A & P 4

basic unit of all living things

• ex: bacteria
• simple cells
• most are unicellular organisms
• dont have true nucleus

• exs: fungi, plants, animals (humans)
• have a true nucleus
• have organelles (subcellular structures)

• plasma membrane- covers & protects cell, controls what gets in and leaves, forms links to other cells, & "flies a flag" to identify the tissue or organ that the cell comes from as well as the individual that it belongs to
• cytoplasm- gives the cell its shape, it's comprised of cytosol (mixture of water, salts, & structural proteins(cytoskeletal)) & organelles (tiny organs that carry out essential cell functions, EXCEPT THE NUCLEUS)
• nucleus- contains genetic (info is stored) library for the cell (control center) DNA & RNA

• 1. lipids consist of polar head groups (hydrophilic-water soluble) with non-polar tails (hydrophobic-fat soluble)
• 2. lipids arrange themselves into two layers- head groups facing intra and extracellular solutions (cookie in oreo) & lipid tails form layer in between (creme in cookie)
• 3. lipids can move side-to-side, but never flip from outside to inside or vice versa
• 4. proteins are embedded in the lipid "sea" free to float around side-to-side, but never flip over
• 5. protein arrangements can be in one of two broad categories: peripheral proteins(associate with either extra/intracellular lipid heads) or integral proteins (span membrane w/ hydrophobic amino acid residues hanging out w/ lipid tails in hydrophobic core of cookie)

loosely associated w/ cell memebrane & lie either completely on outside or completely on inside of cell (they do NOT cross lipid bilayer)

span cell membrane from outside to inside cell (they DO cross lipid bilayer)

tells us how easily a substance can cross the plasma membrane

• because of the distribution of lipids & proteins embedded in it, membrane allows some substances across, but not others
• water is a special case

• gases- PASS EASILY
• small, fat-soluble molecules- PASS EASILY
• charged ions(K⁺, Na⁺, Ca⁺⁺, HPO4⁼, etc..) large, water soluble molecules (proteins)- DON'T PASS

• ion channels
• carriers
• receptors
• enzymes
• linkers
• cell identity markers

• span lipid bilayer & allow charged ions to pass down their concentration gradient (from high concentration areas to low)
• some are open all the time
• some are gated: open and close on demand

• many molecules that cannot cross the cell membrane are "ferried"
• this can occur up or down a concentration gradient(from high to low, or low to high)
• if it occurs against a concentration gradient, energy is required (energy comes from ATP& other molecules that run down their concentration gradient)

• signals outside the cell can affect activities inside the cell
• cell uses receptor proteins to detect an extracellular signal & transduce it to an intracellular signal

membrane proteins responsible for picking up signals from outside the cell

signaling molecule that binds to the receptor

process by which a signal outside the cell is transformed into a change inside the cell

• enzymes are proteins that catalyze(speed up) chemical reactions(blue curve(on bottom), bring reactants together to speed up reaction)
• enzymes on the cell surface catalyze chemical reactions there

"bump" in the energy curve

proteins that catalyze chemical reactions, they can't and don't change the energy profile of the reaction, but instead lower the activation energy

• internal structure of cell must be connected to connective tissues outside the cell
• linkers joing proteins inside & outside the cell

• ways to identify cells that belong to you, & what organ they belong to
• ex: MHC molecules used to match transplant donor & recipient ("flags" must match what's expected by surveillance system or "invader" will be "fired upon' by immune system)
• sugars connected to proteins(glycoproteins) commonly used as "flags"

an area of high concentration (unstopping of perfume bottle) to area of low concentration (air in room where bottle is opened)

• molecules in a gas or liquid can move around(*Brownian motion: random motion of small particles in solution *they zip around and bang into each other, like little billard balls on speed)
• warmer the temp, more movement
• smaller the molecule, more movement
• random movement is seen as diffusion: overtime, concentration of substance will become equal in all parts of the system

• used to move a substance, such as glucose, down its concentration gradient
• only water and gases can move across the cell membrane w/out help
• for everything except water and gases, some sort of escort is necessary

• term that describes the diffusion of solvents across a semi-permeable membrane
• when we combine diffusion of water with a semi-permeable membrane

• increase in volume when the walls of the container are rigid
• by measuring the amount of pressure needed to restore the volume, we can measure osmotic pressure

