UWorld -

how can you tell if something is a strong acid?

any acid that dissociates 100% into ions is called a strong acid. If it does not dissociate 100% if is a weak acid. If the strong acid is not listed here, it is a weak acid.

what is there difference between stereoisomers and constitutional isomers

constitutional isomers differ in atom connectivity where as stereoisomers have the same atom connectivity but differ in spatial orientation

the reaction of a ketone or an aldehyde with a cyanide ion (from NaCN) acting as a nucleophile and attacking the electrophilic carbonyl (C=O) carbon produces a

cyanohydrin

linear sugars can cyclize to become a

hemiketal or hemicetal

glutamate (GLU) (E) and Aspartate (ASP) (E) have what type of charge

negative

acidic and basic amino acids have what type of side chains

negatively charged and positively charged respectively

is tryptophan charged

no

are free fatty acids usually found in the blood plasma?

no, they are usually found as a derivative, such as a triglyceride or phospholipid

gabriel synthesis requires

potassium pthalimide and diethyl bromomalonate

separation of glycerol from a fatty acid sodium salt can be accomplished by

protonation of the negatively charged carboxyl group, which can be achieved by addt'n of a STRONG ACID, such as HCl.

sugars that are six membered rings (five carbon atoms and one O) are considered

pyranoses

Gabriel synthesis includes a SN1 or Sn2 rxn

Sn2

draw and name your common monosaccharides

ribose, glucose, fructose, mannose, galactose

Fragmentation of Data (m/Z) units

see how they did it and in the passage they wrote that 162 MW = one hexose unit

to draw conclusions, from the results of a study on enzyme activity, control experiments should be done to ensure that no confounding factors, such as

side rxns occur

In Strecker Synthesis, if the imine intermediate is planar and has no

stereochemistry, the product is a mixture of L- and D- amino acids

basic reagents in gabriel synthesis

strong bases!!! NaH NaNH2 KH KOH

is the alpha or beta carbon of a carboxylic acid more susceptible to substitution reaction such as bromination?

the alpha carbon (carbon adjacent to the carbonyl carbon) is more susceptible to substitution reactions such as bromination.

alpha carbon

the central carbon atom of each amino acid

why are fatty acids sodium salts soluable in aqueous sol'ns

the charged carboxyl group and sodium ion interact w/ water through ion-dipole interactions

In a Fischer Esterification, which oxygen will always stay?

the oxygen from the alcohol as it is what initially attacks the acid and eventually forms the -OR group of the water

In a Fischer Esterification, which oxygen is removed?

the oxygen from the carboxylic acid

brief summary of gabriel synthesis

1.start with phthalimide 2. deprotonate pthalimide w/ a strong base 3. add an alkyl halide 4.the nitrogen nucleophile will then attack the alkyl halide in an Sn2 rxn & form an N-C bond

Glucose --> Acetyl Co-A how many ATP

2 ATP 4 NADH (2.5 each)= 10ATP

what are the three possibilities of the two products that a retro-aldol condensation can yield?

2 ketones or 2 aldehydes or 1 ketone 1 aldehyde

NADH is how many atp

2.5

Huckel Rule of Aromaticity

4n +2 = pi electrons n is not the number of pi electrons, you set it equal to the number of pi electrons. N has to be a non-negative integer! "n comes from algebra, not from chemistry"

Pyran

6 membered ring

Ribose

A five-carbon sugar present in RNA

important carbon-carbon bond forming reactions where two carbonyl compounds (ketones and or aldehydes) are joined together by nucleophilic addition to form the aldol product.

