PROTEIN & ITS STRUCTURES

BY

NWOSU VANESSA CHISOMEBI

MATRIC NO: 2020204265

DEPARTMENT OF BIOCHEMISTRY

FACULTY OF NATURAL SCIENCES.

ANAMBRA STATE UNIVERSITY, ULI

24TH OCTOBER 2023.

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 PROTEIN & ITS STRUCTURES

BY

NWOSU VANESSA CHISOMEBI

MATRIC NO: 2020204265

A SEMINAR REPORT
SUBMITTED TO

THE DEPARTMENT OF BIOCHEMISTRY

FACULTY OF NATURAL SCIENCES.
IN PARTIAL FULFILLMENT OF THE REQUIREDMENT
FOR THE AWARD OF B.SC (HONS) DEGREE
ANAMBRA STATE UNIVERSITY, ULI

SUPERVISOR: PROF. A. ONOCHE

24TH OCTOBER 2023.

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This is to certify that this work was written or carried out by Nwosu Vanessa Chisomebi
(2020204265) under my supervision.

Prof.A. Onoche
Supervisor 24th October 2023

Prof. Nwaka
Head of Department 24th October 2023

Dean
Faculty of Natural Sciences 24th October 2023

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 DEDICATION
I would like to dedicate this work to God for the strength, health and capacity to carry out this
work and to my family Mr. & Mrs. Nwosu Family. I am very much appreciative and thankful
and blessed to have the ultimate support from my family.
With the motivation and support, there is nothing that will stop me from becoming a successful
woman in my near and far future.

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 ACKNOWLEDGEMENT
First of all, I would like to thank the Almighty God for his enduring Grace, guidance and
protection that has bestowed upon me during this seminar project.
I wish to extend my sincere gratitude to my seminar supervisor Prof. A. Onochie, former Dean
of Natural Science for his valuable guidance and encouragement which has been absolutely
helpful in successful completion of this seminar.
I am indebted to Prof. Nwaka, Professor & Head of Department of Biochemistry for his valuable
support.
I am also grateful to my parents and friends for their timely aid without which I wouldn’t have
finished my seminar successfully. I extend my thanks to all my well-wishers and all those who
have contributed directly & indirectly for the completion of this work.
I would also like to thank Mr. Kennedy Ozorjiri and Miss Iwuchukwu Chinaza for their
stimulating discussion for the sleepless nights of research, guidance from the start to the
completion of the study.

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 Table of Contents
Chapter One Pages
1.1 General Introduction………………………………………………………..9

Chapter Two: Overview of proteins

2.1 General properties of proteins……………………………………………….10
2.1.1 Classification of proteins…………………………………………………….10
2.2 Protein synthesis …………………………………………………………….
2.3 Relationship between DNA, RNA and Protein…………………………...…

Chapter Three: Protein structures

3.1 Configuration and Conformation……………………………………………..
3.2 Levels of protein structures…………………………………………………..
3.3 Factors that stabilize the different protein structures…………………………
3.3 Primary Structure…………………………………………………………….
3.4 Secondary structure ………………………………………………………...
3.5 Tertiary structure……………………………………………………….......
3.6 Quaternary structure………………………………………………………..

Figures
Fig 1 Diagram of the central Dogma of Molecular Genetics……………………..
Fig 2 Diagram of Configuration…………………………………………………….
Fig 3 Diagram of Conformation…………………………………………………….

Chapter Four
Conclusion………………………………………………………………………...

Chapter Five
Reference………………………………………………………………………….

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 Table of Index

Table Page
1.1 General Introduction

2.1 General Properties of Protein

2.1.1 Classification of proteins

2.2 Protein synthesis

2.3 Relationship between DNA, RNA & Protein

3.1 Configuration and Conformation

3.2 Levels of Protein Structures

3.3 Factors that stabilize the different protein structure

3.4 Secondary Structure

3.5 Tertiary Structure

3.6 Quaternary Structure

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 List of Figures

Figures Page
Fig 1 The central Dogma of Molecular Genetics
Fig 2 Diagram of Configuration
Fig 2 Diagram of Conformation

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 SEMINAR TOPIC
PROTEIN AND ITS STRUCTURE

CHAPTER ONE

1.1 GENERAL INTRODUCTION

The word protein is derived from a Greek word “Proteios” which means primary. As the name
shows, the proteins are of paramount importance for biological systems. Out of the total dry
body weight ¾th are made up of proteins. Proteins are used for the body building all the major
structural and functional aspects of the body are carried out by protein molecules. Abnormality
in protein structures will lead to molecular diseases with profound alterations in metabolic
functions.

