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Bio Sci 93 Study Guide Mid Term 1 Shaffer

by: Dana Roach

Bio Sci 93 Study Guide Mid Term 1 Shaffer Bio Sci 93

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Dana Roach

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Here is a study guide for Shaffer's first midterm of the Fall 2015 quarter.
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This 32 page Study Guide was uploaded by Dana Roach on Saturday October 10, 2015. The Study Guide 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 148 views. For similar materials see DNA TO ORGANISMS in Biology at University of California - Irvine.


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Date Created: 10/10/15
Bio Sci 93 Study Guide Shaffer Mid Term 1012 Describe the steps of the scienti c process or method in your own words using the terms hypothesis prediction experiment and analysis The Scientific Method is comprised of various steps including Making an observation farming a question from that observation creating a hypothesis possible and falsifiable explanation fer the observation ferming a prediction based on the hypothesis testingexperimenting recording the result and finally analyzing the result The conclusion of this process may lead to more observations and more questions and therefbre lead to further experimentation That is the nature of the scientific method What is the difference between inductive reasoning and deductive reasoning Provide an example of each Inductive Reasoning Deriving generalizations from specific observations Ex The sky is blue Deductive Reasoning Extrapolate specific data from generalizations Ex If the dead battery hypothesis is correct then the flashlight should work if you replace the batteries with new ones Can an experiment prove that a hypothesis is true Why or why not A hypothesis CANNOTbe proven true because we can never control all variables and understand or know why things happen exactly There are good clues provided as to why which are discovered through the scientific method but they cannot be proven as the only influencing factors and therefbre cannot be proven to be true How is the quotrealquot scienti c process or method different from the textbook scienti c process There is typically a lot more backtracking or rethinking or tinkering with a hypothesis the procedures experiment set up etcm With textbook there are only a few steps that move in a fOrward direction Furthermore the scientific process is constantly building upon itself One question leads to an experiment which causes people to ask new questions to test Also science in the real world is influenced by the community and culture which the experiment is taking place in Different cultures will have different things that they consider important and therefore different questions will arise as being important to answer How is a theory different from a hypothesis A hypothesis is a single idea that answers an individual question Hypotheses are very specific but theories on the other hand are much more broad in scope that is general enough to formulate new specific hypotheses from Furthermore theories are generally supported by a larger set or sets of data can be tested over and over again and conclude with the same or similar data Theories because they are so well tested and have recreateable results are often adopted in science to explain things in nature How is science different from technology Firstly the goal of science is to explain and understand phenomena in nature while technology aims to apply scientific knowledge for a specific purpose Science is often driven by curiosity or the need to know in order to satisfy cultural or social demands whereas technology at its core must ask the question of should we do it How is science in uenced by society How does society bene t from science Science is influenced by society by dictating what questions are being asked what resources are available and can be used in an experiment which ultimately deems how reliable and accurate the data can be Furthermore society can benefit from science by answering long unanswered questions allowing for ways in which minority groups can rise to equality granting more opportunities to create a level playing field in society for all people What is the difference between an element and a compound Element A substance that cannot be broken down to other substances by chemical reaction Compound Substance consisting of two or more different elements combined in a fixed ratio Of the 92 natural elements 2025 are essential elements necessary for an organism s life and ability to reproduce Humans need 25 Plants need 17 CHON make up 96 of living matter Trace elements are required in tiny units by organisms How do neutrons protons and electrons interact to form an atom Examine Figure 24 for a model of a helium atom Atom the smallest unit of39matter that still retains the properties of an element Subatomic particles parts of atoms Neutrons neutral subatomic particle in nucleus Protons positively charged subatomic particles in nucleus Electrons negatively charged subatomic particles zipping around the edge of atoms Daltonamu What is a covalent bond How do covalent bonds function to create molecules Covalent bond the sharing of a pair of valence electrons by two atoms Mblecules two or more atoms held together by a covalent bond What is the difference between a single bond and a double bond Single bond a pair of shared electrons Double bond a set of bonds in which two atoms are sharing two pairs of valence electrons What is the valence of an atom How does valence allow you to determine how many bonds an atom can form What is the valence of hydrogen oxygen nitrogen and carbon valence The bonding capacity of an atom usually equals the number of unpaired electrons required to complete the valence shell of the atom What is electronegativity How does electronegativity result in nonpolar covalent bonds and polar covalent bonds Electronegativity the attraction of a particular atom fer the electrons of a covalent bond Polar Covalent bonds when an atom is bonded to a more electronegative atom and the electrons of the covalent bond are not shared equally causing polarity in the bond where the electron leans closer to one side or the other Nonpolar covalent bonds when the two atoms of the same element are equally sharing the pair of electrons in the covalent bond Define the fellowing terms and provide an example of each Examine Figure 212 fer an example of ionic bonding Ionic bond Bond formed between two atoms of opposite charge the ions do not need to have acquired their charge by an electron transfer with each other