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Foundations of Bio 1 Unit 2

by: Abhishek Mishra

Foundations of Bio 1 Unit 2 BIOSC 0150

Abhishek Mishra
GPA 3.83
Foundation of Biology 1

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Everything you need to know for the second test.
Foundation of Biology 1
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This 13 page Bundle was uploaded by Abhishek Mishra on Monday January 19, 2015. The Bundle belongs to BIOSC 0150 at University of Pittsburgh taught by Kaufman/McGreevy in Spring2015. Since its upload, it has received 88 views. For similar materials see Foundation of Biology 1 in Biological Sciences at University of Pittsburgh.

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Date Created: 01/19/15
72 Eukaryotic Cell Structures and Their Functions Wednesday October 8 2014 809 PM Location of DNA The benefits of organelles Com partmentalization also offers two key advantages 1 Incompatible chemical reactions can be separated 2 Chemical reactions become more efficient Internal membranes and organelles Key differences of Prokaryotes v Eukaryotes 1 Eukaryotic chromosomes are found inside a membranebound CytOSkEIEton compartment called the nucleus 2 Eukaryotic cells are often much larger than prokaryotes 3 Eukaryotes cells contain extensive amounts of internal membrane 4 Eukaryotic cells feature particularly diverse and dynamic cytoskeleton Overall size The Nucleus Chromosomes do not float freely 0 Each chromosome occupies a specific area which will vary over the course of cell replication and different cell types Nucleolus 0 Where mRNA is manufactured 0 large and small ribosomal subunits are assembled Ribosomes Not considered organelles because they are not surrounded by membranes Manufacture proteins Endoplasmic Reticulum ER Portions of nuclear envelope extended into the cytoplasm Continuous with nuclear envelope Single structure containing two regions of distinct structure and function 0 Rough ER I Ribosomes associated with the rER synthesize proteins that will be III Inserted into the plasma membrane III Secreted to the cell exterior III Shipped to an organelle 0 As proteins are manufactured by the rER they move to the interior of the rER the lumen 0 Within the lumen proteins undergo folding and other types of processing 0 Smooth ER I Contains enzymes that catalyze reactions involving lipids I Reservoir of Ca Golgi Apparatus Products of rER pass through the Golgi before they reach their final destination Consists of discrete flattened membranous sacs called cisternae stacked on top of one another Has polarity O Cis surface is closest to the nucleus 0 Trans surface is oriented towards the plasma membrane In between within the cisternae rER39s products are processed and packaged for delivery Lysosomes Function as recycling centers 0 Contain about 40 enzymes specialized for hydrolyzing different types of macromolecules I Proteins I Lipids I Nucleic acids I Carbohydrates D Amino acids nucleotides sugars and other molecules that result from hydrolysis leave the lysosome via transport proteins in the organelles membrane 0 Enzymes are collectively called acid hydrolases because under acidic conditions pH 50 they use water to break monomers from macromolecules O Proton pumps in the lysosomal membrane maintain an acidic pH in the lumen of the lysosome by importing hydrogen ions Module 2 Page 1 Bacteria and Archaea Eukaryotes Inside nucleus membrane bound plasmids extremely rare In nucleoid not membrane bound plasmids also common Large numbers of organelles many types of organelles Extensive internal membranes only in photosynthetic species limited types and numbers of organelles Extensiveusually found throughout volume of the cell Limited in extent relative to eukaryotes Most are larger than prokaryotes Usually small relative to eukaryotes Endomembrane System Acid hydrolases gt Synthesized in ER Processed in Golgi Shipped to Lysosome Wye1340 39awlr de Mums 13 c L a Y Plasma membrane Vacuoles Cells of plants fungi and certain other groups lack lysosomes Instead they contain a prominent organelle called a vacuole Large can take as much as 80 ofthe plant cells volume Some vacuoles contain digestive enzymes but most act as storage units 0 Inside seeds cells may contain large vacuoles filled with proteins Digested to provide amino acids for growing seeds 0 Cells that make up flower petalsfruits contain vacuoles filled with colorful pigments 0 Can be packed with noxious compounds that protect leaves and stems from being eaten by predators Peroxisomes Virtually all eukaryotic cells contain globular organelles called peroxisomes Have a single membrane and originate as buds from the ER Different cells can have different peroxisomes but all are centers of redox reactions 0 Liver cells contain enzymes that remove electrons from or oxidize the ethanol in alcoholic beverages O Glyoxysomes leaves of