MC 2: BIOCHEMISTRY

1st Semester, AY: 2021-2022

RESOURCE UNIT
FACULTY-IN-CHARGE :
COURSE CODE AND TITLE : MC-2 Biochemistry
PROGRAM / YEAR / SCHEDULE : BSN - 1st YEAR

WEEK 9: NOVEMBER 8 - 12
I. LEARNING OUTCOMES
a. Describe structure of proteins and its existence.
b. Analyze and explain the protein denaturation.
c. Present a case study on Protein deficient in children and adults.
d. Test the color reactions of proteins.

II. TOPIC/S
Topic: Proteins
● Definition/ Importance/ Properties/ Denaturation
● Color Reaction
● Structure
● Classification
APCAS Core Value: Integrity
Integration: Discussion of the Topic

III. ACTIVITIES

PART 1: REAL-TIME CLASS SESSION via GOOGLE MEET

P - Pre-Test (10 min.) (should not be posted in g-classroom)

Describe the structure of proteins and its importance.

L - Lesson Presentation ( 80 mins)

Proteins

A - Activity- Seatwork (20mins) -must be posted in google classroom

Explain the following:
1. Structure of Proteins
2. Protein denaturation
3. How to Test the Color reactions of proteins.
4. Importance of Proteins

W - Weekly Assignment (10mins)

Scope of Pre-test: Nucleic acids
Rubrics: Relevance 5 pts.
Content 5 pts.
Explanation 5 pts.
Timeliness 5 pts.

(Lab) (Protein) Egg yolk (hot water, milk, vinegar, calamansi juice, clorox)

PART 2: SELF-DIRECTED LEARNING via GOOGLE CLASSROOM (60mins)

L - Lecture Reading
PROTEINS

➔ Proteins are large, complex molecules that play many critical roles in the body. They do most of
the work in cells and are required for the structure, function, and regulation of the body’s
tissues and organs.

Protein Structure

➔ Proteins are made up of hundreds or thousands of smaller units called amino acids, which are
attached to one another in long chains. There are 20 different types of amino acids that can be
combined to make a protein.
➔ The sequence of amino acids determines each protein’s unique 3-dimensional structure and its
specific function. Amino acids are coded by combinations of three DNA building blocks
(nucleotides), determined by the sequence of genes.
➔ Within a protein, multiple amino acids are linked together by peptide bonds, thereby forming a
long chain. Peptide bonds are formed by a biochemical reaction that extracts a water molecule
as it joins the amino group of one amino acid to the carboxyl group of a neighboring amino acid.

LEVELS OF PROTEIN STRUCTURE

Primary Structure - The simplest level of protein structure, primary structure, is simply the sequence of
amino acids in a polypeptide chain.

Secondary Structure - Hydrogen bonding between amino groups and carboxyl groups in neighboring
regions of the protein chain sometimes causes certain patterns of folding to occur. Known as alpha
helices and beta sheets, these stable folding patterns make up the secondary structure of a protein.

Tertiary Structure - The ensemble of formations and folds in a single linear chain of amino acids —
sometimes called a polypeptide — constitutes the tertiary structure of a protein. The tertiary structure
is primarily due to interactions between the R groups of the amino acids that make up the protein.

Quaternary Structure - Many proteins are made up of a single polypeptide chain and have only three
levels of structure (the ones we’ve just discussed). However, some proteins are made up of multiple
polypeptide chains, also known as subunits. When these subunits come together, they give the protein
its quaternary structure.

The final shape adopted by a newly synthesized protein is typically the most energetically favorable one.
As proteins fold, they test a variety of conformations before reaching their final form, which is unique
and compact. Folded proteins are stabilized by thousands of noncovalent bonds between amino acids.
In addition, chemical forces between a protein and its immediate environment contribute to protein
shape and stability. For example, the proteins that are dissolved in the cell cytoplasm have hydrophilic
(water-loving) chemical groups on their surfaces, whereas their hydrophobic (water-averse) elements
tend to be tucked inside. In contrast, the proteins that are inserted into the cell membranes display
some hydrophobic chemical groups on their surface, specifically in those regions where the protein
surface is exposed to membrane lipids. It is important to note, however, that fully folded proteins are
not frozen into shape. Rather, the atoms within these proteins remain capable of making small
movements.