Ex NaCl Ion An atom that is charged from a polar covalent bond because either it stole an electron or had one stolen from it making it oppositely charged from the other atom it is bonded to Cation Positively charged ion Na Anion Negatively charged ion Cl Salt ionic compounds compounds formed by ionic bonds table salt NaCl What is a hydrogen bond Hydrogen bond the attraction between a hydrogen and an electronegative atom H2O or NH3 water is boomerang shaped Ammonia looks like a tripod What are van der Waals interactions They are the results of electrons being unevenly distributed at times and are everchanging regions of positive and negative charge that enable all atoms and molecules to stick to one another Complete the following table to summarize your knowledge about types of bonds and molecular interactions Relative bond Bond type Bond formed by strength Examples covalent Sharing electrons Strong H2O Iomc Cations and anions Strong When dry NaCl weaker when wet Hydrogen and Hydrogen electronegative Weak NH3 atoms Van der Waals Nonpolar covalent Inqw39dually weak Simultaneously Gecko feet bonds strong Why is molecular shape so important to determining molecular function It determines howbiological molecules recognize and respond to one other with specificity Biological molecules often bind temporarily to each other by forming weak bonds but only if their shapes are complementary Ie morphine De ne the following terms and provide an example of each from the formula 2H2022H20 Chemical reaction the making and breaking of chemical bonds leading to changes in the composition of matter Reactant starting materials Product The end results of the chemical reaction What does it mean when a reaction has reached chemical equilibrium The point at which the reactions offset one another exactly no effect on the net concentrations of reactants and products though not necessarily that the reactant and products are equal in concentration What is a polar covalent bond and what is a polar molecule Why is a water molecule considered to be polar Polar Covalent bonds when an atom is bonded to a more electronegative atom and the electrons of the covalent bond are not shared equally causing polarity in the bond where the electron leans closer to one side or the other Polar molecule the unequal sharing of electrons resulting in a molecule with overall charge that is unevenly distributed A water molecule is polar because the oxygen region of the molecule has a partial negative charge and each hydrogen has a partial positive charge because the oxygen is pulling the electrons closer since it is a more electronegative atom than hydrogen 1 Electronegativity is the ability to attract other atoms electrons to form a covalent bond 2 Because similar charges repel each other and opposite charges attract each other so H would attract 0 3 If that were the case water would not bond with each other changing what water is and resulting in significantly weaker surface tension De ne the following terms and explain how they are related to dissolving table salt into a boiling pot of water Solution A liquid that is completely homogeneous mixture of two or more substances Solvent the dissolving agent of a solution water most times Solute the substance being dissolved Agyeous solution which the solute is dissolved in water water is the solvent What are the similarities and differences between hydrophobic substances and hydrophilic substances Give an example of each Hydrophilic LOVES water vinegar or cotton Hydrophobic HATES water vegetable oil often nonpolar covalent bonds create a lot of the hydrophobic characteristics Neither has to necessarily dissolve in water De ne the following terms and give an example of each if applicable Hvdroagn ion Formed when a water molecule shifts from one to another molecule leaving behind an electron creating a hydrogen ion a single proton with a charge of 1 Hydroxide ion The water molecule from above that has lost a proton ELECTRON with a charge of l Hvdronium ion When the proton attaches to another water molecule making H30 Acid substance that increases the hydrogen ion concentration of a solution Base substance that reduces the hydrogen ion concentration of a solution Is NaOH an acid or a base Why Is H2CO3 an acid or a base Why Base indirectly reduces H concentration by dissociating to form hydroxide ions which combine with hydrogen atoms to make water molecules Carbonic acid is a weak acid because it reversibly releases and accepts back hydrogen ions What does the pH scale measure What is the equation for calculating pH pH scale measures the compressed range ole and OH concentrations by using logarithms It is the negative logarithm base 10 of the hydrogen ion concentration When moving up on the pH scale from 5 to 6 what is the equivalent change in the number of hydrogen ions 10x What is a buffer Give two examples of a buffer Substance that minimizes changes in the concentrations of H and OH in a solution Carbonic acid H2CO3 is an example in conjunction with bicarbonate Acetic acid is also a buffer What is a functional group How do functional groups contribute to molecular properties Functional group chemical groups directly involved in chemical reaction With its own properties such as shape and charge that defines how it will react in a characteristic way They contribute to molecular properties by predefining how to molecules will combine and react together Only 6 of the 7 functional group are chemically reactive Methyl group is nonreactive but instead serves as a tag on biological molecules 6 out of 7 are hydrophilic and therefore increase the solubility of organic compounds in water Complete the following table for the seven most important biological functional groups Structure Polar or non draw it polar Other properties Examples Chemical group Forms hydrogen bonds with oxygen Hydroxyl Polar to dissolve sugars Ethanol Names and in 00 Carbonyl Moderately It s present in Acetone polar sugars forms Propanol ketones with ketoses and carbonyl in carbon skeleton and aldehydes with aldoses and carbonyl as end of the carbon skeleton Carboxyl Polar Acts as an acid Carboxylic acid or organic acid Acetic acid Amino Polar Acts as a base Amine Glycine Sulfhyd ryl Polar Can react to stabilize protein structures like hair structure ie curly vs straight Thiol Cysteine Phosphate Polar Contributes 1 when inside phosphate chain or 2 when at end When attached confers to react with water and release energy Organic phosphate Glycerol phosphate Methyl Nonpolar Affects the expression of genes when on DNA or on proteins bound to DNA Methylated compound 5Methyl cytosine What is a polymer What is a monomer Give a biological example