BIO 024 (Biochemistry)

STUDENT ACTIVITY SHEET BS NURSING / FIRST YEAR

Session # 7

LESSON TITLE: PROTEINS (Peptides, (Protein Structures

and Denaturation)
LEARNING OUTCOMES: Materials:
At the end of the lesson, the nursing student can: Slide Presentation, Hand-outs, Pen, Notebook
1. Name and describe the bond that links the amino acid
together. References
2. Identify the parts of peptide Espino-Cabatit (1988) Biochemistry 12th ed. UST
3. Explain how peptide bond form. Press, Manila
4. List the characteristics of peptide bond Nelson, C. (2013). Lehninger’s principles of
5.Describe what is meant by the term primary, secondary, biochemistry. In Journal of Chemical Information
tertiary, and quaternary structure of protein and know the types and Modeling (Vol. 53, Issue 9).
of bonds and interactions that stabilize each of these https://doi.org/10.1017/CBO9781107415324.004
structures.
6.Discuss the process of protein denaturation.

LESSON PREVIEW / REVIEW (5 minutes)

Watch the video about the internal chemical bonds of hair and pay attention to important details.
Here’s the video link: https://www.youtube.com/watch?v=C6SDKsUTdhM

MAIN LESSON (50 minutes)

PEPTIDE BONDS
- Are chains of amino acid.
- Two amino acid molecules can be covalently joined through a substituted amide linkage, termed a peptide bond,
to yield a dipeptide. Such a linkage is formed by removal of the elements of water (dehydration) from the alpha
carboxyl group of one amino acid and the alpha-amino group of anothe
- Peptide bond formationis an example of a condensation reaction, a common of reactions in living cells.
- Three amino acids can be joined by two peptide bonds to form a tripeptide; similarly, four amino acids can be
linked to form a tetrapeptide, five to form a pentapeptide, and so forth.
- When a few amino acids are joined in this fashion, the structure is called an oligopeptide. When many amino
acids are joined, the product is called a polypeptide.
- Although the terms “protein” and “polypeptide” are sometimes used interchangeably, molecules referred to as
polypeptides generally have molecular weights below 10,000, and those called proteins have higher molecular
weights.
NAMING A PEPTIDE:
● Change the ending of the 1st succeeding amino acids into –yl but retain the name of the last amino acid
Glycine - glycyl Glutamic acid - glutamyl Tryptophan - tryptophyl

Alanine - alanyl Lysine - lysyl Methionine - methionine

Valine - valyl Histidine - histidyl Cysteine - cysteyl

Leucine - leucyl Arginine – arginyl Cystine - cystyl

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 Isoleucine - isoleucyl Phenylalanine - Serine - seryl
phenylalanyl

Aspartic acid - aspartyl Tyrosine - Tyrosyl Threonine - threonyl

CHARACTERISTICS OF PEPTIDE BOND

i. The peptide bond is a partial double bond.

ii. The C–N bond is ‘trans’ in nature and there is no freedom of rotation because of the partial double bond
character.
iii. The distance is 1.32Å which is midway between single bond (1.49Å) and double bond (1.27Å).
iv. The side chains are free to rotate on either side of the peptide bond.
v. The angles of rotation, known as Ramachandran angles, therefore determine the spatial orientation of the
peptide chain . (Dr GN Ramachandran did pioneering work on the structural aspects of proteins during 1950s and
1960s).

PROPERTIES OF PROTEINS:
I- PHYSICAL
● Generally, CHON are colorless, odorless and tasteless except protein hydrolyzates
● Varied solubility in solvents such as acids, bases and salt solutions
● Form colloidal dispersion, thus do not pass through membranes
● Molecular weightsof some of the proteins are: Insulin (5,700); Hemoglobin (68,000); Albumin (69,000);
Immunoglobulins (1,50,000);
● Those of low molecular weight are soluble in H2O
● Those of high MW are macromolecular are totally insoluble in water
● Shapeof the proteins also vary. Thus, Insulin is globular, Albumin is oval in shape, while Fibrinogen molecule
is elongated. Bigger and elongated molecules will increase the viscosity of the solution.

