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Week 3 Notes Shaffer Bio Sci 93

by: Dana Roach

Week 3 Notes Shaffer Bio Sci 93 Bio Sci 93

Marketplace > University of California - Irvine > Biology > Bio Sci 93 > Week 3 Notes Shaffer Bio Sci 93
Dana Roach

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Here are the notes from Week 3 after our Midterm
Class Notes
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This 12 page Class Notes was uploaded by Dana Roach on Sunday October 18, 2015. The Class Notes belongs to Bio Sci 93 at University of California - Irvine taught by WOOD, M., GREEN, K., BUSCIGLIO, J. in Fall 2015. Since its upload, it has received 17 views. For similar materials see DNA TO ORGANISMS in Biology at University of California - Irvine.

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Date Created: 10/18/15
Week 3 Notes Reading guide for lesson 7 Chapter 6 pages 97 to 112 Complete this reading guide as you read the textbook pages listed above You might not have to read every word on every page rather pay close attention to the questions in this guide and answer them as you work through the textbook Also pay close attention to the terms that are underlined these are key terms that you should know the de nitions of and be able to apply in new situations Start at concept 62 on page 97 De ne the following components that all cells have Plasma membrane membrane enclosing the cytoplasm Cytosol semifluid jellylike substance in which subcellular components are suspended Chromosomes structures that carry genes in the fOrm of DNA Ribosomes tiny complexes that make proteins according to instructions fOrm the genes How are eukaryotic cells different from prokaryotic cells We are skipping the details on prokaryotic cells for now we will come back to them later in the class Eukaryotic cells contain the organelle called the nucleus in which most of the DNA is stored whereas in a prokaryotic cell it is stored in the nucleoid Furthermore eukaryotic cells lack flagellum fimbriae and a cell wall all of which prokaryotic cells have Skip to gure 68 on page 100 Examine the animal cell in Figure 68 on page 100 This is a overview gure that will be useful as a reference point as you read about organelles in next few pages We are skipping plant cells for now we will come back to them when we talk about photosynthesis later in the class Describe the structure and function of each of the following cellular components Examine Figure 69 for visual representations of these structures Nucleus Circular structure in the center of the cell comprised of the nuclear envelope nucleolus and chromatin The nucleus is the storage facility of DNA and the starting point fer DNA translationtranscription and protein synthesis Nuclear envelope double membrane enclosing the nucleus separating it from the cytoplasm perfbrated by pores continuous with Endoplasmic Reticulum ER Each membrane is a lipid bilayer with associated proteins are separated by a space of 2040nm The nuclear side of the envelope is lined by the nuclear lamina netlike array of protein filaments that maintains the shape of the nucleus by mechanically supporting the nuclear envelope Nuclear matrix a framework of protein fibers extending Nucleolus Nonemembranous structure involved in the production of ribosomes a nucleus has one or more nucleoli Ribosomal RNA is synthesized in here Chromosomes structures that carry the genetic infbrmation Chromatin material consisting of DNA and proteins visible in dividing cell as individual condensed chromosomes proteins that make up chromosomes How are molecules regulated from entering exiting the nucleus Pore complex lines are intricate protein structures that plays an important role in cell entry and exit regulation including proteins and RNAs as well as large complexes of macromolecules Answer concept check 63 question 3 on page 104 in the space below 3 On a molecular level it becomes more condensed chromatin material which you can see What are ribosomes made of Where do these components come from What is the major function of ribosomes Examine Figure 610 for visualizations of ribosomes They are made of two subunits of ribosomal RNA and proein What is the difference between free and bound ribosomes One is free and floating in the cytoplasm the other is bound to the endoplasmic reticulum What components of the cell are part of the endomembrane system What functions does the endomembrane system perform in the cell Nuclear envelope the endoplasmic reticulum the Golgi apparatus lysosomes vesicles and vacuoles and the plasma membrane Synthesizes proteins transports proteins into membranes and organelles or out of the cell metabolism and movement of lipids and detoxification of poison Describe the structure and function of the smooth endoplasmic reticulum See Figure 611 for a view of the smooth ER Smooth ER is a component of various metabolic processes including the synthesis of lipids metabolism of carbohydrates detoxification of drugs and poisons and storage of calcium ions It is like the Rough ER but lacks ribosomes on the outside Describe the structure and function of the rough endoplasmic reticulum ER See Figure 611 for a view of the rough ER Studded with ribosomes Glycoprotein production and phospholipid production and vesicle production Write one sentence comparing the smooth and rough ER Smooth lack ribosomes and is pertinent to ion storage and detoxification where as rough ER is pertinent to protein