Kaplan MCAT Biochemistry Review.docx - Kaplan MCAT...

Kaplan MCAT Biochemistry Review
CHAPTER ONE: AMINO ACIDS, PEPTIDES, AND PROTEINS
1.1 Amino Acids Found in Proteins
One-letter Three-letter Amino acid Side chain polarity Side chain charge Side chain aromaticity
A Ala Alanine Nonpolar — —
C Cys Cysteine Polar — —
D Asp Aspartic acid Polar Negatively charged —
E Glu Glutamic acid Polar Negatively charged —
F Phe Phenylalanine Nonpolar — Aromatic
G Gly Glycine Nonpolar — —
H His Histidine Polar Positively charged Aromatic (imidazole ring)
I Ile Isoleucine Nonpolar — —
K Lys Lysine Polar Positively charged —
L Leu Leucine Nonpolar — —
M Met Methionine Nonpolar — —
N Asn Asparagine Polar — —
P Pro Proline Nonpolar — —
Q Gln Glutamine Polar — —
R Arg Arginine Polar Positively charged —
S Ser Serine Polar — —
T Thr Threonine Polar — —
V Val Valine Nonpolar — —
W Trp Tryptophan Nonpolar — Aromatic
Y Tyr Tyrosine Polar — Aromatic
 Amino acids are found in their L, or S, form (exception : Cys).
 –ate: denotes deprotonated (anion) form of an –ic acid
 Glycine is the smallest and only achiral amino acid.
 Methionine and cysteine are the only amino acids with sulfur in their side chains.
1.2 Acid-Base Chemistry of Amino Acids
 At low pH, ionizable groups are protonated . At high pH, ionizable groups are deprotonated .
o Under acidic conditions, more H + is available to protonate these groups.
 pK
a
: pH at which half of the molecules in a species are protonated
o pH < pK
a
: protonation
o pH > pK
a
: deprotonation
o pH = pK
a
: buffer region
 Amino acids with ionizable side chains have 3 pK
a
values.
o pK
a
of carboxyl terminus ≈ 2
o pK
a
of amino terminus ≈ 9–10
o pK
a
of ionizable side chain: variable
 Zwitterion : dipolar ion; molecule with both a positive and negative charge
o At physiological pH, the carboxyl end is deprotonated, and the amino end is protonated.
 Isoelectric point (pI) : average of two pK
a
values at which net charge is 0; point at which pH = pK
a
o Acidic ( negative ) and neutral amino acids have low pI.
o Basic ( positive ) amino acids have high pI.

1.3 Peptide Bond Formation and Hydrolysis
 Peptide bond : bond between carboxyl and amino groups in amino acids
o Peptide bond formation is condensation or dehydration reaction (loss of H
2
O)
o Can resonate → limited backbone rotation → increased rigidity
 Amino acids that enzymes cleave will be provided if needed. We do not need to memorize them.
o These enzymes always cleave after the carboxyl end.
1.4 Primary and Secondary Protein Structure
 1° structure : amino acid arrangement (analogous to letters)
o Stabilized by peptide bonds
 2° structure : folded structure based on amino acid backbone interactions (analogous to words)
o Stabilized by hydrogen bonds
o α-helix : rodlike; forms keratin
o β-sheet : parallel or antiparallel
o Proline forms kinks in the middle of α-helices and β-sheets, so it is found in the turns
between chains of β-sheets and at the beginning of α-helices.
1.5 Tertiary and Quaternary Protein Structure
 3° structure : 3D structure of polypeptide chain (analogous to sentences)
o Stabilized by van der Waals forces , hydrogen bonds , ionic bonds