Term
| Define: differential centrifugation |
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Definition
| Centrifugation that separates based on solubility. Insoluble materials sediment into a pellet (cells and organelles); soluble materials (proteins) remain in the supernatant. (3.3) |
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Term
| What's the first step of centrifugation? |
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Definition
Homogenization of cells (breaking the plasma membrane) which leaves most of the membrane-bound organelles intact. (3.4) |
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Term
Define: velocity centrifugation |
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Definition
Subcellular components are separated in a gradient (sucrose), and proteins separate into bands or zones of proteins of different mass (size). The only downside is that we cannot determine precise molecular weight because variations in shape affect sedimentation rate. (3.7) |
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Term
Define: equilibrium centrifugation |
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Definition
Separates cellular components based on buoyant density (without regard to size or shape). Uses a steep sucrose/CsCl gradient. Bands are produced, with those on the bottom containing components with the highest buoyant density. (3.10) |
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Term
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Definition
The separation of molecules in a mixture under the influence of an applied electric field. (3.11)
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Term
| What is the step-by-step process of SDS-Polyacrylamide Gel Electrophoresis? |
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Definition
1) Gels are cast between a pair of glass plates by polymerizing acrylamide into polyacrylamide chains and cross-linking the chains into a matrix 2) The proteins are exposed to negatively-charged SDS before and during the gel electrophoresis (which unfolds the protein, making mass the only factor) 3) Smaller proteins migrate faster than larger proteins through the gel 4) Molecular weight can be estimated by comparing the distances traveled with the distances of proteins of known molecular weight (3.11)
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Term
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Definition
The process of removing small molecules from macromolecular solutions (desalting protein containing solutions).
A protein solution is placed in a semipermeable bag and the bag is immersed in a hypotonic solution, drawing salts out of the protein solution. (3.16)
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Term
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Definition
| Separating a complex mixture based on its differential affinities for the media through which it is passed. Types of chromatography include gel filtration chromatography, ion-exchange chromatography, and affinity chromatography. (3.17) |
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Term
Define: gel filtration chromatography |
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Definition
Separates proteins that differ in size
When passed through a column of porous beads, smaller proteins become temporarily trapped in pores and move more slowly through the column than larger proteins (3.17)
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Term
Define: ion-exchange chromatography |
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Definition
Separates proteins based on charge
Uses a column of beads that are either negatively or positively charged. If column is positively charged, proteins with a net negative charge (acidic) stick to the column. Neutral and basic proteins flow through unimpeded
Acidic proteins are eluted from the column by an increasing concentrations of salt (3.19)
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Term
Define: affinity chromatography |
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Definition
Separates proteins based on affinity for a specific ligand. The ligand is covalently attached to the beads in the column, and proteins with high affinity for the ligand bind to it.
The bound protein is then eluted with a concentrated solution of the ligand (3.21)
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Term
| What are 8 uses of a membrane? |
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Definition
Barrier to toxic molecules
Help accumulate nutrients
Carry out energy transduction
Facilitate cell motion
Assist in reproduction
Modulate signal transduction
Mediate cell-cell interactions
Forms compartments (3.28) |
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Term
| What are four functions of the proteins embedded in a cell membrane? |
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Definition
Provide anchors for cytoskeletal fibers
Bind signaling molecules
Passage across the membrane
Regulate fusion of the membrane (3.30) |
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Term
T/F: Fatty acid side chains found in membranes have an odd number of carbon atoms. |
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Definition
| False. It's an even number of carbon atoms, usually 16, 18, or 20. (13.34) |
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Term
| What's the most common phospholipid in the cell membrane? |
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Definition
| Phosphatidylcholine. (3.35) |
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Term
| What does cholesterol do for membranes? |
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Definition
| At physiological temperatures, the cholesterol molecule interacts with the fatty acids of the membrane phospholipids and causes increased packing of the lipid molecules and hence a reduction of membrane fluidity. (3.36) |
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Term
| What is the composition of a cell membrane? |
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Definition
| Two layers of phospholipid molecules whose polar head group faces water and fatty acyl chains form a hydrophobic interior, along with embedded proteins and cholesterol molecules. (3.37) |
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Term
| What do the flippases do? |
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Definition
| Flip phospholipid molecules from one leaflet of a membrane to the other (from inner to outer, or from outer to inner). (3.41) |
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Term
| Mary, mary, quite contrary, how does your membrane grow? |
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Definition
| Phospholipids are synthesized in the cytosol, and are added to the cytosolic side of the lipid bilayer. Flippases transfer molecules to the other layer, thus evening out the membrane and making it more symmetrical. (3.44) |
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Term
| Break it down: how much of a membrane is composed of [phospho]lipid, how much is composed of embedded proteins? |
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Definition
| It's about 50%/50%. The proteins are incredibly important! (3.45) |
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Term
| What are the two types of membrane proteins? |
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Definition
Integral and peripheral (intrinsic and extrinsic).
Intrinsic proteins have one or more segments embedded in the bilayer.
Hydrophobic amino acids interact with the fatty acyl groups to anchor the protein in the bilayer.
Peripheral proteins are bound to the membrane indirectly by interactions with integral membrane proteins, or by interactions with lipid polar head groups. (3.46) |
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Term
| What type of protein secondary structure crosses a membrane more easily? |
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Definition
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Term
| What's a transport protein? |
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Definition
When an integral protein in a plasma membrane, it transports things across the membrane.
