Unit 2 Notebook - Cells PDF

Lecture 4 Cells Cell Theory 1. All living organisms are composed of 2. Cells are the smallest unit of 3. New cells come only from pre-existing cells by Microscopy  2 types o Light microscope  uses light for illumination  Magnifies up to 1000 – 2000x...

Lecture 4 Cells Cell Theory 1. All living organisms are composed of 2. Cells are the smallest unit of 3. New cells come only from pre-existing cells by Microscopy  2 types o Light microscope  uses light for illumination  Magnifies up to 1000 – 2000x o Electron microscope  uses a beam of electrons for illumination  Magnifies up to 20,000 – 100,000x  Light microscope o advantage: can view organisms o disadvantage: limited magnification prevents seeing and smaller organisms  Electron microscope types o Scanning electron microscope (SEM)  advantage: can view high magnification of  disadvantage: views only o Transmission electron microscope (TEM)  advantage: can view inside the cell  disadvantage: views only slices Cell structures  All cells have these four structures: o o o o  Structures of cells are called which means “little organs” o each performs a specific function for the cell Basic cell types  cells: “before the nucleus” o simple cell structure o have a nucleus: do not have a nuclear membrane around the DNA  Eukaryotic cells: “ nucleus” o more complex cells o a nucleus with a nuclear membrane around the DNA Prokaryotic cells  Two categories of prokaryotes: o Bacteria  Small cells, 1 μm – 10 μm in diameter  Very in environment and our bodies  Vast majority are harmful to humans  Some species cause disease o Archaea  Also small cells, 1 μm – 10 μm in diameter  Less common  Often found in environments  Prokaryotic cell structure o Plasma membrane: regulates the of substance in and out of cells o Cytoplasm: everything contained within the membrane o Nucleoid region: region in the cytoplasm where is located o Ribosomes: organelles that synthesis o Cell wall: rigid structure outside of the plasma membrane that the cell and helps maintain its shape o Capsule: jellylike coating that protects the cell from and physical damage and also helps to evade the immune system o Pili: appendages used for o Flagella: appendages used for Eukaryotic cells  Vary in shape, size, and organization depending on cell type and species  DNA is enclosed inside a  Many of the cell’s organelles are surrounded by membranes which the cell  Cell membranes o Divide cytoplasm into compartments o Each compartment can then perform different  Structures of eukaryotic cells o Plasma membrane: what substances can move in/out of the cell  also used for cell adhesion  also used to send/receive signals in/out of the cell o Cytoplasm: includes inside the plasma membrane (cytosol, organelles, cytoplasm)  o Nucleus  Nuclear membrane: structure enclosing the nucleus.  Nuclear pore: regulates substances in/out of the nucleus  Chromatin: Stretched out. When condensed, called chromosomes o Ribosomes: site for synthesis to take place o Endoplasmic reticulum (ER):  ER: studded with ribosomes and functions in protein synthesis and sorting  smooth ER lacks ribosomes and functions in the synthesis and modification of o Golgi bodies (complex): stack of flattened, membrane bound compartments  transport materials between stacks  function in packaging, processing, and proteins to locations inside or outside of the cell o Lysosome: contains that perform hydrolysis to digest damaged organelles or bacteria o Mitochondria:  “ ” of the cell  Makes o Cytoskeleton: 3 types of fibers in the cell that supports, organizes, and moves cell structures  Example: microtubules o Motor proteins: Transport from one part of the cell to another on the o Centrosome: Region of the cell ( ) where microtubules are formed and radiate outward o Flagella: involved in cell movement o Cilia: short, tend to cover all or part of the cell surface; involved in cell movement or attachment  Structures unique to animal cells (not in plant cells) o Lysosomes o Cilia/flagella  Structures unique to plant cells (not in animal cells) o : provides structure, support and protection to the cell o Plasmodesmata: between plant cells for communication o Central vacuole: and support o Plastids (3 types depending on what type of plant cell):  chloroplast: found in green plant cells and contains the pigment  chromoplast: fund in cells and contains the pigment carotenoids  amyloplast: found in potato cells and stores Lecture 4: Activity 1 – Prokaryotic cell Using the word bank, label the prokaryotic cell from memory. Check your notes to make sure it is labeled correctly. Word Bank: Capsule Cell wall A= Flagellum B= Nucleoid (DNA) C= Pili D= Plasma membrane E= Ribosomes F= G= Lecture 4: