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by: Rima Notetaker

Biology123…Cusic.pdf BY 124

Rima Notetaker
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Dr. Raut

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These are biology 123 notes for the first exam in Dr. Cusic's class. Hopefully they are helpful!
Dr. Raut
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"Can you just teach this course please? lol :)"
Alison Tromp

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This 22 page Bundle was uploaded by Rima Notetaker on Friday September 4, 2015. The Bundle belongs to BY 124 at University of Alabama at Birmingham taught by Dr. Raut in Summer 2015. Since its upload, it has received 174 views. For similar materials see in Biology at University of Alabama at Birmingham.


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Date Created: 09/04/15
Biology 123 Photosynthesis C02 water sugar 02 Science a body of information about the material world which has been collected by rigorous critical observational methods and is subjected to continuous testing and retesting deals with supported hypothesis and not absolute truth Natural phenomena have natural causes 0 Example head ache because of not eating lunch Hypothesis educated guess 0 Can have more than one 0 Can testify or falsify a hypothesis Controlled experiment have a control group and experimental group to nd something out about the experimental group Theory more broad than hypothesis has evidence to support it Law higher than theory ultimate science Technology helps science progress Biology study of life 0 Teratology study of monster birth effects and defective embryos Properties of life 0 Order 0 Regulation regulate certain body temperature 0 GrowthDevelopment o Reproduction 0 Response to the environment something gets cold they bundle up 0 Energy food is energy for humans Order Biological organization 0 Atoms l molecules l cells l tissue l organs l organ systems organisms l populations l communities ecosystems l Biosphere Energy Processing 0 Metabolism how we use energy use sunlight as energy Photoautotrophs make their own food Heterotroph do not produce their own food use cellular respiration eating Cellular Respiration sugar 02 l C02 water use ATP as energy Chemotrophs Use chemicals for foodenergy 0 Growth and Development 0 Mitosis cells continuously divide and help grow Reproduction o Offspring contain DNA and a mixture of genes from parents offspring resemble parents 0 Asexual elongates and splits in two bacteria 0 Response to the Environment 0 May be fast or slow 0 Regulation 0 Regulate temperature pH glucose levels 0 Regulation uses feedback mechanisms Negative Positive Evolutionary adaptation 0 Living things change to adapt to their environment camou age 0 Charles Darwin evolution through natural selection survival of the ttest o Cilia line trachaea o If you y you are light weight birds don t have teeth and one ovary so they weigh less and can y 0 Trace elements elements needed in very small amounts 0 Proton positive 0 Neutron neutral 0 Electron negative 0 Atomic number unique is the identi er number of protons Mass number number of protons and neutrons 2 electrons ll the rst shell and 8 in the second shell Isotopes different arrangements 0 Hydrogen Bond molecules with partial charges being attracted to one another positive to negative and vise versa 0 Just because a molecule has hydrogen does not mean it is a hydrogen bond Vander Waals Interaction o Molecules are constantly breaking and forming new bonds helps geckos stick to walls WATE R Hydrogen bond formed when a hydrogen atom covalently bonds to one electronegative atom is also attracted to another electronegative atom USUALLY oxygen or nitrogen Bond in a water molecule is polar covalent bond Water moves from high to low concentrations 0 Cohesion causes water to cling together 0 Causes surface tension measure of how difficult it is to stretch or break the surface of a liquid Adhesion clinging of water to hydrophilic substance lmbibition to soak up anything water moves into will imbibe soak up 0 Speci c heat amount of heat that must be absorbed or lost to change one gram of a substance one degree Celsius 0 Measured in calories amount of heat that will raise or drop the temperature of one gram of water one degree Celsius Heat of Vaporization 580 calories for 1 gram of water to vaporize Liquidleas Evaporative cooling