of each Polmer a long molecule consisting of many similar or identical building clocks linked b covalent bonds Carbohydrates proteins and nucleic acids are all examples Pol yacet ylene Starch Monomer Are the smaller molecules that are the repeating units that serve as the building blocks of a polymer However some have other functions of their own Dblucose Enzzme Specializedmacromolecules that speed up catalyze chemical reactions How are dehydration and hydrolysis reactions similar and different They both involve water Dehydration removes the H20 molecules where as hydrolysis adds water Dehydration Reaction When monomers are connected by a reaction in which two molecules are covalently bonded to each other with the loss of a water molecule One monomer contributes a hydroxyl OH group while the other gives a hydrogen H Hydrolysis Reaction Polymers are disassembled to monomers by the process that reverses dehydration by breaking the monomers by adding a water molecule to the chain A hydroxyl group connects to one monomer and an H connects to another Why is there such a diversity of biological polymers even though there are a limited number of biological monomers Though there are only about 4050 common monomers and a few rare ones arrangement of these monomers is key They can be sequenced and arranged in almost an unlimited number of ways Complete the following table about the types of carbohydrates Carbohydrate include sugars and polymers of sugars Contains Polar Description Function what or Example functional non 3 groups polar Monosaccharid Molecular Major nutrient Carbonyl Polar Glucose g formulas that source for cells and and are some in hydroxyl Galactos multiple of the photosynthesis e unit CH20 Carbon skeleton 37 Carbons long Trioses 3C And the carbon skeletons also Pentoses 5C sen9613 raw maternal form and Hexoses organic 6C Spatial molecule arrangement synthesns such around asymmetric as amino acnds and fatty acids carbons also creates diversity Two monosaccharid es connected Nutritional by glycosidic source of Maltose Disaccharides linkage monosaccharid Hydroxyl Polar and covalent bond es for sucrose formed by organisms dehydration rxn Storage material for NRG building material used Macromolecule for structural s With a couple SU M or 1001000 roptgction Glycoge Polvsaccharides monosaccharid pFunction39 Hydroxyl Polar n and es joined by Cellulose I d determined by g yCOS39 39C its sugar anage monomers and positions of glycosidic anages How is a disaccharide formed from monosaccharides How is a polysaccharide formed from monosaccharides Disaccharides are formed by removing water molecules dehydration between two monosaccharides that are then covalently bonded Meanwhile polysaccharides are formed similarly but on a large scale connecting different disaccharides into long chains Complete the following table about the types of polysaccharides Structural Functional Found in what characteristics characteristics organisms Polymer of glucose14 Spt ggysilglg tsltc Starch linkages unbranched p p Plants alpha links glucose represents stored energy Polysaccharide comprised of a polymer HydrOIYS39S Of It GI CO en of lucose that is like releases glucose Humans or most y g amglo ectin but more when demand for animals y Branched sugar increases Polysaccharide Major component of glucose but different tough cell walls in ring structure than lam cells most starch glycosidic p abundant organic linkages have different Cellulose rin structure beta compound on earth Plant cells g Enzymes that digest links can be grouped starch are unable to together to make micro digest cellulose due to fibrils Straight molecule the beta links that is never branched Polysaccharide that is extremely strong beta Carbohydrates used Chitin links Glucose monomer by arthropods to build Arthr ssdis and of chitin has a nitrogen exoskeletons 9 containing appendage What property do all lipids share with each other Lipids one class of large biological molecules that does not include true polymers and are generally not big enough to be considered macromolecules They are grouped together because they all mix poorly with water which is a distinctive trait Lipids hydrophobic behavior is caused by their molecular structure and consist mostly of hydrocarbon regions How do fatty acids and glycerol molecules make up fag How many fatty acids and glycerol molecules are in a single fat molecule Can you draw a basic depiction of a fat Examine Figure 59 for an example Fats Are constructed from two kinds of small molecules glycerol and fatty acids Glycerol an alcohol where each of its three carbons bears an hydroxyl group Fatty Acid has a long carbon skeleton 1618 carbons in length Carbon at one end of the skeleton is part of a carboxyl group giving it the name fatty acid The rest of the skeleton consists of hydrocarbon chain making them hydrophobic Three fatty acids are each joined to glycerol by an ester linkage a bond fOrmed by a dehydration reaction between a hydroxyl group and a carboxyl group Also called triacylglycerol or triglyceride What is the difference between a saturated fatty acid or fat and an unsaturated fatty acid or fat What do these terms tell you about whether a fat is liquid or solid at room temperature turat d fattv acid is when there are no double bonds in the molecule letting hydrogen atoms saturate the Carbons whereas unsaturated fat is when double bonds are present between carbon atoms and one fewer hydrogen atom on each doublebonded carbon Most naturally occurring unsaturated fatty acids are cis double bonds which cause kinks in the hydrocarbon chain where they occur rypically saturated fats are solid at room temperature because the molecules are packed closely together On the other hand unsaturated fats are liquid at room temperature because the kinks in the hydrocarbon chains make it difficult to tightly pack the molecules together Oleic acid is shown below Is oeic acid a saturated or unsaturated fatty acid If it were part of a fat would the fat be liquid or solid at room temperature Why unsaturated because it has a double bond at the end It will be liquid at room temperature What is a trans fat Why are trans fats thought to be harmful to health Trans Fats Hydrogenating vegetable oils means that unsaturated fats have been synthetically converted to saturated fats by adding hydrogen leading to unsaturated fats with trans double bonds They are harmful because they can lead to atherosclerosis plaque build up in the arteries and blood vessels How does a phospholipid differ structurally and functionally from a fat In what part of a cell are phospholipids abundant Phospholipid Key component for cell membranes similar to fat molecule