Even though proteins are considered macromolecules, they are too small to visualize, even with a
microscope. So, scientists must use indirect methods to figure out what they look like and how they are
folded. The most common method used to study protein structures is X-ray crystallography. With this
method, solid crystals of purified protein are placed in an X-ray beam, and the pattern of deflected X
rays is used to predict the positions of the thousands of atoms within the protein crystal.

Importance of Proteins
- Protein is required for the growth and maintenance of tissues. Your body’s protein needs are
dependent upon your health and activity level.
- Enzymes are proteins that allow key chemical reactions to take place within your body.
- Amino acid chains of various lengths form protein and peptides, which make up several of your
body’s hormones and transmit information between your cells, tissues and organs.
- A class of proteins known as fibrous proteins provide various parts of your body with
structure, strength and elasticity.
- Proteins act as a buffer system, helping your body maintain proper pH values of the blood and
other bodily fluids.
- Proteins in your blood maintain the fluid balance between your blood and the surrounding
tissues.
- Proteins form antibodies to protect your body from foreign invaders, such as disease-causing
bacteria and viruses.
- Some proteins transport nutrients throughout your entire body, while others store them.
- Protein can serve as a valuable energy source but only in situations of fasting, exhaustive
exercise or inadequate calorie intake.

Physical Properties of Proteins

1. Colour and Taste

Proteins are colourless and usually tasteless. These are homogeneous and crystalline.
2. Shape and Size
The proteins range in shape from simple crystalloid spherical structures to long fibrillar
structures. Two distinct patterns of shape
have been recognized :
A. Globular proteins- These are spherical in shape and occur mainly in plants, esp., in
seeds and in leaf cells. These are bundles formed by folding and crumpling of protein
chains. e.g., pepsin, edestin, insulin, ribonuclease etc.
B. Fibrillar proteins- These are thread-like or ellipsoidal in shape and occur generally in
animal muscles. Most of the studies regarding protein structure have been conducted
using these proteins. e.g., fibrinogen, myosin etc.
3. Colloidal Nature
Because of their giant size, the proteins exhibit many colloidal properties, such as; Their
diffusion rates are extremely slow and they may produce considerable light-scattering in
solution, thus resulting in visible turbidity (Tyndall effect).
4. Denaturation
Denaturation refers to the changes in the properties of a protein. In other words, it is the
loss of biological activity. In many instances the process of denaturation is followed by
coagulation— a process where denatured protein molecules tend to form large
aggregates and to precipitate from solution.
5. Amphoteric Nature
Like amino acids, the proteins are amphoteric, i.e., they act as acids and alkalies both.
These migrate in an electric field and the direction of migration depends upon the net
charge possessed by the molecule. The net charge is influenced by the pH value. Each
protein has a fixed value of isoelectric point (pl) at which it will move in an electric field.
6. Ion Binding Capacity
 The proteins can form salts with both cations and anions based on their net charge.
7. Solubility
The solubility of proteins is influenced by pH. Solubility is lowest at isoelectric point and
increases with increasing acidity or alkalinity. This is because when the protein molecules
exist as either cations or anions, repulsive forces between ions are high, since all the
molecules possess excess charges of the same sign. Thus, they will be more soluble than
in the isoelectric state.
8. Optical Activity
All protein solutions rotate the plane of polarized light to the left, i.e., these are
levorotatory.

Chemical Properties of Proteins

1. Hydrolysis
Proteins are hydrolyzed by a variety of hydrolytic agents.
A. By acidic agents: Proteins, upon hydrolysis with conc. HCl (6–12N) at 100–110°C for 6
to 20 hrs, yield amino acids in the form of their hydrochlorides.
B. By alkaline agents: Proteins may also be hydrolyzed with 2N NaOH.
2. Reactions involving COOH Group
A. Reaction with alkalies (Salt formation)
B. Reaction with alcohols (Esterification)
C. Reaction with amines
3. Reactions involving NH2 Group
A. Reaction with mineral acids (Salt formation): When either free amino acids or proteins
are treated with mineral acids like HCl, the acid salts are formed.
B. Reaction with formaldehyde: With formaldehyde, the hydroxy-methyl derivatives are
formed.
C. Reaction with benzaldehyde: Schiff ‘s bases are formed
D. Reaction with nitrous acid (Van Slyke reaction): The amino acids react with HNO2 to
liberate N2 gas and to produce the corresponding α-hydroxy acids.
E. Reaction with acylating agents (Acylation)
F. Reaction with FDNB or Sanger’s reagent
G. Reaction with dansyl chloride
4. Reactions involving both COOH AND NH2 Group
A. Reaction with triketohydrindene hydrate (Ninhydrin reaction)
B. Reaction with phenyl isocyanate: With phenyl isocyanate, hydantoic acid is formed
which in turn can be converted to hydantoin.
C. Reaction with phenyl isothiocyanate or Edman reagent
D. Reaction with phosgene: With phosgene, N-carboxyanhydride is formed
E. Reaction with carbon disulfide: With carbon disulfide, 2-thio-5-thiazolidinone is
produced
5. Reactions involving R Group or Side Chain
A. Biuret test
B. Xanthoproteic test
C. Millon’s test
D. Folin’s test
E. Sakaguchi test
F. Pauly test
G. Ehrlich test
 6. Reactions involving SH Group
A. Nitroprusside test: Red colour develops with sodium nitroprusside in dilute NH4OH.
The test is specific for cysteine.
B. Sullivan test: Cysteine develops red colour in the presence of sodium 1, 2-
naphthoquinone- 4-sulfonate and sodium hydrosulfite.