I- CHEMICAL PROPERTIES
- Observed when there are changes in chemical composition
A. Amphoteric / ampholyte
● Possess both a positive and negative ion
● Due to the presence of -COOH (proton donor)
● Due to the presence of –NH2 (proton acceptor)
● Are generally good buffers
B. Proteins are precipitated by:
a. Organic acids
Eg. Trichloroaceticacid, Phosphomolybdic acid,
b. Inorganic acids
Eg.
c. Salts of heavy metals
Eg. CuSO4, Pb(Ac)2 , HgCl2,
Salts of Copper, Zinc, Lead, Cadmium and Mercury are toxic, because they tend to precipitate normal
proteins of the gastrointestinal wall. Based on this principle, raw egg is sometimes used as an antidote for
mercury poisoning.
d. Alkaloidal reagents – reagents of plant origin
Eg. Tannic acid, Picric acid, Sulfosalicylic acid, Tungstic acid, Phosphotungstic acid,
e. High concentration of a neutral salt solution or “salting out”
● Process which lead to the destruction of the destruction of the 4 levels of organization of CHON
● As a general rule, higher the molecular weight of a protein, the salt required for precipitation is lesser.
f. Alcohol( powerful protein precipitating agent)

LEVELS OF ORGANIZATION OF CHON:

1. PRIMARY STRUCTURE (1o)
- Linear arrangement of amino acid in a polypeptide chain joined together by means of peptide
linkages
- Denotes the number and sequence of amino acids in the protein.
- The higher level of organizationsare decided by the primary structure.

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 - Insulin is an example of protein with primary level of organization. It has two polypeptide chain. The
Chain A (Glycine Chain) has 21 amino acids, and Chain B (Phenylalanine) chain has 30 amino
acids.

❖ 2 CHARACTERISTICS OF A PEPTIDE LINKAGE:

a. A strong bond – due to the electron delocalization towards the carbonyl group
b. Exhibit geometric isomerism
a. cis isomer – both above or both below; both left or both right
b. trans isomer – 1 above and 1 below; 1 left and 1 right
c. due to the restricted rotation in the double bond, groups attached to C and N may be projected on the
same side
1. SECONDARY STRUCTURE (2o)
- Involves folding of polypeptide chains due to it – boding of peptide bonds
- refers to particularly stable arrangements of amino acid residues giving rise to recurring structural
patterns.
- the steric relationship of amino acids, close to each other.
2 TYPES OF SECONDARY STRUCTURE: (Pauling (Nobel prize, 1954) and Corey described the alpha
helix and beta-pleated sheet structures of polypeptide chains in 1951.)
A. ALPHA HELIX – formed due to intramolecular H- bonding
- the helix is held by hydrogen bonds between the oxygen atom in a carbonyl group of one amino
acid and the hydrogen atom of the amino group that is just four amino acid units farther along the
chain. Proline and glycine disrupt the regularity of the alpha helical backbone conformation.
- It is the most common and stable conformation for a polypeptide chain.
- It is a spiral structure.
- It is generally right-handed.Left handed alpha helix is rare, because amino acids found in proteins
are of L-variety, which exclude left handedness. Proline and hydroxyproline will notallow the
formation of alpha helix.
▪ INTRAMOLECULAR – within the molecules / peptides
KNOWING THE RIGHT HAND FROM THE LEFT.

B. BETA- PLEATED SHEAT – due to intermolecular H- bonding

- the pleats are formed by similar hydrogen bonds between continuous sequences of carbonyl
and amino groups that are further separated on the backbone of the polypeptide chain
▪ INTERMOLECULAR – between different peptide

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 ▪ H-BOND – a weak bond due to the weak attraction between a α+H and lone pairs of an atom
- Represented by dotted lines