Aldol Condensations

6

Terpenes are made up of two or more five-carbon groups known as isoprenes. The triterpenoid lanosterol, a steroid precursor, is shown below. How many isoprene units are present in lanosterol? A.3 B.4 C.6 D.8

Fischer Esterification is ______ catalyzed while Transesterification is ________ catalyzed

acid base Makes sense- the two processes oppose eachother

is an amine group acidic or basic

basic,

Multiple peaks with the same m/z in mass spectrum of an unsaturated molecule could correspond to what type of isomers

cis/trans

Induction is an electronic property in which

electrons are donated through sigma bonds

Soaponification

hydrolysis of ester bonds with a strong base

this happens when a molecule looses electrons and the number of carbon-heteroatom bonds increases

oxidation

glyceraldehyde can be derived from what

oxidation of glycerol

this happens when a molecule gains electrons and the number of carbon-heteroatom bonds decreases

reduced

answer to previous flashcard

see pic

lipids that are primarily found in adipocytes for energy storage

triaglycerols

sugars are classified by their

1. Stereochemistry 2. number of carbons in the sugar 3. number of carbohydrate units in the molecule, and the functional groups present in the sugar

FADH is how many ATP

1.5

CAC how many ATP?

2 ATP 2 FADH2 (1.5 EACH) -> 3 ATP 6 NADH (2.5 EACH) -> 15 ATP

esters can be formed under acidic conditions via

Fischer Esterification; using a carboxylic acid & an alcohol

all strong bases are

OH- compounds so a base based on some other mechanism, such as NH3 (which does not contain OH- ions as a part of its formula will be a weak base)

what are the basic amino acids?

Lys (K), Arg (R), and Histidine (H)

a technique that ionizes molecules in a sample, and ions can fragment. The ions are accelerated toward a magnet, deflected according to mass and detected. A plot of ion mass abundance VS m/z ration fragments is generated; fragments of the sample can be identified by the m/z difference between two peaks.

Mass Spectrometry

is H20 a byproduct of a dehydration reaction?

yes

is an esterification rxn reversible

yes

is thymine aromatic?

yes

are mesylates good leaving groups?

yes, chlorides, bromides, and tosylates/mesylate groups are excellent leaving groups in nucleophilic substitution rxns, due to resonance delocalization of the developing negative charge on the leaving oxygen

Does Fischer Esterfication involve loss of a water molecule?

yes, an esterification is a condensation rxn in which an ester is formed from a cooh and alcohol

how do you determine whether a substance is an acid or a base (donor or acceptor)

you can look at the number of hydrogens it has. decreased H+ = acid increase H+ = base

name three steps in an aldol condensation rxn

deprotonation of the alpha carbon on one of the substrates resonance stabilized enolate forms nucleophilic addition of the enolate to the other carbonyl substrates yields the aldol product

hydrolysis of triglycerides and phospholipids release

free fatty acids

how can you tell is something is a weak base?

if it is less than 100% ionized in a solution, it is a weak base. There are very few strong bases, and any base not listed is a weak base

the products of a retro-aldol rxn depend on what two things

1. substituents on the carbonyl carbon 2. substituents on the Beta-hydroxy ketone

what is the final step of the Gabriel Synthesis rxn?

Decarboxylation, which is not sterospecific

why would deprotonation/protonation of an alcohol not make it a good leaving group?

Deprotonation of the alcohol creates a negative charge on the alcohol oxygen atom, making it a nucleophile rather than a leaving group. Alternatively, protonation of an alcohol would create a strong electrophile and a good leaving group in the form of water.

Electron Donating VS Electron Withdrawing

EWD - pull electrons away from an adjacent atom toward themselves, creating a dipole with a partial negative charge on the electronegative atom and a partial positive charge on the adjacent atom. EDG - an atom or functional group that donates some of its electron density into a conjugated pi system

Fischer Esterification Pneumonic

Ester loves Fisch, Carbs, & alcohol

what rxn is this: 1. Take the big Phthalimide molecule & add some strong base. 2. R-x (with x being the halide you want to replace with the amine in the Pthalamine) and 3. NH2 Nh2 to fill the empty amine that will be given to the R-X *you get R-NH2

Gabriel Synthesis

Gabriel Synthesis Pneumonic

Gabriel is a Strong Basic Alkylholic who likes Pthoties!!

