HTHS Mod 4

the basic unit of all living things

• Eukaryotes
• Prokaryotes

• the name means they have a "true" membrane-bound nucleus
• complex cells w a nucleus and subcellular structures (membrane-bound organelles)
• all fungi, plants and animals (including humans) are eukaryotes

• subcellular structures
• tiny organs that carry out essential cell functions

• simple cells
• include bacteria and are mostly unicellular (one celled) organisms
• don't have true nucleus
• their DNA is spread out through the cell and is not collected into packed structures
• differ in some metabolic pathways from eukaryotes

Plasma membrane, cytoplasm, and nucleus

• a protective covering that regulates what comes into or leaves from the cell
• "plasma" implying it's liquidity in nature
• forms a link to other cells
• "flies a flag" to identify the tissue or organ that the cell comes from, as well as the individual that cell belongs to
• basically a "Lipid sea" with protein "icebergs" floating in it (either integral or peripheral proteins
• *because of markers specific to individuals, is a challenge when transplanting organs

• Gives the cell it's shape
• Contains cytosol and organelles (organelles are fruits and nuts in fruitcake)
• a gelatin-like substance, plus structural fibers and organelles (but not the nucleus)

• the control center of the cell; contains the genetic library for the cell
• DNA and RNA are made in the nucleus
• "Library" with "cookbooks" entitled: how to Make a New Cell, How to Make the Proteins You Need, etc.

• in the cytoplasm, the mixture of water, salts and proteins in which the organelles float
• *the solvent (water) and solutes (salts & dissolved proteins) which make up soluble part of the cytoplasm 
• (cake part of "fruitcake)
• the solution = cytosol

• deoxyribonucleic acid - the genetic material that must be reproduced and read without error, generally never altered or destroyed
• thought of as blueprints of plans for the cells of the body

those cells that are not part of the reproductive system

made in nucleus exported into cytoplasm where it carries out it's work: making proteins

• the new model for cell membranes, proposed by Singer and Nicholson in 1973
• Has lipid "sea" w protein "icebergs" floating in it
• Proteins are integral or peripheral

• Polar (hyprophilic, water-soluble) head groups with non-polar tails.
• They arrange themselves into two layers, w head groups facing facing extracellular and intracellular solutions (like "bread" of sandwhich, w tails forming "peanut butter")
• can move side-to-side, but never flip from outside to inside, or vise-versa

• free to float around side-to-side, but like lipids, can not flip over
• protein arrangements can be in 1 or 2 broad categories: peripheral proteins or integral proteins

• transmembrane proteins
• embedded in bilayer, some can go from one side to the other (completely through the bilayer, allowing transport of other molecules into/out of the cell)
• span the membrane w hydrophobic amino acid residues hanging out w the lipid tails in the hydrophobic core of "sandwich"
• "Integral proteins are present in the membrane"

• loosely associated w cell membrane and lie completely inside or outside of cell
• Inside: link cytoskeleton to membrane
• Outside: link cell to connective tissue or to other cells

molecule that has both polar (hydrophilic) parts and non-polar (Hydrophobic) parts

• phosphate heads are kinda the bread, on outside
• the two fatty acid tails are kinda the inside, or mayo, of sandwich; some tails can be saturated (therefore straight, making it squeeze more tightly to others) and some tails can be mono/poly unsaturated (causing a bend or kink, so more loose.)

• Actually gives our cell membranes a little integrity, a little less liquid
• Too much cholesterol makes the membrane too stiff

Different shapes mean different functions

tells us how easily a substance can cross the plasma membrane

• what defines a cell
• *the cell lets some things pass (water and cell nutrients must be allowed into the cell)
• *The cell doesn't let other things pass (the "guts" of the cell shouldn't leak out, toxic substances shouldn't leak in)

• water movement through lipid bilayers, pores, and plasma membranes
• 90% of water use this to pass through membrane 
• important for kidney function

• water and gases
• EVERYTHING ELSE REQUIRES SOME SORT OF ESCORT

• things that are small
• neutrally charged
• lipid soluble

hormone that is used to help bring sugar into cells.

the physiological role

• ion channels
• carriers
• receptors
• enzymes
• linkers
• cell identity markers
• "I can't really enjoy linked flags"?