2 FORMS OF H-BOND:
a. INTRAMOLECULAR H- BOND – within the molecule
b. INTERMOLECULAR H-BOND – different compounds are involved either similar or non-identical
2. TERTIARY STRUCTURE
- Furthermore unfolding of polypeptide chains due to formation of bonds like H-bond, peptide bond,
covalent bond, disulfide bond, ionic bond, and hydrophobic interactions.
- denotes the overall arrangement and inter-relationship of the various regions, or domains of a
single polypeptide chain.
- denotes three dimensional structure of the whole protein.
- defines the steric relationship of amino acids which are far apart from each other in the linear
sequence, but are close in the three-dimensionalaspect.
- The process by which a polypeptide chain assumes a large-scale, three-dimensional shape is
called protein folding. 
- Domain is the term used to denote a compact globular functional unit of a protein
- The arrangements of the tertiary structure elements in a protein form a “fold”. A typical example is
calmodulin, the calcium binding regulatory protein which regulates intracellular calcium level.

3. QUATERNARY STRUCTURE
- Most complex aspect of protein strand
- Involves polypeptide chains tightly woven with each other
- results when the proteins consist of two or more polypeptide chains held together by noncovalent
forces.
- It is stabilized by relatively weak interactions.
- Hemoglobin is an example of protein with quaternary structure.

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DENATURATION OF PROTEINS
● Destruction of the secondary, tertiary and quaternary structures of CHON leading to changes in its
physical, chemical and biological characteristics
● Involves transformation of a well-defined folded structure of a protein formed under physiological
conditions, to an unfolded state under non-physiological condition.
2 TYPES OF DENATURATING AGENTS:

1. PHYSICAL
- Includes heat, UV rays, high pressure
● Many human proteins denature at temperature above about 45*C, which is one reason that humans
cannot withstand high fever or exposure to high temperature for a long time.
● Heat can be used to disrupt hydrogen bonds and non-polar hydrophobic interactions. This occurs
because heat increases the kinetic energy and causes the molecules to vibrate so rapidly and violently
that the bonds are disrupted.
●  Medical supplies and instruments are sterilized by heating to denature proteins in bacteria and thus
destroy the bacteria.
2. CHEMICAL
- Acids, bases, organic solvents, heavy metals, detergents
- Changes:
a. Physical- increased viscosity
b. Chemical –decreased solubility (ppt. is formed)
c. Biological – increased digestibility by enzymes (loss of hormonal and antigenic action)

● Strong acids and bases change the pH of the solution containing proteins and therefore change the
ionization of acidic and basic side chains, leading to disruption of ionic bonds.
● Heavy metals, because they are charged, also bind to charged side chains, disrupting salt bridges (ionic
bonds).
● A 70% alcohol solution is used as a disinfectant on the skin. This concentration of alcohol is able to
penetrate the bacterial cell wall and denature the proteins and enzymes inside of the cell.
● Alcohol denatures proteins by disrupting the side chain intramolecular hydrogen bonding.
● Heavy metal salts act to denature proteins in much the same manner as acids and bases. Heavy metal
salts usually contain Hg+2, Pb+2, Ag+1 Tl+1, Cd+2 and other metals with high atomic weights. This reaction is
used for its disinfectant properties in external applications. For example, AgNO3 is used to prevent
gonorrhea infections in the eyes of new born infants. Silver nitrate is also used in the treatment of nose
and throat infections, as well as to cauterize wounds. This same reaction is used in reverse in cases of
acute heavy metal poisoning. In such a situation, a person may have swallowed a significant quantity of a
heavy metal salt. As an antidote, a protein such as milk or egg whites may be administered to precipitate
the poisonous salt. Then an emetic is given to induce vomiting so that the precipitated metal protein is
discharged from the body.
● Detergents are amphipatic in nature and proteins have hydrophobic and hydrophilic sides, the detergent
is attracted to these and forces the protein apart and denatures the proteins.
● An alkylating agent cannot denature protein such as iodoacetic acid.

A. Hydrolysis
- By acids, bases and protein – splitting enzyme (proteinase/protease)
- Opposite of peptide formation\

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 Example:
Protein ------ Proteoses ------- Peptones ------ Polypeptides --------- Dipeptides -------- Amino acids
Advantages of Protein Denaturation
1. The study of denaturation of protein helps in the field of proteomics.
2. To determine the concentration of protein in any given food samples.
Denatured proteins are easily digested in the stomach as compared to undenatured proteins.