Activity 2 – Eukaryotic animal cell Put the number that corresponds to the structure next to the name of the structure. Then match the structures with their correct functions (you can pick the text boxes up to move them or use lines to connect). Letter STRUCTURES FUNCTIONS Centrosome Organelle that contains genetic material. Chromatin Cytoplasm Organelle that Organelle that makes makes ATP. lipids.Powerhouse of the cell Golgi complex Genetic material (DNA) wrapped around proteins. Mitochondria Microtubule organizing center where centrioles are located Nucleus Organelle studded with ribosomes that makes proteins. Plasma membrane The liquid and organelles located inside the cell membrane. Ribosomes Organelle that packages and ships proteins. Rough ER Tiny organelles that make proteins. Smooth ER Structure surrounding the cell that regulates what can enter and leave the cell Reference. Molecular Biology. OpenStax. CC BY 4.0 Lecture 4: Activity 3 – Eukaryotic Plant Cells Use the word bank to label the plant cell. Try to do it from memory, but you can use your notes to check your work. Cell wall Mitochondria Central Vacuole Nucleus Chloroplast Plasma membrane Cytoplasm Ribosomes Cytoskeleton Rough ER Golgi complex Smooth ER A= B= C= D= E= F= G= H= I= J= K= L= Unit 1 Exam Review – Lecture 4 1. List the three parts of cell theory. 2. Answer the following questions regarding light and electron microscopes. a. What type of microscope magnifies better? b. What type allows you to view living organisms? c. What type allows you to view 3D surfaces? d. What type would you use to view organelles inside a cell? 3. What four structures are found in all cells? 4. What is the main difference between prokaryotic cells and eukaryotic cells? 5. What are the two types of prokaryotic cells? 6. Organelles being surrounded by membranes allows cells to perform different in each compartment. 7. Be sure to review the information from lecture 4 activities 1, 2, and 3. Be able to label the three cell types and learn the functions from activity 2. 8. Match the organelle or structure to the function.  9. Try labeling the three cell types without looking at your notes. A= 1= B= 2= C= 3= D= 4= E= 5= A= F= 6= B= G= 7= C= 8= D= 9= E= 10= F= G= H= I= J= K= L= Lecture 5: Membrane Transport To-do list  Membrane structure  Membrane transport  Bulk transport Membrane Structure  The membrane is a  Phospholipids are molecules o region faces in away from the water o region faces out towards the water  Four membrane components  o Phospholipids: main component o : transport, attachment, enzymes o Carbohydrates: self-markers, receptors  Attached to a protein:  Attached to a lipid: o Cholesterol  Amphipathic molecule  Only found in  plasma membrane  Fluidity of membranes o Membranes are and highly o Lipids rotate freely around their long axis and within the membrane leaflet o of lipids from one leaflet to the opposite leaflet requires and Membrane Transport  The plasma membrane is (allows passage of some ions and molecules but not others)  Passive transport o Requires (no ATP needed) o Moves the concentration gradient (high  low) o 2 types  Simple diffusion  Facilitated diffusion o Simple diffusion  Requires  Moves the concentration gradient  can diffuse directly through the membrane (must be nonpolar) o Facilitated diffusion  Requires   Moves the concentration gradient  Some solutes diffuse through the membrane with the help of a o Osmosis: facilitated diffusion of across the membrane through the help of protein  Tonicity: the measure of (effect surrounding solution has on a cell)  Isotonic: solute concentrations on both sides of the membrane (in and out of cell)  Hypertonic: Solute concentration is in solution outside of the cell  Hypotonic: Solute concentration is in solution outside of the cell  Osmosis in freshwater protists  Freshwater protists have to survive in a strongly  To prevent osmotic lysis, take up water and discharge it outside the cell  Using vacuoles to remove excess water maintains a  Active Transport o Requires (uses ATP) o Moves the concentration gradient o Goes through  Bulk Transport  Exocytosis: Material inside the cell is packaged into and excreted out of the cell  Endocytosis: Material outside the cell enters the cell and is transported through the cell in a vesicle o : cell eating (solid particles) o Pinocytosis: cell (liquid) o Receptor-mediated endocytosis: requires receptors and clathrin Prof Will provide Activities 1 and 2! Unit 2 Exam Review – Lecture 5 1. Define the term amphipathic molecule and give two examples. 2. List four main components of cellular membranes and state their functions. 3. What is the purpose of a self-marker? 4. What are two requirements for flip flop of lipids to take place? 