Cell Bio Exam 3 Review Questions PDF

Lecture 15: Cytoskeleton Describe the structures and main functions of the 3 types of cytoskeleton components. 1. Name the 3 types of cytoskeleton, their location, and their main function a. Intermediate Filaments: Withstands mechanical stress. Found...

Lecture 15: Cytoskeleton Describe the structures and main functions of the 3 types of cytoskeleton components. 1. Name the 3 types of cytoskeleton, their location, and their main function a. Intermediate Filaments: Withstands mechanical stress. Found inside muscle cells and skin cells. b. Microtubules: highways for intracellular transport and segregation of chromosomes. Found in the centrosome inside the cell c. Actin Filaments: cortex stabilization, cell movement, muscle contraction. Found beneath the plasma membrane 2. Describe the structure, assembly, and function of intermediate filaments. a. A single polypeptide wraps around another one to form a dimer. The head of the dimer attaches to another one but in the antiparallel direction. Due to the identical ends, there is no polarity. When 8 of them bind together they form a tetramer. Tetramers bind together at the ends and form a filament. Form a network in the cytoplasm, surround the nucleus, and extend into the cell periphery and at cell junctions (desmosomes). 3. Name an intermediate filament protein. a. Keratin and lamin 4. How are intermediate filaments structurally different from actin and microtubules?  a. IFs are single proteins bound together to form a filament. Microtubules are dynamic, long, hollow, stiff tubes. Actin filaments are made from a twisted chain of monomers and are flexible. 5. What is the function of nuclear lamins? a. DNA replication, RNA transcription, nuclear and chromatin organization, cell cycle regulation, cell development and differentiation, nuclear migration, and apoptosis. 6. Describe the structure, assembly, and function of microtubules a. Microtubule subunits stack on top of each other to form a filament. Then they attach to other filaments until they make a hollow tube with a plus and minus end. Grows in the plus and minus ends are anchored to the nucleus. Always growing and shrinking unless stabilized, and then it stops. 7. What are the protein subunits of microtubules called? a. Alpha tubulin and Beta tubulin 8. What do we mean by the plus end of the microtubule? a. It’s the end that gets new dimers added on the fastest 9. What is an MTOC? a. Microtubule Organizing Center. This organizes the location, number, and orientation of the microtubules. It starts near the nucleus and orients the same way. 10.What is meant by the dynamic instability of microtubules? a. The growing and shrinking of microtubules to catch molecules 11.How does GTP hydrolysis control dynamic stability?  a. Tubulin binds to GTP which leads to continued growth and the dimers bind tighter to neighbors. GDP leads to instability and collapse 12.What do microtubule capping proteins do? a. Stabilize the microtubule 13.Describe the structure, assembly, and function of actin a. Made of actin monomers that form a twisted chain with a plus and minus end for polarity for transport. ATP hydrolysis binds new monomers to the plus end while ADP pulls off monomers at the minus end. Can help the cell move and determine cell shape 14.What do we mean by actin treadmilling? a. New actin monomers get added to the plus end faster than the minus end, and monomers at the minus end come off, giving it a treadmilling effect. 15.How can actin structure be modified? a. A severing protein cuts a filament in half so now there are more free ends to make filaments. Bundling proteins group filaments together. Cross-linking protein sets filaments up so they cross each other 16.What is the role of myosin? Which direction does it move in actin? a. Generates force and movements toward the plus end 17.Compare and contrast the 3 cytoskeleton proteins. Intermediate Filaments Actin & Microtubules Protein polymers Protein polymers Symmetrical Plus and minus ends Structural backbone Structural backbone & dynamics Connects cells to tissue Thoroughfare for transport Understand how the cytoskeleton and its associated motor proteins move things around in the cell. 1. What are the two motor proteins that walk along microtubules to move cargo? a. Kinesin: plus end-directed; synapse b. Dynein: minus end-directed; toward body 2. Compare dynein and kinesin a. Both use ATP hydrolysis to move along microtubules. Kinesin stretches the ER along microtubules like a net; starts at the nucleus (- end) and stretches out to grab things (+ end). Dynein pulls the Golgi towards the nucleus. 