• a difference from one side of the membrane to the other
• we can move with that difference or against that difference
• If we move with the gradient (high → low concentration) no energy required
• If we move against the gradient (low → high concentration) requires energy
• Ex: think of reservoir of water, and creek running out of it. Easy to open gates to release water (high level-concentration- to low level). Harder to swim up creek against current

• Remember because of non-polar tails of lipids, prevents ions (which are charged) from crossing cell membrane
• Ion channels allow ions to pass down concentration gradient (from high concentration to low concentration)
• Some are open all the time (like leaky faucet, constantly dripping)
• Some are gated, open and close on demand

• basically act as "ferries"; transports many molecules that cannot cross the cell membrane
• can occur up of 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 or other molecules that run down their concentration gradient)

• Na⁺/K⁺ pump, or Na⁺/K⁺ ATPase
• names tell us that the carrier requires energy to run: pumps need energy, cellular energy comes from ATP

• membrane proteins
• signals outside the cell can affect activities inside the cell
• cell uses receptor proteins to detect an extracellular signal and transduce it to an intracellular signal (through transduction)
• Ex: water-soluble hormones, connects to receptors, receptors carry "signal" from hormone to inside cell and initiates change inside of cell.

taking one form of energy and turning it into another

• membrane proteins
• proteins that catalyze (speed up) chemical reactions (bring reactants together to speed up reaction)
• very specific; decreases amount of energy required for reaction to take place (lower activation energy)
• enzymes on cell surface catalyze chemical reactions there

not part of the reaction, but it speeds up the reaction

• the internal structure of the cell must be connected to the connective tissues outside the cell
• join proteins inside and outside the cell

the structural proteins within the cell

molecules always diffuse from an area of high concentration (as in the unstopping of a perfume bottle) to an area of low concentration (the air in the room where the bottle is opened)

• membrane proteins, "flags"
• a way to identify cells that belong to you and what organ they belong to
• What they look at, "typing" (actually the MHC molecules) for blood transfers and organ transplants

• Over time, differences in temperature, pressure, and chemical potential equilibrate in an isolated physical system
• Ex: your warm feet, barefoot, standing on a cold tile floor. Your warm heat goes to tile... heat moves from high temp to low heat

• the sum of random events
• going from organized to disorganized (would go against nature to go from disorganized to organized, cause that takes energy)
• High entropy = high disorder; low entropy = low disorder
• diffusion is a kind of entropy
• Ex: pile of toothpicks  just dropped, not likely to pile up neatly.

the random motion of small particles or even molecules in a liquid or gas

• (simple diffusion)molecules in a gas or liquid can move around (brownian motion; they just zip and bang around into each other, like billiards)
• Affected by temp: the warmer it is, the more movement
• Affected by molecular size: the smaller the molecule, the more movement
• The random movement is seen as diffusion: over time, the concentration of the substance will become equal in all parts of the system

• solvent = "dissolver"
• solute = "dissolvee" (think of a "Ute" football player being stomped to the ground, dissolving)

• diffusion: solutes move
• osmosis: solvents move
• (in osmosis, solutes cannot move)

• the passive movement of water across a semipermeable membrane
• describes the diffusion of solvents across a semipermeable membrane
• "If solute can't move, then solvent has to move"

• the amount of force required to equalize volume
• Ex: think of the U shaped tube, with water and sugar solution, separated by semi-permeable membrane; putting a plug on the sugar side to keep volume the same.

• describes the concentration of salts
• because water can pass freely across membrane, concentration of water is critical for maintaining cell integrity
• *hypertonic, hypotonic, or isotonic

• high salt concentration = low water concentration
• water moves from high concentration to low, so it flows out of cell
• high concentration inside cell
• cell becomes "crenated" or shriveled
• *Think of a skinny person. Their spine sticks out and they are "hyper"

• low salt concentration = high water concentration
• water moves from high concentration to low, so it flows into cell.
• Low concentration inside of cell, "watered down"
• cell becomes  swollen or "bloated"
• Think of a swollen or fat person, they have "hypo" energy

• no net movement of water; meaning you will still have some movement, in and out, but no change in concentrations
• water concentration is equal, inside and outside
• Ideal for cells, keeping normal shape

• when cell is hypertonic, meaning water has flown out of cell and left it highly concentrated. 
• dehydrated; cell shrivels up and take on spiny shape, which is not good if RBC needs to slide easily through blood vessels
• *"when I was skinny, I had no problem being "creatively naked"".

