UNIVERSITY OF

EDUCATION LAHORE (MULTAN

CAMPUS)
Assignment on

STRUCTURE AND FUNCTION OF PROTEIN

Submitted by

Anila Khushi
Roll no

Bsf2105304
Submitted to

Mam Faiza Rao

Department

Zoology (Evening)
 The Structure and Function of
Proteins

What Are Proteins?

Introduction
Proteins are fundamental macromolecules essential to all forms of life. They are involved in virtually
every cellular process and play critical roles in the structure, function, and regulation of the body's tissues
and organs. Understanding proteins—what they are, how they function, and why they are so crucial—is a
cornerstone of molecular biology, biochemistry, and medicine.

Basic Characteristics of Proteins

1. Composition and Structure

Proteins are composed of amino acids, which are organic molecules that contain both an amino group
(-NH₂) and a carboxyl group (-COOH). These amino acids are linked together by peptide bonds to form
polypeptide chains. Each protein is made up of one or more of these chains that fold into specific three-
dimensional shapes, which are critical for their functions.
The sequence of amino acids in a protein is determined by the genetic code within DNA. This sequence
dictates how the protein will fold and what function it will perform in the cell (Alberts et al., 2002).

2. Protein Synthesis
Proteins are synthesized through a process called translation, which occurs in the ribosomes of cells.
The genetic code from DNA is transcribed into messenger RNA (mRNA), which is then translated into a
polypeptide chain by ribosomes. Transfer RNA (tRNA) brings the appropriate amino acids to the
ribosome, where they are assembled into a protein according to the sequence specified by the mRNA
(Alberts et al., 2002).

Importance of Proteins
Proteins are crucial for virtually all biological functions. They are involved in:

 Cell Structure and Function: Proteins maintain cellular integrity and facilitate various cellular
processes.
 Metabolism: Enzymes drive metabolic pathways essential for energy production and
biochemical synthesis.
 Communication: Signaling proteins regulate physiological processes and maintain homeostasis.
 Defense: Immune proteins protect the body from diseases and infections.
 Dysfunctions or abnormalities in proteins can lead to a range of diseases, from genetic disorders
caused by mutations in specific proteins to conditions like Alzheimer’s disease, which involves misfolded
proteins aggregating in the brain (Hardy & Selko, 2002).

2. Levels of Protein Structure

The structure of proteins is organized into four levels:

 Primary Structure: The linear sequence of amino acids in a polypeptide chain. This sequence is
determined by the gene encoding the protein.
 Secondary Structure: Local folding of the polypeptide chain into structures such as alpha
helices and beta sheets, stabilized by hydrogen bonds.
 Tertiary Structure: The overall three-dimensional shape of a single polypeptide chain, formed
by interactions among secondary structures.
 Quaternary Structure: The assembly of multiple polypeptide chains (subunits) into a functional
protein complex (Berg et al., 2002) ...

Protein Structure
1) Primary Structure
The primary structure of a protein refers to its unique sequence of amino acids. This sequence is
determined by the genetic code and dictates the protein's subsequent folding and function. The sequence
is crucial because even a single change in the amino acid sequence can alter a protein's function and lead
to diseases, such as sickle cell anemia, where a single amino acid substitution in hemoglobin causes
significant health issues (Ingram, 1957).
2) Secondary Structure
 The secondary structure of a protein involves local folding patterns within the polypeptide chain.
The two most common secondary structures are alpha helices and beta sheets. Alpha helices are
right-handed coils stabilized by hydrogen bonds between backbone amide and carbonyl groups,
while beta sheets consist of extended strands connected laterally by hydrogen bonds, forming a
sheet-like structure (Rose et al., 1985). These structures are crucial for the overall stability and
functionality of proteins. The secondary structure of a protein is very important to fulfill the
functional characteristics of the protein.


Figure: Secondary structure of the protein

 The secondary structure of the protein is solely stabilized by hydrogen bonds.