plants are packed with enzymes that oxidize fats to form a compound that can be used to store energy for the cell 0 Plant seeds are packed with enzymes responsible for releasing energy from stored fatty acids The young plant uses this to grow Mitochondria Powerhouse of the cell Composed of two membranes 0 Outer layer defines surface 0 Inner surface is connected to a series of saclike cristae Solution within the inner membrane is called the mitochondrial matrix Most enzymes and molecular machines responsible for synthesizing ATP reside within the cristae and the matrix Contains small circular DNA 0 Only codes for 37 genes I Includes genes that code for ribosomal RNA produces some but not all proteins necessary 0 Most genes responsible for mitochondria function reside in nucleus Chloroplasts Double membrane analogous to a mitochondria Contains hundreds of thylakoids arranged into stacks called grana Region outside is called stroma 0 Contains enzymes that use energy from photosynthesis to produce sugars Contains copies of circular chromosome and small ribosomes Cytoskeleton Common to all eukaryotic cells 0 Extensive system of protein fibers Give cell shape and structural stability Moving cell and material within the cell Organizes all the organelles and other cellular structures into a cohesive whole The Cell Wall In fungi algae and plants 0 Outer cell wall in addition to plasma membrane Rods or fibers composed of carbohydrates running through a stiff matrix made of other polysaccharides and proteins Nucleus Ribosomes rER sER Endomembrane Golgi system Lysosomes Vacuoles Membrane Double envelope openings called nuclear pores None Single contains receptors for entry of selected proteins Single contains enzymes for synthesizing phospholipids Single contains receptors for products of rER Single contains proton pumps Single contains transnorters Module 2 Page 2 Components Chromosomes Nucleolus Nuclear Lamina Complex of RNA and proteins Network of branching sacs Ribosomes associated Network of branching sacs Mitochondria and Chloroplasts Grow and divide independently of cell division through a process that resembles bacterial fission Biologists believe that mitochondria and chloroplasts were once freeliving bacteria Endosymbiosis theory suggests that ancestral eukaryotes ingested mitochondriachloroplasts and Established a mutually beneficial relationship with them Function Information storage and transmission Ribosome subunit assembly Structural support Protein synthesis Protein synthesis and processing Lipid synthesis and processing Enzymes for synthesizing or breaking down lipids Stack of flattened distinct cisternae Acid hydrolases catalyze hydrolysis reactions Variespigments oils carbohvdrates water or Protein lipid and carbohydrate processing Digestion and recycling Variescoloration storage of oils system Lysosomes Vacuoles Peroxisomes Mitochondria Chloroplasts Cytoskeleton Plasma membrane Cell Wall quotquotUquotI 3939 products of rER Single contains proton pumps Single contains transporters for selected molecules Single contains transporters for selected macromolecules Double inner contains enzymes for ATP production Double plus membranebound sacs in interior None Single contains transport and receptor proteins None Module 2 Page 3 Acid hydrolases catalyze hydrolysis reactions Variespigments oils carbohydrates water or toxins Enzymes that catalyze oxidation reactions Catalase processes peroxide Enzymes that harvest energy from molecules to make ATP Pigments Enzymes that use light energy to make sugars Actin filaments Intermediate filaments Microtubules Phospholipid bilayer with transport and receptor proteins Carbohydrate fibers running through carbohydrate or protein matrix Digestion and recycling Variescoloration storage of oils carbohydrates water or toxins Oxidation of fatty acids ethanol or other compounds ATP production Production of sugars via photosynthesis Structural support movement of materials in some species movement of the whole cell Selective permeabilitymaintains intracellular environment Protection structural support 73 Putting the Parts into a Whole Thursday ctober 9 2014 105 AM Within a cell each component correlates its structure with its function in the same way the overall size shape and composition of a cell correlates with its function Structure and Function at the Whole Cell Level Examples 0 Cell in pancreas I Manufactures and exports digestive enzymes III Packed with rER and Golgi bodies 0 Cell from testis I Exporting steroids and lipids ii sER 0 Cell from a leaf I Specialized for absorbing light and manufacturing sugar III Hundreds of chloroplasts 0 Cell from brown fat I Stored energy of fat gt heat III Packed mitochondria The Dynamic Cell Imaging techniques the differential centrifugation and electron microscopes only allow us to see cells in a snapshot static way At the scale of the cellribosomeorganelle O Gravity is