sweat cools humans 0 Molecules evaporate and take heat with them 0 Moles Numerical mass 0 Example sucrose C12H22011 C 12 x 12 H1 x 22 016 x 22 Molarity Number of soluteg Avogadro39s Number 6022x1023 o pH power of hydrogen in French 0 pH logH Buffer neutralizes acids and bases 0 COOH Carboxyl groupdrops hydrogen so hydrogen donorAcid o NH3 Amino groupBase CHAPTER 4 Carbohydrates Lipids Proteins Nucleic acid RNA and DNA Hydrocarbons consist only of hydrogen and carbon 0 Good energy sources 0 Carbon likes to form rings 0 Store fat in adipose cells and take energy in the bonds and use them as ATP lsomers 0 Structural isomers single chain and branches 0 Cistrans isomers double bond carbon bent shape off of Carbons Cis two x s are on same side of double bond Trans two x s are on opposite side of double bond 0 Enantiomers left and right hand molecules are same just oppoge L left and D right isomers FIGURE 49 Important Study Functional groups 0 Functional groups 0 Hvdroxvl drouo Alcohols Has OH Speci c name usually ends in o Polar because of the electronegativity of OH example ethanol Hydrogen bonds with water example ethanol o Carbonyl group C double bond O Keytone carbonyl group is in the structure Aldehyde carbonyl group is attached to the end of the structure 0 Carboxyl group Organic acids C double bond O with OH COOH Can act as an acid 0 Amino group Amines Acts as a base Can pick up a hydrogen Includes NITROGEN o Sulfhydryl group Thiols lnclues SULFUR 2 stabilize protein structure 0 Phosphate group Organic phosphate lncudes PHOSPHATE Have potential to react with water and release energy 0 Methvl drOUD Methylated compounds Adding methyl group to DNA or molecules bound to DNA regulates gene action Estradiol makes females look like females Testosterone makes males look likes males ADP adenosine diphosphate ATP reacts with water to produce inordanic phosohate and ADP and energyl Carbohydrates 0 Energy and short term energy storage 0 Form structure structural components of cells 0 Two ways to name sugars o By how many carbons Triose Pentose o By their functional groups Aldose Ketose SHOULD BE ABLE TO COUNT OXYGENS HYDROGENS AND CARBONS WHETHER IT IS A TRIOSE PENTOSE AND HEXOSE SUGAR AND IDENTIFY FUNCTIONAL GROUPS Dehydration Reaction condensation reaction 0 Removes a water molecule to form new bonds 0 Has a helper called enzyme catalyst Hydrolysis 0 Break down a polymer 0 Adds water molecules to break bonds Animals store glycogen and plants store starch Cellulose many brils made of glucose molecules in the cell wall 0 In cell walls of plants 0 Most abundant in world 0 Second function of carbohydrates gives plants structure Chitin 0 Forms exoskeleton of arthropods snakes and insects 0 Contains nitrogen 0 Cell wall of fungi o Is in surgical thread for stitches KNOW DEHYDRATION AND HYDROLYSIS UNDERSTAND THAT GLUCOSE IS WEHRE WE GET PRIMARY ENERGY DEFRENTIATE MONOSACHARIDES DISACHARIDES AND POLYSACHARIDES Lipids fats 0 Very diverse o Hydrophobic 0 Fatty acids always have equal number of Carbons 0 Includes carboxyl group 0 Saturate something means to ll it up 0 Saturated fats are usually solids 0 Not good for us 0 Unsaturated fats 0 Better for us Adding Hydrogen can make unsaturated fats into saturated fats Dimorphism 2 shapes 0 Neutral fats 0 Long term energy storage Phospholipids 0 Function is structure 0 Includes phosphate group which is hydrophilic 0 Has a hydrophilic phosphate head and two hydrophilic tails Membranes 0 Made of phospholipids 0 Heads face the water and the middle is the tails Steroids 0 Cholesterol is in plasma membrane and makes sex steroids Proteins 0 Most diverse in form and function 0 Depend on tting into something like puzzle pieces Enzymatic proteins 0 Selective acceleration Storage proteins 0 Storage of amino acids eggs seeds of plants Defense proteins 0 Protects against disease antibodies Transport proteins 0 Transport substances hemoglobin Hormonal proteins 0 Coordination of an organisms activities insulin Contractile and motor proteins 0 Movement Receptor proteins 0 Response of cell to chemical stimuli Structural protein 0 Support keratin Protein is a polymer made of monomers called amino acids Primary structure 0 linear arrangement of amino acids Secondary structure 0 hydrogen bonding make an alpha helix 0 Bring strands together to make bonds between it beta pleated sheet silk and scales Tertiary structure 0 Have the helix and pleated sheet