Biochemistry : Biochemistry

Study concepts, example questions & explanations for Biochemistry

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Example Questions

Example Question #4 : Toll Like Receptors

What are some characteristics of toll-like receptors?

I. Toll-like receptors are transmembrane proteins characterized by an extracellular domain and a cytoplasmic tail containing the toll receptor domain.

II. Toll-like receptors can be activated by viral double-stranded RNA.

III. Toll-like receptors alert immune cells to the presence of bacterial infections.

IV. Toll-like receptors are expressed in antigen presenting immune cells (dendritic cells).

Possible Answers:

II, III, and IV

II and III

I and II

I, II, and III

I, II, III, and IV

Correct answer:

I, II, III, and IV

Explanation:

Toll-like receptors can be activated by bacterial components such as lipopolysaccharide, peptidoglycan, flagellin, and bacterial DNA. Toll-like receptors activate transcription factors and immune regulatory factors.Activation triggers the production of pro-inflammatory cytokines such as interleukins.

Example Question #1041 : Biochemistry

Which of the following is true regarding ligand-gated ion channels?

Possible Answers:

They respond to changes in voltage

They are found on phospholipid bilayers

They facilitate the repolarization of a nerve

They transport uncharged and charged molecules

Correct answer:

They are found on phospholipid bilayers

Explanation:

Ligand-gated ion channels are activated by a ligand. Upon activation, the ion channels open and allow for passage of ions through the membrane. They are usually found on membranes such as plasma membrane and organelle membranes and facilitate the exchange of ions between cytoplasm and the extracellular matrix (or inside of organelles). Since all membranes found in a cell are phospholipid bilayers, ligand-gated ion channels are found on phospholipid bilayers.

Example Question #2 : Ligand Gated Ion Channels

A researcher is analyzing the distribution of ion channels in the nervous system. He finds that a type of ion channel is a lot more abundant in the neurons than in the glial cells. What can you conclude about this ion channel?

I. It is a lot faster than G protein-coupled receptor (GPCR)

II. It responds to changes in voltage

III. It is involved in depolarization

Possible Answers:

II only

III only

I and III

II and III

Correct answer:

I and III

Explanation:

To answer this question, we need to know the distribution of ion channels in the central nervous system. There are two kinds of ion channels: voltage-gated and ligand-gated. Voltage-gated channels respond to voltage changes whereas ligand-gated channels respond to ligand binding. Upon activation, both types of ion channels allow passage of ions across a membrane. In CNS, voltage-gated channels are typically found on the glial cells (supporting tissue of CNS) whereas ligand-gated channels are typically found on neurons.

A characteristic of ion channels is that they have a much quicker effect than receptors that utilize second messengers (like G protein-coupled receptors). Recall that depolarization in a neuron occurs when neurotransmitters (ligand) bind to receptors on the postsynaptic membrane. Upon binding of neurotransmitters, these receptors will open and allow for the flow of ions, which leads to depolarization.

Example Question #1 : Ligand Gated Ion Channels

G protein-coupled receptor is an example of __________ ion channel and the insulin receptor is an example of __________ ion channel.

Possible Answers:

None of these

ligand-gated . . . ligand-gated

ligand-gated . . . voltage-gated

voltage-gated . . . voltage-gated

Correct answer:

None of these

Explanation:

G protein-coupled receptor (GPCR) is a receptor that is activated by the binding of a ligand; however, it acts through a second messenger molecule (cAMP). This means that the activation of GPCR activates cAMP, which activates subsequent signaling pathways. GPCRs are not involved in the influx and efflux of ions; therefore, they aren’t ion channels.

Insulin receptor is a type of a receptor tyrosine kinase. Upon binding, insulin activates the RTK which eventually leads to activation of genes for the glucose transporters. This increases the glucose uptake by the cells. Similar to GPCR's, insulin receptor does not allow movement of ions across the membrane; therefore, it isn't an ion channel.

Example Question #1042 : Biochemistry

Which of the following is true regarding second messengers?

Possible Answers:

They are activated by ligand gated and voltage gated ion channels

They are activated by ligand gated ion channels

None of these

They are activated by voltage gated ion channels

Correct answer:

None of these

Explanation:

Signaling receptors can be divided into two categories: ion channels and second-messenger utilizing receptors. Ion channels are activated by voltage changes (voltage-gated) or ligand binding (ligand-gated) and they tend to increase the flow of ions into and outside of cell. Receptors, such as G protein-coupled receptors, are activated by ligand binding; however, they signal the cell by activating second messenger molecules such as cAMP.

