BIOLOGY 285 Study Guide - Quiz Guide: Arginine, Hydrophobic Effect, Ice Pack
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Published on 16 Nov 2020
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Peptide Bonds
Question 1 Draw two amino acids sitting side by side unbonded, then draw them with a peptide
bond connecting them. What type of reaction is this? What is a product of the reaction?
Two amino acids connect through a dehydration reaction resulting in a peptide bond between
them and a water molecule.
Amino Acid Chemistry
Question 2 A. Consider the structure of Tyrosine. Draw it. Is it considered a polar or non-polar
amino acid? Why is its classification a bit ambiguous (it is sometimes classified as non-polar)?
(hint: discuss the chemistry of the R group)
B. Draw another amino acid. Label its functional groups. Say something about the chemistry of
its R group (categorization, types of interactions it would make in different levels of structure,
etc).
This is a structure of Alanine, a non-polar (hydrophobic)
amino acid. The R group will not do much in primary
structures since only the backbone is connected by peptide
bonds. Because it is hydrophobic and has no hydrogen
donor/acceptor atoms in the side chain, Alanine will
probably fold its R group facing in the protein to avoid
interactions with water. In tertiary and quaternary structures,
Alanine side chains are frequently engaged in van der Waals
interactions and sometimes paired cysteines allow for
disulfide bonds.
Tyrosine is a polar amino acid
because the R-group contains an
-OH group that allows it to
participate in hydrogen bondings.
Its classification is a bit ambiguous
because the R-group has both polar
and non-polar characteristics.
Secondary Structure
Question 3 A. Remembering that the amino acid chains projecting from each polypeptide
backbone in a beta sheet point alternately above and below the plan of the sheet, consider the
following protein sequence: Leu-Lys-Val-Asp-Ile-Ser-Leu-Arg-Leu-LysIle-Arg-Phe-Glu. Do
you find anything remarkable about the arrangement of the amino acids in this sequence when
incorporated into a beta sheet? Can you make any predictions as to how this Beta sheet might be
arranged in a protein?
By taking a closer look at the side chain chemistry of each amino acid above, I can see
that they alternate in non-polar and polar amino acids. In this case, the beta sheet will have a
polar side and a hydrophobic side. I predict that this sequence will bond, either side, with similar
strands resulting in a beta sheet with a hydrophobic side and a polar side. In a protein, the beta
sheet will be positioned where the hydrophobic side is facing the protein’s interior and the polar
side on the surface, exposed to water.
B. Although alpha helices are common components of polypeptide chains, they need to be of a
certain minimum length. To find out how chain length affects alpha helix formation, you
measure the circular dichroism (a measure of helicity) for a series of peptides of increasing
lengths. Why is there essentially no helix formation until the chain is at least six amino acids
long?
Alpha helices form hydrogen bonds every 4 residues. So, the carbonyl oxygen of the first
amino acid bonds with the amino nitrogen of the fifth residue. Anything less than 5 residues will
not form a helix. However, the singular hydrogen bond between the first and fifth backbone
alone is not enough to stabilize to the structure of the helix and for it to be detected. Any chain
greater than six amino acids long will only increase its stability and the chances of it to be
detected.
Protein Folding
Question 4 A. What are the two termini of a polypeptide chain? What functional groups are on
either end?
The N-terminus has an amine-group (-NH2) at the end and the C-terminus has a
carboxyl-group (-COOH) at the end.