production Describe the structure and function of the Golgi apparatus What is the difference between the quotcisquot and quottransquot sides of the Golgi apparatus See Figure 612 for a view of the Golgi It is the warehouse fbr receiving sorting shipping and manufacturing Products of the ER come here and are modified and stored and then sent off to other parts of the cell Manufacture some macromolecules like polysaccharides Consists o f flattened membranous sacs cisternae These sacs on opposite sides of the stacking differ in thickness and molecular composition Cis and Trans face Cis on the same sidefuse with the Golgi apparatus trans give rise to vesicles that pinch off and travel to other sites Describe the path that vesicles may take from the ER through the Golgi apparatus and to other parts of the cell Molecular identification tags are added to golgi products to distinguish where they are being sent to The vesicles also have docking sites on other organelles that they target How might biomolecules be modi ed as they pass through the Golgi apparatus Their carbohydrates may be modified by removing sugar monomers and substituting others Describe the structure and function of lysosomes See Figure 613 for a view of lysosomes Membranous sac of39hydrolytic enzymes that are used to digest macromolecules Some are made from budding from the trans face of the Golgi apparatus Lysosomes carry out intracellular digestion by fusing with food vacuoles from phagocytosis Compare and contrast the processes of phadocvtosis and autophagy Phagocytosis is of food autophagy is breaking down broken organelles What are vacuoles How do they function in animal cells Large vesicles derived from the ER and Golgi A Transfer food and water into animal cell Large central vacuole contains cell sap in plant cells and is a repository of inorganic ions Review Figure 615 for a summary of the endomembrane system Answer concept check 64 question 3 on page 108 in the space below 3 mRNA in ER sent to Golgi A modified and then shipped back Describe the function of mitochondria Are they present in animal cells In plant cells See Figure 617 for a view of mitochondria We are skipping chloroplasts for now we will cover them later in the class Mitochondria the sites of cellular respiration metabolic process that uses oxygen to drive the generation of39ATP by extracting energy from sugars fats and other fuels Often called the powerhouse of the cell In plants the chloroplasts are the sites of photosynthesisMitochondria and chloroplast have similar evolutionary origins The endosymbiont theory is a great example of biological evolution Describe the endosymbiont theory in your own words in the space below Endoszmbiont theorv theory that states than an early ancestor of eukaryotic cells engulfed an oxygenusing non photosynthetic prokaryotic cell and eventually formed the relationship with the host cell in which it was enclosed merging into a single organism eukaryotic cell with mitochondria How many membranes does a mitochondrion have What are the roles of cristae and the mitochondrial matrix Two membranes enclose the mitochondrion and are comprised of a phospholipid bilyar with unique embeddd proteins The outer membrane is smooth while the inner membrane is convoluted with folds called cristae The inner membrane divides the mitochondrion in two internal compartments The first is the intermembrane space narrow region between both membranes and the second compartments is the mitochondrial matrix The matrix has lots of different enzymes as well as mitochondrial DNA and ribosomes The enzymes catalyze some steps of cellular respiration The cristae give the inner membrane a larger surface area allowing for more productivity Answer concept check 65 question 3 on page 112 in the space below 3They are not part of the endomembrane system because they have a whole different function and do not participate in protein lipid or macromolecule production and excretion What are peroxisomes How do they function in animal cells Peroxisomes specialized metabolic compartment bound by a single membrane which contains enzymes that remove hydrogen atoms from various substrates and transfer them to oxygen producing hydrogen peroxide As a by product This is used to break down fatty acids into smaller molecules to be transported to mitochondria and used for fuel for cellular respiration They are responsible for alcohol break down In plant cells specialized peroxisomes called glyoxysomes convert fatty acids to sugar Complete the following table to summarize your knowledge of animal cell components Structural What would happen Component description Functions If a cell lost this organelle features component Nucleus Round in the center Store DNA It couldn t produce of the cell with proteins or replicate ribosomes all over it and channeltransport proteins embedded in them Large and small unit Make proteins by Proteins wouldn t R39bosome of protein round transcribing mRNA be produced synthesis of lipids Looks like weird metabdis quot f Toxms WOUId Smooth coral Network of carbohydrates overwhelm the cell endoplasmic membranous sacs detoxification and it would lack reticulum and tubes of drugs and proper nutrient poisons and leveb storage of calcium ions Rough endoplasmic reticulum Like a maze of membranous sacs and tubes studded with ribosomes Glycoprotein production and phospholipid production and vesicle production Proteins could not be produced Golgi apparatus Like pita bread