CHECK FOR UNDERSTANDING(30 minutes)

1. Which of the following bonds are not involved in tertiary structure?

A. Hydrophobic interactions C. Peptide bonds
B. Hydrogen bonds D. Ionic bonds
ANSWER: ________
RATIO:___________________________________________________________________________________________
_________________________________________________________________________________________________
2. Unfolding of native proteins
A. Oxidation C. Renaturation
B. Reduction D. Denaturation
ANSWER: ________
RATIO:___________________________________________________________________________________________
_________________________________________________________________________________________________
3. The following are factors affecting the denaturation of proteins, EXCEPT
A. pH change C. Charge
B. Organic solvents D. Heat
E. Alcohol
ANSWER: ________
RATIO:___________________________________________________________________________________________
_________________________________________________________________________________________________
4. The primary structure of protein represents
A. Linear sequence of amino acids joined by B. Three-dimensional structure of protein
peptide bond C. Helical structure of protein
D. Sub-unit structure of protein
ANSWER: ________
RATIO:___________________________________________________________________________________________
_________________________________________________________________________________________________
5. An average protein will be denatured by the following, EXCEPT:
A. Detergent C. Iodoacetic acid
B. Heating at 90*C D. pH 10
ANSWER: ________
RATIO:___________________________________________________________________________________________
_________________________________________________________________________________________________
6. Which of the following are known as helix breakers?
A. Proline and Glycine C. Valine
B. Isoleucine and leucine D. Threonine
ANSWER: ________
RATIO:___________________________________________________________________________________________
_________________________________________________________________________________________________
7. B-pleated sheets are the examples of
A. Primary structure C. Tertiary structure
B. Secondary structure D. Quaternary structure
ANSWER: ________
RATIO:___________________________________________________________________________________________
_________________________________________________________________________________________________

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 8. The following can precipitate proteins, EXCEPT:
A. Phosphotungstic D. Mercury
B. Tannic acid E. None of the choices
C. Copper (II) Sulfate
ANSWER: ________
RATIO:___________________________________________________________________________________________
_________________________________________________________________________________________________
9. Tertiary structure of protein is maintained by:
A. Peptide bond C. Di-sulfide bond
B. Hydrogen bond D. All of the above
ANSWER: ________
RATIO:___________________________________________________________________________________________
_________________________________________________________________________________________________
10. The chain of amino acids folds and coils on itself
A. Primary D. Quaternary
B. Secondary
C. Tertiary
ANSWER: ________
RATIO:___________________________________________________________________________________________
_________________________________________________________________________________________________

RATIONALIZATION ACTIVITY (THIS WILL BE DONE DURING THE FACE TO FACE INTERACTION)
The instructor will now rationalize the answers to the students. You can now ask questions and debate among yourselves.
Write the correct answer and correct/additional ratio in the space provided.

1. ANSWER: ________
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RATIO:________________________________________________________________________________________
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3. ANSWER: ________
RATIO:________________________________________________________________________________________
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RATIO:________________________________________________________________________________________
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5. ANSWER: ________
RATIO:________________________________________________________________________________________
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RATIO:________________________________________________________________________________________
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7. ANSWER: ________
RATIO:________________________________________________________________________________________
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8. ANSWER: ________
RATIO:________________________________________________________________________________________
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9. ANSWER: ________

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 RATIO:________________________________________________________________________________________
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10. ANSWER: ________
RATIO:________________________________________________________________________________________
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LESSON WRAP-UP(5 minutes)

You will now mark (encircle) the session you have finished today in the tracker below. This is simply a visual to help you
track how much work you have accomplished and how much work there is left to do.

You are done with the session! Let’s track your progress.

MUDDIEST POINT
Instruction: Answer the question: “What was the muddiest point/ most unclear or confusing in the discussion? Use the
space provided below for your answer.

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