Biology POB II Review Paper

POB II: Exam II Review
Chapter 6: tour of the cell
Microscopy:
• Microscopes provide a window to the cell.
• Most important tool in cytology
• Resolution has improved understanding of cells. o Resolving power – the smallest distance between two objects that allows them to be seen as distinct objects. o Resolving power of the human eye is 0.1 mm
• Light microscope – uses glass lenses and visible light to form a magnified image of an object. o Resolving power of about 100 nm (.0002 mm) o Advantage: View of cells and organelles o Disadvantage: Cannot visualize ribosomes o Types of light microscopy:
 Brightfield microscopy- passes light directly through specimen. Very little contrast (will show natural colors).
 Brightfield stained
specimen- same as above except dyes have stained specimen. WE USE
 Phase contrast – useful for viewing living cells. Increases contrast of unstained cells.
 Differential interference contrast- exaggerates contrast making image appear almost 3D.
 Fluorescence – shows location of specific molecules with the use of fluorescent dyes or antibodies.
 Confocal – uses lasers and special optics for optical sectioning of fluorescently stained specimens. Clearer Picture than fluorescence.
• Electron microscopes –use powerful magnets to focus an electron beam. o Electron micrograph- the image created. o Resolving power of .2 nm o Scanning electron microscope - electrons are directed at the surface of the cells, providing a 3D image. Electrons don’t penetrate. o Transmission electron microscope – allows you to see inside of the cell. Specimen is sliced thin so that electrons can penetrate.
• Cell fractionation – rupturing cells, followed by systematic centrifugation to take cells apart, separating out organelles. o Cells must be ruptured with care so as to not break the internal membrane bound compartments.
 Mortar and pestle, glass homogenizer, blender, or place cell in a hypotonic solution so that it pops. o Differential centrifugation – when cell suspension is placed in a centrifuge to create large forces causing the components of the suspension to pellet at the bottom of the tube. (Burst cell, separates more dense.) o Centrifuge- lab instrument that spins materials at high speeds.
View of the Cell o Every cell is composed of one or more prokaryotic or eukaryotic cells. o Cells come from preexisting cells o All cells have certain features in common: plasma membrane, cytosol, chromosomes, and ribosomes. o Cells must maintain a surface area –to-volume ratio (SA/V) that is beneficial for metabolic processes to occur.
 As a cells volume increases, so does surface area. Not to the same extent
 Volume is related to the amount of chemical activity a cell can undertake.
 Surface area indicates its ability to exchange nutrients and waste products with the environment.
 If a cell was larger, its waste production would outwork its ability to deal with that waste.
 Cells maintain a large SA/V ration by being small in volume
 The large amount of surface area is important for many biological functions. o Prokaryotic and eukaryotic differ in size and complexity
Prokaryotic
• From Greek meaning pre-nucleus (nucleoid)
• Generally smaller in size
• No membrane bound organelles
• Have cell walls
• Have smaller ribosomes.
• Includes kingdoms eubacteria and archeabacteria
• Generally single celled organisms, often seen in chains, clusters, or colonies.
• Some can use light energy to generate needed materials
• Others can generate needed materials from inorganic compounds.
• Some are chemoheterotrophs
• Some move with the aid of flagella
• Pilli – used for attachment to substrates or used for conjugation.
• Biofilm – conglomeration of bacteria or different species that form a polysaccharide coat so that they are hard to get rid of.
Eukaryotic
• Meaning “true nucleus” o Red blood cells have no nucleus
• Found in plantae, fungi, protista, and animalia
• Have membrane enclosed compartments which isolates certain molecules and chemical reactions. o Some reactions (proteins) are built into the walls of the compartment. o Membranes are a phospholipid bilayer.
 Each different membrane has a special set of proteins and lipids for specific functions.
• More complex cells.
• Have complex internal cytoskeleton and membranous compartments
• Membrane and specialized compartments are organelles o Not all organelles are equally abundant in all cells. o Components between plant and animal cells differ. (figure 6.9)
 Chloroplasts
 Vacuole
 Plasmodesmata
 Lysosomes
 Flagella
 Centrioles
: Nucleus
• DNA resides in the nucleus. o This information may be translated into proteins on the surface of ribosomes. o Normally the largest organelle = 5μm, which is larger than many prokaryotic cells. o Genome – the collection of genes for an organism o Double membrane enclosed nucleus is defining feature of a eukaryotic cell
 The two membranes are very close together and are perforated by nuclear pores.
• Pores are approx. 9nm in diameter and connect the interior of the nucleus (nucleoplasm) with the cytoplasm.
• Each pore is surrounded by 8 protien granules to allow material to pass in and out.
 Under an electron microscope, you can visualize the two membranes that make up the nuclear envelope.
• Nuclear envelope – normally a stable structure except during mitosis or meiosis when it breaks into small vesicles. o Vesiculate – to become vesicles
• Sometimes nuclear envelope folds towards cytoplasm and is continuous with the ER. o Inside the nucleus DNA combines with proteins to for a fibrous complex called chromatin.
 this is surrounded by the aqueous nucleoplasm (liquid and dissolved particles)
 Near the periphery of the nucleus, the chromatin interacts with the nuclear lamina .
 Nuclear Lamina – cytoskeleton of the nucleaus formed by a net array of proteins called lamins (keratin proteins) . Gives nucleus its shape, makes nuclear envelope rigid.
• Nuclear lamina depolymerizes when the nucleus breaks down for cellular reproduction. Since they are polymers they depolymerize (take polymers apart). o Most of DNA is in a tangled mess called chromatin (ramen noodles). Only when the cell is ready to divide will it form chromosomes (bowling pins). o Each contains one, usually linear, molecule of DNA that carries the hereditary information and directs protein synthesis. o Nucleolus – dark circle in the nucleus that houses 10-20% of the cell’s RNA is This is where rRNA and proteins come together to form ribosomal subunits.
 These subunits leave the nucleus and are assembled into functional ribosomes in the cytoplasm.
 Nucleoli disappear as cellular/nuclear division approaches and reappear after cell division.
Ribosomes build a cell’s proteins o Ribosomes are found in three places in the cell:
 Cytoplasm :
 attached to the ER
 in the mitochondria (chloroplast) o Serve as the site of protein synthesis under the direction of nucleic acids. o Are involved in the translation of proteins. o Prokaryotic and eukaryotic ribosomes are similar in that both have two different sized subunits.
 Eukaryotic ribosomes are larger than prokaryotes o The chemical makeup of ribosomes includes rRNA and proteins (50+) o Ribosomes make primary structure. Primary protein structure is most important. o Ribosomes sit on the membrane of the ER and also in between. o Ribosomes bind mRNA and tRNA in order to translate hereditary information into primary protein structure. o Ribosomes are found free in the cytoplasm attached to the ER, and in the mitochondria.
The Endomembrane system
• Regulates protein traffic and performs metabolic functions
• Much of the volume of the cell is taken up by its extensive internal membrane system.