• braking or rupture of cell, from being hypotonic
• "cellular lysis" is rupture of cells
• *"YOU LYED SED! I'm breaking up w you"

• hemo = blood; lysis = bursting
• in a hypotonic solution, when red blood cells will swell until they burst

• relates to how do we want to manipulate the movements of water into or out of cells
• isotonic: will not make cells shrink or swell
• hypertonic: if a pt has edema and need to draw water out of cells
• hypotonic: if a pt is dehydrated or needs water in cells

• no energy needed
• always goes w gradient
• so always goes from high → low concentration (of thing being transported)
• spontaneous, just happens, NO ENERGY

both diffusion and osmosis are examples

• majority of Na⁺ needs to be high outside of cell, which is our primary extracellular cation
• majority of K⁺ needs to be high on inside of cell, which is our primary intracellular cation
• to keep homeostasis, need to maintain this environment

• always goes against gradient
• used to move an ion against its concentration gradient
• goes from low → high concentration
• requires energy (ATP)
• With sodium/potassium pump, moves both ions against their concentration gradients (so Na+ moves out, K+moves in), splits ATP for energy to do this (ATPase)

only water and gases move this way across cell membrane (no help)

• protein channels or carriers in the cell membrane which facilitate the diffusion of substances
• (remember, larger molecules and charged molecules have to be "escorted" even if the concentration is higher outside than inside)

• channel which is open all the time (in cell membrane)
• assists the movement of ions through membrane

• great example is glucose
• specific proteins are made in such a way that as glucose binds it it, it changes shape and allows glucose to enter cell

• sorting particles based on size
• each filtration medium (ex: the filter paper in coffee maker) has specific "pore size"
• Kidneys are great example

a solution which has particles that stay dispersed over time

• solution that has even larger particles than a colloid, and these settle to bottom of a container over time
• -like muddy water

• Adenosine triphosphate; the "energy currency" of the cell
• more accurate to think of a molecule that "contains energy", not necessarily is energy

increases entropy and so needs no energy input

• also referred to as Na⁺/K⁺ ATPase
• Na⁺ gradient: high outside, low inside; K⁺ gradient: low outside, high inside
• pump wants to move both against gradient
• 3 Na+ out, 2 K⁺ in
• inside of cell becomes more negative (pump is electrogenic)

• 1. sets up sodium gradient (primary)
• 2. Sodium gradient used to drive molecules into or out of cell (secondary)

• requires energy, breaking bonds releases energy
• So, when bonds are made, energy is stored within bond. To use energy, bond is broken

• 1. 3 Na+ bind to pocket in pump protein
• 2. 3 Na⁺ expelled from cell, ATP split to ADP + P+energy 
• Energy released can now be used by transporter to move ions across membrane.
• 3. When that happens, K⁺ pocket is exposed in protein, so 2 K⁺ climb in pocked
• 4.  The 2 K⁺ enter the cell, pump is reset to bind 3 more Na⁺
• *Think of K+ (Kunz's) coming in the house, as Na+ (Nan Black) is leaving the house.

"set up" secondary active transport, which is only possible because of primary

using the gradients we set up in primary active transport to move other ions/molecules against their concentration gradients

• antiport system
• symport system
• This secondary active transport moves two or more molecules

• move two or more molecules in opposite directions to drive the pump
• Think of example of water "mill" will (as in the Sodium/Calcium antiporters), as Sodium runs through will (turning it), Calcium can be "lifted" out of cell

• two or more molecules move in the same direction to drive the pump
• again, think of example of water "mill" will, as the gate is opened for sodium to come into the cell, other molecules get "dragged in" w it

• Think of reservoir example. The plasma membrane becomes the dam, Sodium becomes the water. Therefore, we "dammed up sodium ions" outside the membrane (making a high concentration of sodium outside).
• We have created potential energy(because now the sodium wants to go were there are lower concentrations... ⇒back inside the cell
• (just as we use water power from dams to turn turbines and create power.)