but has two fatty acids attached to the glycerol compared to the three The third hydroxyl group of glycerol is joined to a phosphate group instead which has a negative charge in the cell Typically an additional charged particle or polar molecule is attached to the phosphate group The parts of39a phospholipid act differently the hydrocarbon tails are hydrophobic while the phosphate group and its attachments are hydrophilic So when mixed into water they self arrange into bilayers shielding the hydrophobic portions from water What are steroids Steroids have very different structures from fats and phospholipids so why are they classi ed as lipids Steroids Are lipids characterized by a carbon skeleton consisting of four fused rings Different steroids are identified by chemical groups attached to the rings D39Cholesterol type of steroid crucial for animal cell membranes and acts as the precursor from which other steroids are synthesized Though they are different from fats they still are composed of the glycerol and fatty acids therefore are classified as lipids What is the difference between a bolybebtide and a brotein Protein 50 of dry mass of39most cells Regulate cell development and movement Are extremely important Biologically functional molecule composed of the same 20 amino acids linked in unbranched polymers forming polypeptides which are folded and coiled into specific 3D structures PolegptidQ The bond between amino acids is a peptide bond and so the polymer of amino acids is called a polypeptide Catalyst enzyme kind of protein that speeds up chemical reactions with out being consumed by the reaction itself They are different because polypeptides are a chain of amino acids while proteins are coiled up versions of polypeptides attached together Proteins consist of multiple polypeptides What are some of the different functions that proteins have They serve many purposes There are enzymatic proteins defensive proteins storage proteins transport proteins hormone proteins receptor proteins contractile and motor proteins and structural proteins each with their own specific purpose such as speed up reactions protect cells save energy move substances coordinate cell activity respond to stimuli movement or support What is an amino acid What is it composed of Amino Acid an organic molecule with both an amino group and a carboxyl group At the center of an amino acid is the alpha carbon with four partners the amino group a carboxyl group a hydrogen atom and the R groupside chain What are the ways that structural characteristics of amino acids can in uence their properties The structural characteristic of the R group that is attached to the alpha carbon controls what kind of amino acid it is and also decides whether the amino acid is nonpolar polar hydrophobic hydrophilic acidic or basic alkaline What is a peptide bond What does it link together and what reaction is used to form it A covalent bond that is joined together through dehydration It links to amino acids and a carboxyl group Repeated over and over again in a polypeptide which then acts as the back bone of a polypeptide chain with various amino acids attached Protein function is exquisitely linked to protein structure Complete the following table to compare the four levels of protein structure What kinds of Level Description Structural features bonds hold it together Primary sequenacceidif ammo Linear chain Peptide bonds Secondary Coiled folded patterns of amino acids Alpha helix delicate coil held together with hydrogen bonds every fourth amino acid Beta sheet two or more strands of polypeptide chain are laying side by side and are connected by hydrogen bonds between parts of the parallel segments of the polypeptide backbone Hydrogen bonds My Over all shape of polypeptide resulting from R chain interaction and bonding H dro hobic Interaction where the hydrophobic sections end up clustered at the core to avoid contact with water Disulfide bridde covalent bonds form between two cysteine monomers with sulfhydryl groups on their side chains when they are close together by folds of the protein Hydrogen bonds ionic bonds disulfide bridges Quaternary An aggregation of polypeptide sub units Two or more tertiary structures mixed together What happens to a protein s structure and function when it denatures It looses its structure so it is unable to carry out its proper function Answer concept check 54 question 3 in the space below 1Hydrogen bonds between polypeptide backbone help give secondary structure structure The atoms of the side groups give tertiary 2 Alpha and Beta rings for glucose A side by side B upside down Alpha and Beta secondary structure alpha helix versus beta sheet Alpha and Beta hemoglobin 3In the center because they are hydrophobic What is a nucleic acid What three components make up a nucleotide Nucleic acids are polymers made up of nucleotides Two Types Deoxyribonucleic acid directs its own replication and RNA replication and Ribonucleic acid controls protein synthesis through mRNA All of which is called gene expression Nucleotides have a five carbon sugar a nitrogen containing base nitrogenous base and one or phosphate groups Gene discrete unit of inheritance Polvnuclgotidgg nucleic acids are macromolecules that exist as polymers comprised of nucleotide monomers Nucleoside The portion of the nucleotide without any phosphate groups Nitrogenous base called that because they tend to take up hydrogen ions from the solution acting as bases What are the differences between the nitrogenous bases pyrimidines and purines List the names and oneletter abbreviations for each type Pyrimidines C T U has one 6 membered ring of Carbon and Nitrogen atoms Cytosine Thymine Uracil Purines A G Larger and has 6 membered rings fused with 5 membered rings hdenine Guanine Deoxzribose sugar in DNA lacking an oxygen on the second carbon ring Ribose sugar in RNA Phosphodiester Linkage phosphate groups that link the sugars of two adjacent nucleotides which then leads to the creation of the sugar phosphate backbone How does the sequence of nucleotides in DNA in uence the amino acid sequence of a protein Amino acids are comprised of nucleotides which are the building blocks of DNA which provide translation of the proteins that will be created out of other amino acids Describe the structure of a DNA molecule using the terms double helix and antiparallel Has two strands that spiral around each other forming a double helix that are staggered in height but run parallel Sugar phosphate backbones are on the outside of the helix Nitrogenous bases link together in center of the helix Two strands held together by hydrogen bonds between base pairs Eh and T DC and C Strands