Protein Structure and Function

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Questions and Answers

Which of the following best describes the role of protein kinases?

They catalyze the removal of phosphate groups from proteins.
They promote the degradation of proteins.
They catalyze the addition of phosphate groups to proteins. (correct)
They facilitate the binding of ligands to proteins.

Covalent modifications of amino acids play minor roles in protein function.

False (B)

What is the general effect of adding a phosphate group to a protein through phosphorylation?

Phosphorylation can induce major structural changes, alter protein activity, change protein solubility, or create new recognition sites for other proteins to bind.

Phosphorylation is reversible through the action of enzymes known as protein ______.

phosphatases Signup and view all the answers

Match the following post-translational modifications with their primary effects on protein function:

Phosphorylation = Can alter protein activity and create binding sites. Ubiquitylation = Targets proteins for degradation or alters their location. Proteolytic cleavage = Removes amino acids from the original sequence. Signup and view all the answers

Why is the 3D complementarity of binding sites crucial for ligand-protein interactions?

It ensures strong and specific binding between the protein and its ligand. (A) Signup and view all the answers

Ligand binding is generally irreversible due to the strength of covalent bonds involved.

False (B) Signup and view all the answers

Explain the concept of 'strength in numbers' for ligand-protein binding.

The overall strength of ligand binding is not just about one strong interaction, but rather the cumulative effect of many weak, noncovalent bonds that collectively provide a strong and stable interaction. Signup and view all the answers

A ______ is the term used to describe a molecule that binds to a protein.

ligand Signup and view all the answers

Match each term with its correct definition regarding protein-ligand interactions:

Dissociation constant (Kd) = Measure of the affinity between a protein and its ligand; lower values indicate stronger binding. Association constant (Ka) = Measure of the affinity between a protein and its ligand; inverse of the dissociation constant. Ligand = A molecule that binds to a protein. Signup and view all the answers

What is the role of GEFs (guanine nucleotide exchange factors) in GTP-binding protein signaling?

They catalyze the exchange of GDP for GTP, activating the protein. (D) Signup and view all the answers

GTP-binding proteins are only regulated by direct phosphorylation.

False (B) Signup and view all the answers

Explain the function of GAPs (GTPase-activating proteins) in regulating GTP-binding proteins.

GAPs enhance the GTPase activity of GTP-binding proteins, causing them to hydrolyze GTP to GDP, thereby inactivating the protein and turning off the signaling pathway. Signup and view all the answers

GTP-binding proteins are active when bound to and inactive when bound to .

GTP, GDP Signup and view all the answers

Match each regulator with its function in GTP-binding protein regulation:

GEF = Activates a GTP-binding protein by exchanging GDP for GTP. GAP = Inactivates a GTP-binding protein by promoting GTP hydrolysis. Signup and view all the answers

What is the significance of multiple modification/interaction sites on proteins?

It allows proteins to act as molecular integrators, responding to multiple signals. (A) Signup and view all the answers

Proteins can only be regulated by a single type of post-translational modification at any given time.

False (B) Signup and view all the answers

How can phosphorylation and dephosphorylation act as opposing regulatory mechanisms on a protein's activity?

Phosphorylation can activate a protein by inducing a conformational change or creating a binding site, while dephosphorylation can reverse these effects, returning the protein to its original inactive state. Signup and view all the answers

Cyclin Dependent Kinases (CDKs) are regulated by phosphorylation at one site, ______ at another, and binding to another protein (cyclin).

dephosphorylation Signup and view all the answers

You are studying a protein that is turned on by phosphorylation at a specific serine residue. What do you expect would happen if the serine is mutated to aspartic acid?

The protein will always be turned on (A) Signup and view all the answers

How does covalent modification of a protein's amino acid side chains affect its properties?

Covalent modification alters the chemical properties of the side chains, influencing protein structure and function. Signup and view all the answers

What is proteolytic cleavage and how does it modify a protein?

Proteolytic cleavage is the removal of amino acids from the original translated sequence of a protein. This can activate or inactivate a protein or change its localization. Signup and view all the answers

A protein has multiple potential modification sites, but not all are used simultaneously. What does this suggest about the regulation of protein function?

This suggests complex regulation, where modification at different sites may have distinct or opposing effects, influencing protein activity in a context-dependent manner. Signup and view all the answers

Describe the process of protein phosphorylation and its effect on protein function.

Phosphorylation is the addition of a phosphate group to a protein, typically on serine, threonine, or tyrosine residues. This modification can change the protein's activity, structure, or binding affinity. Signup and view all the answers

Explain why phosphorylation can lead to major structural changes in a protein.

Each phosphate group adds two negative charges, which can cause electrostatic repulsion, disrupt existing interactions, or create new interactions within the protein. Signup and view all the answers

How can phosphorylation create a new recognition site on a protein?