 The hydrogen bonding will take place mainly between the carboxyl oxygen of one peptide bond
and the amino hydrogen of another peptide bond.
 The main purpose of the formation of secondary structures is to reduce the polarity associated
with peptide bonds so that higher-order structures can be generated.
 CD spectroscopy can be used to study the secondary structure of the proteins, and the
Ramachandran plot can be used to determine the feasibility of the occurrence of secondary
structure.
 α-helix was the first-ever secondary structure proposed by Linus Pauling in 1951. The β- pleated
sheet was the regular secondary structure proposed by Linus Pauling and Robert Corey in 1952.
 Both the structures, α-helix, and β- pleated sheets were published in “The General of Biological
Chemistry”.
  These two forms show regular secondary structural levels, which are well-known for many
functional proteins.
 The common irregular secondary structure is the random coil form.

Helical formation of protein

The amino acids in the protein structure will be arranged in linear passion. However, in biological
conditions, sequences of amino acids will fold regularly or irregularly by molecular attractions to give
suitable structure to the protein to become metabolically active.

Types of regular right-handed α-helix

Basically, three types of regular right-handed helical structures have been studied, such as α-helix, 3 10
helix, and π (pi) helix.

Alpha helix form

 Involves intrachain hydrogen bonding and the most common α-helix is right-handed and contains
3.6 amino acid residues per turn. The distance between adjacent amino acid residues is known as
helical rise and the distance will be 1.5Å or 15nm and helical pitch of 5.4 Å (0.54nm).
Helical pitch = (Helical rise per residue × No of residues in a loop).

 For every amino acid residue, the helix turns by 1000. The helical repeat occurs every 5 turns or
18 amino acids, which means the same kind of amino acids is repeated for every 5 turns in a
single peptide strand.
 In the regular right-handed α-helix, we can find a hydrogen-bonded loop, which will be formed
by hydrogen bonding between carboxyl oxygen of Ath amino acid and amino hydrogen of A+ 4th
amino acid.
 Every hydrogen-bonded loop contains 13 atoms; therefore, this regular right-handed α-helix is
represented as 3.613.
 The aromatic amino acid, proline strongly de-stabilizes the regular α-helix because the amino
nitrogen of proline lacks hydrogen atom for the formation of the hydrogen bond. Hence, the un-
bonding nature of the proline disturbs the α-helix formation. If proline is incorporated into the
peptide sequence, then it forms a kink in the protein. In a few cases, by chance, if proline is
present, then it completely collapses the functional properties of the proteins.
 Glycine is the simple and basic structure of amino acid, which strongly de-stabilizes the α-helix,
because it contains only hydrogen atoms as a highly flexible side chain, hence it causes
immediate disturbance in the regular turns of the polypeptide. Therefore, this amino acid is
represented as a hinge amino acid.
 While the amino acids such as arginine and aspartate contain high polarity in their side chains;
hence, they also disturb the regular α-helix.
 However, hydrophobic amino acids such as alanine, valine, leucine, methionine, etc. are the most
suitable amino acids for the formation of regular α-helix.
  The best examples for α-helix contained protein structures include α-keratin, myoglobin, and
hemoglobin.

310-helix
 This helix contains three amino acids per turn and ten atoms per hydrogen-bonded loop.
 In 310 helices, the hydrogen bond can be formed between the carbonyl oxygen of Ith residue and
amino hydrogen of i+3rd amino acid residue (H bond pattern between i and i+3).
 This loop contains 3 residues per turn, consecutive amino acids make an angle of 120° around the
helical axis, a helical rise per amino acid of 2 Å, and a helical pitch of 5.8-6 Å (helical rise per
residue × No of residues in a loop).

pi helix
 pi helix (π–helix) is another type of secondary structure present in some proteins. 15% of known
protein structures contain these short pi–helices. Biologists believe that the formation of the pi
helix is due to evolutionary adaptations derived from a single amino acid insertion into an α-
helix.
 π helix or 4.416 helix contains 4.4 amino acids per turn and 16 atoms in the hydrogen-bonded loop.
 The hydrogen-bonded loop can be formed by hydrogen bonding between carboxyl oxygen of Ath
amino acid and amino hydrogen of A+5th amino acid.

