Philippine Science High School – Cagayan Valley Campus 3rd Quarter

Bio 2: Fundamentals of Biology II Peptides and Proteins: Overview

Republic of the Philippines

Department of Science and Technology
PHILIPPINE SCIENCE HIGH SCHOOL – CAGAYAN VALLEY CAMPUS
Bayombong, Nueva Vizcaya

Bio 2: Fundamentals of Biology II

PEPTIDES and PROTEINS: OVERVIEW
Prepared by: Joel C. Magday, Jr.

“When life gives you lemons, you ask for something higher in protein!”

Name: _____________________________________________ Yr. & Sec.: _____________

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Philippine Science High School – Cagayan Valley Campus 3rd Quarter
Bio 2: Fundamentals of Biology II Peptides and Proteins: Overview

PEPTIDES and PROTEINS: OVERVIEW

A. Functions of Proteins

• Establishment and Maintenance of Structure. Structural proteins are responsible for the
shape and stability of cells and tissues (e.g. collagen, histones).
• Transport. A well-known transport protein is hemoglobin in the erythrocytes. It is responsible
for the transport of oxygen and carbon dioxide between the lungs and tissues.
• Protection and defense. The immune system protects the body from pathogens and foreign
substances (e.g. immunoglobulin).
• Control and Regulation. In biochemical signal chains, proteins function as signaling
substances (hormones) and as hormone receptors (e.g. somatotropin).
• Catalysis. Enzymes, with more than 2000 known representatives, are the largest group of
proteins in terms of numbers (e.g. alcohol dehydrogenase, glutamine synthetase).
• Movement. The interaction between actin and myosin is responsible for muscle contraction
and cell movement.

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Philippine Science High School – Cagayan Valley Campus 3rd Quarter
Bio 2: Fundamentals of Biology II Peptides and Proteins: Overview

B. Structure of an Amino Acid

R
|
H2N – C – COOH
|
H

C. The 20 Amino Acids of Proteins

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Philippine Science High School – Cagayan Valley Campus 3rd Quarter
Bio 2: Fundamentals of Biology II Peptides and Proteins: Overview

D. Formation of Peptide Linkages

E. Protein Structure
a. Primary Structure
The specific amino acid sequence of a protein determined by the nucleotide sequence of
the gene that encodes the protein. Because the R groups that distinguish the various amino
acids play no role in the peptide backbone of proteins, a protein can consist of any sequence
of amino acids.

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Philippine Science High School – Cagayan Valley Campus 3rd Quarter
Bio 2: Fundamentals of Biology II Peptides and Proteins: Overview

Lysozyme is an enzyme that attacks bacterial cell walls. It is found in secretions such as
tears and in the white of eggs. Lysozyme has the following primary structure (129 AA):

(NH2)KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTD
GSTDYGILQINSRWWCDNGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGG
MNAWVAWRNRCKGTDVQAWIRGCRL(COOH).

The primary structure of lysozyme (linear map).

b. Secondary Structure
It consists of regular, repeated patterns in different regions of a polypeptide chain. In an α-
helix the polypeptide chain twists around in a spiral, each turn of the helix taking 3.6 amino
acid residues. This allows the nitrogen atom in each peptide bond to form a hydrogen bond
with the oxygen four residues ahead of it in the polypeptide chain. All the peptide bonds in
the helix are able to form such hydrogen bonds, producing a rod in which the amino acid
side chains point outward.

α-helix position of a single H bond.

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Philippine Science High School – Cagayan Valley Campus 3rd Quarter
Bio 2: Fundamentals of Biology II Peptides and Proteins: Overview

A β-pleated sheet is formed from two or more polypeptide chains that are almost
completely extended and lying next to one another. In a β sheet, lengths of polypeptide run
alongside each other, and hydrogen bonds form between the peptide bonds of the strands.
This generates a sheet that has the side chains protruding above and below it. Along a single
strand the side chains alternate up then down. Because the actual geometry prevents them
from being completely flat, they are sometimes called β pleated sheets.
• parallel β sheet – all of the strands in the β sheet are running in the same direction.
• antiparallel β sheet – strands alternate in direction.
The polypeptide chains in β sheets are fully extended unlike the chain in an α helix.

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Philippine Science High School – Cagayan Valley Campus 3rd Quarter
Bio 2: Fundamentals of Biology II Peptides and Proteins: Overview

c. Tertiary Structure
The whole three dimensional arrangement of the amino acids in the protein which often
has protrusions, clefts, or grooves on the surface where particular amino acids are
positioned to form sites that bind ligands and, in the case of enzymes, catalyze reactions
within or between ligands.

Motifs or common patterns occur in tertiary structures (e.g. many proteins with different
functions show a β-barrel structure where β sheet is rolled up to form a tube like the green
fluorescent protein. Often the tertiary structure is seen to divide into discrete regions).

Green fluorescent protein molecule comprises a β-barrel and a central α helix.

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Philippine Science High School – Cagayan Valley Campus 3rd Quarter
Bio 2: Fundamentals of Biology II Peptides and Proteins: Overview

Domains are separately folded regions of a single polypeptide chain (e.g. the calmodulin’s
single chain is organized into two domains joined by only one strand of the polypeptide
chain).

Calmodulin is composed of two very similar domains.

d. Quaternary Structure
When two or more polypeptide chains associate to form a functional protein; the individual
chains are referred to as subunits of the protein. The subunits need not be the same.
Hemoglobin, for example, is a protein composed of two α-chain subunits and two β- chain
subunits.

The structures of hemoglobin.

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Philippine Science High School – Cagayan Valley Campus 3rd Quarter
Bio 2: Fundamentals of Biology II Peptides and Proteins: Overview

PROBLEM SOLVING

1. The endorphins are a group of naturally occurring compounds in the brain that act to control
pain. The active part of an endorphin is a pentapeptide called enkephalin which has the
structure Tyr-Gly-Gly-Phe-Met. Draw the structure of enkephalin.

2. Oxytocin is a hormone secreted by the posterior pituitary that acts as a neurotransmitter and
plays an important role in reproduction. It is sometimes known as the “love hormone.”
Oxytocin is a peptide of nine amino acids (i.e. a nonapeptide). The sequence is CYIQNCPLG.
Draw the structure of oxytocin.

Copyrighted material is used in this lecture. The lecturer invokes the principle of “fair use.”
Prepared by:
Joel C. Magday, Jr. | Special Science Teacher | Philippine Science High School – Cagayan Valley Campus
References:
Koolman, Color Atlas of Biochemistry, 2nd ed., © 2005 Thieme
Reece, J., Urry, L., Cain, M., Wasserman, S., Minorsky, P., & Jackson, R. (2014). Campbell Biology (10th ed., p. 1038).
United States of America: Pearson Education, Inc.

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