• There are connections between many of the membranes, suggesting that there may be a single endomembrane system. o Vesicles (sacs of membrane) are involved in the transfer between components of the endomembrane system. (UPS)
Endoplasmic reticulum
• Manufactures membranes and performs many other biosynthetic functions.
• Lumen – interior compartment that is separate from the cytoplasm.
• So extensive it accounts for over half of all cellular membranes in a eukaryotic cell.
• Parts are continuous with the outer nuclear membrane.
• Consists of a network of membranous tubules and sacs called cisternae. (Latin for liquid reservoir)
Rough ER –
• the portion of the ER with ribosomes attached o Protiens used outside the cytosol: secreted proteins, placed in membranes, or moved into membrane organelles o These proteins enter the lumen due to a special amino acid signal sequence.
 Signal sequence – is the address to where the proteins should go. o The proteins mature into their tertiary structure and some have carbohydrates attached.
 Makes these proteins glycoprotiens (sugar protein)which helps in directing the protein to the right part of the cell and involved in some protien’s function. o Transport vesicle bud like bubbles from the ER to take cargo to other parts of the cell. (golgi)
 When vesicle and Golgi fuse, the vesicle membrane becomes the Golgi membrane, and empties contents into the lumen.
The smooth ER –
• The portion of the ER with no ribosomes attached o These are more tube shaped and less flattened o Diverse metabolic processes occur here.
 Site of Carbohydrate metabolim
 phospholipid, steroid, fatty acid biosynthesis
 toxic substances can also be detoxified here. o If a cell is involved in a lot of protein production for export then they will be packed with ER.
 Ex. Gland cells and antibody producing cells
The Golgi apparatus
• Finishes sorts and ships cell products
• Exists in most eukaryotic cells
• Consists of cisternae and small membrane enclosed vesicles. o Sacs lay together like a stack of saucers
• Phospholipids and ogliosaccharides are altered in the passage through the cisternae of the Golgi.
• Cells that specialize in secretion have extensive Golgi networks
• In many cells, individual stacks for a network. o Cis Golgi – is the bottom stack that lies nearest the nucleus or rough ER o Trans Golgi – is the top portion of the stacks and is nearest the plasma membrane o Medial Golgi- lies inbetween
• Vesicles from rough ER  move to and fuse with cis Golgi to empty contents into lumen  vesicles move from cis to the medial  trans golgi  vesicles leave golgi to travel to other membranes. [ the membrane of two vesicles may fuse resulting in a larger vesicle with mixed contents.]
• How does Golgi sort, package, and send? o Can be an aminio acid sequence, glycolysation, or phosphorylation. o Proteins in the trans golgi recognizes signals and package the protein for shipment to its final destination.
Lysosomes
• Are digestive compartments
• Lysosomes that originate in part from the Golgi apparatus contain digestive enzymes that accelerate macromolecule breakdown.
• Lysosomes contain enzymes that can digest all the major macromolecules: protein, polysaccharide, nucleic acid, and lipid breakdown. o Low internal pH of the lysosome is necessary for normal enzyme function
• This organelle is the site of breakdown for food or foreign material taken up by phagocytosis.
• Phagocytosis is the process that a cell uses to bring in materials from outside the cell inside a membrane bound vesicle called a phagosome. o This may fuse with a lysosome from the Golgi to form a secondary lysosome. o Digestion then occurs
• Lysosomal digestion and phagocytosis are extremely important to white clood cell function. (white blood cells identify and attack foreign objects) o Autophagy – engulfing own cellular components
Vacuoles
• Have diverse functions in cell maintenance
• Filled with an aqueous solution containing many dissolved particles.
• Simple in structure vacuoles have diverse functions
• Plants(central vacuole) cannot excrete all waste products stored here also for storage of ions
• Can give turgor, stiffness to the cell
• Some color pigments used for plant reproduction are stored here
• May be used to store and digest foods, food vacuole
• Contractile vacuole in fresh water protists is used to get rid of excess water
Mitochondria and Chloroplasts change energy from one form to another
• Main energy transformers for cells o Cells use energy to transform raw materials into cell specific materials that are involved in: growth, reproduction and movement. o This occurs in the mitochondria of all eukaryotic cellsand the chloroplasts of cells that can harvest energy from sunlight. o These organells haver their own ribosomes and DNA
 Responsible for making proteins important for their function as energy powerhouses.
Mitochondria
• Utilization of glucose as an energy source begins in the cytosol then moves to the mitochondria.
• Takes partially degraded fuel molecules and changes them from potential chemical energy into the useable form ATP.
• ATP is not a storage form of energy, but a participatory form that can be used to run many cellular processes.
• Production of ATP in the mitochondria using fuel molecules and O2 is aerobic cellular respiration.
• Mitochondria are about the same size as bacteria.
• Electron microscopy has shown us that mitochondria have two membranes, and outer and inner.
• Outer membrane: o Protective offering little resistance to substance moving into and out of the mitochondria.
• Inner membrane: o Has many fold called cristae o Give greater surface area for energy producing reactions to occur. o Has large proteins involved in cellular respiration. o Inside inner membrane is the mitochondrial ______. Which contains enzymes, ribosomes, and mitochondrial DNA.
 Mitochondrial DNA (circular) encodes for some mitochondrial proteins.
 Function almost like separate small organisms
 If the cell requires more energy they have more mitochondria.

Plastids
• Photosynthesize or store materials
• Found only in plants and certain protists.
• A familiar plastid is the chloroplast which contains the green pigment chlorophyll and is the site of photosynthesis
• Light is converted to energy of chemical bonds, provides food for the plant and for other organisms.
• Chloroplasts have a double membrane like mitochondria. o Chloroplasts contain membrane structures that look like stacks of pancakes – called grana. o The circular stacks that make up grana are called thylakoid.
 A Single membrane sack made of phospholipids and proteins
 Contain chlorophyll and carotenoids
 Used to harvest lightenergy and convert it to glucosefrom CO2 and H2O o Fluid inside the chloroplast is the stroma and contains the grana, ribosomes, enzymes, DNA. o Not all plant cells have chloroplasts
• Other types of plastids include the chromoplasts and leucoplasts o Chromoplasts – may be important just for color ( tomato color from carotenoids) o Leucoplasts – are involved in storage of starch and
fats.
• The fact that mitochondria and chloroplasts have their own DNA (circular) and ribosomes led in part to the theory of endosymbiosis. o Proposes that larger prokaryotesengulfed smaller ones and these may have become the first eukaryotic cells (with organelles) o Mitochondria and chloroplasts also have double membranes and ribosomes that are similar to prokaryotes.
Peroxisome
• Degrades H2O2
• Small organelles with a granular interior and a single outer membrane
• Within peroxisomes, highly reactive and toxic peroxides are found. That result from chemical reactions in the cell.
• These peroxides are detoxified in the peroxisome (catalase)
Cytoskeleton
• Network of fibers extending throughout the cytoplasm, that organizes structures and activities in the cell.
• Gives structure helps with cell function.
• Light and electron microscopy have elucidated the cytoskeleton
• Plays a major role in organization and activities throughout the cell.
