Alexi Julia Go

BSN 1
BIOCHEM MODULE 3 – PROTEINS

Lesson 1 – ENHANCEMENT ACTIVITY/OUTCOME

1. What is the general name for the building block (monomers) from which a protein
(polymer) is made?
- The monomers that make up proteins are called amino acids.
2. What element is always present in proteins that is seldom present in carbohydrates and
lipids?
- The element that is always present in proteins and is not present in carbohydrates and
lipids is nitrogen.
3. What percent of a cell’s overall mass is accounted for by proteins?
- Proteins account for approximately 20% of a cell’s overall mass.

Lesson 2 – ENHANCEMENT ACTIVITY/OUTCOME

1. Which of the following structures represent α-amino acid
a. α-amino acid
b. not
c. not
d. α-amino acid
2. What is the major structural difference among the various standard amino acids?
- There are 20 standard amino acids. They are classified as either nonpolar amino acids or
polar amino acids. There are 9 nonpolar amino acids that have nonpolar side chains and
are hydrrophobic. The 11 polar amino acids are hydrophyllic and are classified into 3
types: polar neutral amino acids, polar acidic amino acids, and polar basic amino acids.

There are 6 polar neutral amino acids, these are amino acids that are polar but neutral.
There are 2 polar acidic amino acids. These amino acids contain a second carboxyl group
in their side chain. And lastly, there are 3 polar basic amino acids. These amino acids
have a second amino chain group on their side chain.
3. With the help of Table 2.1, determine which of the standard amino acids have a side
chain with the following characteristics.
a. Contains an aromatic group: Phenylanine, Tyrosine, Tryptophan, Histidine
b. Contains the element sulfur: Methionine, Cysteine
c. Contains a carboxyl group: Aspartic acid, glutamic acid
d. Contains a hydroxyl group: Serine, Threonine
4. What is the distinguishing characteristic of a polar basic amino acid? Polar acidic amino
acid?
- You can distinguish these polar amino acids based on their side chains. Polar acidic
amino acids contain a carboxylic acid group in the side chain. Polar basic amino acids
contain an amine group in the side chain.
5. In what way is the structure of the amino acid proline different from that of the other 19
standard amino acids?
 - Proline is unique among the standard amino acids in that it does not have both free α-
amino and free α-carboxyl groups. Instead, its side chain forms a cyclic structure as the
nitrogen atom of proline is linked to two carbon atoms.
6. What amino acids do these abbreviations stand for?
a. Ala – Alamine
b. Leu – Leucine
c. Met – Methionine
d. Trp – Tryptophan
7. Which four standard amino acids have three-letter abbreviations that are not the first
three letters of their common names?
a. Isoleucine (Ile)
b. Tryptophan (Trp)
c. Asparagine (Asn)
d. Glutamine (Gln)
8. Classify each of the followingn amino acids as nonpolar, polar neutral, polar acidic or
polar basic.
a. Asn – Polar neutral amino acid
b. Glu – Polar acidic amino acid
c. Pro – Nonpolar amino acid
d. Ser – Polar neutral amino acid

Lesson 3 – ENHANCEMENT ACTIVITY/OUTCOME

1. To which family of mirror-image isomers fo nearly all naturally occurring amino acids
belong?
- Nearly all naturally occurring amino acids belong to the family of enantiomers.
2. Draw fischer projection formulas for the following amino acids.
Lesson 4 – ENHANCEMENT ACTIVITY/OUTCOME
1. At room temperature, amino acids are solids with relatively high decomposition points.
Explain why.
- Due to its existence in the form of zwitter ion, there exists a very strong intermolecular
attaction which is responsible for high melting point of amino acid and its solidity at
room temperature.
2. Draw the zwitterion structure for each of the following amino acids.