5. What do I mean by moving “with” the concentration gradient? 6. What are the two types of passive transport, and which requires a protein channel to take place? 7. Beneath each image, state the tonicity of the solution and whether the water is moving into or out of the cells. 8. What structure is needed for freshwater protists to prevent bursting? 9. What structure is used for the bulk transport of substances in and out of the cell? 10. Name three types of endocytosis and state what type of substance is being transported. 43 Lecture 6: Energy, Enzymes, and Metabolism Energy = ability to promote change or do work  Kinetic energy =  Potential energy = due to structure or  Chemical energy = the potential energy stored in  Free energy = the portion of a system’s energy that is available to do work Chemical reactions  Exergonic reactions = o Free energy is by reaction o Example: the hydrolysis of ATP  Endergonic reactions = o Energy is to drive reaction (absorb energy) o Example: the production of ATP  Rate of a reaction o A reaction may be but it could take years to occur o One solution to this problem is Enzymes  Catalyst = an agent that the rate of a chemical reaction being consumed during the reaction  Enzymes = catalysts in living cells  Ribozymes = with catalytic properties  Activation energy o An initial input of energy is needed to start a reaction this is NOT o Common ways of overcoming activation energy  Large amounts of  Using to lower activation energy o How enzymes lower activation energy  in reactants  Expose reactants to environment  reactants together to facilitate bonding  Enzymes: o DO reactions o Do NOT supply to a reaction, so they CANNOT make an reaction occur spontaneously 44  Enzyme properties: o Enzymes are very specific: only bind to its (enzyme catalase only breaks down substrate hydrogen peroxide) o After the reaction, enzymes are released and can continue to catalyze further reactions o Enzymes are affected by the environment  Most enzymes function maximally in a of temperature and pH  Inhibitors also affect enzyme function  Competitive inhibitors bind to the and prevent the substrate from binding  Non-competitive inhibitors bind to the and alters the shape of enzyme so the substrate cannot bind Metabolism  Metabolic pathway = a set of. Each reaction is coordinated by a specific.  Metabolic pathways in cells perform a specific purpose and are very well controlled  Two types of metabolic pathways o Catabolic pathway - reactants or cellular components   Used for building blocks  Used for to drive endergonic reactions o Anabolic pathway - reactants or cellular components   These pathways must be coupled with reactions for the free energy required to drive the reaction 45  Name Date: Analyzing Graphics: Enzymes 1. Enzymes act on substrates. Label the enzyme, substrate, active site, and products on diagram. Answer true or false to the following statements based on the graphic: a. Enzymes interact with many different substrates. b. Enzymes change shape after a reaction occurs. c. An enzyme can be reused with a new substrate. d. The substrate is changed in the reaction. e. If the shape of the enzyme changed, it would no longer work. f. When all substrates are used, the reaction stops. 2. Enzymes speed up the reaction by lowering the activation energy needed for the reaction to start. Compare the activation energy with and without the enzyme. Identify the part of the graph that shows: a) Overall energy released during reaction b) Activation energy with enzyme c) Activation energy without enzyme www.biologycorner.com 46 3. Enzymes work best at optimal temperature and pH values. For example, the enzyme, pepsin, in your stomach must be able to function in a highly acidic environment to break peptide bonds found in proteins. Acidic or basic conditions can disrupt the hydrogen bonds between the loops of the protein chains. If this disruption occurs near the active site, the enzyme can become distorted and not fit the substrate perfectly. The rate of reaction is reduced as more enzymes become denatured. a) What is the optimal pH for pepsin? For lipase? b) Do you think lipase is an enzyme that is found in the stomach? Why or why not? 4. Enzymes can be inhibited. Inhibitors can slow down or stop enzymatic reactions. There are two types of inhibition: competitive and allosteric. Answer true or false to the following statements based on the graphic: a) Increasing the number of inhibitors will decrease the overall rate of reaction. b) Allosteric inhibitors block the active site. c) Allosteric inhibitors change the shape of the enzyme. d) Adding a competitive inhibitor will increase the number of products in the reaction. e) Competitive inhibitors bind to the substrates. www.biologycorner.com 47 Unit 2 Exam Review – Lecture 6 1. What type of potential energy is found stored in molecular bonds? 