Roles of cytoskeleton
• Support, motility, and regulation: o Most obviously involved in support for the cell (scaffolding) o Involved in several different types of motility : cell movement includes movement of the cell and movement of objects inside the cell. o Motility involves the interaction of cytoskeletal components and motor molecules.
 Dynein and kinesin o Three types of cytoskeletal components: microtubules, microfilaments, and intermediate filaments.
Microtubules:
• Long hollow cinlinders that radiate from the microtubule organizing center and are made of the globular protein tubulin.
• Microtubule organizing center in many cells (animal) is the centrosome which contains two centrioles.
• Tubulin – a dimer made of two subunits: α and β tubulin.
• Microtubules grow by adding tubulin dimers to one end.
• Polymerization  grows at one end
• Deplymerization  shortens on one end o Thirteen rows, or protofilaments, of tubulin dimers surround the central cavity of the microtubule. o There is a positive and a negative end to microtubules giving them polarity and making them dynamic structures.
• Functions of microtubules include: o Controls the arrangement of cell walls o Areas of a cell changing shape o Tracks for cargo movement in the cell (dynein and kinesin) o Distribution of chromatids to daughter cells during mitosis and meiosis o Used for cilia and flagella
 Structure as well as movement o Many structures possess whiplike appendages, cilia and/or flagella o Cilia and flagella have similar structure.
 The total number of microtubules is 20
• Have a 9 + 2 arrangement
• 9 fused pairs of microtubules (doublets) around two single microtubules.
 Movement is due to the sliding of the microtubules along one another.
 Sliding is due to the motor protein called dynein (towards positive end) [ important in arm like motion] which attaches to both microtubules and marches them past one another.
 Kinesin is another motor protein used in cargo transport (in vesicles) along microtubules toward the negative end.
 At the end of each microtubule is a basal body the 9 doublets exist in the basal body [anchor], but there are no central microtubules.
• Each doublet is accompanied by another microtubule, making 9 sets of 3.
Microfilaments
• Actin filaments
• Actin is important in cell structure. Important proteins associated with actin.
• Actin is assembled into a long chain of globular actin (G actin) subunits. o G actin has a distinct head and tail for formation of filamentous actin (F actin) o [G is a subunit to F] o Two chains of filamentous actin form a double helical structure called a microfilament. o Formation of filamentous actin is reversible – depolymerization o Microfilaments can be very stable as well as giving specific shapes when interacting with specific actin binding proteins (ABPs).
 Form beneath the plasma membrane
• Microfilaments are well known in their role in motility: amoeboid movement, muscle cell contraction, and cytoplasmic streaming. o Help extend the pseudopodia in amoeboid movement. o Actin interlaced with myosin, myosin acts as a motor protein to walk along actin filaments causing muscle cell contractions. o Actin and myosin interactions in plant cells cause a circular movement of cytoplasm, cytoplasmic streaming.
Intermediate filaments
• Stabilize cell structure and resist tension
• 5 types that have similar structures and are composed of the keratin family of proteins. o Include lamins of the nuclear envelope o May help to hold organelles in position o Provides tissue rigidity by forming desmosomes between cells. [ spot welds]
• Defects in the components associated with the cytoskeleton can result in genetic disorders. o Loss of functional spectrin and ankyrin (actin associated proteins) results in hemolytic anemia (spherocytosis). o The most common form of muscular dystrophy (1 in 3,500 male children), progressive loss of muscle cells, is caused by a mutation in the dystrophin gene which encodes for a protein that attaches actin filaments to the muscle cell plasma membrane.
Extracellular components and connections between cells
Cell walls of plants
• A semi rigid structure outside of the plasma membrane consisting primarily of polysaccharides (cellulose). o Gives support, limits cell volume, and can control water movement.
• There are connections between plant cells called plasmodesmota. o Link plant cells allowing diffusion of water, ions, small molecules and many proteins between the cells ensuring their uniform concentration
Extracellular matrix
• Function in support, adhesion, movement, and regulation
• Multicellular organisms have complex extracellular matrix o Composed of collagen (most abundant protein in mammals) and other glycoprotiens. o Collagen is embedded in a network of woven proteoglycans. o Some cells are attached to the ECM by fibronectins and integrins. o Secreted by cells, some have large amounts of extracellular matrix (bone and cartilage) others have little (brain)
 Cells embedded in bone secrete collagen and the ionic solid calcium phosphate that gives bone its characteristic rigidity. o Epithelial cells that line body cavities spread as a sheet over the basal lamina (basement membrane), a form of extracellular matrix. o Some extracellular matrix proteins can be spectacular
 Proteoglycan is made of approximately one hundred proteins attached to an enormous polysaccharide.
• Functions of the extracellular matrix: o Physical properties: skin, cartilage, and other tissues. o Filter materials o Orientation of cell migration during embryonic development and during tissue regeneration. o Cell to cell signaling.
Intracellular junctions
• Help integrate cells into higher levels of structure and function.
• Allows cells to be organized into tissues, organs, and organ systems.
• Function to allow cells to adhere to one another, interact and communicate aall throufh direct contact and special protein patched ( cell adhesion proteins)
• Three of these cell surface junctions include: tight junction, desmosomes, and gap junctions.
• Tight junctions: o Are specialized structures that link adjacent epithelial cells lining a lumen or cavity. o Limit the passing of materials from the limen and inhivit the movement of the membrane proteins. o Thus, membrane proteins on the apical surface (faces lumen) differ from those on the basolateral.
 Helps ensure directional movement of substances through the cell and into the body o Runs entire length
• Desmosomes: o Specialized structures associated with the plasma membrane that hold adjacent cells together much like spot welds or rivets. o Consists of plaque on the cytoplasmic surface of the plasma membrane attached to keratin fibers of the cytoplasm and adhesion proteins in the plasma membrane. o The adhesion proteins pass from the plaque of one cell to the plaque of another. o Keratin fibers are made of the protein keratin and are intermediate filaments.
• Gap junctions: o Facilitate communication between cells. o Made of specialized protein channels called connexons that span the plasma membrane of adjacent cells. o Small molecules and proteins may pass through these channels, but not large proteins, nucleic acids, or organelles. o In some nerve cells and in the vertebrae heart gap junctions allow for the direct passage of electrical signals. POB II: Exam II Review
Chapter 7: Membrane Structure and Function
Cellular membranes
• Are fluid mosaics of lipids and proteins
• Plasma membrane- is the edge of life and like all membranes, it is selectively permeable.
• Selectively permeable – allows some substances to cross more easily than others.
• Staple ingredients of a membrane are lipids (phospholipids) and proteins. o Phospholipids are amphipathic.
 Amphipathic – they have a hydrophobic portion and a hydrophilic portion. [ polar head, 2 nonpolar tails, and a glycerol] o Proteins and lipids interact in the fluid mosaic model.
 Fluid membrane with proteins embedded into it.
• Membranes are abundant and essential.
• Isolate cellular environments from the outside and from each other.
• The hydrophobic bilayer makes them good barriers
• Membranes do more than define compartements, they process material energy and information. o Including communication with the extracellular environment and other cells.