3. Draw the structure of serine at each of the following pH values.

4. Explain what is meant by the term isoelectric point.

- The isoelectric point of an amino acid is the point at which the amino acid has no net
electrical charge. It is an important characteristic for any amino acid, because every
amino acid has at least two acid–base (titratable) groups. At the isoelectric point, an
amino acid does not dissolve in water. This property helps in the separation of different
amino acids formed by the hydrolysis of proteins.
5. Glutamic acid exists in two low-pH forms instead of the usual one. Explain why.
- Glutamic acid is a polar acidic amino acid. This amino acid has two carboxylic (-COOH)
groups and one amino group. One carboxylic (-COOH) group is positioned at alpha
carbon atom and another carboxylic (-COOH) group is positioned at side chain.
6. Predict the direction of movement of each of the following amino acids in a solution at
the pH value specified under the influence of an electric field. Indicate the direction as
toward the positive electrode or toward the negative electrode. Write “isoelectric” if no
net movement occurs.
a. Towards the negative electrode
b. Towards the positive electrode
c. Towards the positive electrode
d. Towards the negative electrode
7. A direct current was passed through a solution containing valine, histidine and aspartic
acid at a pH of 6.0. one amino acid migrated to the positive electrode, one migrated to the
negative electrode, and one did not migrate to either electrode. Which amino acids went
where?
 - The aspartic acid migrated to the positive electrode. Histidine migrated to the negative
electrode and lastly, valine did not migrate to either electrode.

Lesson 5 – ENHANCEMENT ACTIVITY/OUTCOME

1. When two cysteine molecules dimerize, what happens to the R group present?
- Cysteine is unique among coded amino acids because it contains a reactive sulph-hydryl
group. Therefore, two cysteine residues may form a cystine (disulfide link) between
various parts of the same protein or between two separate polypeptide chains.
2. What chemical reaction involving the cysteine molecule produces a disulfide bond?
- The chemical reaction that involves the production of disulfide bond with cysteine
molecules is called a cysteine oxidation.

Lesson 6 – ENHANCEMENT ACTIVITY/OUTCOME

1. What two functional groups are involved in the formation of a peptide bond?
- Peptide bonds form between the carboxyl group of one amino acid and the amino group
of another through dehydration synthesis.
2. Write out the full structure of the tripeptide Val-Phe-Cys.

3. Explain why the notations Ser-Cys and Cys-Ser represent two different molecules rather
than the same molecule.
- The primary structure of a protein is decided by sequences of amino acids. Notations Ser-
Cys and Cys-Ser represent two different molecules because they differ in biological
activiity. The order of amino acids in peptides matter because it determines the function
of the protein.
4. There are a total of six different amino acid sequences for a tripeptide containing one
molecule each of serine, valine and glycine. Using the three-letter abbreviations for the
amino acids, draw the six posisble sequences of aminoo acids.

5. Identify the amino acids containd in each of the following tripeptides..

a. Serine, Alanine, Cysteine
b. Aspartic acid, Threonine, Asparagine
6. How many peptide bonds are present in each of themolecules in problem 5?
a. Three peptide bonds
b. Three peptide bonds
 7. With the help of table 2.1, assign an IUPAC name to each of the following small
peptides.
a. Ser-Cys: Serylcysteine
b. Gly-Ala-Val: Glycylalanylvaline
c. Tyr-Asp-Gln: Tyrosylaspartylglutamine
d. Leu-Lys-Trp-Met: Leucyllysyltryptophylmethionine
8. What are the two repeating units present in the “backbone” of a peptide?
- The peptide backbone consists of repeating units of N-H 2, CH, C double bond O; N-H 2,
CH, C double bond O.

Lesson 7 – ENHANCEMENT ACTIVITY/OUTCOME

1. Contrast the structure of the hormones oxytocin and vasopressin in terms of
a. What they have in common:
- Oxytocin and vasopressin are related pituitary non-apeptides; they consist of nine amino
acids in a cyclic structure.
b. How they differ:
- These molecules differ by only two amino acids, at position 3 and 8 (isoleucine and
leucine in oxytocin are replaced by phenylanine and arginine in vasopressin,
respectively). They also vary in function. For oxytocin, these functions include uterine
smooth muscle contraction during parturition, ejaculation, milk ejection from the
mammary glands and complex social behaviour, while for vasopressin they include
regulation of peripheral fluid balance and blood pressure, as well as central implications
in memory, learning and stress-related disorders.
2. Contrast the binding-site locations in the brain for enkephalins and the prescription
painkillers morphine and codeine.
- Enkephalins are released at synapses on neurons involved in transmitting pain signals to
the brain and act as an intrinsic pain-suppressing system, hyperpolarizing the post-
synaptic membrane and thus inhibiting pain signals. Opioids or painkillers attach to
proteins called opioid receptors on nerve cells in the brain, spinal cord, gut, and other
parts of the body. When this happens, the opioids block pain messages sent from the
body through the spinal cord to the brain.
3. What is the unusual structural feature present in the molecule gluthathione?
- The unusual feature is that the Glutamic acid is joined in a peptide bond at the side chain
carboxyl rather than the alpha-carboxyl.