• TONICITY describes the concentration of salts
• because water CAN pass freely across the cell membrane, the concentration of water i critical for maintainin cell integrity
• HYPERTONIC=high salt concentration=low water concentration (water moves from high concentration to low, so it flows out of cell)
• HYPTONIC=low salt concentration=high water concentration (water moves from high concentration to low, so it flows into cell)
• ISOTONIC=no net movement of water (water concentration is the same inside and outside the cell)

NO ENERGY needed

• only water and gases move by simple diffusion across the cell membrane
• larger molecules and charged molecules have to be "escorted", even if the concentration is higher outside than inside
• protein channels or carriers in the cell membrane facilitate the diffusion of substances

potassium ions & glucose

• potassium concentration is low outside th cell, high inside
• potassium "wants" to leave the cell
• it CAN'T (the non-polar lipid tails in the membrane repel charged ions like K⁺
• a protein forms a gated channel to allow K⁺ to pass as needed

• glucose concentration is high outside the cell and low inside
• cell NEEDS glucose, alot!
• glucose "wants" to move from outside(high concentration) to inside(low concentration)
• it CAN'T (the non-polar lipid tails in the membrane repel large, water-soluble molecules like glucose)
• a rotein glucose carrier facilitates the diffusion of glucose

• sorting particles based on size
• each filtration medium has a "pore size"
• if mater CAN fit into pore, it stays in solution- if CAN'T fit, than it's trapped

• particles in a colloid stay dispersed over time
• a suspension has even larger particles than a colloid, and these settle to the bottom of a container, given time (muddy water)
• blood is a suspension, colloid, & a solution

• Kidney- cells and most proteins are left in blood, while small molecules (such as water, salts, & glucose) are able to pass through the filter)
• GLOMERULI- filtration system in the kidneys

• REQUIRES ENERGY
• when molecules are moved against their concentration gradient (from low to high concentration)

• Na⁺ is high outside, low inside
• K⁺ is low outside, high inside
• Na⁺/K⁺ pump moves both against their concentration gradients (Na moves out, K moves in) splits ATP for energy to do this (ATPase)

since 3 positive charges are pumped out for every 2 allowed in, the cell is made more negative inside by the pump

• step 1: Na high out, low in- K low out, high in- pump wants to move BOTH against their gradients- ATP is used as energy source- 3 Na bind to pocket in pump protein
• step 2: 3 Na expelled from cell- ATP split to ADP + P + energy * goal of pump is to maintain concentration of extracellular cation Na & intracellular cation K
• step 3: K pocket exposed- P released
• step 4: 2 K enter cell- Pump is reset to bind 3 more Na

• opposite direction
• 2 ions move in opposite directions to DRIVE the pump

• same direction
• a molecule & an ion move in the same direction to DRIVE the pump

• require energy from ATP
• materials move into a cell in a vesicle formed from the plasma membrane
• 3 types of endocytosis: phagocytosis, pinocytosis (bulk-phase endocytosis), & receptor-mediated endocytosis

• small, spherical sac(little blister or bladder)
• transports a variety of substances from one structure to another w/in cells
• also import materials from & release materials into extracellular fluid

• cell surface proteins (receptor proteins) bind a substance of interest, & then signal the cell to begin the process of pinching off a vesicle
• ex: LDL particles are taken into the cell by this process so that the lipd may be used for cell membrane

intracellular receptors, makes protein membrane

cell metabolism membrane repair

• cell's way of eating things
• solid material
• important process for the defense of the body against invaders
• when the invaders are detected, specialized white blood cells known as macrophages & neutrophils (examples) surround and kill the invading cells

• liquid material
• akin to phagocytosis, but is used to bring liquids into the cell
• cell makes a pit, then seals it- in the process, a vesicle-ful of liquid is incorporated into the cell ("swallowing" a tiny ball of liquid)

• the way the materials are removed from the cell (cellular waste)
• used to send materials out of the cell in bulk
• process is active, requires energy
• material to be moved is packaged in a vesicle ("littl bladder") - surrounded by membrane -vesicle fuses with cell membrane, expelling the material from the cell
• reverse endocytosis
• ANOTHER USE OF EXOCYTOSIS is to place markers on the cell membrane "fly a flag"

