Study Guide Exam 2 PDF

Chapter 5 1. What are the major tenets of the cell theory? - Cell theory is an important unifying theory of biology: - Cells are the fundamental units of life - All organisms are composed of cells - All cells come from preexisting cells - Modern cells evolved from a...

Chapter 5 1. What are the major tenets of the cell theory? - Cell theory is an important unifying theory of biology: - Cells are the fundamental units of life - All organisms are composed of cells - All cells come from preexisting cells - Modern cells evolved from a common ancestor 2. Why is surface area so important in cell function? - Cells constantly interacting with the external environment; it needs resources from the external environment, and it has to release things out to the external environment - The cell surface area is at the point where there is interaction between the environment and the inside of the cell - Volume of a cell increases at a rate than is large than the area of the cell, there is point where the inside of the cell becomes too large to have an effective amount transfer of nutrients inside and outside of the cell. - Most cells are small because of a high surface area- to volume ratio is essential - As volume increases, chemical activity increases, along with the need for resources and waste removal - Surface area becomes limiting. Thus, large organisms consist of many small cells 3. Distinguish between magnification and resolution, what are the advantages of the light and electron microscope a. To see most cells, we use microscopes, i. Magnification: increases apparent size ii. Resolution: Clarity of magnified object -- minimum distance two objects can be apart and still be seen as two objects b. Two basic types of microscopes: iii. Light microscopes: glasses lenses and light; resolution = 0.2 um iv. Electron microscope: electromagnets focus an electron beam; resolution = 0.2 nm c. Many different techniques can be used in microscopy 4. What is the primary function of the cell membrane? - The cell membrane: - **A selectively permeable barrier (key)** - **Based on interaction with environment, protein that are found on the surface, the protein that can come in and out of the cell are strictly regulate; The cells need something it can pull it in, if it doesn't need something it can push it out. It maintains things are generally inside on the inside, and what's out, being outside.** - Allow cells to maintain a constant internal environment - Is important in communication and receiving signals - Often has proteins for biding and adhering to adjacent cells 5. Understand the various organelles discussed in the class, distinguish between the various structures. Know the roles for each organelle and general differences in organelles found in animal and plant cells. d. Two types of cells: v. Prokaryotic (Bacteria and Archaea): have no membrane enclosed internal compartment vi. Eukaryotic (Eukarya): have membrane enclosed organelles in which different functions occur e. Features of Prokaryotic cells: vii. Enclosed by a cell membrane viii. DNA located in a region called nucleoid ix. Cytoplasm: the rest of the cell contents x. Ribosomes: site of protein synthesis f. Prokaryotic Cells are the simplest cells xi. Most Prokaryotes have a rigid cell wall outside of the cell membrane xii. Bacteria cell walls contain peptidoglycan, and some have an additional outer membrane xiii. Some bacteria have a slimy capsule of polysaccharides xiv. Bacteria that carry out photosynthesis have an internal membrane system that contains the molecules needed for photosynthesis xv. Cytoskeleton: System of protein filaments that maintain cell shape and play role in cell movement and cell division xvi. Some Prokaryotes swim using flagella, made of the protein flagellin xvii. Pili are hair-like structure projecting from the cells surface. They help bacteria adhere to other cells xviii. Fimbriae are shorter; they help cells adhere to surfaces such as animals cells g. Eukaryotic cells contain organelles xix. Eukaryotic cells are about 10 times larger than those of prokaryote s xx. Membrane enclosed organelles carry out specific unction xxi. Most eukaryotic calls have a similar organelle xxii. Organelles were first studied using light microscopy and then electron microscopy xxiii. Stain target to specific molecules helped determine chemical composition of organelles xxiv. Cell fractionation separates organelles by size or density for chemical analysis xxv. Ribosomes: site of protein synthesis 1. Similar structure in prokaryotes and eukaryotes 2. Consist of two subunits: Ribosomal RNA (rRNA) and more than 50 different protein molecules xxvi. Nucleus -- usually largest organelle 3. Contains most of DNA 4. Site of DNA replication 5. Site where gene transcription is turned on or off 6. Assembly of ribosomes begins in a region called nucleolus 7. The nucleus is surrounded by the nuclear envelope -- double membrane 8. Nuclear pores in the envelope control movement of molecules across the envelope 9. The outer membrane is