so it starts interacting and folding itself up 0 Have hydrogen bonding between R groups 0 Hydrophobic interactions and van der Waals interactions 0 Disul de bridge two sul des with CH2 o Polypeptide backbone Quaternary structure 0 When two or more chains interact with one another 0 CoHagen 0 Has more than one polypeptide chain that interact with one another Hemoglobin 0 Has two alpha chains two beta chains and iron heme 0 Oxygen binds at the heme o Conjugative protein When only the heme or only the iron interacts with proteins and oxygen CENTRAL DOGMA Sicklecell disease Protein is not folded correctly 0 Primary structure one amino acid is wrong 0 Secondary exposed hydrophobic region in beta subunit 0 Quaternary beta subunits attach to alpha subunits like normal but the beta subunit is deformed 0 Function capacity to carry oxygen is reduced Denature 0 when we change the protein 0 Cooking an egg the heat messes up the structure of the egg Renature 0 Can x the structure of a protein if its not too denaturedrearranged Chaperonin 0 Help fold proteinsamino acids correctly 0 Nucleic Acids 0 Large macromolecules 0 DNA is the brains Tells RNA what to do Double stranded molecule 0 RNA does the work Single stranded molecule Phosphodiester linkage o Prymidines o Cytosine o Thymine in DNA 0 Uracil in RNA 0 Purine o Adenine o Guanine Adenine always bonds to Thymine AND Guanine always bonds to Cytosine CHAPTER 5 0 Cell Theory 0 Living matter is composed of cells 0 Chemical reactions of a living organism take place in cells 0 Cells come from other cells 0 Cells contain the hereditary information have DNA of the organism of which they belong human have human DNA this information is passed on from parent cell to daughter cell Magni cation o How big is the object 0 Contrast 0 Measure of clarity Resolving power 0 Minimum distance between two points that can still be distinguished as two separate points 0 Microscopes have better resolving power than the human eyes 0 Shorter the wavelength the better the resolving power Know difference between electron better resolution since shorter wavelength and light microscopes 0 Prokaryotic cells 0 Circular chromosomes No membrane bound organelles Have a nucleoid region since it is not membrane bound Ribosomes where we put amino acids together to make proteins Plasma membrane outside of plasma membrane there is a cell wall De nes cell plasma membrane 0 Some bacteria have a capsule on the outside of the cell wall reason why its difficult to kill some kinds of bacteria 0 Flagella Help move 0 Fimbriae hair like structures around the bacteria 000 O Help them stick onto surfaces Can be modi ed to pass genetic material from one to another Eukaryotic cells 0 Animal cells do not have a cell wall 0 Plasma membrane Hydrophobic region Hydrophilic region Phospholipids Proteins o Nucleus brain of the cell Directs what is going on Membrane bound organelle Pores holes in the nuclear membrane Contains Chromatin DNA Protein Nucleolus dark spot in the nucleus 0 Makes ribosomal RNA rRNA Nuclear Lamina Ray of nucleic laments Maintains shape 0 Cytoplasm Space between plasma membrane and nucleus 0 Cytosol Stuff in the cytoplasm Liquidsemi uid o Ribosome Put together amino acids to make the polypeptide chain Subunits only come together when they start doing work 0 Large subunit 0 Small subunit Free ribosomes Hang out in the cytosol o Endoplasmic reticulum ER Smooth Proteins made here are used in the cytoplasm of the cell 0 Has enzymes that synthesizes lipids Make phospholipids Carbohydrate production and storage 0 Detoxi es things that go into the cell is in liver Glycogen is broken down into glucose Rough Ribosomes on the surface 0 Make certain types of proteins They end up in three places 0 1 Leave the cell 0 2 Enclosed in other organelles o 3 Become proteins associated with plasma membrane Lumen Transport vesicles 0 Little packagespockets 0 Glycoprotein 0 Have sugar attached to the protein 0 Golgi Apparatus 0 Packages and distributes things 0 Two faces Cis face 0 Stuff comes in Trans face 0 Shipping side 0 Makes hyaluronic acidgue that sticks cells together 0 Cisternae Folds in the Golgi Apparatus oTransport vesicles Little pocketsbubble that holds something membrane bound 0 Vesicles are small oVacuoles ARE BIG Lysosome o Known as suicide cells 0 Little baggies that contain Hydrolytic Enzymes Those enzymes are sometimes called Zymogens lnactive enzymes Can