3. What powers the movement of motors? a. ATP hydrolysis 4. Which domain of the motor protein binds cargo? Which domain binds the cytoskeleton? a. The tail binds cargo and the head binds actin 5. Given an example of how kinesin and dynein help position organelles? a. In neurons, kinesis transports vesicles with neurotransmitters to the axon terminal while dynein transports vesicles back to the cell body. 6. What is the motor protein that walks along actin? a. Myosin 7. What are the functions of myosin? a. Binds, releases, and rebinds to move along an actin filament and move cargo where it needs to go Appreciate how actin, myosin, and calcium work together to carry out muscle contractions. 1. Provide a stepwise description of how an action potential leads to muscle contraction. a. The electrical signal travels from neuron to muscle i. Neurotransmitters are released at the nerve terminal by a neuron which triggers an action potential in the muscle cell’s plasma membrane. The signal travels into tubes that connect to the sarcoplasmic reticulum b. An action potential in the muscle cell releases calcium into the cytoplasm of the muscle cell i. Voltage-gated ion channels open since calcium needs to flow into the muscle cell c. Calcium binding proteins move, exposing myosin binding sites on actin i. Without calcium, actin is covered by troponin and tropomyosin. The calcium binds troponin, which moves tropomyosin out of the way and lets myosin bind to actin. This doesn’t activate the motor protein, only exposes the binding site so it stops working  d. Myosin moves along the actin filaments i. Myosin moves actin filaments, contracting a muscle cell. The cell can contract about 33%. This is coordinated across many muscle cells in milliseconds. e. Action potential releases calcium which causes a conformational change in tropomyosin which exposes binding sites 2. What is the role of calcium in muscle contractions? a. Exposing binding sites by binding to troponin which removes tropomyosin 3. Other than calcium, what else is needed for muscle contractions? a. Magnesium, potassium, ATP, acetylcholine, and vitamin D Lecture 16: Endomembrane System Describe the endomembrane system and how proteins and other molecules move between organelles in this system. 1. What functions do organelles serve? a. Organelles compartmentalize functions that aren’t compatible with each other. They provide more lipid surface area to carry out functions that need a membrane. Organelles can highly concentrate molecules in a small space. 2. What is the endomembrane system? a. A class of organelles with specific jobs for production, quality control, and control of all secreted proteins and all membrane proteins. It internalizes things from outside the cell. 3. Name the process used to bring molecules into a cell.  a. Endocytosis 4. Name the process used to move molecules out of a cell. a. Exocytosis 5. What are the 3 mechanisms by which proteins are sorted in a cell? a. Transportation through the nuclear pores, transportation across the membranes, and transportation by vesicles 6. Which sorting method requires that proteins remain unfolded? a. Transportation across membranes 7. What determines where a protein goes in a cell? How did scientists figure this out? a. Signal sequences direct proteins to the correct compartment. Scientists did a genetic experiment and found that without the signal sequence, a particular process wouldn’t happen. 8. What are the ER, Golgi, and lysosomes and what do they do? a. The ER synthesizes most lipids and synthesizes proteins for distribution to many organelles and the plasma membrane. b. The Golgi is an organelle that modifies, sorts, and packages proteins to be either secreted or delivered to another organelle. c. Lysosomes are in charge of intracellular degradation and recycling. Describe the basic structure/function of the nuclear pore and how directionality of import/export is achieved. 1. How do large molecules enter/exit the nucleus? a. They need a special escorting protein. They also need nuclear import receptors and nuclear export receptors. 2. What is the nuclear pore? Describe its structure a. A double membrane that acts as a gate for letting molecules across. Has a ring-like structure of proteins outside the membrane and a nuclear basket inside. Highly controls what goes in and out. 3. What determines if a protein gets sorted into the nucleus? How can this be tested? a. The nuclear localization signal turns on and all proteins go toward the nucleus. The signal provides access and concentration. 