continuous with the endoplasmic reticulum 10. DNA combines with proteins to form chromatin in long, thing thread chromosomes 11. Before cell division, chromatin condenses, and individual chromosomes are visible in the light microscope Mitochondria presence from in both animal and plant h. Plants cells: xxvii. Cell wall xxviii. Certain vacuoles: small molecules in water are stores, add stiffness to the structure of the plant structure. xxix. Presence of Chloroplast: photosynthesis that occur 6. What is the endomembrane system? - Endomembrane system: interconnected system of membrane enclosed compartments. Important because allow for the proper processing of protein, the coordinate protein folding. - Tiny, membrane surrounded vesicles shuttle substance between various components - In the living cells, the membranes and the materials they contain are in constant motion 7. Distinguish between primary and secondary lysosomes, what is the specific role for each in endocytosis? What is their role in exocytosis? i. Lysosome: Contain digestive enzyme that hydrolyze macromolecules into monomers xxx. Break down large macromolecules and their components into origin building blocks to use for making new molecules. j. Primary Lysosomes: originate from the Golgi apparatus k. Food molecules enter the cell by phagocytosis -- a phagosome is formed l. Phagosomes fused with primary lysosomes to form secondary lysosomes. Enzymes hydrolyze food molecules m. Waste are ejected by exocytosis 8. What is the cytoskeleton? What are the three major categories of cytoskeletal proteins? Know figure 5.17 n. Cytoskeleton serves as a structural unit within inside of the cell; helps maintain cell structure, movement, and it organize the internal components of the cells o. Microtubules: structures found disperse throughout the cells; the road of the cells and all things inside of the cell attach to microtubules; they infrastructure of the cells p. Microfilaments: microfilaments make up the shape of the cell and allow motility and movement of the cell q. Intermediate filaments: underline structure of the cell r. 9. Understand how organelles move within the cell, what is the function of the cytoskeleton in this process? s. Things are carried within the cell along microtubules (road of the cell) by motor protein (translocation across microtubules, through plus or minus of microtubules and cannot move by themselves) 10. What is the extracellular matrix? What is the relationship between the proteins in the cell wall and the proteins in the ECM? t. The extracellular matrix: xxxi. Holds cell together in tissues xxxii. Contributes to properties of bone, cartilage skin xxxiii. Filter materials passing between different tissues xxxiv. Orients cell movements in development and tissue repair xxxv. Plays a role in chemical signing u. Many animals are surrounded by an extracellular matrix composed of fibrous protein such as collagen, gel like proteoglycan and other proteins. v. Cell wall is composed of extracellular matrix protein xxxvi. Rigid but flexible support for plants xxxvii. Barrier to diseases organisms xxxviii. Contribute to plant form as growing cells expand w. Extracellular structures are secreted to the outside of the cell membrane x. Example: the peptidoglycan cell wall of bacteria y. In eukaryotes, extracellular structure consists of fibrous macromolecules embedded in gel like medium 11. What is the theory of endosymbiosis? z. Proposes that mitochondria and plastids arose when one cell engulfed another cell a. Most of the ingested cells genes were transferred to the hosts DNA but the symbionts retained specialized functions Chapter 6 1. Describe the fluid mosaic model. What does each word describe in the plasma membrane? - The fluid mosaic model describes the general structure of biological membranes - Phospholipids form a bilayer which is like lake in which a variety of protein float 2. How can phospholipid structure change the local structure of the plasma membrane? - Phospholipids vary in fatty acid chain length, degree of unsaturation, and phosphate groups - Cholesterol is important for membrane integrity and modulates fluidity - Phospholipids polar, hydrophilic head face outward, and hydrophobic fatty tails that face inward membrane 3. Distinguish between peripheral, anchored, and integral membrane proteins - Integral : some portion of the protein embedded into the plasmid membrane - Peripheral: not embedded into the plasmid membrane; outside or inside of the plasmid membrane but not into the plasmid membrane - Lack hydrophobic regions and do not penetrate bilayers - Peripheral membrane proteins are located on one side of the membrane - Anchored: attached to the membrane and have a part of their structure extended out of the membrane - Covalently attached to fatty acids or other lipids 4. What is a protein domain? What is the role of the transmembrane domain? What are some expected characteristics of a transmembrane domain? a. Transmembrane proteins: extend all the way through the phospholipid bilayer with one or more