• Membrane models have adapted to fit new data o Data from many experiments have shown us that membranes are a bilayer
 Allowing them to be barriers
 Proteins are embedded in the membrane. o All of the information has led us to our current fluid mosaic model.(fluid part is phospholipids)
 Phospholipid bilayer with proteins embedded into the membrane.
• Proteins have hydrophobic domains that pass through the membrane and hydrophilic regions on both ends. o Membranes are fluid
 Membranes are NOT static sheets locked rigidly into place.
 Lipids and proteins can flow laterally quite easily even occasionally flipping.
 Unsaturated fatty acids in a membrane decrease its ability to packed easily (by temp) where saturated hydrocarbons pack more easily.
 We have cholesterol in our membranes that help them be more fluid.
• Cholesterol is an important part of animal membranes, it keeps them fluid at low temperatures and yet provides some rigidity.
• Helps counter saturated hydrocarbons
Cell fusion experiment: o Researchers labeled the plasma membrane proteins of a mouse cell and a human cell with two different markers and fused the cells. Then observed the hybrid cell:
 The mixing of the mouse and human membrane proteins indicates that at least some membrane proteins move sideways within the plane of the plasma membrane.
Membrane Proteins and their functions
• A membrane is a collage of different proteins embedded in the fluid matrix of the lipid bilayer
• There are two types of membrane proteins: integral and peripheral. o Intergral membrane proteins:
 Integral membrane proteins penetrate the phospholipid bilayer, most are transmembrane, meaning they pass from one side of the membrane to another. o Peripheral membrane proteins:
 Are not embedded in the bilayer but are attached to exposed parts of integral membrane proteins or phospholipids. Either anchored to an integral protein or thay have a protein tail stuck in the membrane. Phospholipid can anchom trhem by attaching to phosphate head. o Organelle membranes differ greatly in the protein composition of their membrane.
 Ex. Internal membranes of mitochondris and chloroplasts have specialized proteins for energy production. o The two surfaces of a membrane have different properties due to the asymmetric distribution of transmembrane proteins.
 `the different domains of a protein have different properties and transmembrane proteins can have different domains on either side of the membrane.
Six functions for proteins associated with a membrane:
• Transport- getting things across the membrane
• Enzymatic activity ex. Enzymatic activity
• Signal transduction – external signals are transduced to the inside of cell
• Intercellular joining – joins two cells together
• Cell-cell recognition – recognition of foreign, own, and “bad” cells. Helps protect us from cancer, tumors, and other diseases caused by the mistake in the cells.
• Attachment to the cytoskeleton and extracellular matrix – puts cells together to create organelles.
What determines if a membrane protein is peripheral or integral?
• Amino acid side chains have different properties: some are hydrophobic or hydrophilic.
• Integral membrane proteins often have long α helical sections that are hydrophobic ( 20 amino acids) o These are perfect for lying in a membrane o Hydrophilic and hydrophobic forces keep the integral membrane protein in place. o Usually proteins go through the membrane in a α helix form. o To pass through the membrane:
 20 amino acids
 Only hydrophobic
 Α helix o Overall , there are more hydrophobic amino acids on the loops and more hydrophilix amino acids are in the spiral helix. o One reason why α helix is used normallu is because the amino acids used R groups are pointing out.
• How does the integral membrane protein get in the membrane? o Specialized sequences during translation signal for the protein to be inserted in the membrane.
• Some peripheral membrane proteins have specific sequences for the addition of specialized lipids that get inserted into the membrane to keep the protein peripheral to the membrane.
• Protiens are threaded into the membrane by the little mail code packaged on the end of the amino acid sequence.
• Anything that is inserted into the membrane is done either in the ER or in the Golgi.
Membrane carbohydrates
• Are important for cell to cell recognition
• Human red blood cell plasma consists of 40% lipid, % protein, and 8%carbohydrates.
• The carbohydrates are on the outer surface of the membrane and serve as recognition sites. o Often ogliosaccharides
• Carbohydrates can recognize specific extracellular compounds o These carbohydrates are attached to a protein or lipid o The carbohydrates protrude from the lipid or protein into the extracellular environment o Carbohydrates are usually attached to a lipod or a protein which forma a glycolipid and/or a glycoprotein. o The final form of the oligosaccharide are on the outside of the cell pointing out. o Glycocalyx – coating on outside of cell
• Carbohydrates are bound to lipids and proteins as glycolipids and glycoprotiens respectively. [most are attached to proteins]
• Glycolipids are important in recognizing cancerous cells for destruction by the body. o They change their components and are recognized by white blood cells for phagocytosis.
• Most of the carbohydrate is bound to protein. o They re bouns as ogliosaccharide side chains. o Added to the proteins inside the ER and modified in the Golgi o Allows the cell to recognize substances o Great variety of carbohydrates due to the variety of monomers.
Selective permeability
• Determines a membrane’s molecular organization
• Cells must maintain a constant movement of material back and forth across the membrane
• Not all things move across the membrane equally
• Hydrophobic molecules(O2 CO2) easily pass through the membrane
• Transport of ions or polar molecules (hydrophilic) is tightly regulated.
• Certain proteins (transport proteins) play a vital role in controlling the movement of that which cannot pass the hydrophobic barrier. o Transport proteins may actively help molecules across the membrane or form a simple pore for things to diffuse through.
• Movement through the membrane can be active or passive.
Passive transport
• Is diffusion across a membrane
• Diffusion is the tendency for molecules to move from an area of high concentration to low concentration. o It is a result of thermal motion, nothing is ever truly at rest o This is considered “down” the concentration gradient o Requires no work and increases entropy (random mixture)
• Even though the mocement is random the net mocement of particles is directional until equilibrium is reached o Equilibrium does not mean no movement,, it means no net change. Still moving. When the solute cannot move, water will move.
• Diffusion of a substance across a biological membrane is called passive diffusion.
• Passive transport includes: simple diffusion and facilitated diffusion o Simple diffusion requires no energy nor proteins. o Facilitated diffusion uses proteins.
 Passive transport aided by proteins
 Many polar molecules need help in order to diffuse
 Aquaporins are channel proteins involved in helping water (highly polar) across the membrane
 Some channel proteins form simple pores for polar molecules to move through while others act as gated channels.
• Gated channels respond to stimulus to open and close (no energy directly involved)
• Binding of solute molecules may cause the channel to change conformation, allowing the solute to pass.
 Can saturate- when there is more solute than available carriers o Osmosis is diffusion of water
 The movement of water depends on the amount of solute present (not the type).
 Tonicity is the ability of a solution to cause a cell to gain or lose water.
 If two solutions have identical solute concentrations, they are isotonic no matter their chemical composition.
 If the two solutions are not isotonic, then the solution with a high solute concentration is said to be hypertonic to the other solution which is hypotonic.
 Hyper/hypo tonic solutions can cause cells to shrink or expand.
• Hyper has more dissolved particles than the cell, so it causes cell to shrivel.
• Plant cells prefer hypotonic
 Cell survival depends on balancing water uptake and loss.