run opposite direction in regards to 5 0 3 direction One end has phosphate attached to a carbon while on the other there is a hydroxyl group attached to a 3 carbon Complete the following table to compare and contrast DNA and RNA DNA RNA Types of pyrimidines C T C U Types of purines A G A G Type of sugar deoxyribose ribose Contains all genetic Used to transcribe DNA Function information that controls information to create new cell proteins Complete the following table summarizing all types of biomolecules Contains what 7 structural groups Polar or non polar Examples Monosaccharides Carbohydrates disaccharides Polar starch polysaccharides Li ids Fatty acid chains N0n olar Cell membrane p glycerol p lipid bilayer Proteins Polypeptide peptide Both depending on Hemoglobin bonds part of chain Nucleic acids Ammo aC39dS Polar DNA nucleotides What are the major functions of the plasma membrane What does it mean that the plasma membrane is selectively permeable The plasma membrane is the boundary that separates a cell from its surrounding and regulates what enters and exits the cell This is called selective permeability meaning it allows some substances to cross the membrane more easily than other a fundamental characteristic to life The plasma membrane controls the passage of substances What kinds of biomolecules are found in plasma membranes Lipids carbohydrates and proteins are key parts of a plasma membrane Phospholipids are the most abundant lipid in plasma membranes What does it mean that phospholipids are amphipathic How does property affect their orientation in the membrane Phospholipids are amphipathic molecule meaning it has both hydrophilic and hydrophobic regions and are the most abundant lipids in a cell membrane Having these two characteristics leads to the formation of a bilayer with the hydrophilic heads on the outside and the hydrophobic tails on the inside Most membrane proteins are also amphipathic making it so that they reside in the phospholipid bilayer with their hydrophilic parts facing outward What does it mean that this is a uid mosaic model How many different types of molecules can you nd in this drawing Fluid mosaic model model of a cut away of an animal cell showing not only the outside of the cell but also the components and structure of the phospholipid bilayer cholesterol integral proteins phospholipids glycolipids the fibers of extra cellular matrix ECM outside the cell microfilaments of cytoskeleton inside the cell carbohydrates on the extracellular side of the membrane attached to embedded glycoproteins and peripheral proteins on the cytoplasmic side of the membrane What evidence do we have that plasma membranes are uid and not static structures One example of this evidence is the knowledge that a membrane is held together by hydrophobic interaction which are much weaker than covalent bonds leading to rapid horizontal movement Neighboring phospholipids exchange places about 10 7 times per second Proteins move more slowly but can still shift within the membrane if not attached to cytoskeleton or extracellular matrix You couldn t just assume that the proteins don t move because there could be other explanations for the lack of movement such as the noncompatibility of the two animal cells perhaps they need to be the same species or belong to the same biological family or it has to be at a certain temperature Explain how each of the following factors affect membrane uidity a Temperature Membranes remain fluid so long as the temperature decreases until the phospholipids settle and become tightly packed ex bacon grease This temperature limit is dependent on type of lipid b saturation level of fatty acids Membranes remain fluid at lower temps If it has lots of unsaturated hydrocarbon phospholipid tails since they can t be packed tightly together CCh0k en Cholesterol in the membranes affects it at different temperatures At body temperature is makes the membrane less fluid by restraining movement of the phospholipids but in limiting ability to pack tails together is lower the temperature required for a membrane to solidify In this way cholesterol acts as a fluidity buffer for the membrane If phospholipids are the main determinant of a membrane s uidity what kinds of biomolecules affect a membrane s function 2 The membrane lipid composition of the warmer native grass would probably be more liquid and have more movement of phospholipids and proteins where as the cooler native grass would most likely have less movement and more cases of membrane solidification Unless the cool native grass had more cholesterol embedded in the phospholipid bilayer or unsaturated phospholipid tails in which case there would still be reduced movement but less membrane solidification On the other hand the hot grass might need specialty lipids that prevent extreme liquidity of the membrane Compare and contrast the structures and functions of integral proteins and Derinheral proteins Phospholipids are the main fabric of the membrane but proteins determine the membrane s functions Integral proteins penetrate the hydrophobic interior of the lipid bilayer the majority of which are transmembrane proteins spanning the entire membrane The hydrophobic portions of these proteins contain one or more stretches of nonpolar amino acids which are usually curled into alpha helices The hydrophilic parts are exposed to water but some even have hydrophilic channels through the membrane that let substances through Peripheral proteins are not embedded in the phospholipid bilayer but rather lay directly under it that are loosely bonded to the surface of the membrane and are often exposed to the surfaces of the integral proteins Proteins are sometimes held in place by the cytoskeleton or the ECM integrins for example attach to give the cell a stronger framework What is a transmembrane protein Transmembrane proteins proteins that span the entirety of the membrane and connect to both the outside and the inside What are the six major functions of membrane proteins Figure 77 provides a summary Transport Enzymatic activity Signal transduction cellcell recognition intercellular joining attachment to the cytoskeleton and EGM What are the major functions of membrane carbohydrates such as glycolipids and glycoproteins Some carbohydrates are bonded to lipids forming either glycolipids but most are bonded to proteins forming glycoproteins They function as markers that distinguish one cell from another What types of molecules can cross the lipid bilayer without extra help Why can they do this There is a constant movement of small molecules and ions moving across the plasma membrane Other molecules though include nonpolar molecules such as