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Chemistry 2223B- Final Exam Guide - Comprehensive Notes for the exam ( 25 pages long!)


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

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Western
Chemistry 2223B
Final EXAM
STUDY GUIDE

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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
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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
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