• directly using ATP to set up gradients; to run sodium/potassium pumps and to move sodium and potassium against their concentration gradients
• because of primary active transport, secondary transport is possible

• type of active transport which use larger structures called vesicles
• material is to be taken into the cell
• requires energy
• 3 types: Receptor-mediated, phagocytosis and pinocytosis

• type of active transport which uses larger structures called vesicles
• material is to be take out of cell
• requires energy

move large quantities of small things, or to move things too large to fit inside a protein

cell surface proteins (receptor proteins) bind a substance of interest, then signal the cell to begin the process of pinching off the vesicle.

Ex: with LDL. Trouble starts is cell doesn't have right binders, and LDL stays in the bloodstream

• main protein of cell that helps form the vesicle
• gives the vesicle structure

basically a "sorter" of proteins inside the cell.

• 1. Clathrin-coated pit formed (clathrin on cytoplasmic side, receptors of extracellular side) Sides of pit rise as vesicle forms
• 2. vesicle is formed, clathrin coated (receptors and all
• 3. clathrin coating is lost, can open "package"
• 4. vesicle containing LDL (for example) is released, binds with endosome
• 5. endosome separates the receptors from the LDL, puts LDL in own transport vesicle 
• 6.  then binds to lysosome, which by digestive enzymes, releases the LDL

• type of active transport, special example of endocytosis
• phago- = eating; -cyto = cell
• pulls invaders inside cell w vesicle (again, bound to receptors), fuse w lysosome to "beat up" and digest invader, release products by exocytosis 
• ex: white blood cell that engulfs, swallows and digests a microbial invader

• specialized white blood cells
• surround and kill invading cells

• type of active transport, special example of endocytosis
• like phagocytosis, but for liquid instead of solid
• cells forms pit, then seals it, "swallowing" a tiny ball of liquid
• also called bulk-phase endocytosis because it's NOT SPECIFIC like RM or Phago, so forms a big "balloon" and pulls in large amounts of extracellular fluid

• the way materials are removed from the cell
• process is active (requires ATP for energy)
• material to be removed is packaged in vesicle
• vesicle fuses w membrane, expelling material from cell
• Like reverse endocytosis

• markers are placed by exocytosis
• "flag" is sewn inside the cell, then packaged into vesicle
• the material is anchored to the lipid bilayer of the vesicle, so when vesicle fuses w membrane, the flag is raised

• structural
• integrity
• motility
• synthesis
• storage and digestion
• energy production

cytoskeleton 

centrosome

• "cell skeleton" ~ gives basic shape
• Made up of structural proteins needed to move substances around the cell, as well as move cell around it's environment
• a framework for cell to pull against to move or be moved
• Three sizes (made up of different proteins) (from smallest to largest): Microfilaments, intermediate filaments, and microtubules

• smallest structural protein in cytoskeleton
• made of actin
• it gathers together in strands (threads) to make up smallest structure of cytoskeleton

• medium sized structural protein in cytoskeleton
• made up of keratin, vimentin, neurofilaments, lamins, and many other proteins
• are thread like

• largest of structural proteins in cytoskeleton
• made up of the protein tubulin (alpha and beta), plus some microtubule-associated proteins (MAPs)
• built like drinking straws, larger and more rigid than filamentous proteins
• also used as "railroad tracks" in cell to move larger particles from place to place, especially in dividing cells & cells that move stuff over long distance such as nerve cells

• "extensions" that carry out functions
• which enable the cell to move from one place to another and enables cell to change shape
• cell shape specialization supported by cytoskeleton
• look like ruffles or sheets, can see them moving in real time

*recall endocytosis as active transport process (as phagocytosis & pinocytosis) ~ these rely on cell's ability to change shape

• little shaggy hairs which increase the cells surface area
• for cells that have an absorptive function, as in the intestine
• each has microfilament core
• on surface each has glycocalyx
• cell shape specialization supported by cytoskeleton

sugar-protein coat (shell) on surface of microvilli formed by digestive enzymes and cell "flags"

• example of a microtubule-organizing center (MTOC) which are cell locations where microtubules are built (construction site)
• "roots" which microtubules grow out of
• Centrosome = centriole + pericentriolar material

the material around the centriole

• a rigid structure which lines up and then divides the chromosomes in cell division
• formed from microtubules (which come from centrosomes)