• "fruit & gel" of fruitcake
• contains cytosol & subcellular structures (organelles)

• "gel" of fruitcake
• made up of water, solutes, suspended particles, lipid droplets & glycogen granules
• solutes include: K^+, Na^+, Cl^-, HCO3^-, PO4^3-, HPO4^2-, H2PO4^-, other ions, sugar monomers & polymers, amino acid monomers & polymers, & RNA
• some solutes are made other places and then exported into the cytosol (ex: RNA-made in nucleus)

• semi-independent parts
• carries out business of the cell
• 5 main divisions of organelle function: structural integrity, motility, sythesis, storage & digestion, & energy production

cytoskeleton & centrosome

cilia & flagella

• ribosome
• rough endoplasmic reticulum
• smooth endoplasmic reticulum
• golgi complex

• smooth endoplasmic reticulum
• lysosome
• peroxisome
• proteasome

mitochondrion

• structural integrity-structural protein- needed to move substances around the cell, as well as to move te cell around in its environment
• "cell skeleton" is to the cell as the human is to the body
• made up of a # of different proteins that form thread- or tube- like structures
• 3 sizes made up of different proteins: (classified by size, smallest to largest) 1. microfilaments (actin-helps control muscles) 2. intermediate filaments (keratin) 3. microtubules (tubulin)

• cell extensions that carry out this essential function (look like ruffles or sheets, we can see these moving in real time)
• facilitates cell movement along a surface allowing it to sample the environment
• moves cell in its environment
• actin filaments extend lamellipodia

• "little shaggy hairs"
• in cells that need to increase their surface area
• ex: surface of intestines
• villi have microvilli
• each microvillus has a microfilament core
• digestive enzymes & cell "flags" form GLYCOCALYX (sugar-protein coat)

• order from smallest to largest: microfilaments, intermediate filaments, & microtubules
• microfilaments- actin
• intermediate filaments- keratin
• microtubules- tubulin
• microfilaments (2 strands) and intermediate filaments (many different proteins) are thread-like structures, microtubules (hollow tube) are built like drinking straws

• example of Microtubule organizing center (MTOC)
• grow microtubules
• made up of: 2 centrioles & pericentriolar material ((PCM) "clouds")

• microtubule organizing center
• cell locations where microtubules are built, so they represent the origin of microtubules

packed genetic material that must be evenly split between the two daughter cells

• rigid like structure which lines up, and then divides chromosomes
• chromosomes have centrosomes in center/ where microtubules have grown from centriole and attached to chromosomes

• MOTILITY organelle
  hair-like extensions on the cell surface
• usually on luminal (inside) surface of tube-like structures
• moves material on top of the cell
• ex: in the human body- in the lower respiratory tract, where they drive something called the mucociliary escalator

• MOTILITY organelle
• whip-like extension on the cell surface
• usually only one per cell
• in humans, only cell w/ a flagellum is the SPERM cell
• a flagellum moves the cell through material

• they have the same basic structure
• only difference is who gets moved, and who stays put
• at BASE- 9 triplets of microtubules
• at BODY- 9 doublets of microtubules

continually brings mucus, dead invaders, and inhaled crud up from bottom of lungs to the throat, where it is swallowed

• SYNTHESIS organelle
• site of protein synthesis
• combo of a particular subtype of RNA, called ribosomal ribonucleic acid (rRNA), plus proteins
• made up of large & small units
• job is to MAKE PROTEINS
• either found as free ribosomes or associated w/ membranes to make up RER
• free ribosomes synthesize proteins in the cytosol
• also found as part of the organelle ROUGH ENDOPLASMIC RETICULUM (RER)
• HOLE & GROOVE pieces come together to form complete ribosome

• messenger RNA- instruction sheet
• "blueprint"

• transfer RNA- carrier for the raw materials of proteins (amino acids)
• "pieces of puzzle"

• SYNTHESIS organelle
  intracellular network
  ROUGH because of the ribosomes lying on the surface
• collection of membrane bags w/ ribosomes arranged all along the outside
• genetic code material is copied in the nucleus, taken out to the RER to be read
• MAKES PROTEINS

• SYNTHESIS organelle
• intracellular network
• several different organelles w/ similar appearance, so that they cannot be distinguished in electron micrographs of the cell
• function- synthesis (lipis & steroids)
• MAKES FATS

