What is a Protein? (from PDB-101)

Summary

Proteins, 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.