• the packed genetic material that must be evenly split btwn two daughter cells
• HAS CENTROSOME IN CENTER

• cilia
• flagella

• cilium (singular)
• a hair-like extension on cell surface
• usually on luminal (inside) surface of tube-like structures
• moves material on top of cell, cell stays put

best example is in lower respiratory tract, where cilia drive mucociliary escalator

• continually brings mucus, dead invaders and inhaled crud up from bottom of lungs to throat where it is swallowed
• toxic substances in cig smoke paralyze cilia, also smokers inhale more crud than non-smokers. These factors together result in accumulation of crud in smokers' lungs
• driven by cilia in lower respiratory tract

• a whip-like extension of cell surface
• usually only one per cell
• in humans, only cell w flagella is sperm
• moves cell through material, so cell moves

• both have same basic structure
• only difference is who gets moved and who stays put
• at base, nine triplets of microtubules
• as they grow and get further away from base, as in body of cilia or flagella, nine doublet of microtubules (figure 8)

• there is a "rowing" motion; like rowing a canoe or in swimming
• has a powerstroke as it presents full length and max resistance to overlying material (is rigid)
• also has return stroke as it folds to present as little resistance as possible to overlying material (relaxes and bends to side)

uses wave-like, whipping motion, appropriate for swimming

• Ribosome
• Rough ER
• Smooth ER
• Golgi comples

• the site of protein synthesis, makes proteins
• are macromolecular assemblies (little factories) where proteins (+ some nucleic acids) gather together to do a job
• a combination of RNA (Ribosomal ribonucleic acid), plus proteins
• made of large subunit (60S) and small subunit (40S), when brought together forms ribosome
• either found as free ribosomes or associated w membranes to make up the Rough ER

• synthesize proteins in the cytosol
• "free" in cytoplasm, just floating around

• Comes in two types: Rough and smooth
• Endoplasmic refers to "inside the cell"
• "reticulum" is Latin for "network"

• (RER)
• rough endoplasmic reticulum = "rough inside cytoplasm network"
• a collection of membrane bags w ribosomes arranged on surface
• where we are making proteins and "dumping" them on the inside of the "sacks" or bags
• Attached to Nuclear envelope of nucleus

• SER
• three kinds (which all go by the same name): synthesis, storage and digestion
• SER for lipid synthesis (because lipids are made differently than proteins, no ribosomes involved with SER)
• SER for processing of toxins & cellular components; also for calcium storage in muscle (important for muscle cell function) (storage & digestion)

• messenger RNA
• the "instruction sheet"

• transfer RNA
• carrier for the raw materials of proteins (amino acids)
• at the ribosome, amino acids are joined together by peptide bonds to form a protein chain

• also called golgi apparatus
• receives unprocessed proteins from rough ER and modifies them into their final form
• Then it packages the proteins and "tags" them for export to final destination
• Like "UPS pack and mail" store
• is curved, functions are not distributed symmetrically
• Think of Golgi's handle-bar mustache.. haha

YOU ARE! YOU GOT THIS!

• also called entry face
• part of Golgi Complex which receives transported material from the rough ER

• also called exit face
• opposite side at entry (duh)
• gives rise to secretory vesicles to transport material

• 1. protein is synthesized in Rough ER
• 2. Transport vesicles carry "raw", unprocessed proteins to Golgi
• 3. Transport vesicles fuse w cis face of golgi
• 4. As proteins are processed, they are moved from one golgi stack to the next by transfer vesicles (in stacks, unused parts are removed by one set of enzymes &, if a glycoprotein is being produced, the branched sugar groups are added here)
• 5. Last transfer vesicle fused w the trans face of Golgi
• 6. the processed, completed protein is packages into vesicle which is shed from exit face

• can go one of three places:
• If a secretory protein, is packages into vesicle and released from cell by exocytosis
• If a membrane protein (or glycoprotein), packaged into a membrane vesicle which fuses w cell membrane. The protein or glycoprotein then becomes part of cell surface
• If protein is defective or not needed, packaged into vesicle which is directed to lysosome for breakdown and recycling