• SYNTHESIS organelle
• receives unprocessed proteins from the RER & modifies them into their final form
• then packages the proteins & "tags" them for export to their final destination (UPS/post office- it cuts the tags off the gifts the cell wants to send, boxes them w/ packing material as needed to keep them from being broken, & then labels the box to send them to the correct destination)

• faces RER
• receives transported material from the RER

• faces the plasma membrane
• gives rise to secretory vesicles

sacs between the cis/entry & trans/exit faces

• 1. proteins are synthesized in the RER
• 2. TRANSPORT VESICLES carry "raw", unprocessed proteins to the GOLGI
• 3. transport vesicles fuse w/ the entry/cis face of the golgi
• 4. as proteins are processed, they are moved from one golgi stack to the next by TRANSFER VESICLES. in the golgi stacks, the unused part of proteins are removed by one set of enzymes &, if a glycoprotein is being produced, the branched sugar groups are added here
• 5. last transfer vesicle fuses w/ the exit/trans face of golgi
• 6. the processed, completed protein is packaged into a vesicle and the vesicle is shed from the exit/trans face of golgi

• if a secretory protein- packaged into a vesicle & released from the cell by exocytosis
• if a membrane protein (or glycoprotein)- packaged into a membrane vesicle which fuses w/ cell membrane, the proteins or glycoproteins then become part of cell surface
• if protein is defective or not needed, then packaged into a vesicle which is directed to lysosome for breakdown & recycling

• STORAGE & DIGESTION organelle
• stores Ca++ in muscle
• degestive function include: destruction of toxins; recycling of cell membrane; metabolism of carbs; & metabolism of steroids

• STORAGE & DIGESTION organelle
• 100x's more acidic than cell/cytoplasm
• formed from trans/exit face of golgi
• digests things the cell wants to get rid of (cell's "garbage can" or "recycling bin")
• if cell is dying, entire cell is dumped into the "garbage can"
• pH about 5.0
• they're bags of enzymes
• enzymes which work best @ acid pH are inside (hydrolases)

• STORAGE & DIGESTION organelle
• destroy materials for cell
• are membrane-bound
• unique properties: can replicate themselves, make hydrogen peroxide (is toxic& needs to by inactivated by enzyme catalase
• common in liver & kidney (it's the "detox" function)
• break down fatty acids (reaction called beta oxidation) to obtain energy
• generate FREE RADICALS (unpaired electron/ extremely damaging)

• Oxidation
• Is
• Losing
• Reduction
• Is
• Gaining

• STORAGE & DIGESTION organelle
• breakdown proteins
• "paper shredder"
• processes misfolded or malformed proteins
• mostly works on intracellular /mis-folded proteins
• UBIQUITIN tags these for destruction

binds to "bad" protein, then leads the protein to the proteasome which acts like a paper shredder to degrade protein

• ENERGY PRODUCTION organelle
• "POWER HOUSE" of a cell
• makes ATP
• bounded by double-layered membrane (inner & outer mitochondrial membranes-protons(H+) are pumped into space in between, "run" ATP sythesis)
• have their own DNA (inherited only from the mother)

• BUILDUP of smaller molecules into larger ones
• consume ATP & release waste energy as heat
• energy stored in chemical bonds (ENDERGONIC)
• reaction REQUIRES energy

• BREAKDOWN of large molecules into smaller ones
• energy is released from bonds (EXERGONIC)
• create ATP & also release waste energy as heat

• CATABOLIC-foods from the diet are broken into amino acids(proteins), sugars(carbs), & fatty acids(lipids) (used to make ATP)
• ANABOLIC- ATP is then used to make cellular structures which are made of amino acids, sugars, & fatty acids

• we break (dephosphorylation) one phosphate off of Adenosine Triphosphate (ATP)- leaving Adenosine Diphosphate (ADP)
• when we consume (phosphorylation) food energy we turn ADP back into ATP

• digestive system- absorbs nutrients from food
• respiratory system- brings O₂ in, blows CO₂ out
• circulatory system- brings nutrients & O₂ to cells, carries waste & CO₂ away
• excretory system- rids body of waste (urea from proteins in urine & other wastes)

• C₆H₁₂O₆
• primary carb (starting material for cellular energy production)

