orgo uW: Functional groups & biological molecules Flashcards
Inductive Effect
- The inductive effect is an electronic property in which the electrons are donated through sigma bonds.
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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.
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The closer the electron withdrawing group to an atom, the greater the inductive effect that atom experiences. Electron withdrawing groups also make good leaving groups because they can stabilize the negative charge acquired after being eliminated.
- Example: acetic anhydride (greater inductive effect) than N,N-diisopropylisohutyramide)
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The closer the electron withdrawing group to an atom, the greater the inductive effect that atom experiences. Electron withdrawing groups also make good leaving groups because they can stabilize the negative charge acquired after being eliminated.

Oxidation
Reduction
- Oxidation loss of electrons and increase in the number of carbon-heteroatom bonds (see image)
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Reduction gains electrons & the number of carbon-heteroatoms bonds decreases
- reduction can also be viewed as an increase in the number of bonds to hydrogen

Pyranose & aldoses–>hemiacetals
Furnasoes & ketoses–>hemiketals
- 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 a ketone (ketose).
- Furanoses are sugars with five-membered rings (four carbons and one oxygen), and pyranoses are sugars with six-membered rings (five carbons and one oxygen).
- Aldoses cyclize to form hemiacetals, and ketoses cyclize to form hemiketals.

Mannose Derivative

Classifying sugars as L or D

Drawing Conclusions
- 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 reactions occur.
- example:

Mass Spectroscopy
- Mass spectrometry is a technique that ionizes molecules in a sample, and the 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 ratio is generated; fragments of the sample can be identified by the m/z difference between two peaks in the mass spectrum.
- m/z (mass-to-charge ratio)

Aldol condensation reaction & enolate formation
- Protons on an α-carbon (adjacent to a carbonyl) are more acidic than other protons bonded to a carbon atom because the carbonyl oxygen is electron withdrawing, resulting in less electron density around the α-protons.
- Therefore, α-protons have lower pKa values and can be more easily removed by a base to form an enolate, which can be stabilized by charge delocalization.
Acidic & basic Functional groups

Formation of aldol product

Aldol condensation products of diketones

FULL summary of aldol condensation
- Aldol condensations are carbon-carbon bond-forming reactions that require two carbonyl substrates (ketones and/or aldehydes).
- The reaction begins with deprotonation of the α-carbon on one of the substrates, forming a resonance-stabilized enolate intermediate.
- Nucleophilic addition of the enolate to the other carbonyl substrate yields the aldol product, and then deprotonation of the α-carbon, followed by –OH elimination, yields the conjugated product, an α,β-unsaturated carbonyl compound.
Products of retro-aldol reactions

Nucleophiles vs leaving groups

hydrolysis of a glycosidic bond
- A glycosidic bond is the α- or β-linkage between a sugar and an –OH of another molecule.
- Hydrolysis of a glycosidic bond is cleavage of the linkage by addition of H2O, breaking the molecule into two smaller units.
Hydrogen bonding

- Hydrogen bonding is an intermolecular or intramolecular force that occurs between a hydrogen bond donor and acceptor; this type of force helps stabilize molecules.
- Hydrogen bond acceptors are electronegative atoms with a lone pair of electrons (eg, oxygen and nitrogen), and hydrogen bond donors are hydrogen atoms bonded to an electronegative atom.
- Alcohols and amines contain groups that can act as both hydrogen bond donors and acceptors.

In order for decarboxylation reactions to happen, what must be included?
- Decarboxylation is a reaction that removes a carboxyl group from a carboxylic acid with a β-carbonyl, releasing the carboxyl group as CO2 gas.
- A β-carbonyl is necessary for decarboxylation because a cyclic transition state incorporating both carbonyls is formed. Esters with a β-carbonyl can also undergo decarboxylation if they are hydrolyzed to a carboxylic acid first.

Conjugation

L/D Sterochemistry

Determining priority of amino acids

Imine formation
- An imine is an analogue of ketones and aldehydes that contains a carbon-nitrogen double bond.
- Imines are formed from a ketone or aldehyde and NH3 or a primary amine via an acid-catalyzed addition of the amine followed by an acid-catalyzed dehydration.

Acid-catalyzed addition of amine
involves protonation of the carbonyl, nucleophilic attack of the carbonyl by the amine, and deprotonation of the amine.

Acid-catalyzed dehydration
involving protonation of the –OH group, loss of H2O, and deprotonation.

Strecker Synthesis
- is used to make α-amino acids from aldehydes using NH3 and potassium cyanide (KCN).
- The first step of the reaction proceeds with protonation of the carbonyl oxygen by H3O+, followed by nucleophilic attack of the carbonyl carbon by NH3, resulting in dehydration and imine formation.
- Therefore, an aldehyde and NH3 are used to form the imine intermediate in the Strecker synthesis.































































































