What is a Protein? (from PDB-101)

RCSBProteinDataBank

20 Nov 201706:58

Summary

TLDRProteins, composed of 21 amino acids, are essential for various biological functions, from transporting nutrients to facilitating chemical reactions. Their primary structure is a sequence of amino acids encoded by DNA, forming peptide bonds. Proteins fold into secondary structures like alpha helices and beta sheets, which contribute to their three-dimensional tertiary structures. These shapes are crucial for their roles, as seen in hemoglobin's oxygen binding or antibodies' pathogen recognition. The RCSB Protein Data Bank offers more insights into proteins' functions and structures.

Takeaways

🌟 Proteins are essential in the biological world, serving a variety of functions including transport, catalysis, and structural support.
🔍 All proteins are composed of the same 21 amino acids, which are the building blocks of proteins.
💧 Amino acids consist of carbon, oxygen, nitrogen, and hydrogen, with some also containing sulfur or selenium.
🔑 The side chain of an amino acid is what varies and determines its properties, such as being hydrophobic, hydrophilic, or charged.
🧬 The primary structure of a protein is its linear sequence of amino acids as determined by DNA.
🔗 Peptide bonds link amino acids together, forming the protein backbone and releasing a water molecule in the process.
🌀 Proteins can fold into secondary structures like alpha helices or beta sheets, stabilized by hydrogen bonds.
🧬 The tertiary structure is the three-dimensional shape of the protein, influenced by the amino acids' characteristics.
🌐 Globular proteins often have hydrophobic side chains on the inside, while membrane-bound proteins have them on the outside for lipid interaction.
🔑 The function of many proteins is reliant on their three-dimensional shape, such as hemoglobin's ability to bind oxygen.
🔍 Visual representations of proteins, like space-filling, ribbon, and surface diagrams, provide insights into their structure and function.
🌡 The size of proteins, exemplified by hemoglobin at 6.5 nanometers, is significant for their function and interaction within the body.
🏥 The RCSB Protein Data Bank is a resource for learning more about the functions and 3D structures of proteins and other molecular machines.

Q & A

What are the primary functions of proteins in the biological world?
-Proteins serve various functions such as transporting nutrients, facilitating chemical reactions, and building the structures of living organisms.
How many building blocks are there for proteins, and what are they called?
-There are 21 building blocks for proteins, known as amino acids.
What elements make up amino acids, and is there any exception with a different element?
-Amino acids are composed of carbon, oxygen, nitrogen, and hydrogen, with the exception of selenocysteine, which also contains a selenium atom.
What are the three main components of an amino acid?
-An amino acid consists of an amino group, a carboxyl group, and a side chain attached to a central carbon atom.
How does the side chain of an amino acid affect its properties?
-The side chain varies from one amino acid to another and determines its properties, such as being hydrophobic, hydrophilic, or charged.
What is the primary structure of a protein, and how is it formed?
-The primary structure is the linear sequence of amino acids as encoded by DNA, with amino acids joined by peptide bonds, releasing a water molecule each time.
What are the two types of secondary structures that protein chains can fold into?
-Protein chains can fold into alpha helices or beta sheets, both stabilized by hydrogen bonds.
How does the tertiary structure of a protein differ from its secondary structure?
-The tertiary structure refers to the three-dimensional shape of the entire protein chain, determined by the characteristics of the amino acids within it.
What role does the shape of a protein play in its function?
-The three-dimensional shape of a protein is crucial for its function, allowing it to interact with other molecules or perform specific tasks within the body.
Can you provide an example of a protein that relies on its three-dimensional shape for function?
-Hemoglobin is an example of a protein that relies on its shape to form a pocket that holds heme and binds oxygen.
What are some different visual representations of proteins, and what do they show?
-Visual representations include space filling diagrams that show all atoms, ribbon or cartoon diagrams that show the protein backbone and alpha helices, and surface representations that highlight areas accessible to water molecules.
Where can one find more information about the functions and 3D structures of proteins?
-The RCSB Protein Data Bank is a resource where one can learn more about the functions and 3D structures of proteins and other molecular machines.

Outlines

00:00

🧬 Protein Structure and Function

Proteins are essential to life, with roles ranging from nutrient transport to structural support. They are composed of 21 amino acids, which vary in their side chains, affecting their interactions with water and other molecules. The primary structure of a protein is its sequence of amino acids, determined by DNA. This sequence folds into secondary structures like alpha helices and beta sheets, stabilized by hydrogen bonds. The tertiary structure is the three-dimensional shape of the protein, influenced by the amino acids' properties. This shape is crucial for function, as seen in hemoglobin's ability to bind oxygen. Some proteins, like antibodies and insulin, rely on their shape for immune function and glucose regulation, respectively. Proteins can also be represented visually through space filling, ribbon, and surface diagrams to understand their structure and function better.

05:07

🛠️ Specific Proteins and Their Roles

The calcium pump, powered by ATP and aided by magnesium, moves calcium ions to the sarcoplasmic reticulum, essential for muscle contraction. Ferritin is a spherical protein that stores iron in a non-toxic form, with channels for iron entry and exit based on the organism's needs. Inside, ferritin has a hollow space with atoms attached to the interior wall. Collagen is another structural protein, forming a strong triple helix that supports the body, particularly in skin and tendons, by forming elongated fibrils into collagen fibers. The RCSB Protein Data Bank offers more insights into the functions and 3D structures of proteins and other molecular machines, highlighting the complexity and diversity of these biological molecules.