A classic example is an Na+ pump, which pumps Na+ out of cells, and pumps K+ in. (3.49) |
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Term
Define:
glycoprotein and glycolipid |
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Definition
| A protein or a lipid that has a carbohydrate group attached to it. This happens often in the endoplasmic reticulum. (3.52) |
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Term
T/F:
Plasma membranes are completely fluid. |
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Definition
| False. They can be restricted into membrane domains, where a portion of the membrane is (for instance) attached to an organelle, serving as a barrier to fluidity. (3.57) |
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Term
Explain this statement:
"Membranes are selectively permeable barriers." |
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Definition
| Membranes allow only hydrophobic and small, uncharged molecules to pass through unimpeded. Polar molecules need a channel (for instance, a porin) or a gradient (a higher concentration of that molecule/charge outside the cell than inside) to get through the barrier. (3.58) |
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Term
Define:
passive, facilitated, and active transport |
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Definition
Passive transport refers to a molecule moving down a concentration gradient.
Facilitated transport is passive transport, with an added "boost" from proteins.
Active transport requires the use of energy. (3.60) |
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Term
| How much ATP does one person synthesize in a day? |
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Definition
About her bodyweight. (3.62)
(Don't laugh. Would you be surprised if it's on the midterm?) |
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Term
T/F:
Anabolism yields energy. |
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Definition
| False. Hell, no, son. Anabolism is the biosynthetic pathway (energy consuming), whereas catabolism is degradative pathway (energy yielding). (3.64) |
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Term
| What are the end (waste) products of catabolism? |
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Definition
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Term
| Would an anabolic pathway be the exact inverse of its analogous catabolic pathway? Why or why not? |
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Definition
| Nope. There has to be at least one differing step, to ensure that the two can be regulated independently. (Think about it: if all the steps were the same, what regulated one would regulate the other, and not allow for one to happen without the other.) (3.67) |
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Term
| Where do we store electrons? (Both the ion, and the main electron carriers.) |
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Definition
| Electrons are stored in hydride (H:-) ions. Those hydride ions, in turn, are stored in NADH and NADPH molecules (nicotinamide adenine dinucleotide [phosphate]) as well as in FADH2 (flavin adenine dinucleotide). (3.70) |
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Term
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Definition
| Chemiosmosis is the diffusion of ions across a selectively-permeable membrane. More specifically, it relates to the generation of ATP by the movement of hydrogen ions across a membrane. (3.73; thanks, wikipedia) |
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Term
| Why do cells oxidize glucose stepwise to release its energy, rather than all at once? |
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Definition
| Because, dumbass, if we did it all at once we'd lose almost all of its energy as heat. This way, we manage the activation energy and are able to capture free energy with each step. (3.75) |
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Term
| What are the three basic steps of the breakdown of food? |
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Definition
1. digestion of larger molecules into smaller molecules (by the intestine or lysosome)
2. glycolysis, where glucose is converted to pyruvate, and then acetyl CoA (in the cytosol)
3. the citric acid cycle completely oxidizes acetyl CoA to H2O and CO2 (in the mitochondrion). (3.76) |
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Term
T/F:
An average cell has very few mitochondria, randomly placed throughout the cytosol. |
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Definition
| False. An average cell has thousands of mitochondria, and they're located close to where energy will be needed (for instance, sheathing a sperm cell's flagellum). (3.77) |
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Term
| PATHWAY: Steps 1 through 5 of glycolysis, to (glyceraldehyde 3-phosphate) * 2 |
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Definition
Glucose + 1 ATP --> Glucose-6-phosphate (via hexokinase and glucokinase) --> Fructose-6-phosphate (via phosphoglucoisomerase) + ATP --> Fructose 1,6-bisphosphate (via phosphofructokinase) --> 2 * DHAP (dihydroxyacetone phosphate) (via fructose bisphosphate aldolase) --> 2* glyceraldehyde-3-phosphate (G3P) (via triose phosphate isomerase) NOTES: isomerase = enzyme that changes shapes of molecules kinase = phosphorylating enzyme FBP can skip over DHAP, and go straight to G3P using fructose bisphosphate aldolase |
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Term
| Why does glucose get phosphorylated? |
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Definition
| It keeps the glucose from escaping through the cell membrane (remember, it happens in the cytosol) -- since intracellular [glucose] is low, it favors its diffusion. (3.81) |
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Term
| In the process of forming G3P, there are two steps that are most likely to be regulated. What are they, and why are they so likely to be regulated? |
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Definition
The phosphorylation of glucose, and the further phosphorylation of fructose-6-phosphate to fructose 1,6-bisphosphate.
It's because these two steps are large liberators of energy. (3.80 and 3.82) |
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Term
| PATHWAY: Steps 6 through 10 of glycolysis! |
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Definition
2 G3P -(G3P dehydrogenase)-> 1,3-bisphosphoglycerate + 2 NADH -(phosphoglycerate kinase)-> 2 3-phosphoglycerate + 2 ATP -(phosphoglycerate mutase)-> 2 2-phosphoglycerate -(enolase)-> 2 phosphoenolpyruvate -(pyruvate kinase)-> 2 pyruvate + 2 ATP |
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Term
| Account for all ATP and electron oxen in glycolysis. |
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Definition
- 1 ATP in step 1, phosphorylation of glucose - 1 ATP in step 3, phosphorylation of fructose 6-phosphate +2 NADH in step 6, de-H+ of G3P +2 ATP in step 7, dephos. of 1,3-bisphosphoglycerate +2 ATP in step 10, dephos. of phosphoenolpyruvate Total: +2 NADH, +2 ATP |
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