transmembrane domains i. Hydrophobic bc plasmid membrane has hydrophobic core ii. Both hydrophobic and hydrophilic iii. Allow enter and internation with hydrophobic core inside the plasmid membrane b. Domains inner and outer sides can have different functions iv. Regions serve as functional structure; domain hydrophobic and server purpose hydrophobic environment 5. Understand the role of carbohydrates in cell recognition and adhesion. c. Carbohydrates can serve as modification to protein and other molecules and these modifications by carbohydrate allow structural function and signal functions, and allow for **recognition sites** for other cells and molecules v. Glycolipids -- carbohydrate + lipids vi. Glycoproteins -- carbohydrate (Oligosaccharide) + protein; proteoglycans have a higher percentage of carbohydrate 6. Distinguish between the three major cell junctions. What is the role of each junction is cell function? d. Cells junctions are specialized structures that hold cells together vii. Tight junctions: help ensure directional movement of material 1. The hold plasmid membrane of two cells close together so nothing can passes between in between these cells. viii. Desmosomes: are like spot welds 2. Hold structure of cells togethers ix. Gap junctions allow communication 3. Small molecules to be passed through rapidly between cells, communication hubs but really connection that allow transfer of material 7. What is an integrin? What is the relationship between ECM, cytoskeleton, and integrins? - Integrin protein bind to the matrix outside epithelial cells and to actin filaments inside the cells - Proteins that integrate the interstellar cytoskeleton with extra cellular scaffold - Integrins binds matrix to cell 8. Differentiate between active and passive transport. What is the driving force in passive transport? e. Membranes have selective permeability- some substance can pass through, but not others f. Passive transport -- no energy input require (no effort/energy for the cell for things to pass (example, small ions) ) g. Active transport -- energy require (input of energy to allow things to move across the plasmid membrane) h. Energy for passive transport comes from the concentration gradient 9. What is osmosis? What is the role of solutes in osmosis? Be able to recognize and isotonic, hypotonic, and hypertonic solution. i. Osmosis: movement of water and water can move across plasmid membrane freely j. Osmosis: Diffusion of water x. Depends on the relative concentration of water molecules k. Isotonic: equal solute concentration (no gain or lose water) l. Hypertonic: higher solute concentration, low water m. Hypotonic: lower solute concentration, high water 10. How do carrier proteins and channel proteins help in protein transport? n. Carrier protein: Membrane proteins that bind some substances and speed their diffusion through the bilayer xi. Do work; attach to their cargo and help move the cargo across the plasmid membrane o. Channel protein: integral membrane proteins that form a tunnel xii. Then allows movement across the hydrophobic core 11. Differentiate between the various proteins involved in active transport. Why is primary transport coupled with secondary transport? p. Active transport is directional ( requires energy) It involves three kinds of proteins: xiii. Uniporter- moves one substance in one direction xiv. Symporter -- moves two substances in one direction xv. Antiporter -moves two substances in opposite direction q. Primary active transport requires direct hydrolysis of ATP (to move things around) r. Secondary active transport: energy comes from an ion concentration gradient that is established by **primary active transport** xvi. Second active transport capitalize on concentration gradient and it provided energy necessary to allow transportation of a molecule; to generate that concentration gradient cell has to use primary active transport 12. Differentiate between endocytosis and exocytosis. Know the various mechanisms for endocytosis. s. Endocytosis: Brings molecules and cells into a eukaryotic cell xvii. The cell membrane folds inward or invaginates around the material, forming a vesicle xviii. Phagocytosis: molecules or entire cells are engulfed (large things brought into the cell) xix. Pinocytosis: a vehicle forms to bring small, dissolved substances of fluids into a cells xx. Receptor mediate endocytosis: high specific things are brought into the cell via recognition by a receptor t. Exocytosis: some sort of secretory vehicle that has cargo released outside Chapter 7 1. Define a signal transduction pathway and differentiate the different classes of signaling molecules a. A signal transduction pathway: a sequence of events that lead to a cells response to a signal b. Four different kinds of signals i. Autocrine: signal affects the cells that made them (made by a cell to affect itself) ii. Juxacrine: signals affect only adjacent cells (affect nearby cells) iii. Paracrine: signals affect nearby cells (affect nearby cells - farther out) iv. Hormones: Travel to distant