• Movement of water across the membrane and the balance between water and the environment is very important
• Organisms without cell walls have the ability to control watter balance, osmoregulation.
• Cells with cell walls have an ability to withstand bursting when placed in a hypotonic solution die to turgor pressure. o Driving force for growth in plant cells
• Plant cells can go from turgid all the way to flaccid and still survive due to their cell wall.
• Plants can die in a hypertonic solution due to their plasma membrane coming apart from the cell wall, plasmolysis.
Active transport
• Uses energy to move solutes against their concentration gradient
• Active moves molecules from low to high (“uphill”) o Requires ATP and carrier proteins
• Includes specific membrane transporters as well as systems involved in membrane fusion
• Extremely important in keeping cellular concentrations of mall molecules (ions) different inside the cell than outside.
• One common example is the sodium-potassium pump which expels sodium and brings potassium inside the cell o The sodium potassium pump is an integral membrane glycoprotein found in all animal cells.
 The breakdown of ATP into ADP allows the movement of 3 sodium ions out of the cell and 2 potassium ions into the cell.
 The movement of sodium out and potassium in classifies it as an antiporter.
 Different pumps are responsible for the transport of several other ions but only cations are transported by primary active transport
 Other solutes are transported by secondary active transport
 Some ion pumps generate voltage across membranes
• Movement of anions and cations set up a membrane potential across the membrane o The inside of the cell is negatively charged when compared to the outside. Reason it is negative:
 Sodium potassium pump: 3+ ions moved out and 2+ ions move in  charge is less
 Proton pump: moves positively charged protons out of cell  charge is less
• Since the cytoplasm is negative, cations are more likely to diffuse into the cell and anions out of the cell
• Thus, there are two forces acting on an ion concentration gradient the electrical and chemical gradient; this combination is called electrochemical gradient.
• Electrogenic pumps are those involved in generating voltage across a membrane. o the main electrogenic pump in the body is the proton pump (pumps H+) o Cotransport
 Results from a membrane protein coupling the transport of two solutes
 A single ATP powered pump that transports a specific solute can indirectly drive the active transport of several other solutes.
 Protons want to move back in due to the negative charge, the integral membrane protein uses energy created by proton movement to carry large molecules across the membrane.
Exocytosis and endocytosis
• How bulk transport occurs
• Exocytosis – is the process by which materials packaged in vesicles are secreted from the cell. o The vesicle membrane fuses with the plasma membrane (from the golgi) the phospholipids of the two membranes merge and opening to the extracellular environment develops
• The vesicle membrane then becomes part of the plasma membrane
• Used for the secretion of cell wastes, enzymes, neurotransmitters and other cellular secretions.
• Three forms of endocytosis: phagocytosis, pinocytosis, and receptor-mediated endocytosis. o All three involve invagination of the plasma membrane making a small pocket. o This deepening forms a vesicle containing contents from the extracellular matrix o Phagocytosis
 Is a feeding process found in unicellular protists and white blood cells (often the engulfing of an entire cell)
 The phagosome that is formed often fuses with a lysosome (phagolysosome, or secondary lysosome) o Pinocytosis
 “cell drinking”
 Uses smaller vesicles and brings in dissolved particles o Receptor mediated endocytosis:
 Involves specialized reactions that take place at the membrane and trigger uptake
 Ligand – better term for substrate
 Receptor mediated endocytosis is highly specific
 Similar to other endocytosis events except receptors on the plasma membrane bind to specific substances in the extracellular environment
 Often these receptors lie in a region called a coated pit
 Once inside the cell the vesicle may lose its coat and fuse with other vesicles
 Receptor-mediated endocytosis is much more rapid and efficient method of taking up substances out of the cellular environment
 One example of receptor-meidated is how cholesterol gets into a mammalian cell
• Cholesterol is synthesized in the liver and transported in the blood as a lipoprotein.
• These coated pits are depressions of the plasma membrane with receptors on the extracellular surface and coated on the cytoplasmic surface with the protein clathrin.
• After the receptor(s) bind the appropriate substrate the coated pit invaginates and forms a clathrin coated vesicle
• Clathrin may act to strengthen and stabilize the vesicle
• This low density lipoprotein is taken up into cells by attachment to a specific receptor in coated pits
• These LDL particles are engulfed, the receptor is recycled and the LDL containing vesicle fuses to a lysosome
• The LDL particle is digested and the cholesterol is made available to the cell
• A deficient receptor for LDL leads to a dangerously high levels of cholesterol in the blood, hypercholesterolemia. POB II: Exam II Review
Chapter 8: Introduction to Metabolism
Metabolism
o An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamics o Metabolism is the total chemical activity of a living organism o Arises from interactions between molecules within the orderly cell environment o Thousand of reactions occur every instant o Involves multiple chemical reactions
• Chemistry of life is organized into metabolic pathways o Elaborate and complex read map of the thousands of chemical reactions that take place inside of the cell o Enzymes route matter through these pathways by selectively accelerating each step o Enzymes lower activation energy, which speeds up the reaction o Metabolism is concerned with managing the material and energy recourses of the cell o Breaking things down to release subunits and energy or building complex molecules (macromolecules) and using energy o Two basic types of reactions:
 Catabolic reactions – break down complex molecules into simpler ones releasing energy
• Cellular respiration
• Glucose broken into CO2 and H2O
 Anabolic reactions – link together simple molecules to form complex molecules storing energy in chemical bonds
• Protein synthesis from amino acids
 Reaction coupling – takes energy produced by catabolism and uses it for anabolism.
• Ex. Breakdown of glucose and using the energy to produce protein
Forms of energy o Energy – the capacity to do work (rearrange matter) o Two basic types of energy are kinetic and potential:
 Kinetic energy:
• is the energy of action
• Energy that does work (alters the state or motion of matter) can exist as heat, light, electrical, and mechanical.
 Potential energy
• Is the energy of state or position
•
• Stored energy: chemical bonds, concentration gradients, and electrical potentials are all important in biology.
Laws of thermodynamics:
 Energy transformations are subject to two laws of thermodynamics
 First law of thermodynamics - energy is neither created or destroyed it just changes forms
 Second law of thermodynamics – not all energy is used and disorder tends to increase (entropy increases)
• An organism can increase its order at the expense of the order around it o Often in the form of heat or small molecule breakdown
• When energy is transformed some is unavailable to do work o No reaction is 100% efficient
Free energy
• The free energy change of a reaction tells us whether the reaction occurs spontaneously
• Reactions that proceed without energy input are considered spontaneous. While those that do not proceed without energy input are considered nonspontaneous
• Free energy (G) is the portion of a system’s energy that can perform work when temperature is uniform throughout. o Free because it is available to do work o Total energy is called enthalpy (H), unusable energy is entropy (S) o This is affected by absolute temperature (T), in Kelvin (K=C+273) o We are intersested in the change in free energy, therefore the equation is:
 ΔG= ΔH – TΔS
 From a starting state to an ending state o This equation indicates whether free energy is released or consumed by a chemical reaction.