break down every organic molecule 0 Come from rough ER 0 Preform phagocytosis cell eating 0 Autophagy self eat disposes of defective cells 0 AbObtosis o TaySachs Disease The lysosomes don t function properly Die around age 4 Lysosomes surround nerves and causes death O 0 If cells were larger it would take longer to get ride of their waste and longer to divide Have trouble getting oxygen in the cells As things get bigger the surface area doesn t increase at the same rate Peroxisome O 0 Produce and debris hydrogen peroxide Break down fats that are sent to mitochondria to produce energy Central Vacuole O O 0 Storage Holds water Important in the structure of plants Energy related organelles O O Mitochondria plural Contain DNA and ribosomes Makes ATP Takes glucose burns glucose with oxygen takes energy from bonds of glucose transfers energy to bonds of ATP Chloroplasts Contain DNA and ribosomes Found in algae and plants Endosymbiotic Relationship Hypothesis with mitochondria and chloroplast 0 They were once preliving prokaryotic cells that got incorporated with eukaryotic cells but now they cannot live without one another Mitochondria O O O O 0 Includes matrix lntermembrane space Outer membrane Cristae foldscreases Inner membrane Chloroplast 0 00000 Includes thylakoid membranes Granum stacks of thylakoid membrane Inner membrane Outer membrane Stroma stuffing between the granum Pigments Carotenoids yellow pigment Chlorophyll green pigment o Organelles that shape structures 0 Cytoskeleton 3 things Microtubules 0 Little tubes 0 Made up of tubulin 0 Motor protein associated Kinesin Micro laments 0 Made up of actin 0 Helps muscles contract and includes cytoplasmic streaming Motor protein associated myosin Intermediate laments 0 Made up of keratins 0 Help in formation of nuclear lamina Cytoplasmic streaming 0 Like stirring a pot 0 Things move 0 Flagella 0 Long 0 Have dynein proteins 0 9pu52 arrangement of microtubules 0 Cilia o A whole bunch on the cell short 0 9pu52 arrangement Both agella and cilia are made from microtubules o Basal body 0 Put microtubules together o Have triplets instead of pairs of two Centrioles o Have 9pusOH arrangement of microtubulespairs of 3 Cell wall o Plants and bacteria have cell walls ANIMALS NEVER HAVE CELL WALLS Cell wall is a bunch of cellulose 1st cell wall Primary cell wall Middle lamella Contains pectin Sticks plant cells together Is between two plant cells 0 Secondary cell wall 000 O Secreted from the cell Next to cytoplasm Lignin o Is like wood 0 Good and strong 0 In cell walls Peplidoglycan o In bacteria cell wall Extra cellular matrix 0 Not a cell wall 0 In animal cells Plasmodesmata o Openings between cell walls 0 Cell junction in plants ANIMAL CELLS o 3 junctions TightJunction so tight nothing can move between them Desmosome has a plaque so its not too tight and involves a little communication Gap Junction have spaces between them free communication Amphipathic molecules Bilayer phospholipid o Hydrophilic sides face the water 0 Hydrophobic layer in middle Pores o Openings in membrane for water to go through Fluid Mosaic Model of the plasma membrane 0 Mosaic made up of piecesdifferent parts 0 We are made of phospholipids and proteins 0 Proteins and lipids move not static 0 Have 2 types of proteins Integral proteins that span the membrane Peripheral proteins on the side of membrane 0 Cholesterol Big molecule Affects movement of membrane Is a steroid o Unsaturated hydrocarbon Affect movement of membrane 0 Saturated hydrocarbon Affect movement of membrane O O O 0 00000 Figure 68 Figure 619 Glycoprotein Sugar attached to proteins Come from the ribosomes on the Rough Endoplasmic Reticulum Carbohydrate chains Should be on outside of membrane NOT the inside Diffusion Things move from HIGH concentration to LOWER concentration until they reach equilibrium Free energy total energy entropydisorder Things tend to go to disorder Diffusion decrease free energy INCREASE disorder Cells MAXIMIZE diffusion by Cytoplasmic streaming Microvilli Counter current exchange Diffusion is affected by Concentration gradient Temperature and pressure Size and shape of molecules Occur over short distances so are slow Transport by carriers Exocytosis and Endocytosis Chapter 6 Peroxisomes Contain enzymes that produce and degrade hydrogen peroxide 0 Break down fats to send to mitochondria to get energy Glycoxysome fat storing tissue that is found in seeds important