• smooth ER
• lysosome
• peroxisome
• proteasome

• cells "recycling bin" ~ saves and reused parts
• if cell components are malformed, or warn down by age or not needed, they are packaged into vesicle that fuses w lysosome
• here the carbs, lipids and proteins are broken into monomers and reused.
• Formed from trans face of Golgi complex
• "chews up"
• pH is 5, so over 100x more acidic than cytoplasm, so needs membrane to separate from cytoplasm
• enzymes which work best at acid pH are inside (acid hydrolases)

enzymes that break things down w hydrolysis in an acid environment

• "self-breaking"
• part of programmed cell death, or apoptosis
• cell literally throws itself into own garbage can (lysosomes)

• like lysosomes in that they destroy materials for cell & are membrane bound
• Unique Properties: can replicate themselves, makes hydrogen peroxide (H₂O₂) (which is itself toxic and needs to be inactivated by catalase and other enzymes)
• common in liver and kidney ("detox" function of these organs"
• Break down fatty acids in β-oxidation (using fats for energy)

• free radicals (which have an unpaired electron)
• extremely damaging to biological systems and are likely part of cause of diseases such as cancer

• like lysosomes, break down proteins
• Ubiquitin tags these for destruction, then leads protein to proteasome which acts like paper shredder to degrade protein
• New drug Velcade targets cancer cell proteasome, improves survival

• Works on intracellular or  (misfolded-mistake was made in making protein)  proteins:
• factors needed temporarily by cell
• proteins from invaders (ex: viruses)
• mis-folded or mis-constructed proteins

• molecule which is like the hand that brings the paper to the paper shredder
• Once it drags the misfolded protein to the "shredder", it goes off and breaks apart so it's ready to assemble itself again to grab onto another mis-folded protein

• enzyme that breaks down hydrogen peroxide (should it escape from a peroxisome) into water and oxygen
• facilitates the breakdown of alcohol
• Commonly found in liver

mitochondrion

• the "money maker" of cells; produces ATP
• *cells which require larger energy requirements have more mitochondria
• Has own DNA (which is only inherited from mother)
• 2 layered membrane:  has an outer organelle membrane & a folded, inner membrane (which the folded membrane provides more surface area in very little volume)

it bounded by double-layer membrane (inner & outer) into which protons (H+) are pumped into the middle of 2 layers.Then, protons are allowed to run down their concentration gradient & (like a symport system) this produces ATP

• mitochondria DNA
• part of mitochondria in mother's egg. While father's and mother's chromosomes are represented in nucleus, only mother's mtDNA is inherited through maternal line
• This maternal inheritance of DNA has been used to trace movement of human populations over time

• IS NOT ENERGY
• INSTEAD, IT'S AN ENERGY CONTAINING MOLECULE

• Basically all the chemical reaction that go within our body
• The process of metabolism has two components: building (also called synthesis or anabolic)  and  if we are "tearing down) (catabolic)

• the buildup of smaller molecules into larger ones
• Is endergonic 
• we put energy in, energy goes to and is stored in bonds
• consume ATP and release waste energy as heat (making it exothermic)
• ADP + P + energy = ATP

• reactions which require energy
• (ergon- is Greek for energy; so energy goes "en-to" bonds)

reactions in which energy is released (or extracted from bonds)

• the breakdown of large molecules into smaller ones
• energy is released from bonds, making it an exergonic bond; get more energy out than what we put in
• create ATP and also release waste energy as heat (making it exothermic)
• ATP ⇒ ADP + P + energy

• ATP → ADP + P + energy (+ heat)
• Starting with simple molecules such as glucose, amino acids, glycerol and fatty acids
• Anabolic reaction takes place, which transfers energy from ATP to create complex molecule such as glycogen, proteins and triglycerides

• ADP + P + energy = ATP + heat
• Involves catabolic reaction
• If complex molecules are broken down (such as glycogen, proteins, and triglycerides), the catabolic reaction transfers energy from them back into ATP (also releases heat as byproduct) breaking back down to glucose, amino acids, glycerol, and fatty acids.

heat releasing reactions

Adenosine TRIphosphate vs. Adenosine DIphosphate

• What we eat (proteins, carbs and lipids) is broken down into amino acids, sugars and fatty acids.
• The bonds of these molecules are then broken, creating energy (catabolism)
• The energy released is stored as ATP (more correctly, IN ATP)
• Then, the energy from ATP's bonds is recaptured (anabolism) as cellular structures are built from amino acids, sugars and fatty acids.

