Protein | Definition, Structure & Functions

Imagine constructing a massive skyscraper - every beam, wall, and support structure needs the right material. In your body, proteins play that role! They are the building blocks behind your muscles, enzymes, hormones, and even your immune system. Whether you’re growing taller, healing a wound, or simply digesting food, proteins are at work 24/7.

Proteins are a key component of the Biological Molecules chapter in the PMDC syllabus. They are essential for life, playing a crucial role in nearly every biological process. From building and repairing tissues to catalyzing reactions and defending against diseases, proteins serve as the backbone of cellular function. In this topic, we will explore the structure of proteins, their diverse functions, and their significance in maintaining life at the molecular level.

Table of Contents

1. Introduction to Proteins
2. Amino Acids
3. Protein Structure
4. Types of Bonds in Proteins
5. Protein Structure
6. Denaturation of Proteins
7. Classification of Proteins

What is a protein?

Proteins are large, complex biomolecules composed of one or more long chains of amino acids. They are fundamental to life, playing essential roles in cell structure, function, and regulation. From enzymes that speed up chemical reactions to hormones that regulate body functions and antibodies that protect against infections, proteins are involved in nearly every biological process. They are found in all living organisms, from the simplest bacteria to the most complex multicellular organisms like humans.

The structure and function of a protein are determined by the sequence and arrangement of amino acids, which fold into specific three-dimensional shapes to perform their respective tasks. Each protein is unique because it is made from different combinations of 20 standard amino acids, much like how letters in the alphabet combine to form different words.

Since amino acids are the building blocks of proteins, understanding them is crucial to understanding how proteins function. Let's explore amino acids, their structure, types, and how they come together to form functional proteins.

Summary of the definition of proteins and their composition.

Watch this video below to understand important concepts about viruses:

Amino Acids – The Building Blocks of Proteins

Amino acids are the fundamental units that make up proteins. Just as letters form words, amino acids link together in specific sequences to form peptides, polypeptides, and ultimately functional proteins. These molecules are crucial for life, as they determine the structure, function, and properties of proteins.

There are 20 standard amino acids commonly found in proteins, each with a unique structure and function. In addition to these, some proteins also contain non-coded or rare amino acids, which are modified versions of standard amino acids. For example:

• Hydroxyproline (derived from proline) is found in collagen, helping maintain skin and connective tissue structure.
• Hydroxylysine (derived from lysine) contributes to collagen stability.

Structure of an Amino Acid

Each amino acid consists of four key components:

1. Amino group (-NH₂, basic)
2. Carboxyl group (-COOH, acidic)
3. Hydrogen atom (-H)
4. Variable R-group (side chain) that gives each amino acid its uniqueness

The simplest amino acid is glycine, where the R-group is a hydrogen atom (H). If the R-group is CH₃ (methyl group), the amino acid is alanine.

Formation of a Peptide Bond: Two Amino Acids Link Together via a Condensation Reaction, Releasing Water (H₂O)

Chemical Properties of Amino Acids

Amino acids exhibit different chemical and physical properties based on the nature of their R-groups. They can be classified as:

• Acidic Amino Acids → Contain extra carboxyl (-COOH) groups, making them negatively charged.
• Basic Amino Acids → Contain additional amino (-NH₂) groups, making them positively charged.
• Neutral Amino Acids → Have an equal number of amino and carboxyl groups, resulting in no net charge.

You can find additional information about proteins and amino acids here.

Amphoteric Nature and Zwitterions

Amino acids are amphoteric, meaning they can act as both acids and bases depending on the pH of their environment. In a neutral solution, amino acids exist as zwitterions, a dipolar ion where:

• The amino group (-NH₂) accepts a proton (H⁺), becoming NH₃⁺ (positively charged).
• The carboxyl group (-COOH) donates a proton (H⁺), becoming COO⁻ (negatively charged).

This unique property allows amino acids to participate in various biochemical reactions and maintain the pH balance in biological systems.

Understanding amino acids is key to understanding proteins and their diverse functions in the human body, from enzyme activity to muscle contraction and immune response.

The diagrams show that amino acids can act as both acids and bases. In water, they exist as zwitterions, meaning they have both positive and negative charges. This helps them maintain pH balance and take part in important biochemical reactions.