 -ΔG =
• energy released
• exergonic
• spontaneous
 +ΔG =
• Energy consumed
• Endergonic
• Nonspontaneous
 ΔG =0
• Equilibrium
• Results in death of the cell o We will be able to follow the release or consumption of energy during chemical reactions by following the change in free energy
 If a reaction runs spontaneously from reactant A  product B then the reverse (B  A) requires energy
 At some concentrations of A and B the forward and reverse reactions take place at the same rate, this is a _______ equilibrium.
• No observable change I the system, even though individual reactions are still occurring
• Cells never reach total equilibrium, a cell with ΔG = 0 is dead o The ideas of free energy change and thermodynamics are important for understanding how cells function, specifically how biochemical reactions occur
 Exergonic reactions drive endergonic reactions energy coupling a small molecule (ATP) is responsible for mediating most energy coupling in cells
 Reactants have more free energy than the products
ATP
• Powers cellular work by coupling exergonic reactions to endergonic reactions
• Adenosine Triphosphate is the energu form in the cell used for action
• Used for energy and as a building block for DNA and RNA
• Consists of the nitrogenous base adenine fused to ribose which has 3 phosphates attached [rather than the 1 that nucleic acids are normally made of]
• Hydrolysis of ATP yields adenosine diphosphate and an inorganic phosphate ion as well as free energy o at equilibrium there is ten million times as much ADP as ATP, ATP is continuously regenerated o There is more energy in P – P bonds because their charges make them difficult to get together. So it requires more energy to put them together, and thus releases more energy when broken.
• ATP couples exergonic reactions and endergonic reactions o Many enzyme catalyzed reactions (exergonic) can provide the energy to convert ADP to ATP (cellular respiration).
• The breakdown of ATP yield energy for other reactions o Can be through a phosphorylated (phosphate is added, usually an enzymatic process. Enzyme= kinase) intermediate o [dephosphorilation – phosphate is taken. Enzyme = phosphatase]
• ATP lasts less than one minute in the cell and on averae 40kg of ATP per day is produced by a person at rest.
Enzymes
• Are made of proteins
• Speed up metabolic reactions by lowering energy barriers
• ΔG may indicate how far the reaction proceeds to completion but does not indicate the speed of the reaction.
• Exergonic reactions may be fast or slow o Ex. Sucrose hydrolysis is spontaneous but will happen imperceptibly until the enzyme sucrose is added [ could perform benedict’s test to check]
• Activation energy barrier: o Catalyst – any substance that speeds up a reaction
 Does not cause a reaction, merely speeds it up o Most biological catalysts are proteins called enzymes o There are also RNA enzymes called ribozymes – which is RNA that has a catalytic function o Energy barriers must be overcome for a reaction to proceed
 Includes breaking and reforming of chemical bonds
 EX: sucrose hydrolysis requires breaking the chemical bond between glucose and fructose then forming water from H+ and OH – o The energy barrier represents the amount of energy needed to start the reaction, the activation energy.
 Activation energy moves the reactants from stable to unstable, a state called the transition state
• An enzyme lowers the amount of energy required to get to the transition state
 Exergonic reactions need very little activation energy while endergonic reactions need more
 The activation energy is often recovered so it does not affect the ΔG.
 Enzymes act to lower the activation energy, however, they have no effect on equilibrium or ΔG
 Changes activation energy and consequently the reaction rate.
Active site
• Catalysis in enzyme’s active site o Non biological catalysts do not show specifically like protein enzymes do. o Reactants are substrates and they bind to the active site of an enzyme o Enzymes are extremely specific
 Can be so specific that changing a single amino acid can cause the enzyme not to recognize the substrate
 Specificity results from the 3D structure of the enzyme and substrate
• E + S  ES  E + P
• The active site is not rigid, the substrate can cause the enzyme to change the shape of its active site, Induced fit o Like a handshake o EX: hexokinase (the first enzymes of glycolysis that phosphorilates glucose) uses this model for fitting around its substrate, glucose
• Some active sites are more rigis and they fit like a lock and key, lock and key model o EX: the active site of a lysozyme (breaks down bacterial cell walls) neatly fits its substrate o The active site is the enzyme’s catalytic center
 Enzymes use the following mechanisms in order to change a reactant to a product: orientation of substrates, add charges to substrates, or induce strain( push back or bend substrate until it breaks or changes)
Local conditions
• Effects enzyme activity
• Enzyme activity can be altered by environment (ex: temp, pH and salinity), chamicals and concentration of substrate
• Substrate concentration will affect reaction rate o The more substrate, the more possible collisions which leads to more reactions per unit of time (reaction rate) [ more substrate = higher reaction rate] o In an enzyme catalyzed reaction, eventually the enzyme becomes saturated at a certain substrate concentration and rate levels off.
 This means that all available enzymes are bound to a substrate
 Can change environmental factor or add more enzymes
• Some enzymes require added molecules for function o Cofactors are nonprotien inorganic ions that bind temporarily to enzymes and are essential to function
 Ex: copper zinc and iron
 Coenzymes are conbon containing(organic) molecules required for enzyme function
• Enzyme inhibitors o Inhibitors of enzyme function can act reversibly or irreversibly o Irreversible inhibition occurs when an inhibitor binds via a covalent bond (often at the active site) o Reversible Inhibition can occur in two ways:
 Competitive inhibition occurs when the inhibitior and substrate compete for the same active site
 Non competitive inhibition occurs when the inhibitor binds outside the active site but in doing so renders the active site ineffective
• Environmental Conditions o pH, temperature and salinity can affect the function of an enzyme
 for each condition the enzyme has a maximum, minimum, and optimum range for its function

Part of eukaryotic cell Definition / Function
Endoplasmic Reticulum: • Manufactures membranes and performs many other biosynthetic functions.
• So extensive it accounts for over half of all cellular membranes in a eukaryotic cell.
• Parts are continuous with the outer nuclear membrane.
• Consists of a network of membranous tubules and sacs called cisternae.
• If a cell is involved in a lot of protein production for export then they will be packed with ER.
 Ex. Gland cells and antibody producing cells
• Rough ER • The portion of the ER with ribosomes attached
• Vesicles bud from ER to transport cargo.
• Smooth ER • The portion of the ER with no ribosomes attached
• These are more tube shaped and less flattened
• Diverse metabolic processes occur here. o Site of Carbohydrate metabolism o Phospholipid, steroid, fatty acid biosynthesis o Toxic substances can also be detoxified here.
• Lumen interior compartment that is separate from the cytoplasm
Cisternae Flattened Sacs. Latin for Liquid reservoir
Flagellum Are longer whip-like appendages, usually found single or in pairs. Whip-like undulation from one end to another.
Cilia Are shorter whip-like appendages and found in greater numbers. Beat stiffly in one direction and recover flexibly. Swimmers arm.
Peroxisome • Degrades H2O2
• Small organelles with a granular interior and a single outer membrane
• Within peroxisomes, highly reactive and toxic peroxides are found. That result from chemical reactions in the cell.
• These peroxides are detoxified in the peroxisome (catalase)
Cytoskeleton • Network of fibers extending throughout the cytoplasm, that organizes structures and activities in the cell.