hydrocarbons C02 and 02 are hydrophobic and therefore can dissolve the lipid bilayer easily and move across without help What types of molecules cannot cross the lipid bilayer on their own Why can t they How do transport proteins help these molecules through Specific ions and many polar molecules can t cross it on their own They can t cross it because they are hydrophilic and therefore can t pass through These molecules get through with the help of transport proteins also referred to as channel proteins that provide a hydrophilic channel for certain molecules and atomic ions use to travel through the membrane Each transport protein is specific to the substance it transports A specific example is an aquaporin which specifically helps water travel into the cell A carrier protein is another example which holds onto their passengers and change shape in a way that shuttles them across the membrane Answer concept check 72 question 2 in the space below 2 Because water is especially guarded against a cell since too much or too little of it severely affects cell functionality and so the only way it can access into the membrane quickly is through these transport proteins otherwise it would just slowly seep through the membrane and the cell could die in the mean time Describe the structure and the function of the following molecules found in the extracellular matrix Collagen glycoprotein in the EMU of most animal cells that is the most abundant and whose function is to dorm strong fibers outside the cells and which is embedded in a network woven out of proteoglycans Makes up 40 of total protein in the human body Proteoalvcans molecule consists of a small core protein with many carbohydrate chains covalently attached so that it may be up to 95 carbohydrate Fibronectin bind to integrins that attach cells to each other by connecting EGM to EGM Integrins cellsurface receptor proteins that are built into the plasma membrane What is diffusion How does a solute s concentration gradient affect the direction that a solute diffuses Diffusion the result of thermal energy of molecules the movement of particles of any substance so that they spread out into the available space Individual molecules move randomly but a population of molecules may be directional Concentration aradient the region along which the density of a chemical substance increases or decreases Each substance diffuses down its own concentration gradient unaffected by other substances gradients However a solute s concentration gradient can affect the direction the solute diffuses because more concentrated likes to go to less concentrated to become equal and reach equilibrium Why is diffusion considered to be passive transport Passive Transport diffusion of a substance across a biological membrane transport that does not require expending any energy Diffusion is considered passive transport because it occurs spontaneously with no additional energy required The concentration gradient itself represents potential energy and drives diffusion What is osmosis How is it similar to yet different from diffusion Osmosis the diffusion of free water across a selectively permeable membrane whether artificial or cellular It is similar to diffusion in the fact that it has its own concentration gradient of sorts water diffuses across the membrane from region of higher free water lower solute to that of lower free water concentration higher solute The only difference is that osmosis only occurs across a membrane and it is the solvent water moving across rather than the solute Examine Figure 711 and answer the quotwhat ifquot question in the space below If the orange dye was able to cross the membrane the solution would end up moving to the side with more solute thus creating a higher o overall solution on that side However if the two sides were already equal then it would equally mix on both sides slightly raising both De ne the following terms with related to tonicity and give an example of each Tonicity the ability of surrounding solution to cause a cell to gain or lose water that is dependent on solute concentration which cannot cross the membrane relative to the concentration inside the cell Hypotonic having less solute than what s inside the cell leading to the flooding of the cell resulting in lyseing bursting of the cell WATER BALLOON Isotonic same concentration both inside and outside the cell resulting in no net movement across the membrane HVpertonic having more solute than what s inside the cell and so the water in the cell will move to the outside leading to the cell shriveling and dying SALT WATER AND FRESH WATER FISH Osmoregulation the control of solute concentrations and water balance Complete the table below to summarize the effects of tonicity on animal and plant cells For each empty box explain what will happen to a cell placed in that environment and Whyit happens Hypotonic solution Isotonic solution Hypertonic solution Lysed Normal Sh riveled An39mal Ge water floods in Water flows out Turgid normal Turgor pressure Plant cell pressure that Flaccid Plasmolyzed opposesfunher water uptake What is facilitated diffusion How is it similar to yet different than passive transport Eacilitated diffusion the transport of polar molecules and ions across the plasma membrane through the help of transport proteins It is similar to passive transport in the sense that it helps these molecules cross the plasma membrane in a regulate way but it requires the help of specific protein This is still considered passive transport because the solutes are moving down their concentration gradients What are channel proteins ion channels dated channels and carrier proteins How are their structures and functions similar yet different Channel Proteins proteins with hydrophilic corridors that provide corridors for specific molecules or ions across the plasma membrane Ion Channels channel proteins that transport ions Gated Channels corridors into the cell that open or close in response to a stimulus Some are electrical and others only function when the substance it carries binds to the channel garrier Proteins Proteins that carry substances from one side of the membrane to the other They work through passive transport What is active transport How is it similar yet different to passive transport and facilitated diffusion What is required for active transport to work Active Transport pumping a solute across a membrane against the direction of the concentration gradient requiring cells to expend energy Active transport allows a cell to maintain internal regulation of solutes that is different than the outside concentrations Facilitated diffusion passively uses proteins to move solutes across