Lesson 8 – ENHANCEMENT ACTIVITY/OUTCOME

1. What is the major difference between a monomeric protein and a multimeric protein?
- Based on the amount of peptide chains present, a protein can be classified as either
monomeric or multimeric. A monomeric protein is a protein in which only one peptide
chain is present. A multimeric protein, on the other hand, is a protein. Which more than
one peptide chain is present. Large proteins, those with many amino acid residues are
usually multimeric.
2. Indicate whether each of the following statements about proteins is true or false
a. True
b. False
c. False
 d. True

Lesson 9 – ENHANCEMENT ACTIVITY/OUTCOME

 Primary Protein Structure

1. What is meant by the primary structure of a protein?
- The primary structure of a protein is the order in which amino acids are linked together in
a protein.
2. What type of bond is responsible for the primary structure of a protein?
- Primary structure consists of amino acids joined by peptide bonds.
 Secondary Protein Structure
1. What are the two common types of secondary protein structures?
- The two main types of secondary structure are the α-helix and the ß-sheet.
2. The ß pleated sheet secondary structure can be formed through either intramolecular
hydrogen bonding or intermolecular hydrogen bonding. Explain why.
- In a β pleated sheet, two or more segments of a polypeptide chain line up next to each
other, forming a sheet-like structure held together by hydrogen bonds. The hydrogen
bonds form between carbonyl and amino groups of backbone, while the R groups extend
above and below the plane of the sheet cubed. The strands of a β pleated sheet may be
parallel, pointing in the same direction (meaning that their N- and C-termini match up),
or antiparallel, pointing in opposite directions (meaning that the N-terminus of one strand
is positioned next to the C-terminus of the other).
3. Can more than one type of secondary structure be present in the same protein molecule?
Explain your answer.
- Known as alpha helices and beta sheets, these stable folding patterns make up the
secondary structure of a protein. Most proteins contain multiple helices and sheets, in
addition to other less common patterns.
4. What is the function of the “unstructured” secondary structure of a protein?
- Some sections of a protein assume no regular, discernible structure and are sometimes
said to lack secondary structure, though they may have hydrogen bonds. Such segments
are described as being in random coils and may have fluidity to their structure that results
in them having multiple stable forms.

 Tertiary Protein Structure

1. State the four types of attractive forces that give rise to tertiary protein structure.
- The tertiary structure of proteins is determined by a variety of attractive forces, including
hydrophobic interactions, ionic bonding, hydrogen bonding, and disulfide linkages.
2. Give the type of amino acid R group that is involved in each of the following interactions
that contribute to tertiary protein structure.
a. Hydrophobic interaction – Nonpolar R group
b. Hydrogen bond – Polar R groups
c. Disulfide bond - -SH groups
d. Electrostatic interaction – acidic R group and basic R group
3. Identify the type of noncovalent interaction that occurs between the side chains of the
following amino acids and show the interaction using structural representations for the
side chains.
 a. Threonine and asparagine
 The type of noncovalent interaction that occurs between threonine and asparagine
is Hydrogen bonding
b. Aspartic acid and arganine
 The type of noncovalent interaction that occurs between aspartic acid and
arganine is electrostatic interaction.

 Quaternary Protein Structure

1. What is meant by the quaternary structure of a protein?
- A quaternary protein structure is rhe organization among the various peptide chains in a
multimeric protein.
2. Compare the types of noncovalent interactions that contribute to tertiary protein structure
with those that contribute to quaternary protein structure.

Lesson 10 – ENHANCEMENT ACTIVITY/OUTCOME

 Protein classification based on shape
1. Contrast fibrous and globular proteins in terms of
a. Solubility charateristics in water
- Fibrous proteins are insoluble in water while globular proteins are soluble in water.
b. General biochemical function
- Fibrous proteins are structural – which means these proteins helps to maintain cell shape
by providing a scaffolding. Globular proteins, on the other hand, arefunctional – this
means globular proteins carry out a specific biological function in the body

2. Classify each of the following proteins as a globular protein or a fibrous protein.

a. a-Keratin – fibrous protein
b. Collagen – fibrous protein
c. Hemoglobin – globular protein
d. Myoglobin – globular protein

3. Contrast the structures of the proteins a-Keratin and collagen

- Collagen is a protein that is made up of three polypeptide chains forming a helical
structure. Keratin is a protein that exists as an alpha chain or beta sheet linked to various
residues.

