Biochemistry Quiz: Protein Structure and Function

A protein that binds to a GTP molecule and regulates cellular processes by transitioning between an active (GTP-bound) and inactive (GDP-bound) state.

A type of protein structure where multiple polypeptide chains (subunits) come together to form a functional unit. Think of it like a team working together.

Hemoglobin is a protein found in red blood cells that is responsible for carrying oxygen throughout the body. It is an example of a protein with quaternary structure, composed of four subunits.

A protein that forms long, fibrous structures, providing strength and support to tissues. Think of it like the steel beams in a building, providing structural support.

Collagen is a fibrous protein found in connective tissues, such as skin, bones, and tendons. It provides strength and flexibility to these tissues.

The process by which proteins are folded into their three-dimensional shape. This shape determines the protein's function.

A non-protein molecule that is required for the activity of an enzyme, such as a vitamin or mineral.

The protein portion of a conjugated protein. Think of it like the chassis of a car.

A distinct functional and structural unit within a protein. These domains can fold independently and often have specific roles like binding to molecules or regulating activity.

A type of protein domain involved in binding nucleotides like ATP or ADP.

A type of protein domain involved in binding the substrate that the enzyme acts on.

A type of protein domain involved in regulating the activity of the protein. This domain can turn the enzyme on or off, controlling its function.

A small protein domain of about 60 amino acids found in various proteins. Often involved in protein-protein interactions and cell signaling.

The part of the protein that directly performs the catalytic action, breaking down or building up molecules.

A protein domain found in many proteins, including antibodies, responsible for binding to specific molecules.

The flexibility and movement of protein molecules. This is essential for protein function and interaction with other molecules.

A structural motif in proteins, formed by a loop of 3 amino acids, connecting two strands of an antiparallel beta sheet.

A structural motif in proteins made up of 4 amino acids. The first carboxyl group of the turn forms a hydrogen bond with the fourth amino acid, often connecting two strands of an antiparallel beta sheet.

A structural motif in proteins shaped like a loop, formed by more than 7 amino acids. They connect secondary structures and can vary in shape.

A type of loop in proteins, connecting strands of an antiparallel beta sheet. This loop gets its name from its resemblance to a hairpin.

A structural motif in proteins, consisting of 5 amino acids, connecting different secondary structures.

A structural motif in proteins, comprised of 6 amino acids. These turns can be classified into different types.

An amino acid that disrupts alpha helix formation due to its rigid structure and inability to form hydrogen bonds. It can be found at the beginning/end of helices.

An amino acid that acts as a helix breaker due to its lack of a side chain, making it flexible and prone to disrupting the helix structure.

Protein-protein interactions are crucial for many cellular processes, including enzyme reactions, antibody-antigen complexes, large biomolecular assemblies, signal transduction, and more.

Affinity chromatography utilizes immobilized proteins to analyze protein-protein interactions both qualitatively and quantitatively.

Co-immunoprecipitation (Co-IP) involves immunoprecipitating a protein with a specific antibody, indirectly co-precipitating its interacting protein, and helping identify whether two proteins are bound.

Immunoprecipitation experiments can indicate direct or indirect interactions between proteins.

Phage display is a technique used to discover ligands that interact with a protein by displaying modified phages with a library of proteins.

Fluorescence Resonance Energy Transfer (FRET) measures the energy transfer between two fluorophores, which can be used to study protein interactions.

FRET allows for the analysis of protein interactions in real-time and within living cells.

PPI detection methods have advanced significantly, providing valuable insights into various biological processes and offering a promising area for drug discovery.

An experiment that demonstrated that the amino acid sequence of a protein determines its final three-dimensional structure. Anfinsen used the enzyme ribonuclease to demonstrate this by denaturing it with urea and β-mercaptoethanol and then allowing it to refold back into its active form.

The three-dimensional structure of a protein. It's the unique and functional shape that a polypeptide chain assumes after folding.

This paradox proposes that it would take an astronomically long time for a protein to fold into its native conformation if it explored all possible conformations randomly. This would be impossible on the timescale of biological events. It proposes that folding cannot be a random search.

The unfolded state of a protein is very compact, but with little defined structure. It's an intermediate state during folding.

A visual representation of the energy landscape of protein folding. The lowest point of the funnel represents the native state, and the higher points represent unfolded or misfolded states.

The energy landscape in protein folding, where the protein can fold into its native state (correct conformation) or misfold into other states due to an incorrect sequence or even an error in the process.

A set of steps that a protein follows during folding, guiding it to its native state. It avoids exploring all possible configurations, making folding efficient.

The Levinthal Paradox describes the impossibility of a protein finding its correct folded state by randomly trying all possible conformations. This is because the number of possible conformations is astronomically large, and even the fastest folding protein would take an impossibly long time to try them all.

The energy landscape of protein folding represents all the possible conformations a protein can take, with the energy level associated with each conformation. The lowest energy conformation (the 'global minimum') is the stable, folded state of the protein. Misfolding occurs when the protein gets trapped in a local energy minimum, which is a suboptimal conformation with a higher energy level.

Defective protein folding is a process where a protein doesn't fold correctly, leading to non-functional or even harmful proteins. This can be caused by genetic mutations, environmental factors, or errors in cellular machinery.

Chaperones are specialized proteins that help other proteins fold correctly. They prevent misfolding, assist in refolding misfolded proteins, and sometimes degrade damaged proteins.

The Heat Shock Protein (HSP) family is a large group of chaperones involved in protein folding and protection. They are classified based on their molecular weight, with HSP70 being a prominent example.

Chaperonins, a type of HSP (HSP60), are large cylindrical protein complexes that create a protected space where proteins can fold efficiently. They shield the proteins from the surrounding environment, allowing them to fold correctly.

In the context of protein folding, co-chaperones are proteins that assist chaperonins by providing additional functions or interacting with other chaperones. They work together to maintain proper protein folding and prevent misfolding.