L12: Mechanisms of Protein Action

Question 1

What is the approximate number of protein species in human cells due to gene variation and protein modification?

Answer 1

Around 1 million protein species.

Question 2

Why is control of protein function crucial in human health?

Answer 2

Loss of protein control often leads to diseases, including cancer, due to the disruption of cellular pathways.

Question 3

What is a kinase and why is it significant in cellular signaling?

Answer 3

A kinase is an enzyme that transfers phosphate groups to other proteins, playing a key role in signal transduction pathways.

Question 4

What is allosteric regulation?

Answer 4

Allosteric regulation is when a molecule binds to a protein at a site other than the active site, causing a conformational change that affects the protein’s function.

Question 5

Describe the BRAF V600 mutation and its effect on cell behavior.

Answer 5

The BRAF V600 mutation causes the BRAF protein to remain in an active state, leading to uncontrolled cell growth and cancer development.

Question 6

How do mutations in the BRAF gene affect cancer development?

Answer 6

Mutations in BRAF can lock the protein in an active state, leading to constant cell growth signals and potentially contributing to cancer.

Question 7

What is the role of polycystic kidney disease (PKD) proteins PKD1 and PKD2?

Answer 7

PKD1 and PKD2 are transmembrane proteins essential for kidney function and calcium signaling. Mutations cause abnormal kidney cell interactions, leading to cyst formation.

Question 8

What is ubiquitination, and what role does it play in protein regulation?

Answer 8

Ubiquitination tags proteins for degradation by the proteasome, regulating protein levels and function in the cell.

Question 9

How does haemophilia A relate to protein function?

Answer 9

Haemophilia A is caused by a deficiency in clotting factor VIII, leading to poor blood clotting and increased bleeding risk.

Question 10

What is the significance of enzyme pathways in protein function?

Answer 10

Enzyme pathways, whether linear or amplifying, control how proteins interact to produce specific cellular outcomes, often regulated to meet the cell’s needs.

Question 11

Describe feedback inhibition in enzyme pathways.

Answer 11

In feedback inhibition, the end product of a pathway binds to an enzyme in the pathway, changing its shape and halting further product formation.

Question 12

What are protein interaction domains, and what is their function?

Answer 12

Protein interaction domains are structural areas that allow proteins to bind to others, facilitating scaffolding, localization, or regulation of protein activity.

Question 13

How does the localization of proteins within a cell contribute to their regulation?

Answer 13

Proteins can be restricted to certain areas (like the nucleus or cytoplasm), allowing cells to control their activity based on location.

Question 14

What is the role of phosphorylation in protein function?

Answer 14

Phosphorylation adds a phosphate group to a protein, often altering its activity, localization, or interactions with other proteins.

Question 15

What is a GTPase and how does it function as a protein switch?

Answer 15

A GTPase is an enzyme that hydrolyzes GTP to GDP, toggling proteins between active and inactive states and controlling cellular processes like signaling.

Question 16

What is protein hydroxylation, and what role does it play in cancer research?

Answer 16

Protein hydroxylation is the addition of an oxygen atom, which can affect protein function and has been studied in cancer for its role in tumor growth regulation.

Question 17

How does the Ras protein act as a molecular switch in signaling pathways?

Answer 17

Ras binds GTP to become active and transmits growth signals; it becomes inactive when GTP is hydrolyzed to GDP.

Question 18

What effect does calcium signaling have on protein localization?

Answer 18

Calcium levels can trigger proteins to move between the cytoplasm and nucleus, dynamically controlling their activity based on cellular signals.

Question 19

Why are protein modifications like methylation and acetylation important?

Answer 19

They can regulate gene expression, protein stability, and interaction, adding complexity to cellular control mechanisms.

Question 20

What are cyclin-dependent kinases, and what is their role in the cell cycle?

Answer 20

Cyclin-dependent kinases (CDKs) regulate cell cycle progression through phosphorylation, controlling key transitions such as mitosis.

Question 21

What is competitive inhibition in enzyme regulation?

Answer 21

Competitive inhibition occurs when a molecule similar to the enzyme’s substrate binds to the active site, blocking the actual substrate and inhibiting enzyme activity.

