NROS 310 Final Exam

Define what is meant by a dominant and recessive mutation in classical and biochemical terms

- Classical: Recessive: both copies of the gene have to be mutant before showing a mutant phenotype. A dominant mutation is one in which mutation phenotype is seen even if only one copy of the gene is mutant -Biochemical: Recessive mutation tend to result in loss of function of the gene product. Dominant mutation results in proteins that either show a gain in function or a new function, or somehow interfere with the normal protein products from the normal chromosome

Predict the effects of the following mutations on the fate of the developing ectoderm. A) Defective Achaete-scute B) Defective Notch

A) All skin since Asc is responsible for turning on all genes needed to be a neuron B) All neurons since Notch can't trigger inhibition of ASc in the cell nearby and lateral inhibition fails.

Describe process of leukocyte extravasion

1: Endothelial cell express selectins and PAG 2: Leukoctes bind to selectins, slow down and start to roll 3: PAF activates PAF receptors- triggers activation of integrins 4: Integrins bind IgCams on endothelial cells 5: Focal Adhesion form- activate FAK- triggering cytoskeletal changes in leukocyte

What is the evidence that growth cone has all necessary components to respond to axon guidance cues?

A growth cone cut off from its cell body is still able to respond to growth cone cues.

Predict the effects of the following manipulations 1) in the cell with IAP 2) without IAP's A) injection of BCL2 B) Injection of small cytochrome C C) Activation of FAS receptors

A) 1: more resistant to pop 2: more resistant to pop since BCL2 inhibits BAX B) 1: no effect since IAP would prevent 2: trigger apop C) 1: trigger apoptosis since it would active Cas-3 directly 2: same reason as 1

Epigenetic modifications can have long lasting changes in gene expression. A) describe one of these modifications B) Describe the effects of this modification on chromatin structure C) Describe how this modification is passes on to daughter cells

A) Acetylation or methylation of histones of DNA B) cause the opening/condensation of chromatin structure depending on the factor chosen in A C) Modifications are copied as DNA is replicated so that both the DNA and epigenetic changes are transmitted to the daughter cells

Name proteins that these complexes contain A) Adherens Junction B) Focal Adhesion C) Hemidesmosomes D) Gap Junctions E) Desmosomes

A) Actin B) Actin, Integrin C) integrin D) Connexin E) Plakoglobin

What molecule would you target to increase blood pressure and how will you modify it and why does this increase blood pressure?

Add PKG inhibitor to smooth muscle cell causing lack of Ca++ channel phosphorylation -> increase Ca++ -> increase in smooth muscle contraction

What is meant by critical concentration for actin assembly?

Concentration of monomer where polymerization is favored above that concentration and depolymerization is favored below that concentration

Fast axonal transport from axon terminal to cell body

Dynein. MT in axons oriented with (-) end toward cell body and dyne is (-) end motor

Movement of ciliated bacterium

Dynein: Cilia move through activation of a dynenin that mediate the sliding of MT within the cilium.

Movement of vesicle from ER to Golgi

Dynein: MT - end are at the Golgi and dynein is - end motor

Rigor mortis is stiffening of muscles that occurs after death from high Ca++ and low ATP. Why?

Increased Ca++ = troponin to move tropomyosin out of way to allow myosin to bind to actin. Lack of AT means myosin heads stay attached = muscle stiffness.

Predict the effects of treating an animal with HDAC (histone deacetylase) inhibitor on gene expression

Increase: The HDAC will prevent the removal of acetyl groups causing the chromatin to adopt a more open configuration leading to increased expression of genes

Slow axonal transport

Kinesin mediates then + end direction motion of slow axonal transport

Both actin and tubular show dynamic instability A) describe how this process occurs during polymerization of MT and how its regulated

MT grows steadily but periodically falls apart at the end. As MT polymerized, new tubular dimers get added on end in GTP form. Since GTP tubular is more stable that GDP, MT will grow as long as new GTP-tubulin is added to end - this is GTP cap. If end of tubular hydrolyzes the GTP to GDP leaving exposed DGP ends, MT will collapse.

Describe one process that is different between listeria and extension of lamellipod and the proteins that mediate each

Regulation is different. Bacteria trigger nucleation using Alpha actin and the neutrophil triggers nucleation through activation of RAC or CDC42

Describe the positive feedback that triggers activation of mitotic cyclic CDK complex

See notes for details

Describe the mechanisms by which the ER detects misfolded proteins and tries to fold them properly

See notes for pathway

Explain how RAN mediates the export of proteins out of the nucleus. Include the actions of the ran GEF and Ran FAP

See notes for pathway

Explain how RAN mediates the import of proteins into the muscle.