• Gives structure helps with cell function.
• Light and electron microscopy have elucidated the cytoskeleton
• Plays a major role in organization and activities throughout the cell.
Roles of cytoskeleton
• Support, motility, and regulation: o Most obviously involved in support for the cell (scaffolding) o Involved in several different types of motility : cell movement includes movement of the cell and movement of objects inside the cell. o Motility involves the interaction of cytoskeletal components and motor molecules.
 Dynein and kinesin o Three types of cytoskeletal components: microtubules, microfilaments, and intermediate filaments.

• Microfilaments • Actin filaments
• Actin is important in cell structure. Important proteins associated with actin.
• Actin is assembled into a long chain of globular actin (G actin) subunits. o G actin has a distinct head and tail for formation of filamentous actin (F actin) o [G is a subunit to F] o Two chains of filamentous actin form a double helical structure called a microfilament. o Formation of filamentous actin is reversible – depolymerization o Microfilaments can be very stable as well as giving specific shapes when interacting with specific actin binding proteins (ABPs).
 Form beneath the plasma membrane
• Microfilaments are well known in their role in motility: amoeboid movement, muscle cell contraction, and cytoplasmic streaming. o Help extend the pseudopodia in amoeboid movement. o Actin interlaced with myosin, myosin acts as a motor protein to walk along actin filaments causing muscle cell contractions. o Actin and myosin interactions in plant cells cause a circular movement of cytoplasm, cytoplasmic streaming.
• Intermediate filaments • Stabilize cell structure and resist tension
• 5 types that have similar structures and are composed of the keratin family of proteins. o Include lamins of the nuclear envelope o May help to hold organelles in position o Provides tissue rigidity by forming desmosomes between cells. [ spot welds]
• Defects in the components associated with the cytoskeleton can result in genetic disorders. o Loss of functional spectrin and ankyrin (actin associated proteins) results in hemolytic anemia (spherocytosis). o The most common form of muscular dystrophy (1 in 3,500 male children), progressive loss of muscle cells, is caused by a mutation in the dystrophin gene which encodes for a protein that attaches actin filaments to the muscle cell plasma membrane.
• Microtubules • Long hollow cinlinders that radiate from the microtubule organizing center and are made of the globular protein tubulin.
• Microtubule organizing center in many cells (animal) is the centrosome which contains two centrioles.
• Tubulin – a dimer made of two subunits: α and β tubulin.
• Microtubules grow by adding tubulin dimers to one end.
• Polymerization  grows at one end
• Deplymerization  shortens on one end o Thirteen rows, or protofilaments, of tubulin dimers surround the central cavity of the microtubule. o There is a positive and a negative end to microtubules giving them polarity and making them dynamic structures.
• Functions of microtubules include: o Controls the arrangement of cell walls o Areas of a cell changing shape o Tracks for cargo movement in the cell (dynein and kinesin) o Distribution of chromatids to daughter cells during mitosis and meiosis o Used for cilia and flagella
 Structure as well as movement o Many structures possess whiplike appendages, cilia and/or flagella o Cilia and flagella have similar structure.
 The total number of microtubules is 20
• Have a 9 + 2 arrangement
• 9 fused pairs of microtubules (doublets) around two single microtubules.
 Movement is due to the sliding of the microtubules along one another.
 Sliding is due to the motor protein called dynein (towards positive end) [ important in arm like motion] which attaches to both microtubules and marches them past one another.
 Kinesin is another motor protein used in cargo transport (in vesicles) along microtubules toward the negative end.
 At the end of each microtubule is a basal body the 9 doublets exist in the basal body, but there are no central microtubules.
• Each doublet is accompanied by another microtubule, making 9 sets of 3.
Lysosome (animal) • Are digestive compartments
• Lysosomes that originate in part from the Golgi apparatus contain digestive enzymes that accelerate macromolecule breakdown.
• Lysosomes contain enzymes that can digest all the major macromolecules: protein, polysaccharide, nucleic acid, and lipid breakdown. o Low internal pH of the lysosome is necessary for normal enzyme function
• This organelle is the site of breakdown for food or foreign material taken up by phagocytosis.
• Phagocytosis is the process that a cell uses to bring in materials from outside the cell inside a membrane bound vesicle called a phagosome. o This may fuse with a lysosome from the Golgi to form a secondary lysosome. o Digestion then occurs
• Lysosomal digestion and phagocytosis are extremely important to white clood cell function. 9white blood cells identify and attack foreign objects)
Autophagy – engulfing own cellular components
Mitochondria • Has its own ribosomes and DNA
• Utilization of glucose as an energy source begins in the cytosol then moves to the mitochondria.
• Takes partially degraded fuel molecules and changes them from potential chemical energy into the useable form ATP.
• ATP is not a storage form of energy, but a participatory form that can be used to run many cellular processes.
• Production of ATP in the mitochondria using fuel molecules and O2 is aerobic cellular respiration.
• Mitochondria are about the same size as bacteria.
• Electron microscopy has shown us that mitochondria have two membranes, and outer and inner.
• Outer membrane: o Protective offering little resistance to substance moving into and out of the mitochondria.
• Inner membrane: o Has many fold called cristae o Give greater surface area for energy producing reactions to occur. o Has large proteins involved in cellular respiration. o Inside inner membrane is the mitochondrial ______. Which contains enzymes, ribosomes, and mitochondrial DNA.
 Mitochondrial DNA (circular) encodes for some mitochondrial proteins.
 Function almost like separate small organisms
 If the cell requires more energy they have more mitochondria.

Plasma membrane • Are fluid mosaics of lipids and proteins
• Plasma membrane- is the edge of life and like all membranes, it is selectively permeable.
• Selectively permeable – allows some substances to cross more easily than others.
• Staple ingredients of a membrane are lipids (phospholipids) and proteins. o Phospholipids are amphipathic.
 Amphipathic – they have a hydrophobic portion and a hydrophilic portion. [ polar head, 2 nonpolar tails, and a glycerol] o Proteins and lipids interact in the fluid mosaic model.
 Fluid membrane with proteins embedded into it.
• Membranes are abundant and essential.
• Isolate cellular environments from the outside and from each other.
• The hydrophobic bilayer makes them good barriers
• Membranes do more than define compartements, they process material energy and information. o Including communication with the extracellular environment and other cells.
• Membrane models have adapted to fit new data o Data from many experiments have shown us that membranes are a bilayer
 Allowing them to be barriers
 Proteins are embedded in the membrane. o All of the information has led us to our current fluid mosaic model.(fluid part is phospholipids)
 Phospholipid bilayer with proteins embedded into the membrane.
• Proteins have hydrophobic domains that pass through the membrane and hydrophilic regions on both ends. o Membranes are fluid
 Membranes are NOT static sheets locked rigidly into place.
 Lipids and proteins can flow laterally quite easily even occasionally flipping.
 Unsaturated fatty acids in a membrane decrease its ability to packed easily (by temp) where saturated hydrocarbons pack more easily.
 We have cholesterol in our membranes that help them be more fluid.