• major player in metabolism
• 3-carbon molecule
• important intermediate in metabolism

• major player in metabolism
• 3-carbon molecule
• represents a metabolic "dead end"

• "bucket" or "shovel" for 2-carbon molecules
• the 2-carbon molecule that is carried by CoA is an acetyl group (called acetyl-CoA, when carrying)
• important feature- ONLY 2-carbon units CAN fit into the KREBS CYCLE "furnace"

• "buckets"
• protons produced during the KREBS CYCLE are carried by FADH & NAD+
• (there are also electron "buckets" part of the electron transport chain of mitochondria

• these 2 cofactors are NOT consumed in metabolic reactions
• they serve as "hydrogen buckets" carrying hydrogen atoms (H) to where they're needed
• currency to be stored & used later on

• w/out O₂: anaerobic, makes 2 net ATP per glucose molecule
• w/ O₂: aerobic, makes 32-34 ATP per glucose molecule
• 1. GLYCOLYSIS(breakdown glucose)(oxgygen NOT needed) 6Carbons, break them in half: IN-C₆H₁₂O₆ / OUT-2 PYRUVATE (C-C-C), 2 NADH⁺, & 2 ATP (4 ATP-2=2 NET)
• 2. FORMATION OF ACETYL CoA(needs oxygen): IN- 2 PYRUVATE / OUT-2 CO₂, 2 NADH, & 2 ACETYL CoA
• 3. KREBS CYCLE (inner matrix): IN- 2 ACETYL CoA / OUT- (2 CO₂ X 2) 4 CO₂, (3 NADH⁺ X 2) 6 NADH, (1 FADH₂ X 2) 2 FADH₂, & (1 ATP X 2) 2 ATP
• 4. ELECTRON TRANSPORT CHAIN (ETC): for every NADH⁺ you get 3 ATP & for every FADH₂ you get 2 ATP

• does NOT need mitochondria
• 1 glucose molecule is converted into 2 molecules of pyruvic acid (C₃H₄O₃)
• 4 ATPs are made, but 2 are consumed, for a net gain of: 4 made - 2 used=2 net (2 ATPs per glucose)

• w/out O₂: anaerobic pathway only, lactic acid formed as by-product
• w/ O₂: aerobic respiratory pathway, pyruvate(3 carbons) transferred to mitochondrion for further processing

when lactic acid builds up as a result of anaerobic metabolism, the cell becomes more acidic and the cell's metabolism is rendered even less efficient

• operates in a circular fashion, adding & subtracting carbons & giving off electrons as a side product
• these electrons are carried by cofactors called FADH₂ & NADH so they may be used in the ETC
• (x's everything by 2)
• 3 NADH=6
• 1 FADH=2
• 1 ATP=2+2=4 2 from GLYCOLYSIS

• NADH & FADH₂ bring hydrogen atoms to the electron transport chain
• the H⁺ ions (protons) are stripped away & dumped between the inner & outer mitochondrial membranes
• electrons are stripped & used to play hot potato
• finally, protons are allowed to run down their concentration gradient to drive a "turbine" that generates ATP

• if glucose in blood exceeds metabolic needs, then glucose is stored in a readily-available form called GLYCOGEN
• most glycogen is in liver & muscles
• when energy is needed, glycogen is broke down to its 6-phosphate monomers which are then available to provide energy

• taking non-carb sources and making carbs out of them for energy ("making new glucose")
• occurs in the liver

• humans don't store a significant amount of energy as protein (since it's made up of proteins)
• breakdown of proteins in skeletal muscle & other tissues releases large amounts of amino acids
• the 2-carbon backbone of these amino acids can be used for production of glucose

• major component of urine
• it's an amino group or NH₂

• in the disease called diabetes mellitus, cells cannot metabolize glucose, instead they turn to fat stores as an energy source
• fat(lipid) is metabolized by beta-oxidation
• KETONES are produced as a by-product
• (ketosis & metaboic acidosis are signs of diabetes mellitus)
• also beta-oxidation produces hydrogen ions (H⁺) or acid

• every once in a while, the mitochondrial proteins "slip" & make an error in the handling of electrons or protons- formation of free radicals
• common free radicals: superoxide, hydroxide, & peroxinitrite- they react with proteins or lipids and gum up the efficient operation of the cell