Protein denaturation is the net effect of alterations in the biological, chemical, and physical properties of

the protein by mild disruption of its structure. When blood samples are taken for protein analysis, it is

important that they are handled correctly so that no artifacts are introduced that could affect the

investigation and its interpretation. If the protein is allowed to even partially degrade, the assay will not

be accurate. Therefore, it is essential that denaturation is avoided. The ability of plasma proteins to

resist denaturation in a blood sample taken for diagnostic analysis varies between proteins;

consequently, the sample should be handled according to the analysis required. Fortunately, most major

plasma proteins are relatively resistant to denaturation and can be assayed in samples that have been

handled carefully and have been kept away from elevated temperatures. However, separation of plasma

or serum from the blood cells by centrifugation should be performed as early as possible. Thereafter,

many proteins are stable at 4°C for several days and at –20°C for much longer (months to years). Some

proteins are less stable, with enzymes being particularly susceptible to loss of activity with time, while

the stability of the peptide hormone ACTH is so low that samples should be snap-frozen immediately to

preserve the intact peptide.

Color Reactions of Protein

a) Xanthoproteic reaction

➔ The addition of concentrated nitric acid to protein solutions generally causes the formation of a

white precipitate which turns yellow upon heating, the colour becoming orange when the

solution is made alkaline. Insoluble proteins are turned yellow and orange on the surface. The

xanthoproteic reaction is due to nitration of the phenyl rings present in tyrosine, phenylalanine,

and tryptophan to give yellow nitro substitution products, which become orange-coloured upon
 the addition of alkali. Most proteins give the xanthoproteic reaction.

b) Biuret Reaction

➔ When protein solutions are made strongly alkaline with sodium or potassium hydroxide and

when very dilute copper sulphate is added, a purplish to pinkish violet is obtained, the colour

depending upon the complexity of protein. Proteins give a purplish violet colour while proteoses

and peptones give a pink colour. Peptides give a very light pink colour and gelatin gives a blue

colour. This biuret reaction is used as a test for the presence of proteins in biological materials.

It is also used as an excellent method for the quantitative estimation of proteins.

CLASSIFICATIONS OF PROTEIN
Classification based on structural shape:
1. Fibrous protein (Scleroprotein)
➔ We can find these proteins in animals and are insoluble in water. Fibrous proteins are
resistant to proteolytic enzymes and are coiled and exist in threadlike structures to form
fibres. e.g. collagen, actin, and myosin, keratin in hair, claws, feathers, etc.
2. Globular proteins
➔ These proteins, unlike fibrous proteins, are soluble in water. They are made up of
polypeptides that are coiled about themselves to form oval or spherical molecules e.g.
albumin, insulin, and hormones like oxytocin, etc.

Classification based on composition:

1. Simple proteins
➔ These proteins are made up of amino acids only. e.g. albumins, globulins, prolamins, etc.
2. Conjugated proteins
➔ These are complex proteins that are combined with the characteristic of non–amino
acid substance called a prosthetic group. These are of following types:
a. Nucleoproteins: Combination of protein and nucleic acid
b. Mucoproteins: Combination of proteins and carbohydrates (>4%)
c. Glycoproteins: Combination of proteins and carbohydrates(<4%)
d. Chromoproteins: Combination of proteins and coloured pigments.
e. Lipoproteins: Combination of proteins and lipids.
f. Metalloprotein: Combination of proteins and metal ions.
g. Phosphoprotein: Combination of proteins and phosphate group.
3. Derived proteins
➔ When proteins are hydrolyzed by acids, alkalies or enzymes, the degradation products
obtained from them are called derived proteins.

