Study Guides (390,000)
CA (150,000)
Western (10,000)
CHEM (200)
Midterm

Chemistry 2223B Study Guide - Midterm Guide: Nucleophilic Acyl Substitution, Nucleophilic Substitution, Fischer Projection


Department
Chemistry
Course Code
CHEM 2223B
Professor
Len Luyt
Study Guide
Midterm

This preview shows pages 1-3. to view the full 10 pages of the document.
ORGO
TOPIC 3.1: AMINO ACIDS, PEPTIDES, AND PROTEINS PART I
STRUCTURE AND PROPERTIES OF AMINO ACIDS
Terminology
- Amino acids: monomer subunit
- Peptide: 2-50 amino acids
- Protein: >50 amino acids
Amino Acids
- Building block monomers of proteins and peptides
o We can hydrolyze these polymers to break them down in to monomer subunits this
requires high concentrations of acids and high temperatures
o Hydrolysis results in the protonation of both the carboxylic acid and amine functional
groups of the molecule
- Most are -amino acids; amino group is attached to carbon that is to the carboxylic acid
- All are primary amines with the exception of proline (cyclic secondary amine)
- All have a carbon side-chain (R) with the exception of glycine (R = H)
Resonance of the amide bond in proteins
- The amide bond of polypeptides does NOT behave like an amide because it has resonance
structure
o The actual bond is an intermediate between the two resonance contributing structure
Hydrolysis of acid derivatives (i.e. amides, esters, anhydrides)
Acid-Catalyzed Hydrolysis (Nucleophilic acyl substitution)
- Water acts as the nucleophile
1. Acid protonates carboxyl group
2. Water attacks the a-carbon and takes on the positive charge
3. Nitrogen is protonated by removing a hydrogen from the water group good leaving group
is formed
4. Leaving group leaves, one of the hydroxyl groups is deprotonated by H2O or amino group to
reform the carboxylic acid catalyst is regenerated
5. Nitrogen leaving group is protonated to form NH3+ - R
o In acidic conditions, the amine will become positively charged while the carboxyl is
neutral
find more resources at oneclass.com
find more resources at oneclass.com

Only pages 1-3 are available for preview. Some parts have been intentionally blurred.

Base-Catalyzed Hydrolysis (Nucleophilic acyl substitution)
- OH- acts as the nucleophile
1. OH- attacks carboxyl carbon, C=O bond is lost
2. Amino group is protonated by water, good leaving group is formed
3. C=O bond is reformed, ejecting the leaving group
4. Hydroxyl group is deprotonated by base to form water
a. In basic conditions, the carboxyl will become negatively charged while the amine is
neutral
Stereochemistry
- Each amino acid except glycine has a chiral center
- D vs L configuration for amino acids is dependent on the position of the amino group in a
Fischer Projection
- Naturally occurring amino-acids are L-amino acids
o L or D?: Draw the Fischer Projection of the amino acid with the carboxyl group at the
top and the carbon chain running vertically If the amino group of the amino acid is
on the LEFT side, then it is an L amino acid
- D-amino acids are much less common
NOTE: In MOST cases, L-amino acid = S configuration, EXCEPT for cysteine (side chain = -CH2SH),
which is R.
- Usually priority for amino acids is (1 = amino group, 2 = carboxyl group, 3 = side chain, 4 =
H)
- For cysteine, the priority of the side chain is higher than the carboxyl group, this is why it is
R
BE ABLE TO SWITCH FROM FISCHER TO 3D MODEL
THE 20 AMINO ACIDS
- Side chain determine the main chemical properties of the amino acids
- We group amino acids based on the nature of their side chains
Non-polar Amino Acids
- Amino acids with hydrophobic side-chains
- Usually found in abundance proteins that span the cell-membrane
- Usually found on the interior surface of globular proteins (minimizes exposure to water)
Tryptophan is non-polar despite the nitrogen in the side-chain because it is part of an aromatic system
and thus is very stable
find more resources at oneclass.com
find more resources at oneclass.com

Only pages 1-3 are available for preview. Some parts have been intentionally blurred.

Polar Amino Acids
- Amide and hydroxyl groups at the end of side chains create polarity
- Tyrosine is sometimes also classified as non-polar due to relatively hydrophobic ring
Acidic Amino Acids
- Side chain is deprotonated in neutral pH
Basic Amino Acids
- Side chain is protonated in neutral pH
ACID-BASE PROPERTIES OF AMINO ACIDS
The ionization of a weak acid is represented by the following formula:
A B CB CA
If we let Ka = Keq[H2O], the we get the Ka for a weak acid at equilibrium, from which we can derive the
Henderson-Hasselbalch equation
Henderson-Hasselbalch equation
- Allows us to predict the CB to acid ratio of a weak acid at any pH
When pH = pKa of weak acid
pH = pKa + log([A-]/[HA])
0 = log([A-]/[HA])
1 = [A-]/[HA]
Therefore when pKa = pH, we will have a 50/50 ratio of CB to A because [A-] = [HA]
Acid-Base Properties of Amino Acid Functional Groups
- When we exclude the side-chains, acidic conditions result in the full protonation of both the
carboxyl and ammonium groups
pKa for NH3+ = 9 10 (depends on the amino acid)
- It is important to note that this pKa is for the NH3+ group and NOT the pKa for the NH2 group
(~35)
R-NH3+ + H2O <-> R-NH2 + H3O+ NOT R-NH2 + H2O <-> R-NH- + H3O+
pKa for COOH ~ 2
- On its own, a carboxyl group usually has a pKa = 5, BUT the ammonia acts as an EWG which
causes inductive effects, and as a result the COOH in amino acids is more acidic than usual
R-CO2H + H2O <-> R-CO2- + H3O+
E.g. 1
What is the deprotonated:protonated ratio of the carboxyl group in amino acids at a pH of 7.4
7.4 = 2 + log(R-CO2-/R-CO2H)
5.4 = log(R-CO2-/R-CO2H)
R-CO2-/R-CO2H = 250000/1
Therefore at a pH pf 7.4, we have 100% deprotonation of the carboxyl group.
find more resources at oneclass.com
find more resources at oneclass.com
You're Reading a Preview

Unlock to view full version