in converting lipids into carbohydrates Figure 612 Central Vacuole 0 Important in structure of plant cell Figure 615 Figure 616 617 618 Energyrelated Organelles Mitochondria and Chloroplasts o Mitochondria 0 Both plants and animals have mitochondria 0 Contain DNA Endosymbiotic relationship once thought to be preliving prokaryotic cells that became important in developing eukaryotic cells and have an important relationship with each other Power house of the cell where ATP is made 0 Cells that need a lot of energy think muscles need lots of mitochondria o Takes glucose burns it using oxygen gets energy from it transfers energy to bonds as ATP Moves around and divides o Intermembrane space Compartmentalization certain parts function in certain compartments Cristae Chloroplasts 0 Found in algae and plants 0 Also believed to be preliving prokaryotic and have endosymbiotic relationships 0 Where photosynthesis occurs take carbon dioxide and water energy from sunlight o Intermembrane space Thylakoid membranes gt Seen in stacks referred to as grana gt Interconnect with each other Stroma stuffing that lls in around grana o Plastid found in algae and plants Amyloplast stores starch Chromoplasts gt Carotenoids pigment gt Chlorophyll pigment O 0 Figure 620 621 626 627 Table 61 Organelles involved in the shape of cells Cytoskeleton 0 Three structures microtubules micro laments intermediate laments Microtubules 0 Little tubes made up of the protein subunit called tubulin 00 When we need them we make them when we don t need them we break them down Maintains cell shape Think compressionresisting girders Cell motility agella used in movement made up of microtubules Makes up spindle apparatus help in pulling chromosomes apart Motor proteins change chemical energy into movement Kinesin Think cars on an expressway o Micro laments 0 00000 O O Actin two strands of beads wound together Maintenance of cell shape tension of Changes in cell shape Pseudopodium moves around quotfalse footquot Amoeboid movement Myosin motor molecule reaches up to grab an actin and pulls it important in muscle contraction Cytoplasmic streaming Think about stirring a pot and making stuff move around Pinching of cells think drawstring 0 Intermediate laments 0 00000 In between microtubules and micro laments in size Keratins group of proteins it belongs to Maintenance of cell shape Anchor the nucleus and other organelles Form nuclear lamina Cannot assemble and disassemble these Figure 623 624 Cilia and agella o Flagella Only one maybe two Very long Whiplike motion Dynein 9 plus 2 arrangement A whole bunch on a cell Very short Beat together in a civilized manner Same structure as agella Both made in the same structure made of microtubules o In eukaryotic cells all organelles except ribosomes are membrane bound Basal body what makes the cilia and agella grow puts microtubules together 0 0 means no microtubules in the middle look at triplet different agella attached to membrane of the cell Figure 622 Centrioles Similar structure as cilia and agella Microtubules make up the spindle seen in division 0 In the centrosome Like a basal body 92 Figure 628 630 Cell walls 0 Plants bacteria fungi some protists 0 Animal cells never have cell walls 0 A bunch of cellulose aka polysaccharides plants secrete cell walls 0 Sticks together with middle lamella between two plant cells 0 If the cell has to make the cell wall and has the primary and secondary cell wall the primary cell wall will be pushed out 0 Cell wall is outside plant cell Lignin think wood to keep a good strong structure 0 Chitin polysaccharide with nitrogen makes up fungal cell walls Peptidoglycanmurein bacteria cell wall Extracellular matrix 0 Animal cells have this instead of cell walls Figure 632 Plasmodesmata Plant cells have openings between each other to allow communication 0 Animal cells 0 Tight junction membranes of two cells so tightly connected that theres nothing that can move between them Desmosome not as tight Gap junctions free communication similar to plasmodesmata End of chapter concept check mm Figure 72 Lipid soluble substances pass through the plasma membrane faster than water soluble substances Hydrophilic head and hydrophobic tail Amphipathic molecules Blood cells were studied for plasma membrane because they have no organelles Figure 73 Phospholipid bilayer Pores to allow water to go through 0 Some proteins are on the surface and some are