Reference;
http://ecoursesonline.iasri.res.in/mod/page/view.php?id=83589#:~:text=Proteins%20give%20a
%20purplish%20violet,of%20proteins%20in%20biological%20materials.
https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/protein-
denaturation
 https://www.britannica.com/science/protein/Protein-denaturation
https://alevelbiology.co.uk/notes/proteins-physical-chemical-properties/
https://www.nature.com/scitable/topicpage/protein-structure-14122136/
https://microbenotes.com/proteins-properties-structure-classification-and-functions/
https://www.nature.com/scitable/topicpage/protein-structure-14122136/

https://www.youtube.com/watch?v=RSAo9qPV5R4

W - Weekly Assignment
Look for a case study on Protein deficient in children and adults, Then make a
Generalization/Conclusion out of it. In making a generalization/conclusion take note of the following:
Effects of the protein deficiency in children and adults; Importance of protein in the human body and;
Ways on how to prevent protein deficiency.

Laboratory Task 8
Laboratory Task Sheet 8

L - Long Quiz (Weeks-3rd, 5th, 9th, 11th,15th, 17th)

Quiz #1
Some functions of lipids include water-proofing, temperature regulation, and long-term energy storage.
Which of the following is NOT a common type of lipids? (C)
a. Fats
b. Oils
c. Sugars
d. Waxes

Unsaturated lipids are generally liquid at room temperature because their hydrocarbons are
_____________ packed because of their ____________ bonds. (D) 2 PTS
a. tightly; double
b. tightly; single
c. loosely; single
d. loosely; double

Which of the following is an exception to the general rule that unsaturated fats come from plants and
saturated fats come from animals? © 2 PTS
a. Butter from a cow
b. Oil pressed from seeds or olives
c. Wax coatings on a leaf
d. Lard in fatty meats like bacon

Which of these is NOT a typical role for lipids in a living organism? © 2 PTS
a. Provide stored energy reserves
b. Form a structural component of cell membranes & many tissues
c. A source of glucose, when broken down
d. Protection of internal organs, insulation beneath skin

Which of these statements best describes these molecules? (D) 2 PTS

 a. They are both fatty acids.
b. They are both triglycerides.
c. The top one is saturated fatty acid; the lower one is monounsaturated.
d. The top one is a saturated fatty acid; the lower one is polyunsaturated.

Fat is important as a storage molecule. It can provide protection to vital organs as well as warmth. What
form are lipids most commonly stored in? (D)
a. Ceramide
b. Cholesterol
c. Chylomicrons
d. Triacylglycerides

Which of the following molecules make up the basic structure of a cell membrane? (D)
a. waxes
b. steroids
c. fatty acids
d. phospholipids

Which of the following foods contains unsaturated fats? (B)

a. fish
b. olive oil
c. cheese
d. eggs

Why are lipids efficient for energy storage? © 2 PTS

a. They are short chains of nitrogen and oxygen.
b. They are medium chains of hydrogen and oxygen.
c. They are long chains of carbon and hydrogen.
d. All of the following.

How come having excess cholesterol in our arteries is not desirable? © 2 PTS
a. having excess cholesterol makes us weigh more
b. having excess cholesterol increase the blood sugar level
 c. Can block blood flow and lead to heart disease
d. Can block blood stream and lead to heart attack.

Neurotransmitter serotonin is synthesized from the amino acid? (B)

a. Glycine
b. Tryptophan
c. Valine
d. Histidine

Melanin is synthesized by the oxidation amino acid? (A)

a. Tyrosine
b. Threonine
c. Phenylalanine
d. Tryptophan

Proteins are made up of a combination of how many unique amino acids? (B)
a. 10
b. 20
c. 25
d. 50

Amino acids are the building blocks of: (B)

a. lipids and fats
b. proteins and polypeptides
c. Carbohydrates
d. nucleic acids

Which group in the amino acid varies, giving each amino acid individuality? (A)
a. R group
b. Amino group
c. Carboxyl group
d. Hydrogen atom

What is the basic structure of an Amino acid? (B) 2 PTS

a. basic group, aliphatic group, hydrogen and a R side chain
b. acidic group, amino group, hydrogen and a R side chain
c. positively charged group, acidic group, hydrogen and an aromatic group
d. negatively charged group, basic group, hydrogen and an aliphatic group

