BIOCHEMISTRY ASSIGNMENT  One-letter abbreviation: Y

19.4 Draw the zwitterion and give the three- 19.8 Give the name of the essential amino acid
and one-letter abbrevia- that has the following

tion for each of the following amino acids: abbreviation:

a. Trp b. Met c. F d. W

a. lysine The essential amino acids with the given

abbreviations are:
b. arginine
a. Trp:
c. methionine
 Amino Acid: Tryptophan
d. tyrosine
b. Met:
a. Lysine:
 Amino Acid: Methionine
 Zwitterion: NH3+
−CH2−CH2−CH2−CH2−NH−COO−NH3+ c. F:
−CH2−CH2−CH2−CH2−NH−COO−
 Amino Acid: Phenylalanine
 Three-letter abbreviation: Lys
d. W:
 One-letter abbreviation: K
 Amino Acid: Tryptophan
b. Arginine:
So, the names of the essential amino
 Zwitterion: NH3+ acids are: a. Tryptophan b. Methionine
−CH2−CH2−CH2−NH−C(NH2) c. Phenylalanine d. Tryptophan
(NH2)−COO−NH3+−CH2−CH2−CH2
19.10 Draw the Fischer projection for each of
−NH−C(NH2)(NH2)−COO−
the following essential
 Three-letter abbreviation: Arg
amino acids:
 One-letter abbreviation: R
a. l-threonine
c. Methionine:
 Zwitterion: NH3+
−CH2−S−CH3−COO−NH3+−CH2−S−CH3
−COO−
 Three-letter abbreviation: Met b. l-isoleucine

 One-letter abbreviation: M
d. Tyrosine:
 Zwitterion: NH3+
−CH2−C6H4OH−COO−NH3+−CH2−C6H4
OH−COO−
 Three-letter abbreviation: Tyr