cells, usually via the circulator system 2. Define these terms: receptor, ligand, cross talk, agonist, antagonist, and response. c. Receptor proteins have very specific binding sites for chemical signal molecules or ligands v. Ligands fit a three-dimensional site on receptor and causes the receptor protein to change shape 1. Binding reversible and the ligand is not altered d. Cross talk: interaction between multiple signals pathways; one signaling pathway turns on a cell and response another turns off the; interaction within the pathway e. Agonists: have the same effect as ligand (promote pathway, activate pathway, similar etc.) f. Antagonists (inhibitors) bind to the receptor, preventing the ligand from being binding but not setting off signal transduction g. Response: effect of a signaling pathway on the cell 3. What is the medical relevance of receptor K~D~? h. KD is the dissociation constant, a measure of the affinity of the receptor for its ligand. The lower of Kd, the greater the affinity vi. Some receptors have very low KD values, which allows them to bind at very low ligand concentrations i. Drugs function as ligands KD value is important when determining dosages vii. Minimize harms, maximums the effectiveness 4. Distinguish between the molecules that bind a membrane receptor and the intracellular receptors. j. Membrane receptors: large or polar ligands (e.g, insulin) binds to cell membrane receptors viii. Outside of cell k. Intracellular receptors: for small or nonpolar ligands that can diffuse across the cell membrane (e.g, estrogen) 5. Identify the three receptor classes in Eukaryotes and distinguish between them l. Gated ion channels: allow ions to enter or leave the cell m. Protein kinases receptor: catalyze phosphorylation of themselves and or other proteins, which change their change ix. Phosphorylatte through the signaling pathway n. G protein -coupled receptors: signal binding ot the receptor activates a G protein which then activates an effector protein x. Bind or active protein 6. What is the role of the cascade in the signal transduction pathway? What is the role of second messengers in the cascade? o. Reminder: a signal transduction pathway you have a signal and some receptor that initiate transduction pathway and some sort of response. A cascade is a complicated series of events, where multiple protein involved in passing signal down to signal transduction pathway. Cascade, a single activate receptor can initiate the signaling across multiple different protein which then further down active more protein so it can amplification of the signal during the signaling cascade. p. **Idea: protein cascade allows for the amplification of the signal** q. A signaling pathway frequently involves numerous sequential phosphorylation reactions, or a phosphorylation cascade. a small molecule called a second messenger mediates the signal from the activated receptor to start the signaling cascade that follows inside the cell, such as a phosphorylation cascade. 7. What are the various was in which PIP~2~ can act as a signaling molecule? r. Secon messengers: small molecules that mediate some steps in a cascade s. Pip2 a membrane phospholipid, when hydrolysis break down in two molecules: IP3 (released to cytoplasm) and DAG (in membrane) are secondary messenger that signaling pathway t. Phospholipids inside the membrane can be activated in form two secondary messenger to signal within the plasmid membrane or single inside the cell 8. What is the role of phosphorylation in signaling pathways? u. Protein modification, small molecules including phosphate can be both inhibitor or activation. Addition of phosphate does not mean you are activating a protein. v. Phosphorylation in a signaling pathway induces some sort of response: activation or inhibition 9. What role do cell junctions play in signal transduction? w. Gap junction is a ion channel that allow for the rapid movement of ions across cells or between cells; these junction can allow for communication between two cells x. Cells response to signals by: xi. Opening ions channels xii. Changing enzyme activity xiii. Differential gene expression 10. What was the role of intracellular communication in the origin of multicellular life? y. Intracellular communication is an important first step in the ability of the cells to coordinate; it allows the distribution of work between cells; our bodies are made are organelles responsible for allowing us to think, breath, etc. z. Cells are specialized to carry out function that allow an organ to thrive; specialization of cells, cluster of specialized cell into structures and communication between all of of those cells. In order to that happen, the evolution of multicellular they had to aggregate close enough to interaction and the method for internation is intercellular communication. a. The complicated signaling pathway had to be developed early on the evolution of cells and prior to having specialized cells, tissues, complex multiple cellular live interseullar cellular communication needed to happen.