the membrane while passive transport is done independently Examine details of the sodiumpotassium pump a speci c type of active transport Summarize the function of the sodiumpotassium pump in your own words SodiumPotassium pump A protein exists in the membrane and Na binds to it causing phosphorylation by ATP thus changing the shape to be less inclined to Na andmore inclined to K but this process is then reversed when K is then released into the cell Review the differnces of passive and active transport Answer the question associated with the gure in the space below Na is moving out of the cell and K is moving in the cell both against the gradient What is the membrane potential and how does it form How does the membrane potential result in an electrochemical dradient Membrane potential the voltage across a membrane ranging from 50 to 200 millivolts Membrane potential favors the passive transport of cations into the cells and anions out of the cells therefore both drive diffusion of ions one chemical and one electrical Electrochemical gradient the combination of39both the chemical and electrical drive on an ion to move across the plasma membrane Why is it not totally correct to say that an ion diffuses down its quotconcentration gradientquot Why is it more appropriate to say that an ion diffuses down its quotelectrochemical gradientquot Because as in the example of Na the positively charged ion is attracted to the negatively charged inside of the cell and driven by the concentration of Na What is an electrogenic pump What is a proton pump Electroqenic puma a transport protein that generate voltage across a membrane Proton pump the main electronegative pump of plants fungi and bacteria that actively transports protons out of the cell transferring the positive charge to the extracellular solution How does cotransport move molecules across a membrane How do proton pumps contribute to cotransport Cotransport mechanism in which a transport proteincotransporter can couple the downhill diffusion of the solute to the uphill transport of a second substance against its own concentration gradient How do large molecules such as proteins and polysaccharides move across cell membranes They are moved across the cell membranes in vesicles which requires energy Compare and contrast exocytosis and endocytosis in terms of the way they move molecules across cell membranes Give an example of each Exocytosis secretion of certain molecules by the fusion of vesicles with the plasma membrane The vesicle buds from the Golgi apparatus moves along microtubules to the plasma membrane where the specific protein rearrange the lipid molecules of the two bilayers so the two membranes fuse and then the contents of the vesicle spill out The vesicle membrane becomes a part of the cell membrane 7lnsulin production in the pancreas Endocytosis The cell takes in molecules and particulate matter by forming ne vesicles from the plasma membrane Different proteins than exocytosis but the process is just the reverse of it Three types phagocytosis cellular eating pinocytosis cellular drinking and receptor mediated endocytosis a form of pinocytosis D39Cholesterol in the form of lowdensity lipoproteins which act as ligands any molecule that binds specifically to a receptor site on another molecule De ne the three subtypes of endocytosis and give an example of each Phagocytosis cellular eating by extending pseudopodia around it and packaging it within a membranous sac called a food vacuole bacterium and amoeba Pinocytosis cellular drinking in which a cell continually gulps drops lets of extracellular fluid into tiny vesicles Nonspecific to what it transports DPinocytotic vesicles and ECF Receptoremediated endocytosis specialized type of pinocytosis that enable the cell to acquire bulk quantities of specific substances even though they may not be very concentrated in the extracellular fluid D39Cholesterol in the form of lowdensity lipoproteins which act as ligands any molecule that binds specifically to a receptor site on another molecule Complete the following table to summarize transport mechanisms across plasma membranes Direction that Membrane solute moves Energy molecules up down required Examples involved concentration yes no gradient Water Diffusion No Down No nonpolar molecules Faculltated Yes channel Down No Water difoSIon proteins Yes transport Active transport Up Yes Na K proteins Cotransport Cotransporters Up Yes sucrose H cotransporter Exocytosis V9323 GOIg39 Either Yes Insulin Vesicles Endocytosis plasma Either Yes membrane Extracellular Fluid Describe how the following parameters are important to microscopy Magnification The ratio of an object s image size and it s real size Light microscopes can magnify up to 1000 times the actual size of the specimen Resolution Measure of clarity of the image it is the minimum distance two points can be separated and still be distinguished as separate points Light microscopes have resolution up to 02micrometer or 200 nanometers Contrast Difference in brightness between the light and dark areas of an image Staining and labelling cell components helps with this Approximately how big is a frog egg What is the range of sizes for most bacteria How many times smaller is an atom compared to a mitochondrion 13mm Frog egg 110 micrometers most bacteria 10 4 times smaller What is the major difference between a light microscope and an electron microscope Liaht Microsc0pe a microscope where visible light passes through th specimen and then through the glass lenses The lenses refract the light in a way that magnifies the image of the specimen as it is projected into the eyecamera Can see a cell but not some details of a cell such as organelles Electron Microsc0pe microscope that fecuses a beam of electrons through the specimen or onto its surface Resolution is inversely related to the wavelength of the light or electrons Resolution on modern electron microscopes is about 0002nm Complete the following table to help you organize information about types of microscopy Use Figure 63 for help Type Uses light or electrons Description What it is good for Brightfield Light Without staining there is little contrast With staining it kills the cells but gives clear overall look of cell Large cells Ex Epithelial cells Phasecontrast Light Variations in density are amplified to enhance contrast of unstained cells Unstained living cells Fluorescence Light Molecules within a cell can be found using this be labelling them with fluorescent dyes or antibodies Molecules within a cell Confocal Light Uses optical sectioning technique that limits out of focus light to create a single plane of fluorescence in the image 3D reconstruction