Subject Code Chem 3 Reactions and Interactions of Organic and Inorganic

Compounds
Module Code 5.0
Lesson Code 5.3 Structure of Amino Acids and Levels of Protein Structure
Time Limit 30 mins.

AT
Components Tasks TAa
Ab
Target By the end of this LG, the students will have been able to:
0.5
• To describe the structure of naturally occurring amino acids in min
terms of their stereochemistry
• To explain how intermolecular forces and covalent bonding lead to
the different levels of protein structure.
Hook 1.5
min

(Aspartame)

The sweet taste of food is typically associated with sugars or carbohydrates.

However, did you know that aspartame, an artificial sweetener, is actually
a methyl ester of the dipeptide, aspartic acid phenylalanine Asp-Phe? What
is even more interesting is the role that stereoisomerism plays in the taste
of the compound. The natural L-configuration is exhibited by both amino
acids in aspartame but if the configuration of both amino acids is changed
into D-, the resulting compound will have a bitter taste. (Smith 2011)
Ignite 18
Amino Acids: The Building Blocks of Proteins min

The general structure of amino acids

(Figure 1) consists of a stereogenic
carbon to which the following four
different groups are connected: an
unsubstituted amine, a carboxylic
acid, a hydrogen, and a characteristic
side chain (R).
Figure 1. The general structure
of an amino acid. The unsubstituted amine -NH2 and the
carboxylic acid -COOH give the
amino acid its basic and acidic properties, respectively. The side chain R
Chem 3 LG 5.2 Structure of Amino Acids and Levels of Protein Structure | Page 1 of 9
 differentiates one amino acid from another and lead to the following
classification of amino acids:

Acidic Amino Acids – These amino acids have an additional

carboxylic acid group in their R side chain.

Basic Amino Acids – These amino acids have an additional amine

group in their R side chain.

Neutral Amino Acids – These amino acids have neither additional

carboxylic acids nor additional amine groups in their R side chain.

The configuration of the stereogenic α- carbon in amino acids is expressed

though the D- and L- notations, similarly with monosaccharides.
Naturally occurring amino acids (Figure 2) exhibit the L- configuration
and are referred to as L- amino acids. (Smith 2017).

SOMETHING TO PONDER-UPON*
A. Classify the naturally occurring amino acids shown in Figure 2 into
either acidic, basic, or neutral.

B. Which amino acids have two (2) stereogenic centers?

C. Which amino acid does not have a stereogenic center?

* Answers to these non-graded assessments are found in the last pages of the module.

Figure 2. Twenty naturally occurring amino acids with their 3-letter and
single letter abbreviations. The amino acids with an asterisk after
their names are essential amino acids.
Amino acids, in their dry solid states, exist as zwitterions (dipolar ions)
(Solomons 2011). In their zwitterion form, the carboxyl group of the

Chem 3 LG 5.2 Structure of Amino Acids and Levels of Protein Structure | Page 2 of 9
 amino acid is negatively charged and takes on the carboxylate -COO- form
(Figure 3). The amino group, on the other hand, is positively charged and
takes on the ammonium form -NH3+ (Figure 3).

Figure 3. The various ionic forms of amino acids at equilibrium in

aqueous solutions. (Solomons 2011)

In aqueous solution, an equilibrium exists between the zwitterion and the

cationic and anionic forms of the amino acid (Figure 3) (Solomons 2011).
However, the maximum concentration of the zwitterion may be achieved
though pH adjustment. The pH environment at which the maximum
concentration of the zwitterion occurs is referred to as the isoelectric
point pI. (Smith 2017, Solomons 2011)

Levels of Protein Structure

SOMETHING TO PONDER-UPON*
D. How well do we know the following terms? Match the term in
column I with its corresponding definition in column II. Please
accomplish this non-graded exercise before you attend the synchronous
class.
I II
amino acid residue • • a linkage of more than 40 amino acids

dipeptide • • a linkage of more than 3 amino acids

peptide bond • • a linkage of 3 amino acids

polypeptide • • a linkage of 2 amino acids

the amide bond in peptides and
protein • •
proteins
the individual amino acids making up
tripeptide • •
a peptide