inconsequential 0 Dominant forces are charge based electrostatic attractions between molecules and their energy of motion Examples I In one second III Typical cell uses 10 million ATP molecules III Cellular enzyme catalyzes 25000 or more reactions per second III HundredsThousands of new protein molecules Module 2 Page 4 74 Cell Systems I Nuclear Transport Sunday ctober 122 2 14 12 7 AM Nuclear Lamina Provides an attachment point for the chromosomes each of which occupies a welldefined region in the nucleus Specific Centers exist where genetic information in DNA is decoded and processed At these location large suits of enzymes interact to produce RNA messages from specific genes at specific times Nucleolus functions as the site of ribosome assembly Structure and Function of the Nuclear Envelope Bounded by two lipid bilayers and supported by the nuclear lamina Nuclear pore O Extend through both inner and outer membranes 0 Each pore contains 50 different proteins 0 Called the Nuclearpore complex 0 Exit nucleus I Ribosomal subunits and various types of RNAs 0 Enter Nucleus I Nucleotides and proteins involved in DNA replication How do Large Molecules Enter the Nucleus Size was not sole factor Experimental nucleoplasmin ejected in the cytoplasm wound up in the nucleus 0 Cleaved off core segment of nucleoplasmin from the tails I Found that tails were transported into nucleus whereas core was not Nuclearbound proteins are synthesized by ribosomes in the cytosol and given a nuclear localization signal NLS that marks them for transport through the nuclear pores Proteins that are departing the Nucleus have a different signal Energy demanding process Module 2 Page 5 75 Cell Systems II The Endomembrane System Manufactures Ships and Recycles Cargo Sunday ctober 12 2 14 1258 PM Most of the proteins found in peroxisomes mitochondria and chloroplasts are also actively imported from the cytosol These proteins contain special signal sequences like the NLS that target them to the appropriate organelles Entering the Endomembrane System The Signal Hypothesis The signal hypothesis predicts that proteins bound for the endomembrane system have a molecular zip code analogous to the NLS When proteins normally made in the rER are produced in the cytosol they are 20 amino acids longer than usualy 0 Extra amino acids are a quotsend to ERquot signal 0 Removed within the cell ER signal sequence will move proteins in the lumen 0 Step 1 Protein synthesis begins on a free ribosome in the cytosol The ribosomes synthesizes the ER signal sequence 0 Step 2 The signal sequence binds to a signal recognition particle SRP39s a complex of RNA and protein The attached SRP causes protein synthesis to stop 0 Step 3 The ribosome signal sequence SRP complex moves to the ER membrane where it attaches to the SRP receptor 0 Step 4 Once the receptor and the SRP connect the SRP is released and synthesis resumes 0 Step 5 The growing protein is fed into the lumen through a channel and the signal sequence is removed Once inside the rER proteins are folded into their 3D shape via chaperone proteins Addition of carbohydrate side chains via glycosylation results in a glycoprotein 0 Number and arrangement of these sugars changes as the protein matures serving as an indicator for shipment Moving from the ER to the Golgi Proteins are transported in vesicles that bud off the membrane of the ER and dock at the cis section of the Golgi What happens in the Golgi As the proteins move from cisgttrans they are reacted on by a host of sectionspecific enzymes that further modify the carbohydrates added to the protein in the ER How do proteins reach their destination Proteins will accumulate in the respective vesicle budding sites by attaching to receptors These budding sites form into vesicles and the receptors on the cytosolic side of the vesicle directs Module 2 Page 6 it to the intended target Recycling Material in the Lysosome Molecules outside the cell bind into receptors which pinch off the plasma membrane into vesicles The vesicles bind to the early endosome and proton pumps release the vesicles cargo in the early endosome the vesicles are recycled back into the membrane The early endosome receives digestive enzymes from the Golgi and matures into a lateendosome The late endosome matures into a lysosome that recycles materials via autophagy and phagocytosis O Autophagy I Damaged organelle is surrounded in membrane I Delivered to lysosome O Phagocytosis I Cell engulfs a particle I Phagosome is delivered to lysosome Module 2 Page 7 76 Cell Systems I The Dynamic Cytoskeleton Wednesday September 24 ZDM 627 PM unlit rl39lv39 II n mumquot Three distinct cytoskeletal elements in eukaryotic cell actin filaments intermediate filaments and microtubules mil Halb Ivli lrulu m c furmz Actin Filaments Microfilaments Composed of actin gactin and factin Actin is the most abundant protein in animal cells Structure o A completed