4. What are nuclear import receptors? a. Specialized proteins that identify the addresses and small peptides, and allow proteins to move through the nuclear pore 5. Describe the process of nuclear import. a. Import receptors and their cargo bind and release regions of the proteins lining the pore and hop from one to the next 6. How is the directionality of nuclear import/export maintained? a. A cytosolic GAP triggers GTP hydrolysis by RAN that tells a molecule if it’s in the nucleus or cytoplasm. 7. Which form of RAN is high in concentration in the nucleus? Why? a. Ran-GTP. The nucleus has a special enzyme called Ran-GEF that keeps Ran in its GTP-bound (active) form. This enzyme is only found in the nucleus. 8. Which form of RAN is high in concentration in the cytoplasm? Why?  a. Ran-GDP. When Ran-GTP moves out of the nucleus to the cytoplasm, Ran-GAP converts it into its inactive form, Ran-GDP. Understand how immunoprecipitations work and what this can tell you about protein behavior. 1. What is immunoprecipitation? What is it used for? a. Purification of a specific protein using antibody binding. Opens the membrane so everything spills out and the protein you want is bound to its antibody and moves to the bottom. Used to detect protein-protein interactions. 2. What does it mean when two proteins immuno-precipitate together? a. They are physically associated with each other under the experimental conditions used. 3. What are some good controls to use in IP experiments? a. No-antibody control so we know if proteins are just binding to stuff. Recombinant proteins use purified or overexpressed versions of the target protein and its binding partner to confirm the IP works under controlled conditions. 4. If data from IP is shown, can you deduce what it means? a. Maybe Describe the path a protein takes as it is secreted from the cell and understand the structure and main functions of the organelles it visits on its way to the plasma membrane.  1. It starts in the nucleus, where DNA instructions are transcribed into mRNA. The mRNA travels to ribosomes on the rough endoplasmic reticulum (RER), where the protein is synthesized and modified. 2. The RER folds and prepares the protein, then sends it in vesicles to the Golgi apparatus. In the Golgi, the protein undergoes further modifications, sorting, and packaging into transport vesicles. 3. Finally, the vesicles deliver the protein to the plasma membrane, where it is released outside the cell through exocytosis. Lecture 17: Endocytosis Describe the path a protein takes as it enters the cell via endocytosis Understand the structure and main functions of early endosomes, late endosomes, and lysosomes 1. Compare phagocytosis, pinocytosis, and receptor-mediated endocytosis. a. Phagocytosis: the cell engulfs something else and makes it a part of itself b. Pinocytosis: the cell randomly ingests fluid and small molecules into the cell that will benefit it c. Endocytosis: the cell highly regulates what it brings in by enriching which molecules are taken in 2. List the pathway of an internalized molecule via an endosome/phagosome. a. An internalized molecule enters the cell via endocytosis or phagocytosis, forming an endosome or phagosome. It is first sorted in an early endosome or remains in the phagosome,  which matures into a late endosome or fuses with a lysosome to form a phagolysosome. In this compartment, the molecule is either degraded by enzymes, or its components are recycled back to the plasma membrane for reuse. 3. Compare the early endosome to the late endosome. a. Early endosomes are involved in sorting and recycling, while late endosomes specialize in delivering materials for degradation in lysosomes. 4. What is the structure and function of a lysosome? a. The spherical structure has many hydrolytic and degradative enzymes. Degrades material taken up by endocytosis 5. How is the low pH of lysosomes maintained? a. By using proton pumps 6. What is meant by receptor recycling? a. After the surface receptor binds to its ligand, it gets internalized into the cell and returned to the membrane when it needs to be used again. 7. How do lysosomal proteins like degradative enzymes get to lysosomes? Why do they not degrade there? a. They are synthesized in the rough ER and then go to the Golgi to be modified and sorted where they get tagged with the M6P marker. This directs the enzymes to the early endosome which matures into the late endosome and then eventually fuses with the lysosome. b. The enzymes do not degrade in the lysosome itself because they are activated only in the acidic environment of the lysosome,  and the membrane of the lysosome protects the cell from its destructive activity. Analyze data that lead to the discovery of receptor-mediated endocytosis 1. What is the primary symptom of FH patients? a. High blood cholesterol levels 2. In normal cells, what happens to cholesterol biosynthesis when there is no LDL? a. It increases. Cells rely on their cholesterol production through the HMG-CoA reductase pathway. 