This diagram illustrates the amphoteric nature of amino acids, showing how they exist as zwitterions, containing both positive and negative charges

This diagram demonstrates the pH-dependent ionization of amino acids, where they are positively charged at low pH, negatively charged at high pH, and neutral at their isoelectric point.

In the first diagram, amino acids are shown as zwitterions at neutral pH (pH 7), where they carry both a positive charge on the amine group (–NH₃⁺) and a negative charge on the carboxyl group (–COO⁻). This means they act like both an acid and a base. The second diagram shows how amino acids change their charge based on the pH: at low pH (acidic), they gain a positive charge because they pick up protons (H⁺), while at high pH (basic), they lose protons and become negatively charged. At the isoelectric point (pI), the positive and negative charges balance each other, making the amino acid neutral. This pH-dependent behavior is key to how proteins function in biological systems.

A table showing the nature of amino acids and what they are formed by.

Based on nutritional requirements, amino acids are grouped into two classes:

1. Essential Amino Acids

These cannot be produced by the body and must be obtained from food. They are crucial for growth, repair, and overall health.

Examples: Arginine, valine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, and tryptophan.

• Arginine and histidine are called semi-essential amino acids because the body can produce them in limited amounts, but they are still required from diet, especially during growth or recovery from illness.

2. Non-Essential Amino Acids

These can be synthesized by the body as needed, so they don’t need to come from food. They are still important for various bodily functions like tissue repair and enzyme production.

Examples: Glycine, alanine, serine, cysteine, aspartic acid, glutamic acid, asparagine, glutamine, tyrosine, and proline.

Proteins as amino acids are covered in detail in this live class.

Types of Bonds in Proteins

Proteins are large molecules made up of chains of amino acids. These amino acids are linked together by different types of bonds, and each bond plays a role in determining the protein's shape and function. Let’s go through each bond type one by one:

1. Peptide Bond Formation:
2. What is it? A peptide bond is a strong chemical bond that links two amino acids together.
3. How does it work? When one amino acid’s amine group (NH2) reacts with another amino acid’s carboxyl group (COOH), a water molecule is released, and the two amino acids join together. This bond forms the backbone of a protein.
4. Key point to remember: Peptide bonds link amino acids in a protein, and the sequence of amino acids determines the protein’s function.
5. Ionic Bond:
6. What is it? An ionic bond forms between two amino acids or parts of a protein that have opposite electrical charges (positive and negative).
7. How does it work? One part of the protein will have a positive charge (like NH3+), and another part will have a negative charge (like COO-). These opposite charges attract, holding the protein's structure together.
8. Key point to remember: Ionic bonds help proteins fold into their correct shapes and maintain stability.
9. Disulfide Bond:
10. What is it? This bond forms between two cysteine amino acids. Each cysteine contains a sulfhydryl group (–SH), and when these groups come close together, they form a strong covalent bond called a disulfide bond.
11. How does it work? The sulfur atoms from two cysteines join together, creating a sulfide bridge that holds parts of the protein together.
12. Key point to remember: Disulfide bonds stabilize the protein’s 3D shape, especially for proteins that need to be very stable in their final structure.
13. Hydrogen Bond:
14. What is it? A hydrogen bond is a weak attraction between a hydrogen atom attached to an electronegative atom (like oxygen or nitrogen) and another electronegative atom.
15. How does it work? In proteins, hydrogen bonds help maintain the shape by allowing amino acids to interact with each other over short distances.
16. Key point to remember: While hydrogen bonds are weaker than covalent bonds, they are important in holding the protein structure together.
17. Hydrophobic Interactions:
18. What is it? Hydrophobic interactions happen when parts of the protein (usually the side chains of certain amino acids) avoid water because they don’t dissolve in it.
19. How does it work? These hydrophobic (water-fearing) parts of the protein tend to cluster together in the interior of the protein, away from the surrounding water.
20. Key point to remember: These interactions help proteins fold into their functional 3D shapes.

Stages of Protein Formation

Proteins are made up of chains of amino acids, and the structure of these chains depends on how many amino acids are connected together:

• Amino acid = Single building block.
• Peptide (fewer than 50 amino acids) = A short chain of amino acids.
• Peptone (50-100 amino acids) = A medium-length chain.
• Protein (more than 100 amino acids) = A long chain of amino acids that folds into a functional shape.

Configuration of Proteins

Proteins are made of long chains of amino acids that fold into specific shapes. These chains are held together by peptide bonds, forming a linear polymer. The way these chains fold and interact determines the protein’s function.