Proteins contain carbon, Hydrogen, Oxygen and Nitrogen as the major components whole
Sulphur and Phosphorus are minor constituents. All proteins are polymers of amino acids.

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 CHAPTER 2

OVERVIEW OF PROTEINS

Proteins are made up of large numbers of amino acids linked into chains by peptide bonds
joining the carboxyl group of one amino acid to amino group of the next. Some proteins are
composed of only peptide chain while others are composed of two or more polypeptide chains
(multi-subunit proteins) held together by non-covalent bonds (College of Science topic King
Saud University 2010).
The individual polypeptide chains in a multi-subunit protein may be identical or different.
(Indicate peptide bond).

Note: If at least 2 are identical, the protein is said to be Oliganetric and the identical units are
referred to as promoters.

For example, two subunits (homodimer or heterodimer) four sub-units (homotetramer or

heterotetramer). Each protein has a unique amino acid sequence and a well-defined 3-
dimensional structure known as the conformation.

2.1 GENERAL PROPERTIES OF PROTEINS

 It is present in different shapes: Globular and Fribrous

 It comprises of high molecular weight substances.
 All proteins are amphoteric compounds. (They both act as A & B Base Acid).
 The chemical and physical properties depends on the amino acids forming the protein.
 It constitutes more than 50% of the day weight of the cell.
 They precipitate by heat, in alcohol and in their isoelectric point. (It means they look
governed by the favourable entropy change when interaction between water molecules
and non-polar groups of the protein are decreased therefore the PH at which the net
charge of a protein molecule is zero (0).

2.1.1 CLASSIFICATION OF PROTEIN.

Protein can be classified according to three different criteria:

A. Proteins can be classified on the basis of the chemical composition.

B. Proteins can be classified on the basis of shape.
C. Proteins can be classified on the basis of their biological functions.
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According to their chemical composition:

Protein can be classified on the basis of their chemical composition into 2 main classes:

Simple Protein Conjugated Protein

Simple protein: They are those proteins which upon hydrolysis give only amino acids:
Example: Ribo-nucleases.

Conjugated proteins: They are proteins which yield upon hydrolysis amino acids and non-
protein part is called the prosthetic group. Conjugated proteins are classified on the basis of the
chemical nature of their prosthetic groups.

i. Lipo proteins
ii. Metal proteins
iii. Nucleo proteins
iv. Hemo proteins

Classification of proteins; According to their shape

Globular Protein Fibrous Protein

Globular proteins:

 They are generally soluble in water

 The polypeptide chains are tightly folded into a globular shape. Example: Enzyme,
hemoglobin, myoglobin.

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Fibrous proteins:

They are insoluble in water

 Their polypeptide chains are arranged in long strands (elongated on the fibers). Example:
collagen, keratin.

Classification of proteins; According to their biological function.

Proteins can be classified on the basis of their biological functions into:

 Catalytic function (enzymes)

 Transport function (albumin)
 Nutrient and storage proteins (casein)
 Structural function (collagen)

2.2 PROTEIN SYNTHESIS

They are the processes that cells use to create protein

There are 3 main steps that lead to protein synthesis

 Transcription
 Translation
 Post-translational modification

So Transcription: is a process by which a cell make an RNA contemporary copy a piece of a

DNA to form a messenger RNA (MRNA). It therefore carries the genetic information needed to
make proteins in a cell. It carries the information from the DNA in the nucleus of the cell to the
cytoplasm where proteins are made.

Translation: it is the process by which a cell makes protein using the genetic information carried
in messenger RNA. The MRNA is made by copying DNA, and the information it carries tells the
cell how to link amino acid together to form proteins.

Post Translational Modification: it’s the process of changing one or more amino acids in a
protein while they are still attached to the ribosome.