See notes for pathway

Describe how a transcriptional activator can have both short term and long term effects on gene expression

Short term: helping to recruit RNA polymerase Long Term: recruiting the protein that triggers the opening of the chromatin such as histone acetylation

Describe the immediate effects of SSRI on serotonergic synapses. Explain

Strengthen, SSRI's would prevent the re-uptake of serotonin leading to a stronger postsynaptic response.

How can a developing neuron first be attracted by and then repelled by same landmark?

Target can release both attractive and repulsive cues. Growth cone can regulate the receptors it expresses so it doesn't respond to repulsive cue until it reaches the landmark

Which of the steps in moving neutrophil are the same in a moving growth cone?

The fourth step doesnt happen in the growth cone because the growing neuron is elongating rather than moving the entire cell.

Would a cell with non-functional cytochrome C still be able to undergo apoptosis?

Yes because activation of FAS receptors could still trigger activation of caspases

Is there a differenc between an ATP cap and capping protein?

Yes, ATP cap is dynamic and temporarily stabilize growing actin filament. Its formation is subsequent loss are critical for dynamic instability. A capping protein stabilizes an actin filament much more permanently leading to stable filament for stable structures.

Is someone who has cystic fibrosis protected from effects of cholera? why?

Yes, cholera causes dehydration by over-activation of Cystic fibrosis transport receptor. Someone who has cystic fibrosis is homozygous for the CF mutations and has no functional CFTR chloride channels to be affected by the toxin

Is energy required to fill NT vesicles? Where does it come from?

Yes, it is provided by a proton gradient that is generated by a proton pump.

Is it possible to have two copies of a recessive mutation and still not show the expected phenotype? Explain

Yes, the gene interacts with the environment so it is possible to have a nonfunctional protein that has not effect because it is not needed in the current environment

Describe the process by which v-snares are recycled back to the ER membrane

first by untwisting them from the T-snares using NSF and then packaging them as cargo in vesicles traveling back to the ER membrane

Pathway that mediates translocation step of moving neutrophil

rtk -> rho gef -> Rho -> MLCP leading to activation of myosin

Pathway by which NGS causes movement of cell and prevent apoptosis

see notes

Smooth muscle contracion

up Ca++ lead to activation of myosin light chain kinase which phosphorylates myosin and changes its confirmation so that it can interact with actin

How does PINK detect defective mitochondria and trigger their destruction?

when the mitochondrial membrane gradient starts to fail, PINK is unable to get through TIM and TOM and ends up in outer mitochondrial membrane. It then phosphorylates Parkin to activate and trigger the process of destruction

Describe the effective treatment for the symptoms of cystic fibrosis

1. Antibiotics: prevent infection 2: compressive therapy: help mucous out of lungs 3: Lung transplant: Replacing diseased lung tissue with healthy tissue

What are three essential functions of a transcriptional activator protein?

1. Bind DNA- promoter sequence 2: recruit RNA polymerase to trigger transcription 3: Recruit enzymes that promote histone acetylation

How does the injection of double stranded RNA trigger the destruction of target mRNA? Describe 2 necessary steps

1. DsRNA is cut into fragments by dicer 2: fragments are used by the RISC complex to guide it to specific complementary mRNA strands to target them for destruction

Describe the 2 main steps by which injection of double stranded RNA into a cell causes destruction of target mRNA

1. dicer chops dsRNA into fragments 2. RISC complex takes strands and identifies and destroys complementary mRNA targets

Predict effects of mutations on blood pressure A) PDE inhibitor B) Ca++ chelator C) extra activated PPP

A) Decrease by increasing amount of cGMP and activation of PKG B) Decrease. less Phosphorylation of myosin in smooth muscle cell C) increase by decreasing IP3 and resulting Ca++ in endothelial cell

Actin jets cause cell movement. A) does this movement require dynamic or stable cytoskeleton? B) Describe why too little ADF causes slow movement C) Why too much ADF causes slow movement

A) Dynamic because require constant turnover of actin filaments B) little causes reduction in availability of G-actin = slow polymerization rates C) too much = destruction of f-actin before it can provide strong platform for newly polymerized actin to push of

Describe a signaling cascade that uses or results in A) negative feedback B) positive feedback C) Short term effect D) long term effect

A) increase cAMP activated PDE with decreases cAMP B) Caspase 3 triggers that activation of more Caspase3 (apoptosis) C) Phosphorylation of ion channels D) Phosphorylation of transcriptional factors leading to production of new proteins

What is the main problem that would occur with skeletal muscle if A) titin was defective B) troponin was defective

A) muscle sarcomeres could pull apart so actin and myosin were no longer in contact B) muscles would be unable to contract as they couldn't respond to Ca++ signal

Whenever vesicles fuse with target membrane, their v-SNAREs are transferred to the target membrane t-SNARES. For an actively secreting cell this could eventually lead to an accumulation of v-snares in the plasma membrane.. A) How does the cell avoid this? B)What would happened in the cell if NSF was non-functional?