actin filament is two globular units of actin that have coiled around each other via monovalent bonds I Polymerize from head to tail I This asymmetric arrangement results in different polarity on the ends III Plus end polymerizes faster than the minus end 0 Each filament is generally unstable and will growshrink depending on the availability of free actin subunits I Cells regulate lengthlongevity via actin binding proteins that stabilizedestabilize their structure Function o In addition to providing structural support actin is also involved in movement 0 Depends on the motor protein Myosin I Converts potential energy of ATP into kinetic energy of mechanical work I When myosin binds and hydrolyzes ATP to ADP It causes a shape change that extends the myosin head along the actin filament and pulls it III Moves towards the plus end I Cytokinesis Actin filaments form a ring around the membrane and pinch it off during cell division I Cytoplasmic Streaming Directed flow of cytosol and organelles within pant cells I Cell crawling Groups of actin filaments grow and bulge the plasma membrane that extend and move the cell Intermediate Filaments Form a flexible skeleton that helps shape the cells surface and hold the nucleus in place Many types of intermediate filaments exist each consisting of different though similar in size and structure types of protein ex Humans have 70 proteins for intermediates as opposed to actin and tuban Intermediate filaments are not polar each end is identical Not involved in directed movement Serve a purely structural role In eukaryotic cells Example Keratin 20 types of Keratin along skin and surfaces within body that provide enough mechanical strength to resist external forces Several cells can also secrete concentrated Keratin which turns into nails and hair Nuclear Lamins also qualify as intermediate filaments 0 Form a dense mesh under the nuclear envelope and anchor chromosomes 0 Also involved in breakup and reassembly of the nuclear envelope when cells divide hm Wings of tunnlxr39l JL 0 o Microtubules Largest cytoskeletal components in terms of diameter Composed of two poly peptides alpha and beta tubulin that exist as stable protein dimers centric3905 Like actin they also have polarity AlnhndIlhnlin 3 mimic nnrl Module 2 Page 8 Composed of two poly peptides alpha and beta tubulin that exist as stable protein dimers Like actin they also have polarity Alphatubulin gt minus end Betatubulin gt plus end Dynamic and grow faster at plus end compared to minus end Originate from microtubule organizing center MTOC 0 Plus ends grow outward radiating throughout the cell I Plant cells typically have hundreds of MTOC39s I Animal cellsfungal cells have just one near nucleus In animals MTOC contains structure called centrosome 0 Houses two bundles of microtubules called centrosomes I Microtubules do not grow directly from centrioles When ATP is hydrolyzed by kinesin the protein moves along microtubules in a directional manner towards the plus end Flagella and Cilia Moving the Entire Cell Flagella are long whip like projections from the cell surface that function in movement While many bacteria and eukaryotes have flagella the structure is completely differetn in the two groups Bacterial flagella are helical rods made of a protein called flagellin o Create movement by rotating rod like a propeller Eukaryotic flagella consist of several microtubules constructed from tubulin fibers 0 Create movement by undulating whipping back and forth Based on these observations biologists believe these two structures evolved independently Although they have the same function Eukaryotic flagella are closely related to cilia o Flagella are generally much longer and is far less abundant o Underlying organization is identical Axoneme quot92quot arrangement of microtubules o 9 microtubule doublets surrounding 2 central microtubules o Originate from basal body I Identical to centriole O Sporelike proteins connect doublets to central pair Molecular links connects doublets to one another 0 Each doublet has set of arms that connect to adjacent doublet 0 What Provides the Force Required for Movement Energy using process Protein dynein uses ATP to move along microtubules towards the minus end f dynein arms on just one side of axoneme are activated then the movement results in the bending ofthe ciliaflagella which results in a swimming motion Module 2 Page 9 v pair ul centrioms IA ILBI Microtubules growing from nuchmhng Sites on centrosome Inna dynein Ouu dymm arm Nonquot 111 The Cell Surface Monday ctober 132 2 14 454 PM The Structure and Function of an Extracellular Layer Almost all extracellular structures are composed of fiber composites 0 RodsFilamentsFibers I Effective at withstanding stretching and straining forces tension I Resist being pushed or pulled lengthwise 0 Ground substance I Effective at withstanding pressing forces of compression I Gelforming