2. Free energy is the energy available to do work. Answer the following questions about free energy. a. What type of chemical reaction releases free energy (get energy from reaction)? b. To release free energy, is a bond broken or made? c. What type of chemical reaction requires free energy to drive the reaction (lose energy from reaction)? d. Is a bond being broken or made during the type of reaction from question 2c? 3. Describe what is occurring in the image below. Include the following terms: exergonic, endergonic, hydrolysis, dehydration synthesis 4. List three ways enzymes help to lower activation energy. 5. True or false. Enzymes can drive an endergonic reactions by supplying free energy. 6. Review lecture 6 activity 1. Be sure to study all of the material covered in the activity. Then, for extra practice, label the image below. A= B= C= D= 7. What is the difference between catabolic and anabolic pathways? 48 Lecture 7: Photosynthesis Energy  All of life requires energy to grow, reproduce, and carry out other processes that are essential to life  Not all forms of energy can be used to sustain life o Sunlight is an abundant source of energy on Earth, but it cannot directly power and other such reactions that organisms need to stay alive o Sunlight has to be converted into (stored in bonds)  Energy flows through the ecosystem starting with autotrophs o make their own food by harvesting energy from the environment o Most autotrophs get energy from the sun using o Photosynthesis is a metabolic pathway that uses energy from the sun to make from water and CO2 o Autotrophs get energy directly from the sun o must consume autotrophs or other heterotrophs to get energy Composition of light  Light energy travels in  Wavelength: distance between the crests of waves  In the electromagnetic spectrum, wavelength varies from less than a nanometer (gamma rays) to more than a kilometer (radio waves)  Visible light: Photosynthetic pigments  A is a substance that absorbs light energy  Four pigments embedded in the membranes of are involved in plant photosynthesis o 2 chlorophylls:  chlorophyll a  chlorophyll b o 2 carotenoids:  beta-carotene  xanthophyll Wavelengths of light in photosynthesis  Objects appear colored to an observer because they absorb certain wavelengths of light and transmit (reflect) others  is absorbed and used in photosynthesis  used in photosynthesis since it is reflected by the pigment chlorophyll Fall colors  Plants that change color in fall is preparing for a state of dormancy during winter  The nutrients are removed from delicate leaves (could be damaged by cold) into protected parts (like roots) 49  Chlorophyll is not needed during the dormant period and is broken down exposing other photosynthetic pigments that are not usually visible (yellow and orange)  Some plants even begin to make a red/purple pigment called anthocyanin Photosynthesis  Two main steps: o Light reactions o Light independent reactions ( )  Light dependent: o Entering reaction: o Leaving reaction:  Light independent: o Entering reaction: o Leaving reaction: Chloroplasts  Light dependent reactions occur across the  The thylakoid membrane contains millions of light-harvesting complexes that contain the pigment that is needed to harvest light energy  Light independent reactions occur in the of the chloroplast Photosynthesis  “photo-” in photosynthesis means light o The first step requires energy from to drive the reactions o Energy is going into the reaction  endergonic or exergonic? o The energy is needed to use water to make o ATP and NADPH are two molecules that can store the energy to be used in the next step  “-synthesis” from the word photosynthesis means to something o The second step of photosynthesis requires the energy from from the first step to drive the reactions o The energy is needed to use CO2 and water to make Photosynthesis reactants  How do plants get the reactants in the equation?  Plants take in CO2 and release O2 through tiny openings on the underside of leaves called  Plants take in water through the 50 Lecture 7: Activity 1 1) What do you think would happen if autotrophs did not exist? 2) What do you think would happen if herbivores did not exist? 3) What do you think would happen if predators did not exist? 