Question

Fundamentals of Biochemistry Tutorial: Peptides & Proteins

Answer 1

\({\bf{Amino~Acids:}}\)
- proteins are the most abundant macromolecules
- composed of 20 amino acids, covalently linked
- amino acid residue: the result amino acids are linked and water is lost via condensation
- central, chiral carbon (carbon-alpha) linked to an amino group, carboxyl group, H, and R-group, w/ the exception of glycine which isn't chiral because it has 2 hydrogens attached to the central carbon



\({\bf{Effects~on~Acid/Base~Chemistry:}}\)
- if the R-group is not ionizable --> dipolar zwitterion, ampholyte
- both the amino and carboxyl group can carry acidic protons
- the amino group and carboxyl group can both withdraw electrons, lowering pKa
- non-ionizable R group --> 2 distinct pKas on titration curve, ionizable --> 3 distinct
- isoelectronic point (pI): pH at which the electronic charge is neutral
when the charge is negative and above the pI, amino acid moves toward + electrode
farther away from pI --> greater net charge

Answer 2

a lot of biochem teachers ask you to memorize these structures so I would recommend just making 20 flashcards and reviewing them when possible

Answer 3

\({\bf{Peptides~and~Proteins:}}\)
- peptide bond: covalent link between two amino acids, formed by removing -OH from the carboxyl group and -H from the amino group (dehydration)
- this reaction is normally not thermodynamically favorable but the carboxyl group is modified (will specify how later) to make the removal of -OH more favorable. if you remember from orgo, hydroxyl is a very poor leaving group on its own.
- oligopeptide: a few peptides linked
- polypeptide: many peptides linked
- amino-terminal/N-terminal: end of the peptide w/ the free amino group
- carboxyl-terminal/C-terminal: end of the peptide w/ the free carboxyl group

Answer 4

\({\bf{Misc:}}\)
- as w/ individual amino acids, ionizable R-groups influence acid/base behavior
- can approximate the avg. # of amino acids by dividing MW/110.
- avg weight of amino acid is closer to 138 but smaller acids are more prevalent, so the avg. weight is a bit lower in reality.

Answer 5

Source material is section 3.1-3.2 of Principles of Biochemistry 7th edition by Nelson, David L., and Cox, Michael M.