Question 22

How does haemoglobin exhibit allosteric regulation with oxygen?

Answer 22

When one oxygen molecule binds to haemoglobin, it increases the affinity of the remaining subunits for oxygen, facilitating oxygen binding in a stepwise manner.

Question 23

What is proteolysis and how does it control protein function?

Answer 23

Proteolysis is the breakdown of proteins by proteases, often to regulate or eliminate proteins as part of cellular maintenance and signaling.

Question 24

Explain the importance of pH in regulating protease activity, using cathepsin D as an example.

Answer 24

Cathepsin D is activated in acidic conditions, such as in lysosomes, allowing it to function in specific environments and preventing accidental protease activity in neutral pH areas like the cytoplasm.

Question 25

What is RNA interference (RNAi) and how was it used in Mat Coleman’s research?

Answer 25

RNA interference is a technique to inhibit gene expression, used in Coleman’s research to block the activity of a hydroxylase enzyme in cancer cells, which stopped their growth.

Question 26

What role does release factor 1 (eRF1) play in protein synthesis?

Answer 26

eRF1 recognizes stop codons on mRNA during translation, terminating protein synthesis to prevent unnecessary or incorrect protein elongation.

Question 27

Describe the process of ubiquitination and its effect on proteins.

Answer 27

Ubiquitination tags proteins with ubiquitin, directing them to the proteasome for degradation, which helps control protein levels and function.

Question 28

What is the significance of scaffold proteins in cellular signaling?

Answer 28

Scaffold proteins create platforms that organize multiple signaling proteins together, enhancing the efficiency and specificity of cellular signals.

Question 29

How does phosphorylation affect the protein kinase Src?

Answer 29

Phosphorylation of Src holds it in an inactive conformation; dephosphorylation releases it, activating the kinase to promote downstream signaling.

Question 30

What is the impact of protein hydroxylation on cancer cell growth according to Coleman’s research?

Answer 30

Blocking protein hydroxylation impairs cancer cell growth, indicating that hydroxylation supports the synthesis of proteins essential for tumor cell viability.

Question 31

What is the role of histone modifications in gene expression?

Answer 31

Histone modifications, such as methylation or acetylation, alter chromatin structure, thereby influencing accessibility to DNA and regulating gene transcription.

Question 32

Explain the concept of a multi-protein complex with an example.

Answer 32

A multi-protein complex, like the ribosome, is made of numerous proteins and RNA working together to carry out a function, such as protein synthesis.

Question 33

What happens in cells when BRAF is mutated at V600?

Answer 33

The V600 mutation in BRAF causes it to become constantly active, leading to uncontrolled cell growth and contributing to cancers such as melanoma.

Question 34

What is feedback control, and why is it important in metabolic pathways?

Answer 34

Feedback control is when the end product of a pathway inhibits an earlier step, helping to maintain balance and prevent the overproduction of metabolic products.

Question 35

How does a protein’s location in the cell contribute to its regulation?

Answer 35

The cellular localization of a protein (e.g., nucleus or cytoplasm) often determines its activity, allowing the cell to control when and where the protein exerts its function.

Question 36

What is the impact of the GTPase cycle on Ras protein function?

Answer 36

The GTPase cycle toggles Ras between active and inactive forms, controlling downstream signaling pathways related to cell growth and differentiation.

Question 37

How can post-translational modifications like hydroxylation create new drug targets?

Answer 37

Post-translational modifications alter protein function in disease contexts, like cancer, and targeting these modifications can disrupt pathological processes.

Question 38

Describe the dynamic nature of histone modifications and their regulatory impact.

Answer 38

Histone modifications can be quickly added or removed, allowing for rapid changes in gene expression in response to cellular signals or environmental conditions.

Question 39

How does protein synthesis termination involve release factors?

Answer 39

Release factors bind to the ribosome at stop codons, releasing the newly synthesized protein and preventing further elongation.

Question 40

What function do modular domains serve in protein architecture?

Answer 40

Modular domains allow proteins to have distinct regions for specific functions, facilitating interactions and regulation within complex cellular environments.