4) What do you think would happen if decomposers (detrivores) did not exist? Activity 2 Label the chloroplast with the following terms: Granum Intermembrane space Stroma Inner membrane Outer membrane Thylakoid 51 Use the word bank to complete the image on the next page. ATP CO2 Glucose Light dependent reactions Light independent reactions Oxygen Thylakoids Water Light 52 53 Unit 2 Exam Review – Lecture 7 1. Almost all of life is reliant on energy. The energy is then converted into to be stored for later use. When the energy is needed, it is converted to the energy currency of the cell. 2. How do autotrophs get energy? How do heterotrophs get energy? 3. What part of the electromagnetic spectrum is used for photosynthesis? 4. List the four pigments involved in photosynthesis. 5. What color of light is NOT used for photosynthesis? 6. Why do leaves change colors during the fall season? 7. What is the chemical formula for photosynthesis? Put a circle around the reactants and a square around the products. 8. Photosynthesis is divided into two main parts: light dependent and light independent reactions. Answer the following questions about the two parts. a. Where do each set of reactions occur? b. What energy is used to drive the light dependent reactions? c. What molecules provide energy for the light independent reactions? 9. Light dependent reactions are part of an electron transport chain. The first step of this process is the hydrolysis of water that results in: a. that adds to the concentration gradient b. which is a byproduct of photosynthesis c. that move through the transport proteins to provide energy to pump H+ across the membrane 10. When H+ moves back across the membrane with its concentration gradient, it moves through an enzyme called that makes. 11. What reactant of photosynthesis is turned into sugar during the light independent reactions? 54 12. Label the image using the word bank. ADP H2O O2 ATP NADP+ sugar CO2 NADPH A= B= C= D= E= F= G= H= 55 Lecture 8: Cellular Respiration The Mighty Mitochondrion Cellular respiration – Two types:  Aerobic respiration  Anaerobic respiration Aerobic respiration  Uses to make cellular energy   Main form of energy production in eukaryotes and some prokaryotes  Very efficient at making ATP Anaerobic respiration  Prefix “an-”  “without”  Making cellular energy  Not as efficient as aerobic respiration  Main form of energy production in some prokaryotes  Why don’t prokaryotes use aerobic if it is so much more efficient than anaerobic? Aerobic respiration 3 stages:  Glycolysis  Citric acid cycle  Oxidative phosphorylation Glycolysis  Glyco = sugar; lysis = break down  Occurs in  is split into 2  Get 2 ATP from this step Krebs cycle  Occurs in the mitochondrial  Pyruvate is used to make: o 2 ATP o Several NADH and FADH2 to be used later 56 Oxidative phosphorylation  Also called  Occurs in the  32-34 ATP made in this step  Series of proteins that pick up and release electrons from until they transfer them to their final acceptor ( )  Energy from transfer of electrons is used to make a H+ gradient  As H+ flow back into the mitochondrial with their concentration gradient, energy is released to make Anaerobic respiration  Some prokaryotes use molecules other than oxygen as the final electron acceptor  Amount of ATP produced by anaerobic respiration is much than the amount produced by aerobic respiration (not as efficient)  If O2 is not available, electrons can be transferred to an organic molecule instead of going through the  Produces 2 ATP  Two types of anaerobic respiration: o Lactate fermentation – occurs in skeletal muscle o Alcoholic fermentation – occurs in yeast Can molecules other than glucose be used to make cellular energy (ATP)? How? Prof will provide Activity 1 and 2 60 Lecture 8 Activity 3 Photosynthesis Cell Respiration Formula Reactants Products Location Function Found in Animal, Plants or Both Complete the cycle below using the terms: cellular respiration, CO2, glucose, O2, photosynthesis and water 61 Unit 2 Exam Review - Lecture 8 1. What are two types of cellular respiration? Circle the type that requires oxygen. 2. Write the formula for aerobic cellular respiration. Circle the reactants and put a square around the products. 3. Complete the table below about aerobic cellular respiration. Stages # ATP Location Starts with Ends with Glycolysis glucose Krebs cycle Electron transport system 4. Describe the electron transport system of aerobic cellular respiration. Be sure to include the terms: final acceptor, concentration gradient, and ATP synthase. 62 5. Complete the table comparing aerobic and anaerobic respiration. Type of Example # ATP Final Byproduct Examples of products cellular organism acceptor respiration Aerobic Human (most cells) Lactic acid Human fermentation (muscle cells) Lactic acid Yeast fermentation (Lactobacillus) Alcoholic Yeast fermentation (Saccharomyces) 6. Glucose is not the only molecule we ingest. What other types of molecules can be used for aerobic cellular respiration? 63