Beta pleated sheet

 The hydrogen bond formation in the β-pleated sheet is opposite to the α-helix. In an α-helix, the
hydrogen bond formation will be within the same chain (intrachain bonding), but in a β-pleated
sheet, hydrogen bond formation will be between two chains (interchain bonding).
 However, in some cases, bonding can be intrachain, which forms an antiparallel β-pleated sheet
when a respective chain folds back itself to form a hydrogen bond.
 The two chains involved in β-pleated sheet formation are called β-strands. Based on the two β-
strand arrangements, the β-pleated sheet has been divided into two forms, parallel and
antiparallel.

Parallel beta-pleated sheet

 The hydrogen bond formation in parallel β-pleated sheet strictly between interchain.
 In a parallel β-pleated sheet, the two β-strands are arranged in the same directions. It means the
amino terminus of one strand will be close to the amino terminus of the opposite strand.
 Similarly, the C- terminus of one strand will be close to the C-terminus of another strand.
However, this closer proximity of similar groups in the strands develops an intrinsic repulsion,
which leads to a reduction in structural stability.
 The hydrogen bonds between the chains are not compact because an amino acid in one chain
forms hydrogen bonds with two different amino acids in the second chain.

Antiparallel beta-pleated sheet

 The hydrogen bond formation in an antiparallel β-pleated sheet can be formed between interchain
or within intrachain.
  In an antiparallel β-pleated sheet, the two β-strands are arranged in opposite directions. The bond
formation occurs between the amino groups of one strand and the closely located carboxyl
terminus of the other strands.
 The hydrogen bonds are highly compact because amino acid in one chain forms the hydrogen
bonds with single amino acid in the second chain.
 The commercially valuable insoluble proteins of silk, such as fibroin, sericin, etc. are the best
examples of the antiparallel β-pleated sheet-containing proteins.
 Interestingly, in addition to parallel and anti-antiparallel β-sheets, mixed β-sheets are also
possible. It means, we can see both types of above-mentioned sheets in mixed β-sheets. Mixed β-
sheets are only possible when a β-sheet or protein contains three or more β-strands.

3) Tertiary Structure
The tertiary structure refers to the three-dimensional shape of a single polypeptide chain. This shape
is determined by various interactions among the amino acids, including hydrophobic interactions,
hydrogen bonds, ionic interactions, and disulfide bridges. For example, the tertiary structure of enzymes
such as lysozyme is essential for its catalytic activity (Phillips, 1997). The protein’s tertiary structure
allows for the formation of active sites and the precise interaction with substrates.

Figure: Tertiary structure of the protein

4) Quaternary Structure
Quaternary structure is observed in proteins composed of multiple polypeptide chains, or subunits.
The interaction between these subunits can create a functional protein complex. Hemoglobin is a well-
known example of a protein with quaternary structure, consisting of four subunits that cooperate to bind
and release oxygen effectively (Perutz et al., 1960). The quaternary structure is crucial for the
regulation
 and functionality of many proteins.

Image: Quaternary structure of the protein

Example of Quaternary Structure:

♦ Insulin is an extracellular protein that has been stabilized by both covalent and noncovalent
interactions.

♦ Two interchain disulfide bridges are present in insulin between chains a and b.
♦ Hemoglobin's quaternary structure started with the creation of a heterodimer of α and β subunits,
which will be firmly held together by hydrophobic contacts and will not alter shape over time.
♦ The heterotetrametric is formed when two of these heterodimers join. Here, analogous subunit
types communicate via feeble salt bridges that may be broken as hemoglobin changes shape in
response to ligand binding.
♦ Hemoglobin was thought to be myoglobin in muscle because of the similarities between each
subunit. The structure of hemoglobin was represented as mb-mb2.d as mb-mb2. Hemoglobin was
considered myoglobin in muscle cells due to the similarity in each subunit.

Protein Function

Enzymes
Enzymes are proteins that act as biological catalysts, accelerating chemical reactions without being
consumed in the process. They achieve this by lowering the activation energy required for a reaction to
proceed. The specificity of enzymes is determined by the shape and chemical properties of their active
sites,
which bind to substrates. An example is the enzyme amylase, which breaks down starch into sugars (Strayer,
1995).