stacks of membranous sacks comprised of the cis medial and trans face Manufacturing labemngand shipping of molecules to parts of the cell or outside the cell Nothing could be excreted out of the cell Round organelle comprised of Breaks down food Toxin build up and L m m m m r n ysoso e pas a e be e and old organelles lack of nutrients and a hydrolytic enzyme Water and food Transports selective Large veSIcles levels would be too solutes act as food derived from ER high and low Vacuole collectors or pump and Golgi respectively and extra water out of Apparatus cell would shut the cell down 2layer m m r n N w r n e b a OUS Produce ATP from 0 p0 9 0t organelle With functioning no sugar fat and other Mitochondrion intermembrane active transport fuels to power the space and levels uneven cell mitochondrion matrix cell death used in break down ofvanous Round organelle substances and Peroxisome comprised of produces hydrogen Toxin build up plasma membrane peroxide as a product then converts it to water Reading guide for lesson 8 Chapter 11 pages 212 226 Complete this reading guide as you read the textbook pages listed above You might not have to read every word on every page rather pay close attention to the questions in this guide and answer them as you work through the textbook Also pay close attention to the terms that are underlined these are key terms that you should know the de nitions of and be able to apply in new situations Start on page 212 local and longdistance signaling How can cells communicate via direct contact How are gap junctions involved in one of these processes See Figure 114 for examples of cells communicating via direct contact They can directly connect to adjacent cells through connecting the cytoplasm of the two cells through what are called gap cell junctions Animal cells also communicate directly through contact between membranebound cellsurface molecules in cell cell recognition Some examples of local signaling include growth factors through paracrine signaling there is also a more specialized farm of local signaling called synaptic signaling in which an animals nervous system sends electrical signal along a nerve cell triggering secretion of neurotransmitters Hormones are used far longdistance signaling such as endocrine signaling How are paracrine signaling synaptic signaling and endocrine signaling similar yet different In which method are hormones used Examine Figure 115 for details Paracrine signaling when numerous cells simultaneously received and respond to the molecules of growth factor produced by a single cell in the vicinity Synaptic signaling in animals nervous system sends electrical signal along a nerve cell triggering secretion of neurotransmitters Endocrine signaling specialized cells release hormone molecules which travel via the circulatory system to other parts of the body where they reach target cells that can recognize and respond to the hormones These are all forms of signaling used between cells in animal cells and use three different methods for sharing information with other cells Do all cells respond to secreted signaling molecules If not why No not all cells respond This is because only some of the cells have the ability to respond which is determined by whether it has the specific receptor needed to bind to the molecule being sent This signal must be conveyed in the binding and transduced inside the cell before it can respond Brie y describe what happens in each of the three stages of cell signaling Refer to Figure 116 for a visual representation of these steps Reception the signaling molecule binds to the receptor protein on the other cell s surface Transduction The receptor protein then changes initiates transduction in which the signal is converted to a form the elicits specific cellular response If transduction requires more than one change a sequence of changes in a series of different molecules this is called a transduction pathway Response when the transduced signal finally triggers a specific cellular response which could be almost any kind of cellular activity What is a signal transduction pathway If transduction requires more than one change a sequence of changes in a series of different molecules this is called a transduction pathway What is a ligand and how does it interact with cells Ligand a molecule that specifically binds to another molecule often a larger one Ligands bind to other cells and causes a receptor protein to undergo a change of shape sometimes directly activating the receptor allowing it to interact with other cellular molecules For other receptors it can lead to aggregation of two or more receptor molecules leading to molecular events inside the cell Where can receptors be found within a cell There are receptors embedded in the plasma membrane but there are also some located inside the cell What is the largest family of human cellsurface receptors G proteincoupled receptors GPCRs How does a G proteincoupled receptor GPCR function as a receptor Summarize the four steps listed in Figure 118 on page 215 in your own words It functions as a receptor by lLoosely attached to cytoplasmic side the G protein acts as a molecular switch depending on which of the two guanine nucleotides is attached GDP inactive vs GTP active 2Bonding to the extracellular side of the receptor activates it and it changes shape cause GTP to displace GDP 3Active GTP disassociates from the receptor and then moves down the membrane to bind to an enzyme