Molecular Biology Lecture 1: Cell Structure PDF

1.Identify the level of impact for a given scenario in terms of genetics and molecular expression List the levels of the conceptual hierarchy of genetics - Genes are expressed at the MOLECULAR level - Proteins function at the CELLULAR level - Traits are observed at the ORGANISMAL lev...

1.Identify the level of impact for a given scenario in terms of genetics and molecular expression List the levels of the conceptual hierarchy of genetics - Genes are expressed at the MOLECULAR level - Proteins function at the CELLULAR level - Traits are observed at the ORGANISMAL level - Organisms maintain distinctive sets of attributes in the SPECIES - The occurrence of a trait within a species is observed at the POPULATION level Match the details to the corresponding level in the conceptual hierarchy Example: In a given group of 100 individuals, 23% has blue eyes while 47% has brown. What level of conceptual hierarchy are we assessing when we make this observation? - Population level At what level would we observe two different variants for a gene or trait? - Organismal level 2.Summarize the cell structures and functions and Determine the cellular outcomes and cellular behaviors expected for changes in the availability or activity of cellular structures ◦List the cellular structures associated with prokaryotic and eukaryotic cells Prokaryotic Cell: - No membrane-bound organelles - Lack of compartmentalization means cells cant separate contents which impacts biochemical and molecular processes The following is a picture of a prokaryotic cell - No nucleus and the DNA is free in the cytoplasm Eukaryotic Cell - 1. Each compartment is unique to its organelles - 2. Each organelle has a specific job - 3. Each job is specific to maximizing the cells activity - Example: - What type of cell would be expected to have more mitochondria? What function(s) would additional mitochondria enable? - Mitochondria provide energy and Heart Cells need a lot of energy, therefore a lot of mitochondria ◦Match cellular activity with cellular structures Rough ER - Make and package proteins - Ribosomes dock in the membrane - Membrane bound ribosomes synthesize membrane/lysosomal/secreted proteins - Free ribosomes make cytosolic proteins Smooth ER - Detox center, no ribosomes - Metabolism of drugs, lipids, exogenous material - Smooth ER cells exist - in muscles cells to store calcium - In liver to release glucose Golgi - Fedex flattened sac shipping - Sort and Ship proteins - Cis face - Connects rough ER - Trans face - Connects plasma membrane - Many enzymes - Glycosylation of proteins - Synthenzie complex carbs Lysosomes - Digest and Breakdown molecules - Primary lysosome - Not active = no digestion - Secondary lysosome - Active = digestion - Fusion with organelle or vesicle allows for active digestion ◦Identify the consequence for a change in availability or function of a cell structure - Cellular content determines and regulates function (Form=Function) - The presence or absence of organelles is important to function of a cell as part of the specialization and differentiation process - Example cell must lose a certain part of its content, like its nucleus, to become another cell (Red Blood Cells) 3.Explain the process of ribosome anchoring to the rough ER and identify consequences for changes in components involved ◦List the steps of ribosome anchoring and the necessary components to achieve each step - Ribosomes make proteins in the rough ER -> signal recognition particle (SRP) selects and transfers ribosome to the membrane -> docks it on ER - Docking of ribosomes is a conformational change and is mediated by RNA 4.Explain how cellular structures and molecules contribute to the direction and targeting of vesicles and assess the consequences for trafficking if changes to structures and/or molecules occurs ◦Summarize the process of vesicular trafficking/List the steps involved in cellular trafficking via vesicles ◦List the cellular structures involved in vesicular trafficking ◦Match trafficking activity with cellular structures ◦Compare and contrast anterograde and retrograde trafficking in terms of direction, motor proteins involved, and vesicle coat Vesicular Trafficking - How compartments and organelles travel - Anterograde transport - ER -> Golgi -> plasma membrane - Kinesin motor proteins - Retrograde transport - Opposite (membrane -> golgi -> ER) - Dynein motor proteins - COPI and COPII are surface markers for vesicular traffic - COPI is involved in both Antero and Retro transport - Between ER, ERGIC, cis-golgi, and trans-golgi - COPII is involved in Antero transport - Between ER, ERGIC, cis-golgi only - Coats of vesicles = where it goes - Catherin-coated vesicles transport transmembrane proteins (golgi to membrane) - Catherin = to plasma membrane ◦Identify 1 change likely to increase trafficking and 1 change likely to decrease trafficking - Increase trafficking - More ATP available for motor proteins - Decrease trafficking - Less proteins being made, absence of catherin 5.Summarize the mechanisms for the generation of extracellular vesicles in animal and plant cells (links to a future lecture) and explain their role/importance in molecular biology 1.List the 2 mechanisms of animal cell generation of extracellular vesicles  - 1. Endocytosis and formation of early endosome that is transformed into a multivesicular body - 2. Budding of plasma membrane to generate microvesicles 2.Summarize how internal vs. external material can be incorporated into extracellular vesicles - Extracellular vesicles (EVs) are tiny lipid-bound particles released by cells - They can carry various types of cargo, including proteins, lipids, and nucleic acids, both from inside the cell (internal) and from outside the cell (external). 1. Internal Material: ○ Intracellular Cargo: i. This includes proteins, lipids, RNA, and DNA from within the cell. These materials are packaged into EVs during their formation. ii. For instance, as cells produce EVs, they can incorporate internal proteins and nucleic acids into the vesicle. iii. This internal material can be used for intercellular communication, signaling, and even transferring genetic information. 2. External Material: ○ External Cargo: i. This includes substances from the extracellular environment, such as proteins and lipids that are picked up from the cell’s surroundings or from other cells. ii. External material can be incorporated into EVs through processes like endocytosis (where cells engulf extracellular substances) or direct incorporation from the extracellular space. iii. This allows cells to modulate the composition of EVs based on their external environment. 3.List the importance/roles of extracellular vesicles in molecular biology - Communication (transfer of bioactive molecules) - Defense (stimulation of immune response) - Signaling during development (programming)  - Establishment of niches in cancer (metastasis) - Potential in therapeutics/treatment - 1.In a given group of 100 individuals, 23% has blue eyes while 47% has brown. What level of conceptual hierarchy are we assessing when we make this observation? (LO1) - Organismal = visual assessment Population = comparative population - Example: What level of conceptual hierarchy is being described in this situation? 2.What type of cell would be expected to have more mitochondria? What function(s) would additional mitochondria enable? (LO2) - Muscle cells, B cells - More mitochondria = greater capacity to produce energy 3.What type of cell would have expanded smooth ER? What function(s) would additional sER enable? (LO2) - Liver cells (detoxification) - Increased sER = increase capacity for removal of toxins) 4.What would be the consequence if the signal sequence is altered so that it does not associate with the signal recognition particle? If the signal recognition particle could not undergo conformational changes? (LO3) Q1: failure of particle recognition and docking Q2: failure to offload the ribosome at the Er; failure of protein to enter ER downstream consequence: reduced trafficking of proteins to ER; in Q1 only the affected protein/signal sequence would be reduced’ in A2 global reductions in ER protein trafficking could be observed 5.What alterations or functional losses at the cellular level could cause impaired vesicular trafficking? (LO4) - Vesicle coating, ER or golgi function, effects on endo or exocytosis