3. In normal cells, what happens to cholesterol biosynthesis when there is LDL? a. It decreases. The cell takes up LDL and the cholesterol from it inhibits the activity of HMG-CoA reductase. 4. In FH cells, what happens to cholesterol biosynthesis when there is no LDL? a. It remains high. The LDL receptors can’t efficiently take up LDL cholesterol so the cells can’t receive enough cholesterol from the blood and they continue to synthesize cholesterol. 5. In FH cells, what happens to cholesterol biosynthesis when there is LDL? a. It’s not properly regulated. The defective LDL receptors prevent effective uptake so the cells can’t properly suppress biosynthesis and the production of cholesterol remains high. 6. What did Brown and Goldstein find about cholesterol metabolism in normal people?  a. LDL receptors on cells efficiently mediate the uptake of LDL cholesterol. When there is enough LDL, the cell will suppress the internal production of cholesterol and maintain cholesterol balance. 7. What did Brown and Goldstein find about cholesterol metabolism in FH patients? a. The LDL receptors are either defective or absent which prevents the efficient uptake of LDL cholesterol. This causes the cell to not suppress cholesterol biosynthesis properly and leads to high levels of cholesterol in the blood. 8. Draw the two cholesterol acquisition pathways in cells. a. Exogenous Acquisition via LDL: LDL particles are brought into the cell via endocytosis. Then it’s delivered to lysosomes where it’s broken down and free cholesterol is released. The cholesterol can be used for synthesis, stored, or used to regulate cholesterol biosynthesis by inhibiting HMG-CoA reductase. b. Endogenous Synthesis: acetyl-CoA is converted into mevalonate by HMG-CoA reductase. Mevolante is processed into isoprenoid intermediates that form squalene which is then converted into cholesterol. Then it can be used in cell membranes for hormone production or stored in lipid droplets. Lecture 19: The Cell Cycle Describe the 4 main phases of the cell cycle and what happens in each one 1. What is the cell cycle? a. The way a cell passes on its genetic contents to offspring 2. Are all eukaryotic cell cycle durations the same? a. No, it changes between organisms and through development. The rate-limiting step is how quickly a cell can duplicate its genome. 3. What are the 4 main stages of a cell cycle? Explain what happens at each stage. a. G1: cell growth and any mistakes are fixed before replication b. S: DNA replication c. G2: preparation for mitosis d. M: nuclear division, daughter cells are made 4. What stages makeup interphase? a. G1, S, and G2 5. What divisions make up the M phase? a. Cytokinesis and mitosis 6. What is the G0 stage? a. The non-dividing and resting stage 7. Where are the 3 main transition points/ gates in the cell cycle? a. Before entering the S phase from G1, before entering the M phase, and before the duplicated chromosomes are pulled apart Recall how cells duplicate their DNA and other contents before mitosis 1. DNA replication begins and completes during which phase? a. S phase at the origin of replication 2. How are large genomes replicated quickly? a. Multiple replication forks open and work at the same time to replicate large genomes. 3. Which phases of the cell cycle does the mass of the rest of the cell increase? a. G1 and G2 4. How do mitochondria replicate? a. Similar to bacteria through fission. The mitochondria get pinched in half to create replicates and then be passed on. 5. How do ER, Golgi, and cell membranes increase in size? a. The organelles are constantly generated via vesicle trafficking so it’s not a big challenge for each daughter cell to get one of each organelle. 6. When does the centrosome duplicate? a. During S phase 7. What is the function of the centrosome in the cell cycle? a. Grow microtubules to pull sister chromatids apart and make sure each cell gets the right amount of chromosomes during mitosis. Understand how flow cytometry works and analyze basic data from this kind of experiment. 1. State two applications of flow cytometry. a. Controls the flow of cells into a line so its characteristics can be measured. Can sort cells based on their fluorescence 2. If flow cytometry data is shown can you draw logical conclusions? a. Possibly Understand the basic features of cell cycle regulation by CDKs and cyclins 1. What are the two types of proteins required for controlling the cell cycle? a. Cyclins and cyclin-dependent kinases 2. Which cell cycle regulatory protein is always present but activated by another protein? a. Cyclin 3. In the S phase, is S-CDK present? Is M-CDK present? a. S-CDK is present but not M-CDK 4. In the S phase, is S cyclin present? Is M cyclin present? a. S cyclin is present but not M cyclin 5. How are cyclin levels regulated? a. Phosphorylation and dephosphorylation: stops the cell cycle to fix mistakes. Inhibitor proteins: regulate the cell cycle in response to DNA damage to either fix it or die if the damage is too severe. 