Geometric Isomers/Stereoisomers can be separated by

Gas Chromatography because they have slightly different boiling points

enone

Alpha beta unsaturated carbonyl. Stable compound because multiple resonance structures. More susceptible to nucleophilic attack.

Researchers separated fatty acid sodium salts from glycerol by adding HCl and then extracting with hexanes. Which statement correctly describes the extraction process? A.HCl protonates the carboxylate, and the fatty acid is found in the aqueous layer. B.The carboxyl group is deprotonated, and the fatty acid is dissolved in the polar solvent. C.HCl protonates the carboxylate, and the fatty acid is found in the organic layer. D.The carboxyl group is deprotonated, and the fatty acid is dissolved in the nonpolar solvent.

C.HCl protonates the carboxylate, and the fatty acid is found in the organic layer.

Strecker Synthesis Pneumonic

Strecker = (S) Cyanide *Streckers ALways (aldehyde) eat Banana Chocolate Nuts (KCN) AMMongst Cleopatra (Ammonium Chloride).

Name the Rxn: *make ALPHA amino acids from an aldehyde using ammonium chloride (NH4Cl) and Potassium Cyanide (KCN)

Strecker Synthesis

Name the rxn: *Not stereospecific *creates both L and D enantiomers *requires an aldehyde, KCN, and Ammonium Chloride

Strecker Synthesis

lipid precursors to steroids and lipid signaling molecules, and are generally isolated from plants

Terpenes

mass spectrum can be used to identify a molecules fragments by taking the m/z difference between peaks

Mass Spectrum

would you expect thymine, adenine, or imidazole to be aromatic? If so, what resonance structures would you have to write in order to obtain 6 electrons in a cycle?

While only adenine has a six-membered ring with 3 conjugated double bonds (like benzene), all three compounds have some degree of aromatic character. If we consider the Lewis structures shown below, and count the lone pairs on N atoms which are pointing perpendicular to the planes of the rings as contributing to the cyclic array of 2p electrons, we see that both thymine and imidazole are aromatic. Adenine is like naphthalene, an aromatic compound with 10 electrons in a cyclic array of 2p orbitals. The general rule for aromatic compounds is Huckel's Rule, which states that any cyclic array of 4n+2 (where n is any integer) electrons in p type atomic orbitals will have special stability.

sugars are linear carbohydrates made up of

a carbonyl and at least two other carbon atoms

transesterification is the conversion of

a carboxylic acid ester into a different carboxylic acid ester.

Name four carboxylic acid Derivities

1. Acid Halide 2. Anhydride 3. Ester 4.Amide

Aldose

A carbohydrate whose carbonyl group is an aldehyde

a tripeptide contains how many amino acids and how many peptide bonds

3 aa 2 peptide bonds

how many ATP are produced from one glucose?

32-38 theoretical range.

what are all the hydrophilic amino acids (3 categories)

Basic LYS ARG HIS Acidic GLU ASP Polar w/ uncharged R groups SER THR ASN GLN TYR CYS

beta carbon

Carbon separated from carbonyl carbon by alpha carbon (count two over)

(T/F) The Strecker synthesis is used to generate beta-amino acids from an aldehyde using ammonium chloride (NH4Cl) and potassium cyanide (KCN). Because the imine intermediate formed during the reaction is planar (no stereocenters), nucleophilic addition can occur from either above or below the plane. Therefore, the Strecker synthesis is stereospecific reaction.

FALSE!! The Strecker synthesis is used to generate α-amino acids from an aldehyde using ammonium chloride (NH4Cl) and potassium cyanide (KCN). Because the imine intermediate formed during the reaction is planar (no stereocenters), nucleophilic addition can occur from either above or below the plane. Therefore, the Strecker synthesis is not a stereospecific reaction and produces a mixture of L- and D-amino acids.

name the strong acids

HCl HBr HI HNO3 H2SO4 HClO3 HClO4

IntrAmolecular Aldol Condensations

In an Aldol Condensation, the products can form a dicarbonyl compound

ubiquinone is the fully oxidized form of

Coenzyme Q

D amino acids are (R/S)

DaminoR

peptide bond formation proceeds from what terminal to the other?

