereochemistry at a non-anomeric carbon; e.g. galactose is the 4-epimer of glucose

carbohydrates: classification by function

storage: a fuel reservoir; e.g. starches are plant-based fuel storage (amylose or amylopectin), glycogen is animal-based fuel storage. α-linkages generally indicate storage structural: polysaccharides forming support for plants (cellulose), insects (chitin) and/or animals (hyaluronic acid, the glycosaminoglycan in cartilage). β-linkages generally indicate structure

carbohydrates: structure

straight-chain, intermediate and alpha- or beta-ring form: straight-chain and ring forms exist in equilibrium; alpha- and beta-ring forms exist in equilibrium. Transition between forms common unless and until anomeric carbon becomes fixed in a glycosidic bond

protein functional classifications

structural (e.g. maintain the structure of an ear) catalytic (e.g. enzymes) transport (e.g. hemoglobin transports O2) movement (e.g. muscular contractions) messengers (e.g. hormones ) storage (e.g. muscle is a fuel reserve, DNA is an information reserve) protection (e.g. antibodies) regulation (e.g. regulatory proteins) All determined by primary structure

hydroxyl

substituent name when -OH is not the highest priority functional group attached to the parent hydrocarbon

-ane

suffix for alkane compounds

-ene

suffix for alkene compounds

-yne

suffix for alkyne compounds

-ol

suffix for the parent hydrocarbon bearing a hydroxide (-OH) as the highest functional group

-ose

suffix indicating the compound is a carbohydrate

deoxygenated sugar

sugar in which a hydrogen replaces an -OH group; nomenclature = sugar type, locant of deoxygenation + prefix deoxy- (e.g. D-2-deoxygalactose)

alditol

sugar with all carbonyl groups reduced to alcohols; nomenclature = replace -ose with suffix -itol. Common to sugar-free foodstuffs (e.g. glucose aka sorbose becomes sorbitol)

sugar phosphate

sugar with an alcohol in ester linkage with phosphoric acid ((PO₃²⁻); nomenclature = sugar type, sugar name, locant of phosphate group + 'phosphate' (e.g. D-glucose-6-phosphate). Phosphorylated sugars are marked for destruction (i.e. tagged to be used in glycolysis)

common nomenclature

system of naming that predates IUPAC

boiling point (aka b.p.)

temperature at which the vapor pressure is large enough that bubbles form inside the body of the liquid. larger molecules usually have higher boiling points and melting points. This is not because of their higher molecular weights but because they usually have greater surface areas with which to form more intermolecular interactions. This is also why linear molecules tend to have higher MPs and BPs than branched (or more spherically shaped) molecules. Linear molecules will have more surface area than a more spherically shaped molecule

aldehydes: physical properties

terminal carbonyl (C=O) group -electronegative O creates partial positive on C and makes it a target for nucleophiles, partial negative O is target for protonation -no locant given as functional group is in C1 position by definition -dial suffix if functional group is at both ends -polar, but no H attached to the O for h-bonding -m.p. and b.p. higher than corresponding hydrocarbons, but less than alcohols or amines -water soluble at low MW, less polar & less water soluble as MW increases (5-6C+)

3° amine

tertiary amine: the nitrogen atom is bonded to three carbons

alkane structure

tetrahedral geometry about carbons

chirality

the 'handedness' of objects: occurring in pairs, non-superimposable on mirror image

residue

the 'left-overs', i.e. the 'R' of R-groups

alpha-ring form

the -OH on the anomeric carbon projects downward / opposite the direction of the tail

beta-ring form

the -OH on the anomeric carbon projects upward/ in the same direction as the tail

stereoisomerism

the ability of compounds of the same formula and connections to differ in how the atoms are arranged in space

catalysis

the acceleration of a chemical reaction by a catalyst

protonation

the addition of a proton (H+) to an atom, molecule, or ion, forming the conjugate acid

carbohydrates reaction: glycolysation

the addition of an alcohol to a hemiacetal or hemiketal to form an acetal or ketal (i.e. the reaction in which a carbohydrate, AKA glycosyl donor, is attached to a hydroxyl or other functional group of another molecule): a sugar + an alcohol a sugar + a sugar resultant linkage = glycosidic bond

alkene reactions

the carbon-carbon double bond is a site of chemical reactivity as breaking the double bonds into single bonds (an exothermic reaction) creates a more stable (lower energy) molecule: combustion (like any other hydrocarbons, alkenes will burn in a plentiful supply of oxygen to give carbon dioxide and water), hydrohalogenation, acid-catalyzed hydration, halogenation, hydrogenation. Substitution reactions when dealing with polymerization (we did not cover).