Mindmap

Keywords

💡Proteins

Proteins are large, complex molecules that play a crucial role in the structure, function, and regulation of the body's cells, tissues, and organs. They are essential for all life processes and are involved in countless functions, such as transporting nutrients, catalyzing chemical reactions, and building structures. In the script, proteins are described as being composed of amino acids, which are the building blocks that determine their properties and functions.

💡Amino Acids

Amino acids are the basic units that make up proteins. There are 21 standard amino acids, each with a unique side chain that determines its properties. The script mentions that all proteins are made from these building blocks, which are composed of carbon, oxygen, nitrogen, and hydrogen, with some also containing sulfur or selenium. Amino acids are linked together by peptide bonds to form proteins.

💡Peptide Bonds

Peptide bonds are chemical bonds that link amino acids together in a protein chain. They are formed through a dehydration synthesis reaction between the amino group of one amino acid and the carboxyl group of another, releasing a water molecule in the process. The script explains that peptide bonds are what create the protein backbone, which is essential for the protein's structure and function.

💡Primary Structure

The primary structure of a protein refers to the linear sequence of amino acids as encoded by DNA. This sequence determines the protein's identity and is crucial for its function. The script describes how the primary structure is the starting point for understanding how proteins fold into their functional shapes.

💡Secondary Structures

Secondary structures are local folding patterns that proteins adopt, such as alpha helices and beta sheets. These structures are stabilized by hydrogen bonds between the amino and carboxyl groups of nearby amino acids. The script mentions that these secondary structures are important for the protein's overall three-dimensional shape and stability.

💡Tertiary Structure

The tertiary structure of a protein is its three-dimensional shape, which is determined by the characteristics of the amino acids in the chain. This structure is crucial for the protein's function, as it allows proteins to interact with other molecules in specific ways. The script gives an example of hemoglobin, which forms a pocket to bind oxygen, demonstrating the importance of tertiary structure.

💡Globular Proteins

Globular proteins are a class of proteins that have a spherical shape, with hydrophobic side chains typically sheltered inside, away from the surrounding water. This shape is common for proteins that need to be soluble in water but also interact with nonpolar molecules. The script describes how many proteins form globular shapes, which is important for their stability and function in the aqueous environment of cells.

💡Membrane-Bound Proteins

Membrane-bound proteins are proteins that are embedded in or associated with biological membranes. They often have hydrophobic regions that interact with the lipids in the membrane, allowing them to function in the membrane environment. The script mentions that these proteins have hydrophobic residues clustered on the outside, which is essential for their interaction with the membrane.

💡Hemoglobin

Hemoglobin is a protein found in red blood cells that is responsible for transporting oxygen from the lungs to the body's tissues. It has a unique structure that allows it to bind oxygen in the lungs and release it where it is needed. The script uses hemoglobin as an example of a protein whose function is directly related to its three-dimensional shape.

💡Antibodies

Antibodies, also known as immunoglobulins, are proteins produced by the immune system to identify and neutralize foreign objects like bacteria and viruses. They have flexible arms that can recognize and bind to specific antigens, targeting them for destruction. The script mentions antibodies as an example of proteins that protect us from disease by binding to pathogens.

💡Collagen

Collagen is a protein that forms a strong triple helix structure and is found throughout the body, providing structural support in tissues such as skin, tendons, and bones. The script describes collagen as forming elongated fibrils that aggregate to form collagen fibers, which are essential for the body's structural integrity.

Highlights

Proteins have a wide range of functions in the biological world, including transport, catalysis, and structural support.

All proteins are composed of the same 21 amino acids, which vary in their side chains.

Selenocysteine is the only standard amino acid containing a selenium atom.

Amino acids are categorized as hydrophobic, hydrophilic, or charged based on their side chain properties.

The primary structure of a protein is its linear sequence of amino acids as encoded by DNA.

Peptide bonds link amino acids together in a protein, forming the protein backbone.

Proteins can fold into secondary structures like alpha helices and beta sheets, stabilized by hydrogen bonds.

The tertiary structure is the three-dimensional shape of a protein, determined by amino acid characteristics.

Many proteins form globular shapes with hydrophobic side chains sheltered inside.

Membrane-bound proteins have hydrophobic residues on the outside to interact with lipids in the membrane.

Charged amino acids allow proteins to interact with molecules with complementary charges.

The three-dimensional shape of a protein is crucial for its function, as seen in hemoglobin's ability to bind oxygen.

Hemoglobin's four subunits cooperate to pick up and release oxygen in the body.

Different visual representations of proteins, like space filling and ribbon diagrams, provide insights into protein structure and function.

Hemoglobin molecules are about 6.5 nanometers in size and are found in high concentration in red blood cells.

Antibodies have flexible arms that recognize and bind to pathogens, targeting them for immune system destruction.

Insulin is a small, stable protein that regulates blood glucose levels while traveling through the blood.

Alpha Amylase is an enzyme that initiates starch digestion in saliva.

The calcium pump moves calcium ions back to the sarcoplasmic reticulum after muscle contraction, aided by magnesium and powered by ATP.

Ferritin is a spherical protein that stores iron in a non-toxic form and allows iron atoms to enter and exit depending on the organism's needs.

Collagen forms a strong triple helix for structural support in the body, and collagen molecules can aggregate to form collagen fibers found in skin and tendons.

The RCSB Protein Data Bank provides more information on protein functions and 3D structures.