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2.3 RELATIONSHIP BETWEEN DNA, RNA AND PROTEINS

 The flow of information from DNA to RNA to protein is termed as “central dogma”
 The genetic information corresponding to certain protein is stored in the form of
nucleotide sequence in DNA called gene.
 The gene is transcribed in the nucleus into the specific nucleotide sequence called MRNA
molecule that contains the genetic code.
 MRN is translated in the cytoplasm by the ribosome which bind the amino acids charged
in MRNA in a sequence determined by MRNA.

Figure 2.3.1

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 CHAPTER THREE

PROTEIN STRUCTURE

The amount and type of amino acids found in a protein and the sequence in which they
are arranged in the polypeptide chain is a unique characteristics of each protein.

3.1 CONFIGURATION AND CONFORMATION

Configuration is the arrangement in space of substituent groups in stereoisomers covalent

bond while Conformation refers to the spatial arrangement of substituent groups that are free to
assume many different positions, without breaking bonds because of rotation about angle bonds
in the molecule. Proteins in any of their functional folded conformation are called native
proteins.

Figure 3.1.1 Configuration Figure 3.1.2 Confirmation

3.2 LEVELS OF PROTEIN STRUCTURE

Protein structures can be considered at four level:

 Primary structure
 Secondary structure
 Tertiary structure
 Quaternary structure

Note:

- All proteins have their own specific primary structure, amino acides sequence,
determined by the genes.
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 - Different proteins have different extent of secondary structure. Some have none.
- All intracellular globular proteins have a tertiary structure.
- Proteins made of more than one submit (polypeptide) have quaternary structure.

Figure 3.2.1

3.2.2 FACTORS THAT STABILIZE THE DIFFERENT PROTEIN STRUCTURE

LEVEL INTERACTIONS THAT STABILIZE THE STREK

Primary Covalent bond
Secondary Hydrogen bond
Tertiary Ionic bond, Hydrogen bonding (between R groups in the same chain)
Quaternary Ionic bond, Hydrogen bonding (between R group in different chains)

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3.3 PRIMARY STRUCTURE

It is the sequence of an amino acid that makeup its polypeptide chains. The covalent bond is
what connects the amino acids together.

Because of the nature of the peptide bond the backbone of a polypeptide will have a single
primary amine at one end and a single carboxylic acid at the end. (They do not take part in a
peptide bond). Those ends care called N-terminus (primary amines and the c-terminal
(carboxylic acid).

Amino acids are joined together to form proteins. The covalent bond between two amino acid to
the result of a condensation reaction and is called peptide bond. 2 amino acids joined together to
form dipeptide and a longer chain of amino acid is called polypeptide such as the first 20 amino
acids

Characteristics of the peptide bond:

a. The peptide bond is rigid and planar

 The rigid peptide bond omit the number of conformation by polypeptide chains.
b. Trans configuration:
The peptide bond is generally a Trans bond (instead of cis) because of steroid
interference of the R-group when in composition.
c. Uncharged bolt polar:
(The – C = O and – NH groups of the peptide bond are polar and are involved in
hydrogen bonds.

3.4 SECONDARY STRUCTURE

It is the spatial arrangement of amino acid residues that are near one another in the linear
sequence of the polypeptide chain.

The secondary structures are of three types

- The α – helix
- The β – pleated sheets
- Collagen helix

The bonds responsible for stability of secondary.

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The secondary structure is stabilized by a hydrogen bonds between peptide bond groups

α – helix

- It is a spiral structure
- The polypeptide backbone is tightly wound around the long axis of the molecule and the
R – group of amino acid residues protrude outward from the helical backbone.
- Each helical turn includes 3.6 amino acids residues.
- In all proteins the helical twist of the α – helix is right handed.

The bonds responsible for stability of α – helix

It is stabilized by a hydrogen bonds between peptide bond groups which leads to cooking,
forming a spiral, cylindrical helical).

β – pleated sheets

- In the β – conformation, the backbone of the polypeptide chain is extended into a zigzag
rather than a helical structure.
- The zigzag polypeptide chains can be arranged side to form a structure resembling a
series of pleats, such a structure is called a β – pleated sheets.
- The R – groups of adjacent amino acids protrude from the zigzag structure in opposite
directions creating the alternating pattern.
- Hydrogen bonds from between adjacent segments of polypeptide chain β – pleated sheets
are composed of two or more β – strands

The adjacent polypeptide chains in a β – sheet can be either

Parallel Anti-parallel
(having the same amino to (having the opposite amino
carboxyl orientation) to carboxyl orientation)

When two or more β – sheets are layered close together within a protein; the R-groups of the
amino acid residues on the touching our faces must be relatively small.

