Lecture 2: the molecules and mechanisms of life

Question 1

What is a hydroxyl group?

Answer 1

OH functional group

Question 2

What is an oxonium ion?

Answer 2

RH2O+

(compared to the hydronium ion H3O+)

Question 3

Distinguish between a carboxylic acid and carboxylate

Answer 3

carboxylic acid is a carbonyl with OH, whereas carboxylate is a carbonyl that has lost its H+ from the OH, so it’s just O-

Question 4

Distinguish between a carboxylic acid and carboxylic ester

Answer 4

carb. acid = OH functional group on carbonyl
carb. ester = OR functional group on carbonyl

Question 5

What is the molecular formula for acetic acid, acetate, and an acetyl group?

Answer 5

acetic acid: CH3COOH
acetate: CH3COO-
acetyl group COCH3 carbonyl functional group

Question 6

What is an acid anhydride?

Answer 6

Question 7

Distinguish between ammonia and the ammonium ion

Answer 7

ammonia = NH3

ammonium ion = NH4+

Question 8

Distinguish between primary, secondary, and tertiary amines

Answer 8

primary = RNH2

secondary = R2NH

tertiary = R3N

Question 9

What is an alkyl ammonium ion and a quarternary ammonium ion?

Answer 9

alkyl ammonium ion = RNH3+

quarternary ammonium ion = R4N+

Question 10

Distinguish between imine and enamine

Answer 10

Question 11

Distinguish between a thiol and thiolate, sulfide and disulfide, and a thioester

Answer 11

thiol = SH functional group

thiolate lost the H+ from the SH and therefore is a S- functional group

Sulfide = aka thioether R-S-R

Disulfide = R-S-S-R

thioester = carbonyl with an S-R functional group

Question 12

What is phosphoric acid?

Answer 12

H3PO4

Question 13

What is inorganic phosphate

Answer 13

HPO₄^2-

also commonly written as P_i

Question 14

Phosphoric acid is a ____protic acid

Answer 14

tri

Question 15

What is a phosphoryl group vs a phosphate group?

Answer 15

phosphoryl group is the PO3 functional group attached to a molecule

a phosphate group includes the 4th O and is, therefore, the PO4 group attached to the molecule

Question 16

What is a phosphoanhydride and pyrophosphate?

Answer 16

Phosphoanhydride refers to 2 phosphoryl groups bonded to each other, in which is then bonded to an R group of some sort: RPO₄PO₃

Pyrophosphate (aka PP_i) are 2 phosphoryl groups bonded to each other: PO₄PO₃

Question 17

What are the covalent linkages called that bond each of the following monomers to make macromolecules:

1) amino acids bonded into proteins
2) nucleotides bonded into DNA/RNA
3) monosaccharides bonded into carbohydrates

Answer 17

1) AA are bonded into proteins via peptide linkages
2) nucleotides are bonded into DNA/RNA via phosphodiester bonds
3) monosaccharides are bonded into carbohydrates via glycosidic bonds

Question 18

The intermediary between the info stored in DNA and the info manifested in proteins is _____, synthesized using DNA as a template and acting as the tempalte for protein synthesis

Answer 18

mRNA

Question 19

The “native folding” of a protein depends on _______, which then determines the function of the protein

Answer 19

amino acid sequence

Question 20

Distinguish between nucleophiles and electrophiles

Answer 20

nucleophiles are nucleus-loving and, thus, are e- rich and seek to bond with molecules/atoms with a (partial) positive charge

electrophiles are electorn-loving (aka e- deficient) and, thus, are attracted to molecules/atoms with a negative charge or that are e- rich

Question 21

Distinguish between SN1 and SN2 rxns

Answer 21

SN1 generates a carbocation intermediate and, therefore, proceed in a 2-step mechanism. The LG leaves, creating a carbocation (which may be prone to carbocation rearrangement if it produces a more stable cation), and then the Nu attacks the carbocation

SN2 proceeds in a 1-step mechanism and, therefore, generates no intermediates. The Nu attacks the Electrophile at the same time the LG breaks its bond with the electrophile

Question 22

Distinguish between E1 and E2 rxns

Answer 22

E1 rxn creates a carbocation or carbanion intermediate

E2 does not create a carbocation intermediate and, therefore, is a concerted rxn

Both create a C=C, but most rxn mechanisms are prone to the E2 rxn mechanism instead of an E1 rxn mechanism. The dehydration and rehydration of molecules will be the most common elimination rxn seen in biochem

Question 23

alcohols and carbonyls will react together in a nucleophilic carbonyl addition rxn to generate a ____ or _____

Answer 23

hemiacetal or acetal

this type of rxn occurs frequently in carbohydrates; there is a tetrahedral intermediate with this rxn mechanism