N to C terminal

these compounds are made up branches five-carbon groups, called isoprene units, in which the branched end is referred to as the head and the unbranched end is the tail

T E R P E N E ' S

acid amino acids such as (aspartate & glutamate) experience electrostatic interactions with

basic amino acids, such as arginine (opp = attract)

which is more stable, keto or enol?

despite being a reversible rxn, the keto form is more stable and thus favored by equilibrium..

charged amino acids can experience what type of interactions

electrostatic interactions

Tautomers

Isomers that can interconvert by exchanging the location of a proton. two specific forms of the molecule that can interconvert @ equilibrium.

Docosenoic acid is an unsaturated fatty acid, meaning it contains a disubstituted double bond, and can be in the cis or trans form. Both isomers have the same molecular weight and m/z ration, but will come off the GC column at different times, yielding two distinct peaks. Therefore it can be inferred that Peaks A and B are cis/trans isomers of docosenoic acid. (b/c they have slightly different boiling points)

What can be inferred from Figure 1 about the relationship of Peaks A and B? A.Nothing can be inferred about the relationship of the peaks. B.The peaks are fragments of docosenoic acid. C.The peaks are constitutional isomers of docosenoic acid. D.The peaks are cis-trans isomers of docosenoic acid.

a reverse aldol condensation is called

a retro-aldol rxn

what is a keto-enol tutomerization (KET) rxn?

a rxn in which ketone and enol molecule can isomerize or interconvert, typically in an acid or base catalyzed rxn (not limited to just ketones - also aldehydes) *think constitutional isomers

COOH/ CO2H would be a carboxyl group, while HOCH2 would (one O) would be a

aldose/aldehyde

Enal

alpha beta unsaturated aldehyde

Gabriel Synthesis produces

amino acids

Strecker Synthesis produces

amino acids

Peptide bonds are formed from the carboxyl group of one amino acid and the

amino group of another

how do you break an electrostatic interactions

increasing ionic strength of the buffer sol'n (adding salt) removing charge (neutralizing weak acids by dropping pH) coating the protein in a single charge ( adding charged detergent like SDS)

protonation of the fatty acid sodium salt makes it (soluable/insoluable)

insoluable in water because the fatty acid is no longer a charged species, and therefor cannot interact as readily with water (no more NA)

An atom can be substituted with an _____, which can be "followed" in a reaction. This procedure is known as labeling

isotope

what does the number of distinct fatty acids released in the hydrolysis of a triacylglycerol depend on?

it depends on the number of distinct fatty acids

In regards to a saponification rxn, what is meant when it is said "one equivalent of base"

it is defined as the amount of base needed to hydrolyze one ester linkage in a triacylglycerol

what does the saponification of a triacylglycerol with a strong base do?

it releases free fatty acids (sodium salts) and a molecule of glycerol b/c it breaks down the ester bond

the the carbonyl or beta carbon are not bonded to a hydrogen, they will become what

ketones

a six carbon sugar with the anomeric carbon at C2

ketose

what is meant by a catalytic amount

less than one equivalent

un-hybridized VS hybridized p-orbitals

unhybridized orbitals are in the ground state of the atom. Hybridized orbitals are a combination of orbitals some of which are not in the ground state.

the carbonyl carbon of carboxylic acid may be temporarily brominated, but this carbon is susceptible to hydrolysis when

water is added

Esters are

carboxylic acid derivatives

the closer the electron withdrawing group is to an atom, the (greater/less) inductive effect the atom experiences

greater

In Fischer Projection, alochol O stays and carboxylic acid O

leaves

what is the difference between saturated and unsaturated fatty acids

saturated fatty acids do not contain any double bonds unsaturated fatty acids contain double bonds

the cyclic structure of a sugar is classified by the

size of the ring as well as whether the linear form contains an aldehyde (aldose) or ketone (ketose)

what is an electrophile?