embedded in Figure 75 76 78 Fluid mosaic model of the plasma membrane 0 Made up of phospholipids and proteins 0 Two types of membranes peripheral only on one side and integral span membrane 0 Certain physical and biological properties depend on movement Membranes usually uid in body temperature 0 Cholesterol 0 Saturated and unsaturated lipids 0 Type of lipid 0 Lateral movement of lipids and proteins restricted on attachment Glycoprotein Glycolipid Carbohydrates important to help cells recognize each other and stick together in tissues important in recognizing self vs non self Figure 79 710 712 Protein 0 Long polypeptide chain 0 C and N terminus Membrane 0 Transport Enzymatic action Act as receptors for signaling molecules Cellcell recognition 0 Join cells together Connects extracellular matrix and cytoskeleton for communication 0 proteins made in the ribosomes in the rough ER and then join the plasma membrane Figure 711 Don t need to know much information Cell has to bind to two receptors Lacking coreceptors make individuals resistant Figure 712 713 1 Diffusion Molecules have kinetic energy Law of Diffusion things move from higher to lower concentration until they reach equilibrium Free energy total energy plus entropy things go towards disorder diffusion deceases free energy and increase disorder Diffusion is passive transport doesn t require energy More surface area increases diffusion Cytoplasmic streaming Microvilli Counter current exchange think sh breathing through gills maximizes diffusion Not efficient over long distances Affected by the concentration gradient Affected by the size and shape of molecules Affected by temperature and pressure 2 Transport by carriers 3 Endocytosis and exocytosis Figure 714 715 Osmosis diffusion of water 0 Size lipid solubility charge across the membrane 0 Water can move freely across the membrane from higher concentration to lower concentration 0 Remember water has a charge and will attach to other things bound water Osmotic concentration the total solute concentration of a solution Osmotic pressure the measure of the tendency for a solution to take up water when separated from pure water by a selectively permeable 0 Animal cell 0 lsotonic solution have normal cells equal concentrations in cell and solution 0 Hypertonic solutions will have shriveledcrenated cells cell has higher concentration than solution 0 Hypotonic solutions will have lysed cells solution has higher concentration than cell 0 Solution is hypertonic to the cell or cell is hypotonic to the solution 0 Plant cell 0 Cells in hypotonic solution will have turgid cells 0 Cells in an isotonic solution will be accid 0 Cells in a hypertonic solution will be plasmolyzed Figure 717 718 719 0 Transport by carriers Hydrophobic things go through membranes easily 0 Channel protein gated channels 0 Carrier protein picks up things and move them across 0 Transport proteins 0 Uniport carries one thing 0 Symports carry two things in the same direction 0 Antiports carry two things in opposite directions Facilitated transportfacilitated diffusion 0 Does not use energy 0 Goes from high concentration to low concentration 0 Does not use carrier proteins 0 Passive transport 0 Aquaporins protein carriers 0 Sodium Potassium Pump Protein carriers 718 IS IMPORTANT Can hold either sodium or potassium Bind sodium to carrier High sodium concentration outside and low inside Hydrolysis of ATP phosphate changes shape Sodium can t be held anymore so it gets dumped outside of the cell 0 Potassium binds and causes to fall off 0 Shape changes again and potassium gets trapped inside 0 Active transport 0 Protein carrier needed 0 Going from high to low concentration OOOOO o Requires energy Figure 720 721 Voltage electrical potential energy or a separation of opposite charge Membrane potential voltage across a membrane 0 Charges will affect movement if charges are present Electrochemical gradient combines the electrical force membrane potential and the chemical force concentration gradient Electrogenic pump transport protein that generates voltage across the membrane Proton pump 0 Pumps hydrogen ions 0 Requires energy 0 Important in plants cellular respiration and photosynthesis Cotransporter cell 0 Sucrose Figure 722 Endocytosis Phagocytosis cell eating Pinocytosis cell drinking Receptormediated endocytosis Exocytosis Goes from inside to outside


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