• Cholesterol is an important part of animal membranes, it keeps them fluid at low temperatures and yet provides some rigidity.
• Helps counter saturated hydrocarbons
Golgi apparatus • Finishes sorts and ships cell products. Sort, package and send.
• Exists in most eukaryotic cells
• Consists of cisternae and small membrane enclosed vesicles. o Sacs lay together like a stack of saucers
• Phospholipids and ogliosaccharides are altered in the passage through the cisternae of the Golgi.
• Cells that specialize in secretion have extensive Golgi networks
• In many cells, individual stacks for a network. o Cis Golgi – is the bottom stack that lies nearest the nucleus or rough ER o Trans Golgi – is the top portion of the stacks and is nearest the plasma membrane o Medial Golgi- lies inbetween
• Vesicles from rough ER  move to and fuse with cis Golgi to empty contents into lumen  vesicles move from cis to the medial  trans golgi  vesicles leave golgi to travel to other membranes. [ the membrane of two vesicles may fuse resulting in a larger vesicle with mixed contents.]
• How does Golgi sort, package, and send? o Can be an aminio acid sequence, glycolysation, or phosphorylation. o Proteins in the trans golgi recognizes signals and package the protein for shipment to its final destination.
Ribosomes o Ribosomes are found in three places in the cell:
 Cytoplasm :
 attached to the ER
 in the mitochondria (chloroplast) o Serve as the site of protein synthesis under the direction of nucleic acids. o Are involved in the translation of proteins. o Prokaryotic and eukaryotic ribosomes are similar in that both have two different sized subunits.
 Eukaryotic ribosomes are larger than prokaryotes o The chemical makeup of ribosomes includes rRNA and proteins (50+) o Ribosomes make primary structure. Primary protein structure is most important. o Ribosomes sit on the membrane of the ER and also in between. o Ribosomes bind mRNA and tRNA in order to translate hereditary information into primary protein structure. o Ribosomes are found free in the cytoplasm attached to the ER, and in the mitochondria.
Chromatin Fibrous complex.DNA is mostly in this form. Ramen noodles.
Nucleolus Nonmembranous organelle involved in production of ribosomes o Nucleolus – dark circle in the nucleus that houses 10-20% of the cell’s RNA is This is where rRNA and proteins come together to form ribosomal subunits.
 These subunits leave the nucleus and are assembled into functional ribosomes in the cytoplasm.
 Nucleoli disappear as cellular/nuclear division approaches and reappear after cell division.

Nuclear envelope • Double membrane enclosing the nucleus; perforated by pores; continuous with ER. Pores are approx. 9nm in diameter and connect the interior of the nucleus (nucleoplasm) with the cytoplasm.
• Each pore is surrounded by 8 protien granules to allow material to pass in and out.

Vesicle Have proteins in their membrane that interacts with other things.
Plastid • Photosynthesize or store materials
• Found only in plants and certain protists.
• A familiar plastid is the chloroplast which contains the green pigment chlorophyll and is the site of photosynthesis
• Light is converted to energy of chemical bonds, provides food for the plant and for other organisms.
• Other types of plastids include the chromoplasts and leucoplasts o Chromoplasts – may be important just for color ( tomato color from carotenoids) o Leucoplasts – are incolced in storage of starch and fats.
• Chloroplast (plant) • Has its own ribosomes and DNA
• have a double membrane like mitochondria. o Chloroplasts contain membrane structures that look like stacks of pancakes – called grana. o The circular stacks that make up grana are called thylakoid.
 A Single membrane sack made of phospholipids and proteins
 Contain chlorophyll and carotenoids
 Used to harvest lightenergy and convert it to glucosefrom CO2 and H2O o Fluid inside the chloroplast is the stroma and contains the grana, ribosomes, enzymes, DNA. o Not all plant cells have chloroplasts
Cell wall (plant) • A semi rigid structure outside of the plasma membrane consisting primarily of polysaccharides (cellulose). o Gives support, limits cell volume, and can control water movement.
Plasmodesmata (plant) • There are connections between plant cells called plasmodesmota. o Link plant cells allowing diffusion of water, ions, small molecules and many proteins between the cells ensuring their uniform concentration
Centrioles (animal)
Vacuole (plant) • Have diverse functions in cell maintenance
• Filled with an aqueous solution containing many dissolved particles.
• Simple in structure vacuoles have diverse functions
• Plants(central vacuole) cannot excrete all waste products stored here also for storage of ions
• Can give turgor, stiffness to the cell
• Some color pigments used for plant reproduction are stored here
• May be used to store and digest foods, food vacuole
• Contractile vacuole in fresh water protists is used to get rid of excess water
Nuclear lamina  Nuclear Lamina – cytoskeleton of the nucleaus formed by a net array of proteins called lamins (keratin proteins) . Gives nucleus its shape, makes nuclear envelope rigid.
• Nuclear lamina depolymerizes when the nucleus breaks down for cellular reproduction. Since they are polymers they depolymerize (take polymers apart).

Nucleoplasm
Chromosomes The individual form of chromatin. Visible in a dividing cell. “bowling pins”
Endosome
Cristae
Grana o Chloroplasts contain membrane structures that look like stacks of pancakes – called grana.

Thykaloid o The circular stacks that make up grana are called thylakoid.
 A Single membrane sack made of phospholipids and proteins
 Contain chlorophyll and carotenoids
 Used to harvest lightenergy and convert it to glucosefrom CO2 and H2O

Stroma o Fluid inside the chloroplast is the stroma and contains the grana, ribosomes, enzymes, DNA.

Luekoplasts A type of plastid involved in storage of starch and fats
Chromoplasts A type of plastid. be important just for color ( tomato color from carotenoids)
Intracellular junctions: • Help integrate cells into higher levels of structure and function.
• Allows cells to be organized into tissues, organs, and organ systems.
• Function to allow cells to adhere to one another, interact and communicate aall throufh direct contact and special protein patched ( cell adhesion proteins)
Three of these cell surface junctions include: tight junction, desmosomes, and gap junctions.
• Tight junctions o Are specialized structures that link adjacent epithelial cells lining a lumen or cavity. o Limit the passing of materials from the limen and inhivit the movement of the membrane proteins. o Thus, membrane proteins on the apical surface (faces lumen) differ from those on the basolateral.
 Helps ensure directional movement of substances through the cell and into the body o Runs entire length
• Desmosomes o Specialized structures associated with the plasma membrane that hold adjacent cells together much like spot welds or rivets. o Consists of plaque on the cytoplasmic surface of the plasma membrane attached to keratin fibers of the cytoplasm and adhesion proteins in the plasma membrane. o The adhesion proteins pass from the plaque of one cell to the plaque of another. o Keratin fibers are made of the protein keratin and are intermediate filaments.
• Gap junctions o Facilitate communication between cells. o Made of specialized protein channels called connexons that span the plasma membrane of adjacent cells. o Small molecules and proteins may pass through these channels, but not large proteins, nucleic acids, or organelles. o In some nerve cells and in the vertebrae heart gap junctions allow for the direct passage of electrical signals.