can be created from standard image that is blurry but once out of focus light is excluded it is very clear Scanning electron microscopy Electron Micrographs taken with this show a 3D image of surface of a specimen by beam scanning the surface covered in gold film that excited electrons that are detected by a device that translates the pattern of electron into an electronic signal that is sent to a video screen Good for viewing surface of cells Transmission electron microscopy Electron Profiles a thin section of a specimen Aims electron beam through thin section of specimen that has been stained with atoms of heavy Good for viewing internal cellular structure metals that attach to certain cellular structures enhancing density Image displays transmitted electrons and uses electromagnets as lenses to bend the path of the electrons Answer concept check 61 question 2 on page 97 in the space below ggll Fractionation technique for studying cell structure and function which takes the cells apart and separates major organelles and other subcellular structures from one another Centrifuge is used to do this lThey are usually just colored with dye and don t change the density of the cell where as the electron microscopes require the use of stains with heavy metal atoms that alter the density of the cell being investigated 2 Phase contrast for living and scanning electron for hair surface What is the cytoskeleton What three major molecular structures make up the cytoskeleton What are the major roles of the cytoskeleton Cytoskeleton A network of fibers extending through the cytoplasm DiMicrotubules microfilaments and intermediate filaments Roles to give mechanical support the the cell and maintain its shape Balances between opposite forces exerted by its elements Provides anchorage for many organelles and even cytosolic enzyme molecules Can quickly be taken apart in one part of the cell and reassembled in another changing the shape of the cell How do motor proteins interact with the cytoskeleton to achieve cell motility gell motility ability for the cell as a whole to change shape and movement of cell parts Motor proteins proteins that help with the movement of the cell Which interact with the cytoskeleton to allow who cell walls to move along the fibers outside the cell or for vesicles and other organelles often use motor proteins to walk along the cytoskeleton fibers How do microtubules change size using the protein tubulin Microtubulgs are the largest of the three fibers to make up the cytoskeleton microfilaments actin filaments are the thinnest and intermediate filaments are in the middle Microtubules are hollow rods made from globular protein called tubulin Each tubulin protein is a dimer molecule with two subunits that are two slightly different polypeptides alpha and beta tubulin Each end of the tubule grows independently at different rates and can result in one side being thicker than the other since it has a much higher rate What are centrosomes and centrioles See Figure 622 for a microscopic image of these structures What type of microscopy was used to obtain this image Centrosomes where microtubules grow from in an animal cell a region that is often located near the nucleus Centrioles centrosome pair composed of nine sets of triplet microtubules arranged in a ring Light microscope was used to find this photo How do microtubules contribute to the movement of Q and agella How is the motor protein dynein involved Cilia and Flagella microtubule containing extensions that project from eukaryotic cells Microtubules help with the movement by being responsible for the beating pattern of them the two patterns are different Flagellum undulate while cilia move back and forth They are also different in length number per cell and beating pattern But they both have groups of microtubules sheathed in an extension of the plasma membrane Nine doublets of microtubules are arrange in a ring with two single microtubules in its center 92 pattern The microtubule assembly is anchor in a basal body which is similar to a centriole with microtubule triplets in a 90 order The bending movement of39both flagella and cilia involves the proteins called dyneins that are attached along each outer microtubule doublet and consist of two feet that walk along the microtubule adjacent to it using ATP for energy How are micro laments involved in muscle cell contraction along with the motor protein myosin amoeboid movement and cytoplasmic streaming Microfilaments are thin solid rods built from molecules of actin and help with muscle cell contraction by acting as a pulling force Cortical membranes help support the cell s shape and gives the outer cytoplasmic layer cortexa gel consistency Actin filaments andmyosin filaments interact to cause contraction of muscle cells This same interaction is involved in the amoeboid crawling movement of our white blood cells by extending pseudopodia fake foot andmoving toward them Both actin andmyosin interactions in plants lead to cytoplasmic streaming the circular flow of cytoplasm within cells How did intermediate laments get their name Are intermediate laments more or less quotsturdyquot than microtubules and microfilaments Intermediate filaments are named for their diameter which is in between that of microfilaments and microtubules found in the cells of some animals are specialized for bearing tension like microfilaments them though cells They are only including vertebrates and Unlike intermediates are formed from subunits of proteins whose members include keratin and are permanent fixtures of It is found that they are exceptionally sturdy Complete the following table to help you organize information about cytoskeleton components See Table 61 for help Made up of Description Diameter Cellular what Functions of structure nm examples protein Se aration of Hollow 0 chromosomes rods Dimer of mu ed In cell diViSion two 9 p 25nm with shape and into subunits 15nmlumen support cell centrioles Microtubules alpha and tracks for Flagella Cllla in 9 sets of beta tubulin 250 nm organelles triplet polypetides centriole gwde ve3icles microtubule from ER to 3 arranged Golgi in a ring apparatus Prowde Thin solid su ort 7nm pp rods that is shape approx Amoeb0id Actin a tWIsted increases 200nm crawling Microfilaments globular double surface area 92 cytoplasmic protein chain of to absorb arrangemen streaming actin nutrients act t subunits as bearing forces Intermediate Proteins Fibrous 8 12nm Cell shape Dead skin filaments such as proteins support cells keratin coiled into tension cables bearing anchorage of nucleus and other organelles formation of nuclear lamina


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