mixture of polysaccharides The Cell Wall in Plants Primary Cell Walls 0 Fibrous component of primary cell wall is composed of bundles of cellulose called microfibrils I Cross linked by other polysaccharide filaments I Synthesized by enzymes in plasma membrane 0 Space between microfibrils is filled with gelatinous pectin I Hydrophilic can attract and hold large quantities f water I Synthesized in rER and Golgi 0 Primary cell walls defines shape of a plant cell Secondary Cell Walls 0 When plant cells mature and stop growing they can secrete and additional layer of material between the plasma membrane and the primary cell wall 0 The structure of the secondary cell wall varies from cell to cell in the plant and correlates with that cell39s function I Examples 11 Leaves 0 2nd cell wall secretes waterproof wax 11 Stem 0 Contain great deal of cellulose III Woodforming 0 Lignin forms an exceptionally rigid network The Extracellular Matrix in Animals Most animal cells secrete a fiber composite called the extracellular matrix ECM Structural support is one of the ECM39s most important functions Contains much more proteins relative to carbohydrates than a cell wall 0 Fibrous component I Collagen 0 Matrix that surrounds collagen I Proteoglycans Most ECM components are synthesized in the rER processed in the Golgi and secreted from the cell via exocytosis ECM varies depending on the tissue 0 Bone has few cells and lots of ECM Module 2 Page 10 0 Skin cells are packed together will minimum ECM Transmembrane proteins called integrins bind to both the cytoskeleton and the ECM O This cytoskeletonECM linkage keeps the cell anchored in place and helps adjacent cells adhere t one another Module 2 Page 11 112 How Do Adjacent Cells Connect and Communicate Monday October 13 2014 705 PM CellCell Attachments in Multicellular Eukaryotes Epithelium 0 Forms barrier between internal and exterior surfaces Indirect Intercellular Attachments 0 The extracellular space between adjacent plant cells comprises three layers I The primary cells walls of the adjacent cells sandwich and area called them middle lamella iI composed of pectins that are continuous with the primary cells walls ofthe adjacent cells gluing them together 0 The extracellular space between adjacent animal cells integrins connect the cytoskeleton of each cell to the extra cellular matrix I A middlelamellalike layer of gelatinous proteins and proteoglycans run between adjacent cells and along with cytoskeletonECM connections cold cells together Tight Junctions Form a Seal between Cells 0 Cellcell attachment composed of specialized proteins in the plasma membranes of adjacent animal cells prevents solutions from flowing through the space between the two cells 0 Dynamic and variable I can loosen and tighten in response to environmental condition Good at holding cells together but can be broken easily 0 0 Cells Communicate via CellCell gaps o In both plants and animals direct connections between cells in the same tissue help them to work in a coordinated fashion 0 Create channels directly between cells I Can alter which proteins are produce and which are not by regulating gene expression I Can activate or deactivate Gap Junctions Connect Animal Cells via Protein Channels Protein channels along cell membranes that create pores between the cells allow water ions and small molecules 0 amino acids sugars and nucleotides allow rapid passage of regulatory ions or molecules Plasmodesmata Connect Plant Cells via Membrane Channels 0 connects sER of two adjacent plant cells Module 2 Page 12 tight junction zona occludens surface basal surface apical cell protein strands cell 2 113 How Do Distant Cells Communicate Tuesday ctober 14 2 14 1235 AM CellCell Signaling in Multicellular Organisms Most lipidsoluble signaling molecules are able to diffuse across the hydrophobic region of the plasma membrane and enter the cytoplasm of their target cells Large of hydrophilic signaling molecules are lipid insoluble and do not cross the plasma membrane To affect a cell they have to be recognized at the cell surface GProteinCoupled Receptors Step 1 Signaling receptor arrives and binds to a receptor in the plasma membrane Receptor is coupled to a Gprotein Step 2 In response to binding the receptor changes its shape and removes the GDP from its G protein allowing it to bind GTP This changes the Gproteins shape the active subunit of Gprotein splits off Step 3 Active Gprotein subunit binds to an enzyme which leads to the production of secondary messengers 0 small and diffuse rapidly O activate protein kinases Receptor Tyrosine Kinases Step 1 Signaling molecule binds to RTK Step 2 RTK subunits bind to form a dimer and phosphorylyze themselves Step 3 Proteins attach to phosphorylated RTK and form a bridge with Ras a Gprotein Step 4 Ras triggers a kinase Step 5 Cascade occurs Module 2 Page 13


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