Chem 3 LG 5.2 Structure of Amino Acids and Levels of Protein Structure | Page 3 of 9
 The functionality of proteins is strongly dependent on its structure. Amidst
the recent pandemic, a strong interest in protein structure emerges in pursuit
of effective treatments and preventive measures for the corona virus
COVID- 19. One of the ways by which even non-experts can contribute to
this cause is through the gaming platform, FoldIt. https://fold.it/

SUPPLEMENTARY: Follow the link below to a brief video

introduction on FoldIt Games in relation to anti-viral proteins against
COVID-19.
https://youtu.be/gGvlNo3nMfw
There are four (4) levels of protein structure. These are: primary, secondary,
tertiary, and quaternary. The primary structure of proteins pertains to the
specific sequence of amino acids joined together by peptide bonds. It is
worth noting that regardless of the number of amino acid residues present,
there is only one N-terminal amino acid (amino terminus) and one C-
terminal amino acid (carboxy terminus) (Figure 4).

Figure 4. Features of the primary structure of proteins.

The most important feature of the primary structure is the peptide bond –
an amide bond linking the amino acid residues. The stability of the peptide
bond derives from the resonance stabilization of the amide functional group.
(Solomons 2011). The carbonyl carbon of the peptide bond is sp2 hybridized
causing the N-H and C=O bonds of each peptide bond to be oriented at 180o
relative to each other. In addition, rotation about the amide bonds is
restricted but not with the other sigma bonds in the protein backbone (Smith
2017).

The secondary structure of proteins arises due to the hydrogen-bonding

interaction between the N-H of a peptide and the C=O oxygen of another
(Figure 5). These interactions lead to three-dimensional conformations of
localized regions in the protein.

Chem 3 LG 5.2 Structure of Amino Acids and Levels of Protein Structure | Page 4 of 9
 Figure 5. Hydrogen bonding interactions between amino acids in a peptide

Among a variety of possible three-dimensional conformations, the α-helix

and the β-pleated sheet arrangement (Figure 6) is particularly stable. The
defining characteristics of these arrangements are summarized in Table 1.

(n.d.) [Image] (n.d.) retrieved May 28, 2021

http://book.bionumbers.org/wp-content/uploads/2014/08/310-f1-
AlphaBeta-1.png
Figure 6. Ball-and-stick models and ribbon diagram representations of α-
helices and the β-pleated sheets.

Chem 3 LG 5.2 Structure of Amino Acids and Levels of Protein Structure | Page 5 of 9
 Table 1. A comparison of the defining characteristics of α-helices and β-
pleated sheets.
Criteria α-Helix β-Pleated Sheet
No. of Amino Acids per 3.6 amino acids N/A
Turn
Orientations of the N-H Both point along the axis Both lie in the plane of
and the C=O bonds of the helix the sheet
Distance of a pair of Definite: The C=O Not definite: hydrogen
amino acids interacting group of one amino acid bonding occurs between
through a hydrogen is hydrogen bonded to the N-H and the C=O
bond the N-H group four groups of nearby amino
amino acids farther acids
along the chain.
Orientation of the R- R- sidechains extend R- sidechains extend
sidechains outward either above or below
the plane

SOMETHING TO PONDER-UPON*
E. What properties of spider dragline silk are derived from its α-helical
regions and regions of β-pleated sheets?
The tertiary structure of proteins pertains to the three-dimensional shape
adopted by the entire peptide chain. In general, the three-dimensional shape
or conformation which the peptide chain takes maximizes its stability
(Smith 2011). In the aqueous environment of the cytoplasm or blood
plasma, the most stable conformation of proteins is achieved through the
following (Smith 2017):

✓ A larger number of polar and charged groups project outward to the

aqueous environment to promote dipole-dipole and hydrogen-
bonding interactions with water.

✓ Polar functional groups also hydrogen bond with each other and
charged -COO- and -NH3+ groups interact through electrostatic
forces.

✓ Most non-polar groups project within the conformation to

maximize Van der Waals interactions between functional groups.

✓ The covalent disulfide bond which forms among cysteine residues

also helps stabilize the tertiary structure.

The quaternary structure of proteins is the shape adopted when two or

more folded polypeptide chains aggregate into one protein complex. Each
polypeptide chain comprising the quaternary structure is referred to as a
subunit. The highest level of structure of hemoglobin in our red blood cells
is quaternary and is composed of four subunits - all of which are necessary
to the protein’s function (Solomons 2011, Smith 2017).