A) snares are recycled by packaging them as cargo in vesicles traveling back to their membrane of origin. B) v and t-snares would not be able to unwind and the cell would quickly run out of functional snares so vesicle trafficking would stop

Which cytoskeleton motors is most likely to mediate the following? A: ER to golgi B: ciliated bacterium C: Vesicle from cell body to axon tip D: Color change in octopus E: vesicle from golgi to membrane

A: Dynein B: Dynein C: Kinesin D: Kinesin and dynein E: Kinesin and myosin

Predict the effects on vesicle trafficking of the following mutations A: defective Sar-GEF B: defective Cop-I C: Defective arf-GEF D: Defective v-snares

A: Vesicles from Er to golgi will not form B: Vesicles from golgi --> ER not form C: Vesicles will dock but not fuse with target membranes D: Vesicles will form but not be able to pinch off the donor membrane

You have identified a sequence that you believe acts as a nuclear localization signal. Describe an experiment that you could do to show: A) Sequence is necessary B) Sequence is sufficient

A: label protein so you could detect where it goes and then delete you candidate sequence. If sequence was necessary, protein will no longer go to nucleus. B: Could take candidate sequence and attach it to another protein that doesn't normally go to nucleus. If sequence was sufficient, the protein should now go into nucleus

Describe where proteins with the following signal sequence would end up A) Protein with no descernable signal sequence B) Protein with nuclear targeting and mitochondria matrix targeting sequence C) A protein with a mitochondrial inner membrane stop transfer sequence and a nuclear targeting sequence D) A protein with a mitochondrial outer membrane targeting signal

A: stays in cytoplasm B: nucleus or mitochondrial matrix C: Nucleus. mitochondrial inner membrane stop signal will not function unless there is also a mitochondrial matrix targeting signal D) Would end up in mitochondrial outer membrane

Describe three proteins that are similar for listera and extension of lamellipod

ADF, profilin, capping proteins, ARP2/3.

Describe the molecular interactions that resulting in only a select few cells becoming neuroblasts in Drosophilia

ASc -> neural genes Ask -> Delta -> Notch -> Suh -> Espl -> ASc in the nearby cell

What is the difference between ATP cap and capping protein?

ATP cap forms during polymerization of actin filaments and it refers to the presence of actin-ATP at the end of the growing filament. Capping protein binds onto the end of actin filament to stabilize them for the long term

Describe actin polymerization

As a filament is polymerized, new g-Actin gets added to end in ATP form. Some time after it turns into ADP. Since g-actin is stable at end of growing filaments but ADP actin is not stable at end. This is ATP cap. If the actin at the end of filament hydrolyzes the ATP to ADP leaving exposed ADp ends, the filament will depolarize.

Pathway in endothelial cell and smooth muscle in vasculature leading to ACH binding to endothelial cell to relaxation

Blood Pressure Pathway (NO Pathway) with Aschetolcholine acting as ligand to activate pathway

Fast axonal transport

Both kinesin and dynein but in different direction

What is the rate limiting step of polymerization of actin and MT?

Both nucleation . Arp2/3 to trigger nucleation of actin and gamma tubular to trigger MT nucleation

Describe how calcium causes muscle contraction in skeletal muscle

Ca > troponin > tropomyosin movement to allow myosin to interact with actin > contraction

Describe how an increase in Ca causes muscle contraction in skeletal muscle

Ca++ binds to troponin which changes confirmation and causes tropomyosin to move aside to allow myosin to interact with actin to trigger contraction

Why is Ca++ a second messenger but not Na+?

Ca++ can bind to many different proteins and affect their function. Na+ can't

How do cells interact with ECM and how is this regulated?

Cells use integrins to bind to fibronectin and laminin which bind to ECM components. Integrins can be turned on and off

Describe what chaperone proteins do and the roles they they play in the import of protein into the mitochondrial matrix

Chaperones are protein that regulate the folding of proteins and keep proteins destined for the mitochondria unfolded so they can pass through TIM and TOM via thermal ratchet mechanism

ECM is important for cartilage. What molecules in responsible for strength and shock absorbance?