• Polypeptide Chains → A protein can have one or multiple chains of amino acids.
• Multimeric Proteins → If a protein has two or more polypeptide chains, it is called a multimeric protein (e.g., hemoglobin).
• Protein Function → The unique folding of proteins allows them to perform essential roles like enzymatic activity, structural support, transport, and signaling in cells.
• Importance in Cells → Proteins make up 50% of the total dry weight of a cell, highlighting their vital role in life. Proteins also make up cell membrane.

Proteins can be classified based on their configuration, which refers to how their polypeptide chains are arranged and folded. Let's explore this classification next.

Classification of Proteins Based on Configuration

Proteins are large macromolecules made by linking amino acids together in a process called polymerization. Their structure determines their function, and based on their arrangement (configuration), proteins are classified into four levels:

i) Primary Structure: The Protein’s Blueprint

The primary structure is the simplest level of a protein’s organization, consisting of a linear chain of amino acids arranged in a specific sequence. This sequence, coded by DNA, determines the protein’s shape and function.

🔬 Why is it Important?

• Even a single amino acid change can alter protein function (e.g., sickle cell anemia).
• It acts as a blueprint for higher structures like secondary and tertiary proteins.

🧬 Example: Insulin, a hormone that regulates blood sugar levels.

💡 Key Takeaway: The sequence of amino acids is like a set of instructions—it must be correct for the protein to work properly! ✅

ii) Secondary Structure: The First Fold in Protein Shape

After amino acids form a linear chain (primary structure), the chain starts to fold into specific shapes due to hydrogen bonding between amino acids. This folding gives proteins their secondary structure, which helps in stability and function. The polypeptide chain mostly forms right-handed helices and is classified into three main types:

1) α-Helix: The Spiral Coil

• The chain coils into a spiral in a right-handed manner (like a spring).
• Hydrogen bonds between amino acids hold the coil together, making it strong and flexible.
• Examples: Found in keratin (hair & nails), myosin (muscles), epidermis (skin), and fibrin (blood clotting).

2) β-Pleated Sheet: The Folded Sheet

• Instead of coiling, the polypeptide chains lie side by side, forming a zigzag pattern (pleated sheet).
• These sheets can be parallel or anti-parallel, connected by hydrogen bonds for extra strength.
• Examples: Found in β-keratin (feathers) and fibroin (silk fibers), which give them durability.

3) Collagen Helix: The Triple Twist

• Unlike α-helix, this structure has three polypeptide chains twisted together, forming a triple helix (like a rope).
• This unique structure provides strength and flexibility to tissues.
• Examples: Found in collagen (bones, tendons, skin, and connective tissues).

💡 Why Does This Matter?

The secondary structure is critical for proteins to function properly. It gives proteins strength (β-pleated sheet), flexibility (α-helix), and durability (collagen helix), helping them perform roles in muscles, skin, blood, and bones. These structures set the stage for even more complex protein folding in the tertiary and quaternary structures! 🚀

iii) Tertiary Structure: The Protein’s 3D Shape

The tertiary structure is formed when the polypeptide chain folds further, creating a complex, three-dimensional shape. This folding is stabilized by multiple bonds, including covalent, ionic, hydrogen, disulfide bonds, and hydrophobic interactions.

🔬 Why is it Important?

• The 3D shape determines the protein’s function (e.g., enzymes, transport proteins).
• If disrupted by heat or pH changes, the protein loses its shape, a process called denaturation.

🧬 Example: Myoglobin, which stores oxygen in muscles.

💡 Key Takeaway: The tertiary structure gives proteins their unique function—if it’s lost, so is the protein’s ability to work! 🚀

iv) Quaternary Structure: Multi-Chain Proteins

The quaternary structure forms when two or more polypeptide chains come together to create a fully functional protein. These chains are held by hydrophobic interactions, hydrogen bonds, and ionic bonds, ensuring stability and function.

🔬 Why is it Important?

• Many essential proteins require multiple chains to work properly.
• The arrangement of these chains affects protein activity and stability.

🧬 Example: Hemoglobin, which has four polypeptide chains (two α and two β chains) and is responsible for oxygen transport in blood.