mutarotation

the change in specific rotation that occurs when an alpha- or beta-ring form of a carbohydrate is converted to an equilibrium mixture of the two forms

levorotatory

the clockwise (to the left) rotation of the plane of polarized light in a polarimeter

hybridization

the concept of mixing atomic orbitals into new hybrid orbitals (with different energies, shapes, etc., than the component atomic orbitals) suitable for the pairing of electrons to form chemical bonds in valence bond theory

dextrorotatory

the counterclockwise (to the right) rotation of the plane of polarized light in a polarimeter

delocalization

the electrons in a molecule, ion or solid metal are not associated with a single atom or a covalent bond (i.e. they are free to move between pi bonds). In the simple aromatic ring of benzene the delocalization of six π electrons over the C6 ring is often graphically indicated by a circle.

buffer capacity

the extent to which a buffer solution can prevent a significant change in pH of a solution upon addition of a strong acid or a strong base

isoprene unit

the fundamental unit of compounds known as terpenes. It has a molecular formula of C5H8 and can be described as aliphatic or acyclic

parent chain

the longest continuous chain of connected carbon atoms in a hydrocarbon

decarboxylation

the loss of CO2 from a carboxyl group

glycolysis

the metabolic pathway by which monosaccharides (especially glucose) are degraded to pyruvate

cholesterol

the most abundant and important steroid in the human body: fundamental constituents of cell membranes and precursors of other steroid compounds. Component of cell membranes that acts as membrane fluidity modulator: at low temps, cholesterol acts as an impurity and lowers the m.p. of the membrane/increases fluidity; at high temps, cholesterol impedes lateral diffusion across the leaflet as molecules must move around the cholesterol.

alkene addition reaction

the most characteristic alkene reaction is an addition to their carbon-carbon double bond: the double bond is broken and single bonds form in its place between the carbons and two new atoms or groups of atoms. Examples: hydrohalogenation, hydration, bromination, hydrogenation

benzene reactions

the most characteristic reaction of aromatic compounds is substitution at a ring carbon (aka aromatic substitution): halogenation, nitration and sulfonation. Like any other hydrocarbons, benzene will also burn. Aromatic compounds DO NOT undergo addition reactions because that would involve breaking the delocalisation and losing that stability

chair conformation

the most stable conformation of cyclohexane in which all bond angles are approximately 109.5°. Half of the C-H bonds are oriented axially, half of the C-H bonds are oriented equitorially

envelope conformation

the most stable conformation of cyclopentane, four carbon atoms are in a plane and the fifth carbon atom is bent out of the plane like an envelope flap

active transport

the movement of ions or molecules across a cell membrane into a region of higher concentration, assisted by enzymes and requiring energy input

penultimate carbon

the next-to-the-last carbon on the chain

specific rotation

the number of degrees by which an optically active compound rotates the plane of plane-polarized light in a polarimeter

equivalence point

the point in a titration at which there is a stoichiometrically equal number of moles of each reactant present

alpha position

the position immediately after the carbonyl carbon; the H on that position is acidic

Keq

the ratio of concentrations when equilibrium is reached in a reversible reaction (when the rate of the forward reaction equals the rate of the reverse reaction)

isomerism

the relation of two or more compounds, radicals, or ions that are composed of the same kinds and numbers of atoms but differ from each other in structural arrangement (structural isomerism) as is the case for CH3OCH3 and CH3CH2OH, or in the arrangement of their atoms in space and therefore in one or more properties

R-

the symbol used to represent everything besides the functional group (i.e. the "residue")

melting point (aka m.p.)

the temperature at which the solid melts to become a liquid. Larger molecules usually have higher boiling points and melting points. This is not because of their higher molecular weights but because they usually have greater surface areas with which to form more intermolecular interactions. This is also why linear molecules tend to have higher MPs and BPs than branched (or more spherically shaped) molecules. Linear molecules will have more surface area than a more spherically shaped molecule

polarity

the tendency of a molecule, or compound, to be attracted or repelled by electrical charges because of an asymmetrical arrangement of atoms around the nucleus.

