MCAT BIOCHEMISTRY REVIEW

CH. 1: AMINO ACIDS

Sickle cell disease
 6th AA changed from Q  V

1.1 Amino Acids in Proteins


 alpha carbon ADJACENT to carboxylic acid carbon
 alpha carbon connected to:
o NH2 – amino
o COOH – carboxylic acid
o H
o R group: determines properties
 Alpha carbon CHIRAL except glycine
o (S) absolute configuration except cysteine (R)

Nonpolar, Aromatic, Polar, Negative Positive

nonaromatic uncharged nonaromatic (acidic) (basic)
-G -F: plain -S: OH -E: anion is -K: terminal
-A -W: double ring -T: OH glutamate primary
-V system, N -N: CONH2 amide -D: anion is amino grp
-L -Y: OH (relatively -Q: CONH2 amide aspartate -R:+
-I polar) -C: -SH thiol grp delocalized
-M: contains prone to on 3 Ns
Sulfur oxidation -H: aromatic,
-P: forms cyclic imidazole
AA, less flexible,
affects secondary
structure

 Hydrophobic – AA w/ long side chains: A, I, L, V, P

 Hydrophilic – AA w/ charges: K, R, H, D, E, Q+N (amides, CONH2)
MCAT BIOCHEMISTRY REVIEW

1.2 Acid-Base Chemistry of AA

 AA are amphoteric species – can accept/donate proton depending on pH of

environment
o GAIN protons in ACIDIC conditions
o LOSE protons in BASIC conditions
 pKa = pH at which [HA] = [A-]
o pH<pKa (acidic), more [HA]
o pH>pKa (basic), more [A-]
 AAs have 2 pKa values bc of 2 groups that can be deprotonated
o AA w/ ionizable sidechain has 3 pKa values
o Acidic conditions: NH3+, COOH (net +)
o Intermediate conditions: NH3+, COOH (net neutral, zwitterion)
o Basic conditions: NH2, COO- (net -)
 Titrations
o When pH=pKa, solution acts as a buffer (flat part of curve)
o Zwitterion when pH=pI (vertical line)
 Calculating pI (avg of 2 nearest pKa values)
 Neutral AA: (pKa amino grp + pKa carbox grp)/2, ~6
 Acidic AA: (pka R grp + pKa carbox grp)/2, <6
 Basic AA: (pka amino grp + pKa R grp)/2, >6

1.3 Peptide Bond Formation + Hydrolysis

 NC (spelling of my name)*
 C(O)—NH peptide bond (amide)
 Condensation/dehydration rxn (removal of H20)
 Exhibit resonance, C-N has partial double bond character, pi bond causes rotation to be
restricted


 synthesized by ribosomes
 Hydrolysis
o Performed by trypsin and chymotrypsin
o Chymotrypsin cleaves @ COOH end of P, W, Y (chymo rhymes w/ aro)
MCAT BIOCHEMISTRY REVIEW

o Trypsin cleaves @ COOH end of R, K

o Mechanism: add OH to COOH and H to NH

1.4 Primary + Secondary Protein Structure

 Primary – linear sequence of AA coded in DNA, NC
o Stabilized by covalent peptide bonds
 Secondary – INTRAMOLECULAR H BONDS
o Alpha helices – rod-like structure where peptide chain coils clockwise around a
central axis; H bonds b/w carbonyl O and amide H 4 residues down
 Important in keratin- fibrous, structural protein in skin, hair, fingernails


o Beta-pleated sheets – parallel vs antiparallel; pleated shape
 Peptide chains forms rows held together by H bonding b/w carbonyl O
and amide H in adjacent chain
 Fibroin- primary protein of silk fibers


o Proline introduces kink in b-pleated sheets, found in turns b/w chains of b-
pleated sheet, found @ start of a-helix
 Not typically found in middle of these

1.5 Tertiary + Quaternary Protein Structure

 Fibrous – sheets, long strands (ex. Collagen)
 Globular – spherical (ex. Myoglobin)
o Shape a result of protein folding
MCAT BIOCHEMISTRY REVIEW

 Tertiary – 3D shape determined by..

o 1. hydrophilic/hydrophobic interactions b/w R groups
o 2. H bonding
o 3. Acid-base interactions b/w charged R groups, creating salt bridges
 disulfide bonds – oxidation of 2 cysteine molecules
 create loops in protein chain and determine how wavy hair is
 denaturation - loss of tertiary structure + function
 molten globules - intermediate states in protein folding
 protein folding typically takes <1 sec
 hydrophobic R group does not allow solvation layer (H bonding) to form
o rearrange to inside maximize H bonding
o decrease entropy, nonspontaneous process
o hydrophilic R group opposite effect
 Quaternary – not all proteins have this structure, interaction of peptides b/w multiple
subunits
o Represents functional form; ex: hemoglobin, IgG antibodies
o 1. Stabilizing function by reducing surface area
o 2. Reduce amt DNA needed – crucial for viruses
o 3. Bring catalytic sites together
o 4. Induce cooperativity*
 Conjugated proteins
o Covalently attached prosthetic group determine function
 Ex: prosthetic grp of hemoglobin and myoglobin is heme – contains iron
atom in core and binds oxygen

1.6 Denaturation
 Denaturation- protein loses 3D structure, often irreversible, caused by heat and solutes
o Caused by 1. Heat – increased motion
o 2. Solutes - urea – break disulfide bridges, overcome H bonding

CH. 2: ENZYMES
 Enzymes- biological catalysts
 catalysts- only lower ACTIVATION ENERGY required for rxn to proceed
o pH and temp sensitive
o specific to rxn