19.12 Explain why each of the following pairs
are complementary
proteins:
a. beans and oats
Complementary Amino Acids: Beans are often
limited in the amino acid methionine but are
rich in lysine. Oats, on the other hand, are
relatively low in lysine but have a good amount
of methionine. When beans and oats are
consumed together, their amino acid profiles
complement each other, providing a more
balanced and complete set of essential amino
acids.
b. almonds and peanuts
Complementary Amino Acids: Almonds and
peanuts are both rich in protein but have
different amino acid profiles. Almonds are
relatively low in lysine but have a good amount
of methionine, while peanuts are higher in
lysine but lower in methionine. By combining
almonds and peanuts, you can create a more
balanced amino acid profile, making them
complementary proteins.
19.20 Draw the structure for each of the
following peptides, and give
the three-letter and one-letter abbreviations for
their names:
a. prolyl aspartate
Structure: Pro-Asp
Three-Letter Abbreviation: Pro-Asp
One-Letter Abbreviation: PD
b. threonyl leucine
Structure: Thr-Leu
Three-Letter Abbreviation: Thr-Leu
One-Letter Abbreviation: TL
c. methionyl glutaminyl lysine
Structure: Met-Gln-Lys
Three-Letter Abbreviation: Met-Gln-Lys
One-Letter Abbreviation: MQL
d. histidylglycylglutamylisoleucine
Structure: His-Gly-Glu-Ile
Three-Letter Abbreviation: His-Gly-Glu-Ile
One-Letter Abbreviation: HGIE
19.22 Refer to the structure of b-endorphin
1Chemistry Link to
Health: Polypeptides in the Body2 to answer
each of the
following:
a. What is the C-terminus of b-endorphin?
C-terminus of β-endorphin:
The C-terminus is the end of the polypeptide
chain where the carboxyl group (COO-) of the
last amino acid is located.
For beta-endorphin, the C-terminus would be
the carboxyl group at the end of the peptide
chain.
b. What is the N-terminus of b-endorphin?
b. N-terminus of β-endorphin:
The N-terminus is the end of the polypeptide
chain where the amino group (NH2) of the first
amino acid is located.
For beta-endorphin, the N-terminus would be
the amino group at the beginning of the peptide
chain.
 c. Write the amino acid order for b-
endorphin using single-letter
abbreviations.
c. Amino Acid Order for β-endorphin using
single-letter abbreviations:
The specific amino acid sequence of beta-
endorphin can vary, but it is a peptide derived
from the precursor proopiomelanocortin
(POMC). Beta-endorphin is around 31 amino
acids long. The amino acid sequence is typically
represented using single-letter abbreviations for
amino acids.
The amino acid sequence of beta-endorphin
includes amino acids such as Met, Lys, Phe, Tyr,
and others. The exact sequence may vary, and
it's recommended to refer to a specific and
updated source or research paper for the
precise sequence.
19.24 Peptides from sweet potato with
antioxidant properties have the
following sequence of amino acids. Draw the
structure for each
peptide and write the one-letter abbreviations.
a. Asp–Cys–Gly–Tyr
HOOC-Asp-Cys-Gly-Tyr-OH
 One-Letter Abbreviation: DCGY
b. Asn–Tyr–Asp–Glu–Tyr
H2N-Asn-Tyr-Asp-Glu-Tyr-OH
One-Letter Abbreviation: NYDEY
19.26 How can two proteins with exactly the
same number and type of amino acids have
different primary structures?
Here's how two proteins with identical amino
acid composition can have different primary
structures:
1. Sequence Variations:
 Even though two proteins may
have the same number and
type of amino acids, the specific
order or sequence in which
these amino acids are arranged
along the polypeptide chain can
differ.
2. Post-Translational Modifications:
 Post-translational modifications
(PTMs) can introduce variations
in primary structure. Certain
amino acids may undergo
modifications, such as
phosphorylation, glycosylation,
or acetylation, which can alter
the chemical properties of the
protein.
3. Alternative Splicing:
 In eukaryotic organisms, pre-
mRNA undergoes alternative
splicing to produce different
mRNA isoforms. This process
can result in different primary
structures of proteins derived
from the same gene.
4. Genetic Variability:
 Genetic variations, such as
single nucleotide
polymorphisms (SNPs) or
mutations, can lead to changes
in the amino acid sequence of a
protein. These changes, even if
subtle, can affect the primary
structure.
5. Protein Isoforms:
 Some genes encode for multiple
protein isoforms through
alternative splicing or
alternative initiation sites.
These isoforms may share the
same overall amino acid
 composition but have different
primary structures.
6. Proteolytic Cleavage:
 Proteins are often synthesized
as larger precursor molecules
that undergo proteolytic
cleavage to generate smaller
functional proteins. The
cleavage of peptide bonds
results in different primary
structures.
In summary, the primary structure of a protein
is defined by the unique sequence of amino
acids in its polypeptide chain. Even if two
proteins have the same number and type of
amino acids, differences in the specific order of
these amino acids, post-translational
modifications, alternative splicing, genetic
variations, or proteolytic cleavage can lead to
distinct primary structures and, consequently,