London Dispersion Forces

the weakest intermolecular force. LDF is a temporary attractive force that results when the electrons in two adjacent atoms occupy positions that make the atoms form temporary dipoles. This force is sometimes called an induced dipole-induced dipole attraction

Henderson-Hasselbalch equation

to calculate pH of buffer: pH = pKa + log ([conjugate base] / [weak acid])

xylene

toluene + additional methyl group (can be ortho, meta or para)

phosphoric anhydride

two phosphoryl (P=O) groups bonded to the same oxygen atom

lipid bilayer

two rows (leaflets, layers) of complex lipid molecules arranged tail to tail; an arrangement in which hydrophobic tails point towards each other and the hydrophilic heads face outward into the aqueous environment; formed when constituent phospholipid molecules have cylindrical shape

oleic acid

unsaturated fatty acid with formula 18:1cΔ9 Ω-9

lineolic acid

unsaturated fatty acid with formula 18:2cΔ9,12 Ω-6

linolenic acid

unsaturated fatty acid with formula 18:3cΔ9,12,15 Ω-3

arachidonic acid

unsaturated fatty acid with formula 20:4cΔ5,8,11,14 Ω-6 key ingredient of prostaglandins

alkyne

unsaturated hydrocarbon that contains a carbon-carbon triple bond. the parent chain must be configured in order to include all triple bonds. numbering of the carbons is done to assign the lowest locant possible to the triple bond(s).

alkene

unsaturated hydrocarbon that contains at least one carbon-carbon double bond. the parent chain must be configured in order to include all double bonds. numbering of the carbons is done to assign the lowest locant possible to the double bond(s).

pyrimidine base

uracil (RNA), thymine & cytosine

pyrimidine nucleoside

uridine, thymidine & cytidine

fatty acids: physical properties

water insoluble m.p.: saturated fatty acids = relatively high because molecules can pack tightly to maximize LDF; unsaturated fatty acids = lower than corresponding saturated FAs because the cis- double bonds kink the molecules such that they do not pack well and there is less LDF affect; unsaturated fatty acids with trans double bonds = similar to corresponding saturated FAs because they can pack well

lipids

water-insoluble substances classified into four groups: fats & oils (aka triglycerides); complex lipids; steroids; and prostaglandins, thromboxanes, and leukotrienes

solvation

when a substance known as a solute dissolves in another, known as a solvent, it is termed a solution. Solvation is a process where a chemical reaction occurs during this and both the solute and solvent combine to form weak covalent electron bonds. The process of solvation is closely related to dissolution and solubility, with the technical distinction that it creates a stable state in the solution where ionic charges of the solute and solvent cancel each other out to form an overall neutral charge

hybrid orbital

when atomic orbitals mix to form new atomic orbitals. The new orbitals have the same total electron capacity as the old ones. The properties and energies of the new, hybridized orbitals are an 'average' of the original unhybridized orbitals

monosubstituted benzene

when one of the positions on the ring has been substituted with another atom or group of atoms

Le Chatelier's Principle

when the concentration of a species in an equilibrium changes, the equilibrium will shift to minimize that change (i.e. add to product side, reactant side increases to compensate; decrease from reactant side, reactant side increases to compensate)

anhydride reaction: rxn with alcohol

yields one mole ester + one mole carboxylic acid: CH3C(=O)-O-C(=O)CH3 + HO-CH2CH3 → CH3C(=O)-O-CH2CH3 + HO-C(=O)CH3