Collagen gives strength and GAG's such as hyaluronon provide shock absorbance.

Fragile X syndrome is the result of a mutation in a single gene. What is the function of the protein product of this gene (FMRP) and how does it lead to problems with neural functions?

FMRP is an RNA binding protein that regulates where/when RNA gets translated. Its functional loss will impair the ability of a neuron to translate proteins locally at specific synapses

How can the same motor protein drive slow and fast axonal transport?

Fast transport makes strong connections to kinesin and slow things make transient weak connections to kinesin.

What junctional complexes are formed as the growth cone navigates and what are the two main components?

Focal Adhesion: Integrins and actin

Describe how nucleation occurs for MT

Gamma tubulin nucleates MT by forming a ring that they can grow from

Describe how the quality control mechanism in the ER works. Include the actions of both calnexin and glucosyltransferase

Glucosyltransferase detects misfolded protein and tags them with with sugar. Calnexin detects the sugar and tries to refold the protein and the sugar gets removed.

A moving growth cone is attracted to a target because of a diffusible factor. What is the likely signal pathway that leads to the first step in cell movement?

Growth Factor > rTK > PI3Kinase > Cdc42 gef > Cdc42 > Wasp/Arp2/3

Describe what would happen to the import if RAN GEF was present on both sides of the nucleus

Import would cease because Importing would bind RAN-GTP rather than cargo in the cytoplasm

Why are neurons particularly susceptible to problems with protein folding and degradation?

Neurons are generally older than other cells so their proteins are older and neurons tend to be very metabolically active so their proteins have more damage

Can a uniporter be used for active transport? If yes, explain where the energy comes from.

No uniporters only transport things down their electrical gradients since there is no place for energy to come from to drive active transport

Gatorade can be used to treat cholera. Would a sugar free-version of Gatorade also be effective?

No, sugar is needed to drive the Na+/glucose symporter that will help increase the amount of Na+ and therefore water in the cells

Extension of lammelipod as a neutrophil chases bacterium

None- mediated by actin polymerization

What happens to a cell if a lysosome is damaged so that it raptures?

Nothing, the acid hydrolyses that degrade proteins in lysosome only function at low pH. When the lysosome ruptures, the pH quickly buffered by the cytoplasm and the acid ceases to function

What would happen in soluble cadherisns were added to bloodstream?

Nothing. Cadherins dont play role here

How does the difficulty of nucleating MT lead to the efficient movement of things within the cell using motor proteins?

Nucleating MT is hard and wont spontaneously form and will only grow from MTOC. This MT network is organized so that all (-) end are at the MTOC and the (+) and are at the periphery of the cell. This consistent polarity makes MT motor based movements highly efficient.

Rate limiting step for actin polymerization and how is it regulated?

Nucleation is the rate limiting step and is regulated using Arp2/3

How does the over expression of HSP70 affect the progression of aggregation bases diseases like Parkinson's and Alzheimers?

Over expression will decrease the progression of these diseases because the extra HSP70/chaperones will help fold and resolve protein aggregates.

What is the function of P53 and why is a mutation in this protein particularly likely to increase the chances of developing cancer?

P53 responds to DNA damage and when activated, triggers a halt to the cell cycle. A mutation in this process greatly increases the possibility of dividing with DNA damage which increases the overall mutation rate

What would happen if integrins were added to bloodstream?

Prevent leukocyte from attaching to endothelial cell so they would keep rolling along via selectin-sugar interactions

How can mutation in Ataxin-1 cause neurological disease even though the protein itself is non-essential?

The mutant ataxin-1 cannot be broken down by proteasome and builds up causing aggregations which cause problems with processing of other proteins.

Gene

The sequence of genomic DNA that codes for a functional product and all necessary elements to properly regulate its expression

The mutation that causes fragile X is a change in the untranslated part of the gene. Explain how this mutation causes a loss of function even through it doesn't change any of the amino acids in the protein product of the gene

This mutation causes the CGG repeat region in the untranslated portion of the gene to expand triggering the methylation of the DNA and chromatin condensation where this gene resides. Thus the gene is not expressed and is not functional since it is not ever made

Signal transduction by which peptides detects neutrophil tiggers the polymerization of actin

peptide > GPCR > Beta-gamma > PI3Kinase > PIP3 > Rac GEF > RAC > Wasp and Arp2/3 > actin polymerization

What is the most likely type of biochemical change in a protein that results in a recessive and dominant mutation

recessive: Changes in protein that results in a loss of function Dominant: Changes in proteins that result in a gain of functional