 Protein classification based on function

Characterize each of the following proteins in terms of its function classification.
a. Actin – contractile proteins
b. Myoglobin – storage proteins
c. Transferrin -
d. Insulin

 Glycoproteins
1. What two nonstandard amino acids are present in collagen?
- The two non-standard amino acids present in collagen are 4-hydroxyproline and 5-
hydroxylysine, derivatives of the standard amino acids proline and lysine.
 2. What is the function of the carbohydrate groups present in collagen?
- It is most well-known for the structural role it plays in the body. It is present in large
quantities in connective tissue and provides tendons and ligaments with tensile strength
and skin with elasticity. It often works in conjuction with other important proteins such as
keratin and elastin.
3. What is the difference between an antigen and an antibody?
- An antigen is any substance or organism that is unrecognized by our immune system. It
could be anything from bacteria to chemicals, to viruses or even foods. Antigens typically
trigger an immune response. ON the other hand, antibodies are proteins that bind with the
antigen in order to neutralize the latter – or make other elements of the immune system
“aware” of their presence. To summarize – an antigen is a disease agent (virus, toxin,
bacterium parasite, fungus, chemical, etc) that the body needs to remove, and an antibody
is a protein that binds to the antigen to allow our immune system to identify and deal with
it.
4. Describe the structural features of a typical immunoglobulin molecule.
- Each immunoglobulin molecule is made up of two heavy chains and two light chains
joined by disulfide bonds so that each heavy chain is linked to a light chain and the two
heavy chains are linked together.

 Lipoproteins
1. Describe the general overall structure of a plasma lipoprotein.
- Lipoproteins are complex particles that have a central hydrophobic core of non-polar
lipids, primarily cholesteryl esters and triglycerides. This hydrophobic core is surrounded
by a hydrophilic membrane consisting of phospholipids, free cholesterol, and
apolipoproteins.
2. What are the four major classes of plasma lipoproteins?
- There are four major classes of circulating lipoproteins, each with its own characteristic
protein and lipid composition. They are chylomicrons, very low-density lipoproteins
(VLDL), low-density lipoproteins (LDL), and high-density lipoproteins (HDL).
3. What factor determines the density of a plasma lipoprotein?
- Lipoprotein density is dependent on the concentration of triglycerides in the particle.
4. What is the biochemical function of the following?
a. Chylomicrons - Chylomicrons transport lipids absorbed from the intestine to
adipose, cardiac, and skeletal muscle tissue, where their triglyceride
components are hydrolyzed by the activity of the lipoprotein lipase, allowing
the released free fatty acids to be absorbed by the tissues.
b. Low-density lipoproteins - LDL delivers fat molecules to cells. LDL is
involved in atherosclerosis, a process in which it is oxidized within the walls
of arteries.

Lesson 11 – ENHANCEMENT ACTIVITY/OUTCOME

1. Will hydrolysis of the dipeptides Ala-Val and Val-Ala yield the same products? Explain
your answer.
2. Drugs that are proteins such as insulin, must always be injected rather than taken by
mouth. Explain why.
 - Injections remain as the most common means for administering therapeutic proteins and
peptides because of their poor oral bioavailability. oral delivery is restricted due to its low
bioavailability. The main reasons are drug degradation by stomach acids and proteases in
the digestive system and a drug's inability to cross intestinal membrane barriers.

3. Identify the primary structure of a hexapeptide containing six different amino acids if the
following smaller peptides are among the partial hydrolysis products: Ala-Gly, His-Val-
Arg, Ala-Gly-Met and Gly-Met-His.
- Ala2-Gly3-His2-Val-Arg-Met2

4. How many different di- and tripeptides could be present in a solution of partially
hydrolyzed Ala-Gly-Ser-Tyr?

Lesson 12 – ENHANCEMENT ACTIVITY/OUTCOME

1. Which structural levels of a protein are affected by denaturation?

- Denaturation of proteins involves the disruption and possible destruction of both the
secondary and tertiary structures. Since denaturation reactions are not strong enough to
break the peptide bonds, the primary structure (sequence of amino acids) remains the
same after a denaturation process.
2. In what way is the protein in a cooked egg the same as that in raw egg?
- In both states, they have the same amount of protein present in them.