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03AAMO Mamalapat
03AAMO Mamalapat
2. Classify the twenty (20) common amino acids according to their polarity and acid-
base properties (What makes the 20 common amino acids 'common'? Be sure to be
able to visualize the three-dimensional picture of the amino acids. In addition to the
four classic classifications, be sure to know which ones are large, small, aromatic)
The 20 common amino acids share a fundamental structure consisting of an amino
group, a carboxyl group, a central carbon, and a unique side chain (R group). Their
prevalence arises from their role as protein building blocks, contributing diverse properties
based on their distinct side chains.
Serine (Ser, S) /
Threonine (Thr, T) /
Tyrosine (Tyr, Y) /
Asparagine (Asn, /
N)
Polar
Cysteine (Cys, C) /
Glutamine (Gln, /
Q)
Tryptophan (Trp, / /
W)
Phenylalanine(Ph / /
e, F)
Leucine (Leu, L) /
Isoleucine (Ile, I) /
Non-polar Methionine (Met, /
M)
Proline (Pro, P) /
Glycine (Gly, G) /
Valine (Val, V) /
Alanine (Ala, A) /
Lysine (Lys, K) /
Histidine (His, H) /
Basic
Arginine (Arg, R) /
Aspartic Acid /
(Asp, D)
Acidic
Glutamic Acid /
(Glu, E)
3. Point out some of the uncommon amino acids (What makes them uncommon?
What's the relationship between the common and the uncommon amino acids?)
Uncommon amino acids, such as selenocysteine and pyrrolysine, deviate from the
standard set of 20 amino acids found in proteins. These rare amino acids possess unique
structural components that set them apart. Selenocysteine, replacing cysteine's sulfur
atom with selenium, imparts distinct redox properties and plays a role in certain enzymes'
catalytic functions. Pyrrolysine features an extended side chain containing a pyrroline ring,
critical for specific enzymatic reactions in certain organisms.
The relationship between common and uncommon amino acids lies in their shared
biochemical context. While common amino acids form the building blocks of most proteins,
uncommon amino acids expand the repertoire of protein functions. They offer specialized
roles that common amino acids cannot fulfill, contributing to the intricacies of biological
processes. This diversity enhances the functional capabilities of proteins, underscoring
the harmonious collaboration between common and uncommon amino acids in supporting
various cellular activities and promoting evolutionary adaptability.
4. Emphasize the importance of the properties of the side-chains of the amino acids
(Be able to point out the most likely intermolecular force of attraction that each
individual amino acid would participate in)
The R-group, also known as the side-chain, is important because it establishes the
properties and identification of a certain amino acid. Additionally, it affects how efficiently
the protein binds with other amino acids and how the protein is structured. The polarity of
an amino acid is also determined by its side-chains. Hydrocarbon side chain groups tend
to be non-polar; as a result, the intermolecular force of attraction that is present is Van Der
Waals. Polar groups typically have hydrogen and covalent bondings because of partial
charges, while acidic and basic groups typically have ionic bondings and donate or accept
electrons..
5. Illustrate the acidic and the basic properties of amino acids (Be able to write the
acid-base reactions of individual amino acids. Account for the charges of the amino
acids as a function of the pH. What is the significance when the pH of the solution
is less than, equal to, or greater than the pKa of that amino acid?
Amino acids possess both acidic and basic characteristics due to their ionizable
functional groups. In solution, the carboxyl group can lose a proton to become negatively
charged (COO⁻), while the amino group can accept a proton to become positively charged
(NH₃⁺). This results in a zwitterionic form at neutral pH, where both groups are charged,
but the overall charge is neutral. The pH of the solution relative to the pKa of an amino
acid's functional groups dictates its charge state.
When the pH is lower than an amino acid's pKa, the environment is acidic. At this
point, the amino acid's carboxyl group is protonated (COOH) and the amino group is also
protonated (NH₃⁺), leading to a net positive charge. In contrast, when the pH is higher
than the pKa, the environment is basic. Here, the carboxyl group is deprotonated (COO⁻),
and the amino group is neutral (NH₂), resulting in a net negative charge.
7. Illustrate how polypeptides are formed and named (Be able to draw oligopeptides
of a specified sequence from N-terminal to C-terminal)