thus altering it 4 After this interaction it returns to GDP inactive state and moves to original position What happens if cellsurface receptors such as GPCRs malfunction Bacterial infections such as cholera whooping cough and botulism make their victims ill by interfering with G protein function Malfunctions could lead to loss of tate smell and vision since these are all dependent on GPCRs Skip section receptor tyrosine kinases and ion channel receptors go to quotintracellular receptors on page 21 7 Where are intracellular receptors found in the cell How do signaling molecules pass through the cell membrane They are found in the cytoplasm or nucleus of target cells To pass through the cell membrane theymust either by hydrophobic enough or small enough to cross Explain how intracellular receptor signaling pathways can turn on or off gene expression See Figure 119 When the aldosterone receptor is activated it acts as a transcription factor that turns on specific genes Transcription factors are specific proteins that control which genes are turned on Answer concept check 112 question 1 on page 218 in the space below lThe receptor would be embedded in the plasma membrane as that s how the molecules would reach it Transduction often involves many steps What are some examples of these steps What is a bene t to having many steps in a pathway Is the original signaling molecule passed along a pathway through the cell Some steps include activation of proteins by addition or removal of phosphate groups or release of other smaller molecules or ions that act as messengers The benefit of having so many steps is the possibility for greater amplification of the signal Passed though a pathway it results in more molecules activated at the end of the pathway What are protein kinases and protein phosphatases How do they contribute to signal transduction pathways What happens when a protein is phosphorylated or dephosphorylated Refer to Figure 1110 for an example of a phosphorylation cascade Protein kinases and enzyme that transfers phosphate groups from ATP to protein Protein phosphatases enzymes that can rapidly remove phosphate groups from proteins through dephosphorylation 2 Dho phorvlation process of removing phosphate groups Phosphorvlation addition of phosphate group to protein which can sometimes decrease activity of protein The two processes in combination act as an onoff switch for signal transduction pathway What are second messengers What are the two most common second messengers Second messengers small non protein watersoluble molecules or ions that are often involved in signaling pathways that can rapidly spread throughout the cell by diffusion cyclic Am and calcium ions What is cvclic AMP CAMP How is it made by adenvlvl cvclase Cyclic adenosine monophosphate cAMP is a compound whose levels rises when epinephrine and plasma membrane biding occurs in liver cells Adenylyl cyclase in the plasma membrane converts Amp to cAMP in response to extracellular signal Summarize the steps in a GPCR initiated CAMP second messenger transduction pathway as shown in Figure 1112 GDP goes to the receptor gets activated as GTP goes to the enzyme in the plasma membrane adenylyl cyclase creating cAMP which then transduces into Protein kinase A and causes cellular responses Skip section on calcium ions and IP3 go to concept 114 on page 223 Where in the cell may the nal response to a signaling pathway occur It may occur in the nucleus of the cell or in the cytoplasm Describe how a signaling pathway may activate gene expression See Figure 1115 for a visual depiction of this process Signaling pathways may activate genes by activating transcription factors Other times it may regulate the activity of proteins rather than their synthesis directly affecting proteins that function outside the nucleus In your own words describe the steps of the stimulation of glycogen breakdown by epinephrine as summarized in Figure 1116 The receptor is activated by GDP which activates the enzyme producing cAMP activating protein kinase activating phosphorylase activating glycogen phosphorylase creating the response of glucose l phosphate being produced How is a response ampli ed through a signal transduction pathway Elaborate phosphorylation cascade enzyme cascades amplify cell s response to a signal because with each step the number of activated products increases dramatically This stems from the fact that they proteins process multiple molecules of substrate before they become inactive and therefore many are activated which activate others before the originals have even become deactivated again Explain how cell signaling is speci c Why don t all cells respond to the same signaling molecules Examine Figure 1117 for a summary the speci city of cell signaling Not all cells respond to the same signaling molecules because different kinds of cells turn on different sets of genes and different kinds of cells have different collections of proteins Certain receptor proteins only accept certain molecules Answer concept check 114 question 3 on page 227 in the space below 3It wouldn t by dephosphorylated so once activated it wouldn t be terminated Read and analyze the quotscienti c skills exercisequot on page 226 You will be answering the questions associated with this exercise as part of your pre class assignment on Mastering Biology You are now ready to complete the precass assignment on Mastering Biology


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