Which of the following are non-essential amino acids? (D)

a. Isoleucine
b. Phenylalanine
c. Histidine
d. Glycine

How many essential amino acids are there? (C)

a. 3
b. 6
c. 9
d. 12
Two amino acids that contain sulfur atoms are: (D)
a. cysteine and serine
b. methionine and serine
c. cysteine and threonine
d. methionine and cysteine

Which of the following statements is most likely to be true of non-polar R groups in aqueous solution? ©
2 PTS
a. They are hydrophilic and found buried within proteins
b. They are hydrophilic and found on protein surfaces
c. They are hydrophobic and found within proteins
d. They are hydrophobic and found on protein surfaces

What is the main difference between essential and nonessential amino acids? (B) 2 PTS
a. The body can function properly without essential amino acids.
b. The body can make nonessential amino acids, but it cannot make essential amino acids.
c. The body can make essential amino acids, but it cannot make nonessential amino acids.
d. The body can function properly without nonessential amino acids.

All of the following amino acids are essential, EXCEPT: (C)

a. Phenylalanine
b. Valine
c. Glutamate
d. Tryptophan

Nine of the amino acids are considered to be essential; the others are not. What makes an amino acid
essential? (D) 2 PTS
a. The amino acid must be obtained by prescription only
b. The amino acid has a higher molecular weight than glycine or alanine
c. The amino acid can not enter cells alone and must be taken in by active transport
d. The amino acid can not be synthesized in the body and must be consumed

Proteins are polymers of _____. (A)

a. amino acids
b. disulfide bridges
c. Glucose
d. peptide bonds

The primary structure of a protein involves: (A)

a. Peptide bonds
b. Hydrogen bonds
c. Hydrophobic forces
d. None of the above

What is a peptide bond? (A) 2 PTS

a. Bond that holds two amino acids together.
b. A bond that holds hydrogen and oxygen molecules together.
c. A bond that holds the phosphate group of one nucleotide and a sugar of a neighboring
nucleotide.
 d. A bond that is formed by the sharing of electrons.

Certain bacteria synthesize toxic proteins which are responsible for many of the problems they cause in
humans. If you were to develop a drug designed to inhibit bacterial protein synthesis without interfering
with normal human protein synthesis, what might be a logical target for the drug? (C) 2 PTS
a. DNA
b. RNA
c. Ribosomes
d. Golgi apparatus

The chemical union of the basic units of carbohydrates, lipids, or proteins always produces the
byproduct: (C)
a. Energy
b. Carbon
c. Water
d. Acid

Which of the following is NOT true about Proteins?

a. They are insoluble in water due to their size & heavy molecular mass.
b. They are the building block of many mammalian tissues, such as muscle or bone.
c. They are stored as a nutrient, since they yield more energy than lipids or carbs.
d. They are useful in cells as both structural components & in chemical reactions.

What macronutrients are insoluble in water? (B)

a. carbohydrates
b. fats
c. minerals
d. salt

The primary structure of a protein is determined by: (B) 2 PTS

a. the hydrogen bonding in the molecule
b. the sequence of amino acids in the protein
c. the way amino acids coil around themselves
d. none of the choices

The secondary structure of a protein is determined by: (B) 2 PTS

a. the sequence of amino acids in the protein
b. the way amino acids coil around themselves
c. the way amino acids fold
d. all of the above

Which level of protein organization is due to interactions between amino acid side chain groups? (C)
a. Primary
b. Secondary
c. Tertiary
d. Quaternary

Which statement is mismatched? (A) 2 PTS

a. The quaternary structure is related to the basic linear structure of a protein
b. The primary structure relates to the basic linear structure of a protein
c. The secondary structure relates to the helical shape of a protein
 d. The tertiary structure is a higher level of protein folding

What is Protein denaturation? (A) 2 PTS

a. Denaturation refers to the changes in the properties of a protein.
b. Denaturation is a process where protein molecules tend to form large aggregates and to
precipitate from solution.
c. Denaturation refers to the changes in the structures of a protein.
d. Denaturation is a process where protein molecules tend to form small aggregates and to
precipitate from solution.

The three-dimensional structure of a protein is determined primarily by: (D) 2 PTS

a. non-covalent interactions with lipids, which provide a folding framework
b. non-covalent interactions with nucleic acids
c. the number of amino acids in the protein
d. the sequence (order) of amino acids in the protein

https://www.andrew.cmu.edu/course/03-231/MCQF05/MCQLec09.htm