• Metabolism is a controlled burning process. Energy is released in smaller, controlled steps, storing energy in ATP as you go.
• In burning, all energy is released in one step.

• Digestive system absorbs nutrients from food
• Respiratory system brings O₂ in, blows  CO₂ out
• Circulatory system brings nutrients and O₂ to cells, carries waste & CO₂ away
• Excretory System rids body of waste (urea from proteins in the urine, feces, etc)

• Simply taking a phosphate away
• ATP → ADP + P     -P

• simply adding a phosphate 
• ADP + P (+energy) = ATP

The main nutrient we use for energy = glucose

can be a proton donor

• Starring Role: Glucose
• Supporting Cast: Pyruvic acid, Lactate acid, Coenzyme A (CoA)

• "pyruvate" in ion form, when acid donates a proton
• "supporting role" in metabolism
• a 3 carbon molecule that is important intermediate in metabolism

• "Lactate" in ion form; when acid donates a proton
• "supporting role" in metabolism
• has 3 carbons, but represents a metobolic "dead end"

• Coenzyme A: two-carbon carrier
• is a sulfur-containing molecule that acts as a carbon carrier
• Think of this as the "shovel" that can hold only two-carbon "lumps of coal"
• Two-carbon "lumps of coal" units are acetate groups
• *fact that only two carbon units can fit into the Krebs cycle "furnace" is important to keep in mind!!!
• When it is carrying an acetyl group, it's called acetyl - CoA
• Actually a B vitamin

a substance which participates in the chemical reaction, but is not consumed by the chemical reaction, but serves specific function

• Flavin adenine dinucleotide (FADH) and Nicotinamide adenine dinucleotide (NAD⁺)
• Are cofactors that are not consumed in metabolic reactions
• Rather, they serve as "hydrogen buckets" carrying hydrogen atoms (H) to where they are needed
• THINK OF THEM AS SAVINGS ACCOUNT - referring to ATP as spendable cash. When we run out, we hit the savings account.
• *Remember H = H⁺ plus e^- (a proton plus an electron)

• also called anaerobic metabolism
• without oxygen, makes 2 net ATP per glucose molecule

• also called aerobic metabolism
• With oxygen, makes 36 - 38 ATP per glucose molecule
• 3 steps: glycolysis, Krebs cycle, the electron transport chain

• Glycolysis: anaerobic metabolism of glucose (sugar-breaking)
• occurs in cytoplasm, does not need mitochondria
• one glucose molecule is converted into 2 molecules of pyruvic acid.
• W/o oxygen, metabolism stops here
• 4 ATP's are made, but 2 are consumed, for a net gain of 2 ATP's per glucose.
• *No O₂ needed, and No CO₂ made

• If oxygen is present, the 6-carbon glucose is converted to 2 pyruvates (3 carbons) which is transferred to mitochondria for further processing (needs to be pyruvate to be able to get into the mitochondria)
• If oxygen is absent, the pyruvate is converted into lactic acid, a metabolic dead end

• When lactic acid builds up as a result of anaerobic metabolism and the cell becomes more acidic, which makes the cell's metabolism rendered even less efficient
• can also interfere w muscle strength during exercise
• *happens when someone is exercising and doesn't get enough oxygen. Can actually change pH of body

• during glycolysis, a 6 carbon glucose is split into TWO 3-carbon molecules of pyruvic acid.
• Therefore, when the pyruvic acid enters the mitochondria, there are TWO 3-carbon molecules of pyruvic acid.

• After glucose is split into 2 molecules of pyruvate, it enters mitochondria
• The steps in aerobic metabolism can only utilize 2-carbon units. Since pyruvate has three carbons, one carbon is let go (which ends up at CO₂)
• From there, the two-carbon units, like lumps of coal, are "shoveled" into the pathway using a carrier called coenzyme A.
• The coal is consumed, the shovel is not.
• Together, the two-carbon acetate group & the coenzyme A "shovel" make up acetyl-coenzyme A

• The combination of the two-carbon acetate group and the coenzyme A "shovel"
• (the 2 carbon acetate group was previously the 3 carbon pyruvate)

the CoA carrier is lost and a six carbon molecule is formed.