Chem 3 LG 5.2 Structure of Amino Acids and Levels of Protein Structure | Page 6 of 9
 Jaddeo (n.d.) [Image] retrieved May 29, 2021 https://png2.cleanpng.com
Figure 7. Ribbon diagram representation of hemoglobin.
Navigate Let’s see how we’re doing so far… 8
For both Levels 1 & 2 min
NON-GRADED FORMATIVE ASSESSMENT

NG1. Draw the 3-dimensional representation (wedge-and dash) for both

the L- and D- isomers of alanine and label them accordingly.

NG2. In your own words, differentiate among the four levels of structure
of protein in terms of: (a) the type(s) of interaction(s) which give
rise to the structure, and (b) the number of peptides comprising the
structure.

GRADED FORMATIVE ASSESSMENT

ALTERNATE RESPONSE. Write “TRUE” if the statement is correct.

Otherwise, supply the correct replacement for the underlined word or
phrase.

5.3.1 Asparagine is a basic amino acid.

5.3.2 Tyrosine is an acidic amino acid.
5.3.3 Glycine, whether naturally occurring or synthetic, is achiral.
5.3.4 There are only two possible conformations (α-helix and β-
pleated sheet) for the secondary structures of proteins.
5.3.5 The tertiary structure of proteins is stabilized through both
intermolecular forces of attraction and covalent bonds.
5.3.6 Reversing the sequence of amino acids in a peptide results into
the same peptide.

Chem 3 LG 5.2 Structure of Amino Acids and Levels of Protein Structure | Page 7 of 9
 Knot There are four levels of structure of protein. The primary structure describes 2
how amino acid residues link together to form the amino acid sequence. The min
secondary structure describes three dimensional conformations in various
regions of the protein which arise from hydrogen bonding between the N-
H of one residue and the C=O of another. The tertiary structure describes
the overall structure of the peptide, with all secondary structures in
consideration. Finally, he quaternary structure describes the position and
orientation of all protein subunits in a protein complex.

Robbie Petrus Justen. The four levels of protein structure. [Image] X-Ray
structure re-refinement. Combining old data with new methods for better
structural bioinformatics - Scientific Figure on ResearchGate. Retrieved on
May 29, 2021. https://www.researchgate.net/figure/The-four-levels-of-
protein-structure-The-primary-structure-describes-how-amino-
acid_fig1_238609063
a
suggested time allocation set by the teacher
b
actual time spent by the student (for information purposes only)

Answer Key:

IGNITE (Something to Ponder Upon)

A.
Acidic Basic Neutral
aspartic acid, arginine, (all other amino
glutamic acid histidine, lysine acids in the table)

B. Isoleucine and Threonine

C. Glycine. Its R sidechain is a hydrogen.
D.

Chem 3 LG 5.2 Structure of Amino Acids and Levels of Protein Structure | Page 8 of 9
 E. Alpha-helical regions impart elasticity to the silk while regions of β-pleated sheets impart
strength.

NAVIGATE (Formative)

Non-Graded Formative Assessment

NG1.

J. David Van Horn. Molecular Structure of L- and D- Alanine [Photo] Positron Annihilation Lifetime Analysis of Left- and Right-Handed Alanine Single
Crystals - Scientific Figure on ResearchGate. Retrieved May 29, 2021. https://www.researchgate.net/figure/Molecular-structures-of-L-and-D-
alanine_fig1_321652957

NG2. Key words:

Level of Structure Types of Interactions No. of Peptides Involved

Primary covalent bonds (peptide One
bond)
Secondary Intermolecular forces (h- One
bonding)
Tertiary Intermolecular forces and One
covalent bonds (cysteine
linkages)
Quaternary Intermolecular forces More than one

References:

Smith, J.G. (2011).Organic chemistry. (3rd ed.). McGraw Hill Education

Smith, J.G. (2017).Organic chemistry. (5th ed.). McGraw Hill Education

Solomons, T.W.G., Fryhle, C.B., Snyder, S.A. (2011).Organic chemistry.

(10th ed).John Wiley& Sons, Inc.

Prepared by: Fiona Paredes Reviewed by: Melba C. Patacsil

Position: Special Science Teacher (SST) II Position: Special Science Teacher (SST) V
Campus: PSHS-CAR Campus: PSHS-CAR

Chem 3 LG 5.2 Structure of Amino Acids and Levels of Protein Structure | Page 9 of 9
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