(+) charge any molecule, ion or atom that is deficient in electron in some manner can act as an electrophile. In other words, the reagent which attacks the negative of the molecule or loves electrons is called electrophile. They are generally positively charged or are neutral species (electron-deficient molecules) with empty orbitals.

Furan

5 membered ring

Name the rxn: *requires Potassium Phthalimide and Diethyl Bromomalonate.

Gabriel Synthesis

Name the rxn: *need strong bases, SN2 rxn, Produce amino acids

Gabriel Synthesis

ene + ol =?

enol

anomeric carbon

the carbon that has two bonds to oxygen

L amino acid are (R/S)

S Laminos

these rxns occur when electrons are transferred from one atom to another

oxidation-reduction

hemicetal

the cyclic sugar that is a aldose

what are the three components of an amino acid

1. an amino group 2. a carboxyl group 3. a side chain all bonded to the same carbon atom - alpha carbon

Gabriel Synthesis & Strecker Synthesis two MCAT facts I should know.

1. both are ways to produce amines & amino acids 2. produce L & D enantiomers (NOT stereospecific)

what are the four rules to be classified as an aromatic ring?

1. conjugated pi bonds in a cyclic structure 2. un-hybridized p orbitals present in each atom in a ring 3. planar geometry, forming a continuous ring of parallel, overlapping un-hybridized p-orbitals 4. 4n+2 pi electrons (Huckel Rule), where n is a non-negative interger

what are the acidic amino acids

Aspartic Acid (D) and Glutamic Acid (E)

what are all the hydrophobic amino acids?

Glycine alanine valine leucine isoleucine proline phenylalanine methionine tryptophan

remember, right side is conjugate acid/base ... why? use the following equation as an example: HCl + H2O --> (H3O+) + Cl-

H3O+ is the conjugate acid, even though H2O is the base, b/c it donates an acid to Cl to turn it back into its conjugate acid.

IntErmolecular Aldol Condensation

In an aldol condensation, the carbonyls can come from separate compounds

if an alcohol were to undergo a substitution reaction, would oxidation of the alcohol improve the leaving group ability? why or why not?

NO! Oxidation of the alcohol forms a double bond to the oxygen atom. It makes the carbon bonded to the alcohol oxygen a strong electrophile susceptible to a nucleophilic attack, but the alcohol leaving group ability is decreased as there are now two bonds holding it in place.

In a retro-aldol rxn, if the carbonyl carbon is bonded to a hydrogen atom before the rxn, what will the product be?

an aldehyde

heteroatom

an atom other than carbon or hydrogen

heterocycle

any cyclic compound that contains at least one heteroatom

what is a mesylate?

any salt or ester of methanesulfonic acid (CH3SO3H). In salts, the mesylate is present as CH3SO3- anion.

In a retro-aldol rxn, the aldol product (B-hydroxy Ketone) or the dehydration product (enone or enal) is heated and treated with base, causing the carbon-carbon bond between alpha and beta to

break

reduction can also be viewed as an increase in the number of bonds to

hydrogen

In peptide bond formation, the amino group of one amino acid looses a

hydrogen atom

a good leaving group containing and electron withdrawing group will do what

enhance the partial positive charge of the electrophile

what happens during hydrolysis of a triacylglycerol

hydrolysis breaks the ester bonds, releasing THREE free fatty acids and glycerol

Is Tryptophan hydrophobic or hydrophilic?

hydrophobic

(T/F) Keto will ALWAYS be more stable than an enol

false, there are some situations where the enol form will provide greater stability to the overall molecule. (see pic) the keto form has a more stable carbonyl, but the enol form allows the pi bond to be a part of a much more stable aromatic system. Therefore, the enol form of this molecule will predominate at equilibrium

sugars that are five membered rings (four carbon atoms & one oxygen atom) are considered

furanoses f = five

stereoisomers arise from disubstituted double bonds that are called

geometric isomers; classified as cis or trans based on the relative positions of the non-hydrogen substituents