6. How can cyclins and CDKs be detected in cells? a. Western blotting, immunofluorescence, flow cytometry, and immunoprecipitation. 7. What are the two major cell cycle checkpoints? a. G1/S to make sure there are no damages or mistakes. G2/M to make sure the cell is ready to be divided. 8. What do we mean by cell cycle arrest? a. Temporarily pausing the cell cycle to allow mistakes and damages to be fixed. 9. How can one control the activity of cyclin-CDK complexes to arrest the cell cycle? a. By inhibiting cyclin synthesis, activating CDK inhibitors (CKIs), or phosphorylating CDKs to block their activity, leading to cell cycle arrest. 10.What decisions are made during the G1/S checkpoint? a. The cell decides if it should continue to replication or if it should stop to fix something. 11.What happens if DNA damage is detected during the G1/S checkpoint? a. The cell cycle stops and repair mechanisms are activated. If the damage is too severe the cell goes through apoptosis. 12.What is the role of p53 in the cell cycle? a. When cell damage occurs, p53 arrests the cell until the damage is repaired. 13.What will a G1/S checkpoint arrest look like by flow cytometry? a. Normally, it would show a large number of cells in the G1 phase and fewer cells in the S phase. 14.Why is p53 called a tumor suppressor? a. Mutations in p53 dramatically increase the risk of cancer 15.What does active S-CDK do? a. Initiates and regulates DNA replication during the S phase 16.What decisions are made during the G2/M checkpoint? a. The cell checks if replication is done and if there’s damage 17.What does active M-CDK do? a. It drives the cell into mitosis. Describe mitosis and how chromosomes are segregated, including the role of microtubules in this process. 1. What are the two crucial parts of the M phase? a. Mitosis and cytokinesis. 2. What happens in metaphase and anaphase? a. Chromosomes line up in metaphase and get separated during anaphase. 3. What is the function of kinetochores? a. Chromosomes attach to spindle microtubules here. 4. What two components are essential to generate tension between sister kinetochores? a. Kinetochore microtubules and the motor proteins dynein and kinesin 5. When is cohesin loaded onto chromosomes? When is it removed? a. Loaded onto sister chromatids during the S phase and is removed in anaphase 6. How do the spindle assembly checkpoints work? a. The cell stops in metaphase until all the kinetochores are under tension and then anaphase happens. Describe cytokinesis and how organelles are distributed to the daughter cells. 1. When and how does the nuclear envelope break down and reform during the cell cycle?  a. Breaks down during late prophase and reforms after anaphase. Phosphorylation of nuclear pore proteins and lamins breaks it down and dephosphorylation reforms it. 2. What happens to mitochondria during the M phase? a. The mitochondria split using fission so the daughter cells have the appropriate amount of mitochondria. 3. What happens to the Golgi during the M phase? a. Breaks down using fragmentation into vesicles which are distributed to the daughter cells. 4. What happens to the ER during the M phase? a. Goes through reorganization and fragmentation into smaller vesicles which are then distributed to the daughter cells. 5. What is cytokinesis? What proteins aid this process in animal cells? What aids this process in plant cells? a. When the cytoplasm is split to form the two daughter cells. In animals, it’s initiated by a contractile ring made of actin filaments and myosin motors. In plant cells, it’s initiated by the fusion of vesicles filled with polysaccharides and glycoproteins. Lecture 20: Cell Death Compare and contrast apoptosis and necrosis 1. What is apoptosis? How is it different from necrosis? a. Programmed cell death. Necrosis is cell death when it experiences injury or infection. 2. Which cell death pathway induces inflammation? a. Necrosis  3. Do healthy cells undergo apoptosis? a. Yes. 4. What is apoptosis used for? a. It prevents uncontrolled growth. It’s a safety system to remove cells that have lost their normal communication and control. Helps regulate cell numbers and tissue morphology. 