different functional properties.
19.30 In an a helix, how does bonding occur
between the amino acids in the polypeptide
chain?
1. Hydrogen Bond Formation:
 The backbone of the
polypeptide chain is involved in
hydrogen bonding.
 The hydrogen bond occurs
between the carbonyl oxygen of
one amino acid and the amide
hydrogen of an amino acid
three or four residues ahead in
the sequence.
2. Repeating Hydrogen-Bonding Pattern:
 The hydrogen bonding in the α-
helix follows a repeating
pattern, with each turn of the
helix involving interactions
between the carbonyl and
amide groups of adjacent amino
acids.
 The hydrogen bond distance is
relatively short, typically around
2.7 to 3.5 Å.
3. Stabilization of Helical Structure:
 Hydrogen bonding stabilizes the
helical structure by forming a
helical ladder-like pattern along
the length of the polypeptide
chain.
 The hydrogen bonds help
maintain the regular and
predictable structure of the α-
helix.
4. Direction of Hydrogen Bonds:
 The hydrogen bonds in the α-
helix run parallel to the helical
axis.
 The directionality of the
hydrogen bonds contributes to
the stability of the helical
structure.
5. Secondary Structure Formation:
 The α-helix is a type of
secondary structure,
representing a local and
repetitive folding pattern within
a protein.
 Hydrogen bonding is a
fundamental force that
contributes to the stability of
various secondary structures,
including the α-helix.
6. Amide Groups' Involvement:
 The amide groups in the
peptide bonds participate in
hydrogen bonding, forming a
helical structure stabilized by
these interactions.
The α-helix is an important structural element in
proteins, and the stability of the helical
conformation is influenced by factors such as
the amino acid sequence, the presence of helix-
promoting or helix-breaking residues, and the
surrounding environment. The specific
sequence of amino acids and their interactions
determine the overall folding and function of a
protein.
19.32 How is the structure of a b-pleated sheet
different from that of a triple helix?
Triple Helix:
The β-pleated sheet and triple helix are two
distinct secondary structures in proteins, each
characterized by different patterns of amino
acid interactions and overall shapes. Here's how
the structure of a β-pleated sheet differs from
that of a triple helix:
β-Pleated Sheet:
1. Arrangement of Polypeptide Chains:
 The β-pleated sheet involves
the side-by-side alignment of
two or more polypeptide
chains, known as β-strands.
 Adjacent β-strands run
antiparallel or parallel to each
other.
2. Interactions:
 The primary interaction in a β-
pleated sheet is the hydrogen
bonding between carbonyl and
amide groups in adjacent β-
strands.
 Hydrogen bonds form a regular
pattern, creating a sheet-like
structure.
3. Overall Shape:
 The β-pleated sheet has a
planar or sheet-like appearance.
 The side chains of amino acids
in each strand extend
alternately above and below
the plane of the sheet.
4. Antiparallel vs. Parallel:
 In an antiparallel β-sheet,
adjacent strands run in opposite
directions, enhancing stability.
 In a parallel β-sheet, adjacent
strands run in the same
direction.
1. Arrangement of Polypeptide Chains:
 The triple helix, also known as a
collagen helix, involves the
winding of three polypeptide
chains around each other.
 The three chains form a right-
handed helical structure.
2. Interactions:
 The stability of the triple helix is
primarily due to interchain
hydrogen bonding between
amino acid residues,
particularly glycine, proline, and
hydroxyproline.
 Collagen, a protein rich in triple
helices, has a unique amino acid
composition that contributes to
the helix stability.
3. Overall Shape:
 The triple helix has a rod-like or
cylindrical appearance.
 It is a continuous helical
structure with three
polypeptide chains closely
wound around a central axis.
4. Role in Collagen:
 The triple helix is a
characteristic feature of
collagen, the most abundant
 protein in the extracellular
matrix of connective tissues.
 Collagen provides tensile
strength to tissues like skin,
tendons, and bones.
In summary, the key differences lie in the
arrangement of polypeptide chains and the
overall shapes of the structures. The β-pleated
sheet involves the alignment of β-strands in a
planar or sheet-like fashion, while the triple
helix consists of three polypeptide chains
wound around each other in a cylindrical
manner, as observed in collagen.
19.34 Write the three-letter sequence for the
amino acid residues in somatostatin, a peptide
that inhibits the release of growth hormone, if
treatment with chymotrypsin and trypsin gives
the following fragments 1see Chemistry Link to
Health: Protein Sequencing2:
reagent
Chymotrypsin
Phe
1. Chymotrypsin Fragments:
 Chymotrypsin cleaves peptide
bonds at the C-terminal side of
large hydrophobic amino acids,
such as phenylalanine (Phe),
tryptophan (Trp), and tyrosine
(Tyr).
 The chymotrypsin fragments
provided are:
 Phe
 Trp
 Lys–Thr–Phe
 Thr–Ser–Cys
 Ala–Gly–Cys–Lys–Asn–
Phe
2. Trypsin Fragments:
 Trypsin cleaves peptide bonds
at the C-terminal side of lysine
(Lys) and arginine (Arg).
 The trypsin fragments provided
are:

Trp  Ala–Gly–Cys–Lys

Lys–Thr–Phe  Asn–Phe–Phe–Trp–Lys

Thr–Ser–Cys  Thr–Phe–Thr–Ser–Cys

Ala–Gly–Cys–Lys–Asn–Phe 3. Combine Information:

Fragments Produced  By combining the information

Trypsin
Ala–Gly–Cys–Lys
Asn–Phe–Phe–Trp–Lys
Thr–Phe–Thr–Ser–Cys
To deduce the three-letter sequence for
the amino acid residues in somatostatin based
on the given fragments produced by
chymotrypsin and trypsin, we can analyze the
information provided. Here are the steps and
the resulting three-letter sequence:
from both chymotrypsin and
trypsin fragments, we can
deduce the three-letter
sequence for somatostatin:
 Ala–Gly–Cys–Lys
 Asn–Phe–Phe–Trp–Lys
 Thr–Phe–Thr–Ser–Cys
4. Three-Letter Sequence:
 Combining the overlapping
sequences from the fragments,
 the three-letter sequence for
somatostatin is:
 AGCKNFFWLKTPFTSC
So, the deduced three-letter sequence for the
amino acid residues in somatostatin is
AGCKNFFWLKTPFTSC.
19.36 What type of interaction would you
expect between the following groups in a
tertiary structure?
a. phenylalanine and isoleucine b. aspartate and
histidine
c. asparagine and tyrosine d. alanine and proline
In a tertiary protein structure, various
types of interactions contribute to the folding
and stabilization of the three-dimensional
shape. Let's consider the potential interactions
between the given amino acid side chains:
a. Phenylalanine and Isoleucine:
 Interaction Type: Hydrophobic
Interactions
 Phenylalanine and isoleucine both have
hydrophobic side chains. In a
hydrophobic environment, these
residues tend to cluster together to
minimize exposure to water.
b. Aspartate and Histidine:
 Interaction Type: Ionic (or Salt Bridge)
Interaction
 Aspartate has a negatively charged side
chain, and histidine has a positively
charged side chain at neutral pH. Ionic
interactions occur between oppositely
charged amino acid side chains.
c. Asparagine and Tyrosine:
 Interaction Type: Hydrogen Bonding
 Both asparagine and tyrosine can
participate in hydrogen bonding. The
oxygen in the asparagine side chain can
act as a hydrogen bond acceptor, while
the hydroxyl group in the tyrosine side
chain can act as a hydrogen bond donor.
d. Alanine and Proline:
 Interaction Type: Various (e.g.,
Hydrophobic Interactions, Van der
Waals Interactions)
 Alanine and proline both have nonpolar
side chains. Their interactions may
involve hydrophobic interactions and
van der Waals forces, contributing to
the stabilization of the protein
structure.
It's important to note that the interactions in a
protein's tertiary structure are dynamic and can
involve a combination of different forces.
Hydrophobic interactions, hydrogen bonding,
ionic interactions, and van der Waals forces
collectively contribute to the folding and
stability of the protein in its three-dimensional
conformation.
19.40 Indicate whether each of the following
statements describes the primary, secondary,
tertiary, or quaternary protein structure:
a. Hydrophobic amino acid residues seeking a
nonpolar environment move toward the inside
of the folded protein. Tertiary Structure
b. Hydrophilic amino acid residues move to the
polar aqueous environment outside the protein.
Tertiary Structure
c. An active protein contains four tertiary
subunits. Quaternary Structure
d. In sickle cell anemia, valine replaces
glutamate in the b-chain. Primary Structure
Let's categorize each statement based
on the level of protein structure it describes:
a. Hydrophobic amino acid residues seeking a
nonpolar environment move toward the inside
of the folded protein.
 Description: This statement refers to
the interior packing of hydrophobic
amino acid residues, which is a
characteristic of the tertiary structure of
a protein.
 Level of Protein Structure: Tertiary
Structure
b. Hydrophilic amino acid residues move to the
polar aqueous environment outside the
protein.
 Description: This statement describes
the arrangement of hydrophilic amino
acid residues on the exterior of a folded
protein, interacting with the aqueous
environment.
 Level of Protein Structure: Tertiary
Structure
c. An active protein contains four tertiary
subunits.
 Description: This statement refers to
the presence of multiple tertiary
subunits, indicating a quaternary
structure. The term "tertiary subunits"
suggests that each subunit has its own
tertiary structure.
 Level of Protein Structure: Quaternary
Structure
d. In sickle cell anemia, valine replaces...
 Description: This statement begins a
description of a mutation at the level of
the primary structure where a specific
amino acid (valine) replaces another
(e.g., glutamic acid) in the hemoglobin
protein.
 Level of Protein Structure: Primary
Structure
19.42 Would the hydrolysis products of the
tripeptide Ala–Ser–Gly be the same or different
from the products in problem 19.41?
Explain.
19.44 What tripeptides could be produced from
the partial hydrolysis of Ser–Leu–Gly–Gly–Ala?
Tripeptides that could be produced
from the partial hydrolysis of Ser–Leu–Gly–Gly–
Ala would result from the cleavage of peptide
bonds within the original sequence. The
possible tripeptides are:
1. Ser–Leu–Gly:
 This tripeptide is formed by
cleaving the peptide bond
between Ser and Leu.
2. Leu–Gly–Gly:
 This tripeptide is formed by
cleaving the peptide bond
between Leu and Gly.
3. Gly–Gly–Ala:
 This tripeptide is formed by
cleaving the peptide bond
between Gly and Ala.
These tripeptides represent the different
combinations that can be obtained by breaking
the peptide bonds in the original Ser–Leu–Gly–
Gly–Ala sequence during partial hydrolysis. The
order of amino acids within each tripeptide
reflects the sequential arrangement in the
original peptide chain.
  Changes:
19.48 Indicate the changes in the secondary and  Secondary Structure: HgCl2
tertiary structural levels of proteins for each of treatment may not directly
the following: impact the secondary structure
of proteins.
a. Tannic acid is placed on a burn.
 Tertiary Structure: HgCl2 is a
b. Milk is heated to 60 °C to make yogurt. denaturing agent and can
c. To avoid spoilage, seeds are treated with a disrupt disulfide bonds, leading
solution of HgCl2 to a change in tertiary structure.