Example Question #1043 : Biochemistry

Second messengers are __________ by receptor tyrosine kinase pathway and are __________ by voltage gated ion channels.

Possible Answers:

not activated . . . activated

activated . . . not activated

not activated . . . not activated

activated . . . activated

Correct answer:

activated . . . not activated

Explanation:

Receptor tyrosine kinase pathway utilizes second messenger molecules to activate molecules in the cell that, subsequently, activate cellular mechanisms. Ion channels allow for flow of ions between membranes; they do not directly activate second messenger molecules.

Example Question #1 : Second Messengers

Which of the following is not a direct function of cAMP?

I. Amplification of signal

II. Phosphorylation of molecules

III. Activation of kinases

Possible Answers:

I, II, and III

I and III

I only

II only

Correct answer:

II only

Explanation:

cAMP is a second messenger molecule that activates several molecules. Second messenger molecules often amplify the original signal, allowing for the signal to travel all across the cell. One of the molecules activated by cAMP is protein kinase C (PKC). This molecule, as the name implies, is a kinase; therefore, it phosphorylates other molecules. Note that this is a function of protein kinase C, not a direct function of cAMP.

Example Question #1044 : Biochemistry

Phosphatidylinositol bisphosphate (PIP2) can be cleaved by phospholipase C to produce lipid-derived second messengers. Which of the following are the two second messengers derived from PIP2? 

Possible Answers:

Inositol triphosphate (IP3) and protein kinase C (PKC)

Protein kinase C (PKC) and nitric oxide (NO)

Diacylglycerol (DAG) and inositol trisphosphate (IP3)

Diacylglycerol (DAG) and protein kinase A (PKA)

Phosphatidylcholine and cyclic AMP (cAMP)

Correct answer:

Diacylglycerol (DAG) and inositol trisphosphate (IP3)

Explanation:

PIP2 gets cleaved into two smaller molecules by phospholipase C, and these two molecules are DAG and IP3. The protein kinases are not produced from this reaction, nor is cAMP or phosphatidylcholine. This is simply a matter of knowing that DAG and IP3 are the two most important lipid-derived second messengers. 

Example Question #1045 : Biochemistry

Cyclic GMP (cGMP) is produced when the enzyme __________ converts the precursor GTP into cGMP. The reaction involves the removal of __________ from the GTP precursor.

Possible Answers:

adenylyl cyclase . . . two phosphate groups

guanylyl cyclase . . . one phosphate group

cGMP protein kinase . . . one phosphate group

cGMP protein kinase . . . two phosphate groups

guanylyl cyclase . . . two phosphate groups

Correct answer:

guanylyl cyclase . . . two phosphate groups

Explanation:

Guanylyl cyclase is the enzyme responsible for catalyzing this reaction, and the reaction involves removing two phosphate groups from guanosine triphosphate to generate cyclic guanosine monophosphate. Adenylyl cyclase performs a similar reaction but the substrate is adenosine triphosphate and the product is cyclic adenosine monophosphate. cGMP protein kinase is a target that is activated by cGMP, but is not involved in this reaction. 

Example Question #2 : Second Messengers

Second messenger cascades are frequently initiated by activation of a G protein-coupled receptor (GPCR). Ligand binding to the extracellular domain of the GPCR triggers a conformation change in the GPCR that permits activation and dissociation of the G protein to which it is associated. What is the biochemical change catalyzed by the activated GPCR that permits activation of its associated G protein?

Possible Answers:

The GPCR exchanges the G protein's bound GDP for a GMP

The GPCR exchanges the G protein's bound GDP for a GTP

The GPCR breaks covalent bonds between the intracellular domain and the G protein

The GPCR opens ion channels, and influx of calcium activates the G protein

The GPCR phosphorylates protein kinases, which phosphorylate and activate the G protein

Correct answer:

The GPCR exchanges the G protein's bound GDP for a GTP

Explanation:

Once the conformation change has been induced by ligand binding, the GPCR can act as a guanine exchange factor (GEF) which exchanges out a bound GDP (lower energy) on the G-protein for a GTP (higher energy). This triggers the dissociation of the G-protein, and it goes on to activate various second messenger cascades within the cell. Generally, addition of phosphate groups in biochemistry signals "activation," and removal triggers "deactivation."

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