Mamalapat, Mohamidin K.

Chem 2065 AY2023-24

Amino Acids and Peptides

1. Correlate the three-dimensional structure of amino acids to its interactions to its

chiral environment ( Be sure to be able to visualize the three-dimensional picture
of the amino acids. Recall the Fischer projection structure from your organic
chemistry.
The three-dimensional structure of amino acids, such as in the Fischer
projection, defines their chiral nature. Chirality influences how amino acids interact with
their surroundings; enzymes recognize specific enantiomers due to their complementary
shapes. Amino acids' R groups dictate their properties: polar R groups engage in
hydrogen bonds, nonpolar one’s cluster in hydrophobic areas, and charged ones partake
in ionic interactions. Such interactions, determined by the amino acids' three-
dimensional arrangement, shape protein folding, stability, and function, elucidating the
profound connection between amino acid structure, chirality, and molecular interactions
in biological systems.

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.

Classificatio Amino 3-D Large Mediu Small Aromati

n Acid Picture m c
 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) /

Methionine (Met, /
M)

Proline (Pro, P) /

Glycine (Gly, G) /

Non-polar 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.

Understanding these shifts in charge is essential in various biological processes.

Amino acids' charge states influence protein folding, enzymatic reactions, and
interactions with other molecules. At physiological pH, amino acids' zwitterionic forms
 dominate, allowing them to contribute to protein structure and function without excessive
repulsion or attraction between charges. The pH-pKa relationship is pivotal in shaping
the behavior of amino acids, providing insights into their roles in maintaining cellular
homeostasis and facilitating biochemical reactions.

6. Describe the nature of the peptide bond as it is formed from amino acids
A peptide bond is created when the carboxyl group (COOH) of one amino acid
bonds covalently with the amino group (NH2) of another amino acid. Thus, an amide (C-
N) bond is formed. During the reaction (the dehydration process), water is lost. The two
atoms share a single pair of electrons. Resonance structure makes it possible for the
peptide bonds (C-N) and (C=N) to hybridize and have a partial double bond character.
The peptide group that connects the two amino acids as a result is planar. This
resonance stabilization makes the peptide connection stronger than a typical single
bond.

7. Illustrate how polypeptides are formed and named (Be able to draw oligopeptides
of a specified sequence from N-terminal to C-terminal)

8. Cite properties (structure-function relationship) of amino acids aside from being

peptides or proteins (neurotransmitters and others)
Amino acids, beyond their role as protein building blocks, exhibit diverse
structural and functional properties. For instance, glutamate functions as a
neurotransmitter, facilitating excitatory neuronal signaling due to its ability to activate ion
channels. GABA, derived from glutamate, acts as an inhibitory neurotransmitter,
 dampening neuronal activity by opening ion channels. Glycine also serves as an
inhibitory neurotransmitter in the spinal cord, promoting muscle relaxation. Taurine, a
sulfur-containing amino acid, aids osmoregulation in cells and supports cardiovascular
function. These examples showcase the varied roles amino acids play beyond protein
synthesis, highlighting their distinct properties in cellular communication and
physiological regulation.

9. Showcase the structure-function relationship of some small peptides with

physiological activity (hormones and others)
Small peptides with physiological activity exemplify the structure-function
relationship in biochemistry. For instance, insulin, a peptide hormone, regulates glucose
metabolism. Its specific arrangement of amino acids enables receptor binding, triggering
cellular glucose uptake. Oxytocin, a peptide neurotransmitter, governs social bonding
and reproductive processes. Its unique structure ensures receptor affinity, fostering
emotional and physiological responses. Moreover, endorphins, short peptides, act as
natural pain relievers. Their specific sequences engage opioid receptors, modulating
pain perception. These examples highlight how the three-dimensional arrangement of
amino acids in small peptides dictates their specific functions, exemplifying the intimate
link between molecular structure and physiological impact.
References:

Biochemistry by Campbell and Farrell (QD415 .C36 2018)