d. Hamburger is cooked at high temperatures to d. Hamburger is cooked at high temperatures

destroy E. coli bacteria that may cause intestinal to destroy E. coli bacteria that may cause
illness. intestinal illness.

Let's analyze the changes in the  Changes:

secondary and tertiary structural levels of  Secondary Structure: High-
proteins for each scenario: temperature cooking may cause
a. Tannic acid is placed on a burn. changes in the secondary
structure due to the
 Changes: denaturation of proteins.
 Secondary Structure: Tannic  Tertiary Structure: Cooking can
acid is not likely to have a direct lead to extensive denaturation,
impact on the secondary disrupting the tertiary structure
structure of proteins. of proteins.
 Tertiary Structure: Tannic acid In summary:
can denature proteins by
disrupting hydrogen bonds and  a. Tertiary Structure (some impact)
hydrophobic interactions,  b. Tertiary Structure (partial impact)
leading to a change in tertiary
structure.  c. Tertiary Structure
b. Milk is heated to 60 °C to make yogurt.  d. Secondary Structure, Tertiary
Structure (extensive impact)
 Changes:
 Secondary Structure: Mild
heating may not significantly
affect the secondary structure
of proteins in milk.
 Tertiary Structure: Moderate
heating can cause partial
denaturation, affecting the
tertiary structure of some
proteins.
c. To avoid spoilage, seeds are treated with a
solution of HgCl2.