• Krebs cycle
• operates in a circular fashion, adding and subtracting carbons and giving off electrons (which are stripped from the H⁺) as a side-product

• citric acid cycle
• tricarboxylic acid cycle
• *referred to as "cycle" because it happens over and over

• The two-carbon acetate, "dumped" in by the "shovel" coenzyme A
• This forms citric acid

• 3 NADH
• 1 FADH₂
• 1 ATP

• 1 Glucose = 2 pyruvic acids, so we go through the cycle twice.
• 1 Glucose = 6 NADH, 2 FADH₂, 2 ATP
• *WTH? only 4 atp (with the 2 made in glycolysis) What happened to 36 - 38?? Well, it's in your "savings account" (NADH and FADH₂), need electron transport

• *Also called oxidative phosphorylation 
• Converts your "savings account" into currency (releases energy saved in NADH & FADH₂)
• Takes energy out of bonds formed and gives us the ability to form ATP

• In oxidation, lose electrons
• in reduction, gain electrons (think of "reducing the charge", so as you gain electrons, your charge becomes more and more negative)

• Kinda like playing hot potato w/ electrons... 
• As electrons are stripped from hydrogen atoms (the hydrogen atoms are taken from NADH and FADH₂), protons are created (H⁺) and pumped into space btwn the inner and outer mitochondrial membrane.
• Electrons go into transport chain (proteins on the inner membrane) and eventually end up attached to oxygen
• These protons are then allowed to run down their concentration gradient to drive ATP synthesis

• NADH =  3 ATP
• FADH₂ = 2 ATP

• A concentration gradient is created as hydrogen ions accumulate in the space btwn the membranes.
• An electrical gradient is created as protons (+ charge) and electrons (- charge) are separated

• potential energy... like damming up all the hydrogens
• This energy is what's used to create ATP 
• Once the concentration gradient is established, opens H⁺ channels. This channel acts as enzyme, ATP synthase. 
• Takes this energy, transfers it to ADP + P = ATP
• Is a symport system

• Glycolysis:  w/o oxygen = 2 net ATP; producing 2 reduced coenzymes = 4-6 ATP
• Formation of Acetyl-CoA (forms 2 reduced coenzymes, release 2 CO₂) : 6 ATP
• Krebs Cycle: 2 ATP
• Electron transport: 22 ATP
• *other

• then glucose is stored in a readily-available form called glycogen
• most glycogen is in liver and muscles

• "making new glucose", occurs in liver
• the production of glucose using the 2-carbon backbone of amino acids from the breakdown of proteins in skeletal muscle & other tissues (which releases large amounts of acids)

• Glycolysis is the breaking down of glucose to form energy
• Gluconeogenesis is the formation of new glucose

medication taken by diabetics, "look like" glucose but "gum up" the active site of the enzyme that makes glucose from fats

• a major component of urine
• amino acid 2-carbon backbones which are fed directly into the Krebs cycle, NH₃ (ammonia) becomes urea

amino acids which cannot be made "from scratch" and must be part of human diet

the process of using fatty acids to feed Krebs cycle

the excess calories are stored as lipids (fat or adipose tissue)

• disease in which the cells cannot metabolize glucose ~ the carbohydrate metabolism is "broken"
• cannot utilize glucose for energy
• instead, they turn to fat stores as energy
• results in ketosis and metabolic acidosis

• a by-product of fat metabolism by beta-oxidation
• have a carbon double-bonded to oxygen 
• sign of diabetes
• Ketoacidosis = exclusively metabolizing fats, therefore producing large amounts of ketones (very acidic)
• because their acidic, also referred to as metabolic acidosis

• carbohydrates (glycogen) and lipids (adipose tissue)
• PROTEINS ARE NOT USED FOR ENERGY STORAGE. We USE our protein cells. However, can be used for emergency backup

• it's normal to form free radicals (through oxidation) with metabolism, and we have cells that take care of that (antioxidants)
• it becomes a problem when the free radicals are in excess (we form too many), damages the lipids in mitochondria, damaging our mitochondria