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
You've reached the end of your free preview.
Want to read all 25 pages?
- Fall '20