💡 Key Takeaway: The quaternary structure allows proteins to perform complex biological functions by combining multiple chains! 🩸🚀

This illustration below shows how a simple chain of amino acids transforms into a fully functional protein. It starts with the primary structure, a linear sequence of amino acids, which then folds into secondary structures like the α-helix. Further folding forms a tertiary structure, creating a unique three-dimensional shape essential for function. Finally, multiple polypeptide chains come together in the quaternary structure, forming complex proteins like hemoglobin, which enables oxygen transport in the blood. This step-by-step organization highlights how structure dictates function in proteins.

From a simple chain to a functional protein, structure shapes function!

Classification of Proteins Based on Function

Proteins are classified based on their function, each playing a crucial role in maintaining biological processes and overall health. By learning about the different functions of proteins, you will be able to understand their significance in various biological processes.

This table above categorizes proteins based on their function, highlighting their diverse roles in the body. Digestive enzymes help break down food, while transport proteins like hemoglobin carry essential substances throughout the body. Structural proteins provide support, forming the cytoskeleton and connective tissues. Hormonal proteins regulate body processes, whereas defensive proteins (like immunoglobulins) protect against infections. Contractile proteins drive muscle movement, and storage proteins store essential nutrients for growth and development. Each protein type is vital for maintaining life and ensuring the body functions properly.

Classification of Proteins Based on Configuration

Proteins can be classified based on their configuration, which refers to how their polypeptide chains are arranged and folded. The two main types are fibrous proteins and globular proteins, each with distinct structures and functions.

• Non-crystalline and elastic.
• Provides structural support in cells and organisms. | Silk, keratin (nails/hair), myosin (muscles), spider web, fibers. | | Globular Proteins | Spherical or ellipsoidal; tertiary or quaternary structures. | - Soluble in aqueous mediums with salts, acids, or bases.
• Can be crystallised.
• Functional proteins like enzymes, hormones, and antibodies. | Hemoglobin, myoglobin, enzymes, antibodies |

If you want to test yourself about your concepts for proteins, attempt these biological molecules MCQs.

Conclusion

Proteins are essential biomolecules that play diverse roles in maintaining life, from catalyzing reactions as enzymes to supporting immune defense and cellular communication. Their structure and function are determined by amino acids, which link together to form complex protein molecules. The unique properties of amino acids, including their classification as essential or non-essential, their chemical behaviors, and their bonding interactions, all contribute to the stability and functionality of proteins. Understanding proteins and their building blocks provides insight into their vital role in biological processes, helping us appreciate their importance in health, nutrition, and medicine.

Frequently Asked Questions

1. What is a simple definition of protein?

Proteins are essential biomolecules made up of amino acids that help in the structure, function, and regulation of the body's cells and tissues.

2. What are proteins in short answer?

Proteins are large molecules composed of amino acids that perform vital roles such as building tissues, transporting substances, and supporting metabolic functions.

3. What are five examples of proteins?

• Hemoglobin – carries oxygen in blood
• Insulin – regulates blood sugar
• Collagen – provides structural support in skin and bones
• Amylase – an enzyme that breaks down starch
• Antibodies – help fight infections

4. What are proteins and their functions?

Proteins serve various functions, including:

• Structural support (e.g., collagen)
• Enzymatic activity (e.g., amylase)
• Transport of molecules (e.g., hemoglobin)
• Hormonal regulation (e.g., insulin)
• Immune defense (e.g., antibodies)

5. What are proteins made of?

Proteins are made of chains of amino acids, which are linked by peptide bonds and contain carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur.

6. What are proteins in food?

Proteins are found in both animal and plant-based foods, such as:

• Animal sources: Meat, fish, eggs, dairy
• Plant sources: Lentils, beans, nuts, soy products

7. What are proteins in biology?

In biology, proteins are macromolecules that perform essential cellular processes, including catalyzing reactions (enzymes), providing structure, and facilitating communication between cells.

Additional Important FAQs

8. What happens if we don't get enough protein?

A lack of protein can lead to muscle loss, weak immunity, slow healing, and severe conditions like kwashiorkor and marasmus.

9. How much protein does the human body need daily?

On average, an adult requires 0.8 grams per kilogram of body weight per day, though needs vary based on age, activity level, and health conditions.

10. What are complete and incomplete proteins?

• Complete proteins contain all essential amino acids (e.g., meat, dairy, soy).
• Incomplete proteins lack one or more essential amino acids (e.g., most plant proteins like beans and grains).