The bond responsible for stability of β – pleated sheets. It is stabilized by a hydrogen bonds
between peptide bond groups.
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Collagen Helix

Collagen is found in connective tissues such as tendons, cartilages, the organic matrix of bone of
the cornea of the eye.

 Collagen molecules consist of 3 polypeptide called α – chains which wrap around each
other in a triple helix forming a rope like structure.
 Collagen is built of recurring subunit structure, triple – stranded tropocollagen (triple
helix) molecules; having distinctive heads.

3.5 TERTIARY STRUCTURE

Tertiary structure refers to the spatial arrangement of amino acid residues that are far apart in the
linear sequence (Tien primary structure), so the polypeptide chain is folded into 3 dimension.

Tertiary structure is a 3–dimensional confirmation of a polymer in its nature folded state. The
unique 3–dimensional stricture of each polypeptide is determined in its native folded state.
Interaction of the amino acid side chains guide the folding of the polypeptide chain to form a
compact structure.

Hydrophobic side chains are buried in the interior whereas hydrophobic groups are generally
found on the surface of the molecule.

Bonds that stabilize tertiary structures are:

a. Non – covalent bonds (between R-groups).

 Hydrophobic interaction
 Hydrogen bonds
 Ionic Interaction bonds

Hydrophobic interactions:

It is the association between Non – polar groups (hydrophobic groups) in the side chain of amino
acids.

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Hydrogen bonds:

A hydrogen bond is a type of attractive interaction between an electronegative atom (such as

oxygen or nitrogen) and electronegative atom.

Iconic interaction (electrostatic interaction):

It is the interaction between opposite charged group of the side chains of amino acids.

3.6 QUATERNARY STRUCTURE

Proteins that are composed of more than one polypeptide chain (subunits) show a fourth level of
protein structure which is quaternary structure. Quaternary structure is the 3 – dimensional
structure of a multi-subunits protein, particularly the manner in which the subunits fit together.

Subunits may either function independently of each other or may work co-operatively as a
hemoglobin.

The interaction between subunits are stabilized by the same forces that stabilize structure (non-
covalent).

Bonds that stabilize quaternary structure:

 Hydrophobic interaction
 Hydrogen bond
 Ionic interaction

Hemoglobin is a simple dig-metric protein. It is found in red blood cells where its main function
is to transport oxygen from the lungs to the capillaries of the tissue.

Quaternary structure of hemoglobin.

The hemoglobin tetramer composed of two identical dimers:

 (αβ ) dimer 1
 (αβ ) dimer 2

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 CONCLUSION

Proteins are built as charts of Amino acids which the fold into unique three-dimensional shape.
Proteins are extraordinary complex molecules.

Of all the molecules encountered in living organisms, proteins have the most diverse functions.
So a basic understanding of the structure of proteins is necessary to comprehend its role in
organisms, proteins characterization involves the use of experimental methods that allow for the
detection and isolation of a protein & its purification, as well as the characterization of its
structure & function. The complex structure & larger size of proteins, as well as the intrinsic
nature of each protein, makes the characterization of proteins inherently more complicated that
the characterization of smaller molecules.

Protein structure influences all aspects biological function, although there is considerable
variation on the structural observed in biological macromolecules they are all unified by being
built from the same 20 amino acids.

A protein can be identified based on each level of its structures, every proteins at list contains a
primary, secondary, tertiary structure, only some proteins have a quaternary structure as well.
The primary structure is comprised of a linear chain of amino acids.

The secondary structure contains regains of amino acids chains that are stabilized by hydrogen
bonds from the polypeptide backbone. The hydrogen bonds create alpha-helix & beta pleated
sheets of the secondary structure. The three dimensional shape of a protein, its tertiary structure,
is determined by the interaction of side chains from the poly peptide backbone.

The quaternary structure also influences the three-dimensional shape of the protein & is formed
through the side chain interactions between two or more poly peptides.

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