5. What changes does a cell undergo during apoptosis? a. The cell membrane bulges. The cell shrinks and condenses apoptotic bodies. Phagocytosis takes back things the cell may need before the contents leak. Understand how cells commit apoptosis and describe the basic processes that give rise to apoptosis. 1. What are the proteins that trigger apoptosis called? a. Caspases 2. How are initiator caspases activated? What do these activated initiator caspases do? a. Become activated after receiving the apoptosis signal. They cleave off and activate other executioner caspases, leading to a cascade of activation. 3. What do active executioner caspases do to initiate cell death? a. Coordinate the destruction of key cellular structures. Golgi fragmentation, action bundle contraction, ER fragmentation, translational shutdown, plasma membrane flip, etc. 4. What are the two main signaling pathways for initiating apoptosis? Example?  a. Intrinsic, internal cell stress/damage: DNA damage, oxidative damage, or other stresses b. Extrinsic, extracellular signals: developmental signals 5. Permeabilization of mitochondrial membrane is seen in which apoptotic signaling pathway? What is released as a result of this and what is its purpose? a. Intrinsic. Cytochrome C is released which activates caspases to start cell death. 6. If you find cytochrome C in the cytoplasm, what does it tell you about the status of the cell? a. It has been released from the mitochondria and apoptosis has started. 7. When extrinsic signals of apoptosis are present, what detects these signals in the target cells? a. Death receptors 8. How do extrinsic signals trigger apoptosis? a. Extrinsic signals of apoptosis are detected by death receptors (Fas) on the cell surface, which recruit adaptor proteins like FADD to form the death-inducing signaling complex (DISC). This activates initiator caspases (caspase-8), triggering a cascade of executioner caspases that dismantle the cell and induce apoptosis. Describe some cellular markers of apoptotic cells that can be used to identify them. 1. What are some standard markers of apoptotic cells?  a. Phosphatidylserine is flipped to the outside of the cell. 2. How does the cell membrane change during apoptosis? What dye can be used to detect this change? a. Annexin V is a dye that can’t pass the membrane but it binds to phosphatidylserine. During apoptosis, the membrane becomes permeable to dyes. The dye will bind to PS and we can tell it’s going through cell death. 3. How does the nuclear DNA change during apoptosis? How can this change be detected by flow cytometry? a. The DNA goes through fragmentation. Flow cytometry can be used to identify cells that have been dyed with DNA dye. 4. Analyze flow cytometry data to identify apoptotic cell populations. a. ok 5. What other technique and marker can be used for analyzing apoptosis? a. Immunoblotting. Cell extracts are treated with cytochrome C, then the samples are analyzed by immunoblotting with an antibody for caspase. Lecture 21: Meiosis Compare and contrast mitosis and meiosis. Feature Mitosis Meiosis Purpose Growth, repair, and Production of gametes for asexual reproduction sexual reproduction Number of Divisions One Two Number of Daughter Cells Two Four Daughter Cell Type Diploid, genetically Haploid, genetically identical to the parent distinct from parent Genetic Variation None, clones Has variation due to crossing over Chromosome Number The same # of Reduces the number of chromosomes as the chromosomes in half parent Crossing Over Doesn’t happen Happens during prophase 1 Phases Prophases, metaphase, Prophase 1&2, metaphase anaphase, telophase 1&2, anaphase 1&2, telophase 1&2 Homologous Do not pair Pair and separate during Chromosomes Behavior meiosis 1 Occurs in Somatic cells Germ cells Distinguish between the mechanisms of meiosis 1 and meiosis 2 1. Meiosis I is the reductional division, where homologous chromosomes pair up, exchange genetic material through crossing over (in prophase I) and are then separated into two daughter cells, reducing the chromosome number by half (diploid to haploid).  2. Meiosis II is the equational division, similar to mitosis, where the sister chromatids of each chromosome are separated and distributed into four haploid daughter cells. Meiosis I ensures genetic diversity through recombination and independent assortment, while meiosis II ensures that each gamete receives a single copy of each chromosome. Understand the consequences of genetic diversity generated during meiosis 1. Genetic diversity allows for the next generation to have a unique genetic combination. It can give them a better genome set based on their environment. Appreciate the consequences of errors during meiosis 1. Errors in chromosome segregation happen in about 10% of meiosis in females. Usually, this leads to miscarriage or disease.