Structural Proteins
Structural proteins provide support and shape to cells and tissues. For instance, collagen, a fibrous
protein found in connective tissues, provides tensile strength and structural integrity to tissues such as
skin, tendons, and ligaments (Burgess et al., 1994). Keratin, another structural protein, strengthens hair,
nails, and the outer layer of skin.

Transport Proteins
Transport proteins are responsible for moving molecules across cell membranes and within the
bloodstream. Hemoglobin, for example, transports oxygen from the lungs to various tissues throughout
the body (Perutz, 1978). Membrane transporters, such as ion channels and carrier proteins, facilitate the
movement of ions and other substances across cellular membranes.

Signaling Proteins
Signaling proteins are involved in transmitting signals within and between cells. Hormones such as
insulin are signaling molecules that regulate glucose metabolism by binding to specific receptors on target
cells (Kahn et al., 2006). These proteins play essential roles in maintaining homeostasis and coordinating
physiological responses.

Regulatory Proteins
Regulatory proteins control various cellular processes, including gene expression and the cell cycle.
Transcription factors, for example, bind specific DNA sequences to regulate the transcription of genes
(Ptashne, 2005). Cyclins and cyclin-dependent kinases regulate the progression of the cell cycle, ensuring
proper cell division and function (Nurse, 1994).

Immune Proteins
Immune proteins, such as antibodies, are crucial for the immune response. Antibodies recognize and
neutralize pathogens, while cytokines act as signaling molecules that coordinate immune responses
(Janeway et al., 2001). These proteins are vital for protecting the body from infections and diseases.

Protein Dynamics and Modifications

Protein Folding
Protein folding is a critical process that determines a protein’s functional structure. Proper folding is
essential for protein function, while misfolding can lead to diseases such as Alzheimer's and Parkinson's.
Molecular chaperones assist in the folding process and prevent misfolded proteins from aggregating
(Hartl et al., 2011).
Post-Translational Modifications
Proteins often undergo post-translational modifications, which can affect their function, location, and
stability. Common modifications include phosphorylation, glycosylation, and ubiquitination. These
modifications play roles in regulating protein activity and interactions (Cohen, 2002).

Protein Degradation
Protein degradation is essential for regulating protein levels and removing damaged or non-functional
proteins. The proteasome and lysosome systems are responsible for degrading proteins, with the
ubiquitin- proteasome pathway being a key mechanism for targeting proteins for degradation
(Hochstrasser, 2009).

Techniques for Studying Proteins

Protein Sequencing
Protein sequencing techniques, such as Edman degradation and mass spectrometry, allow for the
determination of amino acid sequences and post-translational modifications. These methods are
fundamental for characterizing proteins and understanding their functions (Murray et al., 2003).

Structural Analysis
Techniques like X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-
electron microscopy (cryo-EM) are used to determine protein structures at atomic resolution. These
methods provide insights into protein folding, dynamics, and interactions (Rupp, 2010).

Functional Assays
Functional assays are used to measure protein activity and interactions. Enzyme activity assays,
binding studies, and functional tests are essential for understanding how proteins perform their biological
functions (Berg et al., 2002).

Applications and Implications

Medicine and Biotechnology

Proteins are central to many medical and biotechnological applications. Protein-based drugs, such as
monoclonal antibodies and enzyme replacements, are used in the treatment of various diseases.
Additionally, protein engineering and synthetic biology hold promise for developing novel therapeutic and
industrial applications (Cohen, 2007).

Proteomics
Proteomics is the large-scale study of proteins, including their functions, interactions, and
modifications. Advances in proteomics technologies have facilitated the discovery of biomarkers and
therapeutic targets for diseases (Aebersold & Mann, 2003).
Environmental and Agricultural Applications
Proteins also have applications in environmental and agricultural fields. For example, enzymes are
used in bioremediation to break down pollutants, and genetically modified crops with enhanced protein
properties can improve agricultural productivity (Scruton, 2007).

Conclusion
Proteins are fundamental to life, and their diverse functions are closely linked to their complex
structures. Understanding protein structure and function is crucial for advancing our knowledge of
biological processes and developing medical and biotechnological innovations. Ongoing research
continues to reveal new insights into protein dynamics, modifications, and applications, highlighting the
importance of proteins in health and disease.

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