The added phosphate group can create a specific binding motif, such as a phosphotyrosine-binding motif, that allows other proteins with corresponding domains (e.g., SH2 domain) to bind to the phosphorylated protein. Signup and view all the answers

If a protein's activity is turned on by phosphorylation of a specific serine residue, what would be the effect of mutating that serine to alanine?

Mutating the serine to alanine would likely prevent the protein from being activated via phosphorylation at that site, as alanine cannot be phosphorylated. Signup and view all the answers

Describe the role of ubiquitin in protein modification and its two main functions.

Ubiquitin is a small regulatory protein that can be covalently attached to other proteins. It serves as a tag that can either mark proteins for degradation or direct them to specific locations in the cell. Signup and view all the answers

Besides phosphorylation and ubiquitination, name two other covalent modifications that regulate protein function and briefly describe their effects.

Acetylation (helps to create histone code in chromatin) and palmitoylation (drives protein association with membranes). Signup and view all the answers

Define the term 'ligand' in the context of protein interactions.

A ligand is any molecule that binds to a protein. This interaction is crucial for the protein's biological function. Signup and view all the answers

Why is ligand binding to a protein typically reversible?

Ligand binding is generally achieved through noncovalent bonds (e.g., hydrogen bonds, van der Waals forces, electrostatic interactions), which are weaker and more easily disrupted than covalent bonds, allowing for reversibility. Signup and view all the answers

What factors contribute to the strength of ligand binding to a protein?

The strength of ligand binding is achieved through 3D complementarity of binding, optimized by the formation of several noncovalent bonds. In other words, a lock and key fit which is secured by a multitude of weak bonds. Signup and view all the answers

A drug with a high binding affinity for a target protein has a low dissociation constant Kd. Explain the rationale.

A lower dissociation constant represents a lower rate of dissociation of the protein-ligand complex, which means that the ligand binds more tightly to the protein. Higher affinity will also decrease the dissociation. Signup and view all the answers

Explain why amino acids that contribute to a ligand binding site may be far apart on a protein's primary sequence.

The primary sequence determines the order of amino acids, however the protein will fold into a tertiary structure bringing distant aminos acids together to form a binding site. Signup and view all the answers

Which represents a stronger protein-ligand interaction: an antibody binding to a bacterial toxin with a $K_d$ of $10^{-12}$ M, or calmodulin binding to calcium with a $K_d$ of $10^{-6}$ M? Explain.

Antibody binding to bacterial toxin with a $K_d$ of $10^{-12}$ M represents a stronger interaction, because a lower $K_d$ indicates higher binding affinity. Signup and view all the answers

Describe how guanosine triphosphate (GTP) binding can regulate protein activity.

GTP binding is similar to direct phosphorylation, where it induces a conformational change that alters its activity. Signup and view all the answers

How do GTPase-activating proteins (GAPs) influence the activity of GTP-binding proteins?

GAPs increase the rate of GTP hydrolysis, converting the GTP-bound (active) form of the protein to the GDP-bound (inactive) form, thereby turning the protein off. Signup and view all the answers

Explain how multiple modification/interaction sites allow proteins to act as molecular integrators.

Having multiple sites allows a protein's activity to be regulated by multiple inputs. Different modifications or interactions can have additive, synergistic, or opposing effects on the protein's function, allowing the protein to integrate diverse signals and respond accordingly. Signup and view all the answers

How does the addition of a phosphate group to a protein affect its structure and activity?

The addition of a phosphate group can cause major structural changes, activity changes, or changes in protein solubility. Signup and view all the answers

In general terms, how can covalent modifications impact protein function?

Covalent modifications of amino acids play important roles in regulating protein function by changing their chemical properties. Signup and view all the answers

Explain how a protein's function can be regulated by ligand binding, and why this interaction is typically described as reversible.

Protein function is regulated by ligand binding through specific interactions with other molecules. This is reversible because ligand binding is generally achieved by noncovalent bonds. Signup and view all the answers

What is the role of protein kinases and phosphatases in regulating protein activity?

Protein kinases catalyze the addition of phosphate groups to proteins, while protein phosphatases catalyze the removal of phosphate groups from proteins. Signup and view all the answers

How does ubiquitination affect protein function, and what are two potential outcomes of this post-translational modification?

Ubiquitination serves as a tag that can either mark proteins for degradation or direct proteins to specific locations in the cell. Signup and view all the answers

Flashcards

Post-Translational Modifications

Modifications to amino acids after protein synthesis that play roles in protein function.

Phosphorylation

The covalent addition of a phosphate group to a protein, typically to serine, threonine, or tyrosine residues.