Glucose vs Galactose

glu = stuck = oh bottom galactose = lactose n tolerant = upchuck = oh up

the long-chain hydrocarbons on fatty acids greatly increase the

hydrophobicity of these molecules, causing fatty acids to be insoluable in water and soluble in an organic solvent

In peptide bond formation, the carboxyl group of one amino acid looses a

hydroxyl group

Isoprene units can be joined together to form terpenes in one of three ways:

head to tail tail to tail head to head

variables are components of an experiment that change while other components of the experiment are

held constant

for the Haworth Projections, to see whether it is L/D, you check the stereochemistry based on the

highest numbered sugar, aka the chiral center not the whole molecule.

watch this video now

https://www.youtube.com/watch?v=wFYsufJ9XMM

are constitutional isomers the same compounds?

no, although they have the same molecular weight, they have different atom connectivity making them different compounds. MCAT HACK: The passage stated that both compounds are forms of docosenoic acid so they CANNOT be constitutional isomers.

are alcohols good leaving groups?

no, because a good leaving group is a weak base. alcohol has the OH aka strong base. alcohols are weak electrophiles and poor leaving groups; therefore, nucleophiles are unlikely to displace the hydroxyl group (-OH).

compounds with acidic and basic functional groups, such as amino acids with basic and acidic side chains, can form electrostatic interactions w/ each other due to positive-negative charge attraction of the respective functional groups. These interactions can be disrupted by

other charged molecules that complete for binding

NADH is a reducing agent because it

reduces something and in turn gets oxidized

in the electron transport chain, ubiquinone receives two electrons from NADH which

reduces the carbonyl carbons to hydroxyl groups and forms an aromatic ring, yielding ubiquinol

hemiketal

the cyclic sugar that is a ketose

how would you optimize the rxn conditions for a synthesis rxn?

the methodology should be evaluated, analysis and results, including yield of purification. The conditions that give high product yield and easy separation of the product from impurities are considered optimal

if three equivalent of NaOH are used to hydrolyze a triacylglyverol, will the molecule be completely hydrolyzed?

the molecule will be completely hydrolyzed because each equivalent hydrolyzes one ester, and there are three esters in a triacylglycerol molecule

In a retro-aldol rxn, if the beta carbon is bonded to a hydrogen, what will the product be?

the product will be an aldehyde

Gabriel Synthesis & Strecker Synthesis are alike in that

the same outcome is obtained for amino acids produced because there is no sterospecificity

why do EWG make good leaving groups?

they stabilize the negative charge acquired after being eliminated

what are triacylglycerols made of

three fatty acids attached to a glycerol molecule attached via an ester linkage

what makes a good leaving group

weak base: happy and stable on its own. some examples of weak bases: halide ions: (I-, Br-, Cl-) and water (H20), and sulfonates such as toluenesulfonate (OTs) and mehanesulfonate (OMs)

what happens when a nucleophile attacks an electrophile? (in regards to a leaving group)

when a nucleophile attack an electrophile, a bond is formed between the nucleophile and electrophile whereas the bond between the electrophile and leaving group is broken

(T/F) Electronegative atoms or electron withdrawing groups tend to create greater dipoles, partial charges, and better leaving groups, and to have greater inductive effects than less electronegative atoms

true

(T/F) basic nitrogen atoms, such as in pyrimidine and purine, have a double bond placing the lone pair electrons in Sp2 orbital perpendicular to the conjugated p-orbitals containing the pi electrons.

true

(T/F) hexanes are non-polar organic molecules that can readily interact with the protonated fatty acids. Therefore pronated fatty acids will enter the organic layer after extraction with the organic solvent hexanes

true

Strecker Synthesis of Amino Acids

used to make alpha-amino acids from an aldehyde using ammonium chloride (NH4Cl) & Potassium Cyanide (KCN)