Term
| What kind of interactions stabilize a protein's folded structure? |
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Definition
| H-bonds, van der waals,hydrophobic interactions, ionic |
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Term
| Name and describe the 4 levels of protein structure |
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Definition
Primary-chain of amino acids
Secondary-alpha helices, beta sheets
Tertiary-3D globular structure
Quaternary-1+ polypeptide chains |
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Term
| The peptide bond is rigid and planar. Why is this? |
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Definition
| The oxygen and nitrogen share electrons. |
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Term
| Most peptide bonds are in which configuration? |
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Definition
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Term
| What is the significance of the rigid, planar structure of a peptide bond? |
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Definition
| The properties limit the number of conformations that a protein can assume |
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Term
| Which 2 amino acids are rarely found in alpha helices and why? |
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Definition
Glycine-too small
Proline- too rigid |
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Term
| Which 2 amino acids are most prevalent in Fibroin (protein found in silk) and why? |
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Definition
| Glycine and Alanine- small and fit between beta sheets |
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Term
| What kind of bond stabilizes the beta-turn? |
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Definition
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Term
| What type of interactions stabilize the beta-alpha-beta loop? |
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Definition
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Term
| What do you need to do to a protein before you can predict its tertiary structure? |
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Definition
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Term
| What makes glycine and proline well-suited for the beta turn structure? |
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Definition
Gly- small, flexible
Proline-can have cis bonds |
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Term
| Give an example of a structural motif and name the secondary structures involved? |
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Definition
| B-A-B loop, A-A corner (alpha helix) |
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Term
| Name a fibrous protein and the secondary structure it is composed of |
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Definition
| keratin, collagen (alpha helix) |
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Term
| What kind of model shows alpha helices and beta sheets? |
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Definition
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Term
| What type of bond is involved in stabilizing a proteins structure and are important to small molecules? why are they important to small molecules? |
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Definition
| Disulfide linkages are important because the give stability to a molecule with very few other interactions. |
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Term
| Can long range interactions be predicted by analysis of the linear sequence of amino acids? |
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Definition
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Term
| Which type of interactions are responsible for the binding of polypeptides in a protein with quaternary structure? |
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Definition
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Term
| Hemoglobin is an O2 carrying protein found in RBC that has 4 subunits. Each subunit has a prosthetic group. What is the prosthetic group called? What atom actually binds the O2? |
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Definition
| Prosthetic group is called Heme. The O2 actually binds to Fe. |
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Term
| Both Hb and Mb bind O2. The roles concerning the bound O2 differ. What are these roles? |
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Definition
| Hb takes O2 from the lungs to the tissue. Mb takes O2 to the mitochondria. |
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Term
| Describe Hemoglobin's positive cooperativity. |
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Definition
| O2 binding to first site makes binding of O2 to subsequent site easier |
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Term
| Proteins that use cooperativity are termed "______" |
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Definition
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Term
| What kind of change occurs in the protein upon binding of an "effector" molecule? |
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Definition
| Binding of an effector molecule at one site causes a conformational change. |
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Term
| Define cofactor and give an example |
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Definition
| Non-protein additions that are required for the enzymes function. Ex:inorganic ions, coenzymes, prosthetic groups |
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Term
| What is the difference between a holoenzyme and an apoenzyme? Is an apoenzyme active? |
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Definition
Holoenzyme: protein + cofactor
Apoenzyme: protein - cofactor (not active) |
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Term
| Once folded, polypeptides contain stable globular structural units. What are the units called? |
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Definition
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Term
| In the Molten Globule model, what provides the driving force in folding a protein into its tertiary structure? |
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Definition
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Term
| What happens when a protein is exposed to very high temperatures? If it were RNAase, what would you do to renature it? |
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Definition
| High temperatures would denature your protein. Putting the protein on ice would renature it. |
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Term
| In the RNAase denaturing-renaturing experiment, what would the result of forgetting to remove the BME from the soln containing the denatured protein? Will the RNAase be active? |
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Definition
| The disulfide bonds won't reform. It would not be active |
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Term
| The RNAase denaturation-renaturation experiment provided the first evidence for a fundamental hypothesis concerning protein tertiary structure. What was it? |
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Definition
| The sequence of amino acids determines the tertiary structure. |
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Term
| Hemoglobin exhibits positive cooperativity with respect to O2 binding to the heme groups. Could myoglobin, a protein that also binds O2 via a heme, exhibit positive cooperativity? Why? |
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Definition
| No it could not because it only has one subunit (one heme and one polypeptide). More than one subunit is required for positive cooperativity. |
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Term
| Enzymes lower the Ea by partially stabilizing the transition state. This is because the enzyme has a pocket that "fits" the transition state. What would happen if the pocket looked like the substrate in its ground state? Would the reaction be impeded or helped to proceed? Why? |
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Definition
| It will stabilize the substrate which will impede the reaction. |
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Term
| Enzymes use binding energy to catalyze reactions. Explain what is meant by this. What are the 4 energy hurdles it must overcome? |
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Definition
| Enzymes use the binding energy created when the transition state binds to the enzyme pocket. This energy is used to overcome hurdles. Hurdles include entropy reduction, desolvation, induced strain, and induced fit |
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Term
| Using the M'n'M equation, what would happen if [S]>>[kM]? |
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Definition
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Term
| For many enzymes, kM can be used as a measure of the affinity of an enzyme for its substrate. What kind of kM (high or low) would represent a high affinity for a substrate? |
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Definition
| k-1/k1= small/big= low kM value |
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Term
| Define turnover number. What is meant by an enzyme having a turnover number of 30 x s^-1? |
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Definition
| The turnover number refers of the number of substrate molecules converted to product in a given unit of time by a single enzyme molecule at Vmax. A turnover number of 30 x s-1 would mean 30 substrate molecules were converted to product |
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Term
| What does a graph that represents uncompetitive inhibition look like? |
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Definition
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Term
| What does a graph of competitive inhibition look like? |
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Definition
| Both lines cross at Y axis |
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Term
| What does a graph of mixed inhibition look like? |
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Definition
| Both lines cross before Y axis. |
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Term
| What do irreversible inhibitors of enzyme function do? Give an example. |
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Definition
| They bind the enzyme/shut down active site. Ex) Pesticides, nerve gas |
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Term
| Define allosteric regulation. Give an example of where it is used. |
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Definition
Binding of a modulator to one site causes conformational changes in the active site. Ex)Feedback inhibition |
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Term
| Give the functions of the following lipids: steroids, triglycerides, sterols, Eicosanoids,phospholipids,gylcolipids |
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Definition
Steroids- signaling
Trigyl.-energy
Sterols-membrane structure
Eicosanoids-signaling
Phospholipids-Membrane structure
Gylcolipids-membrane structure |
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Term
| Are all cofactors prosthetic groups? |
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Definition
| No, they can be inorganic ions or coenzymes |
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Term
| Covalent cataylsis definition |
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Definition
| Involves substrate enzyme covalent |
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Term
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Definition
| Cleaves peptide bonds next to aromatic residue |
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Term
| T/F: Catalysts affect the rate at which a reaction will reach an equilibrium? |
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Definition
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Term
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Definition
| Lower Ea, partially stabilize transition state and use binding energy |
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Term
| Describe acid-base catalysis: |
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Definition
| Groups in the enzyme aid in transfer of H+. Specific acid/base catalysts (H+ picked up to yield water and general acid/base catalysts (enzyme provides H+ donor/acceptor) |
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Term
| Describe covalent catalysis |
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Definition
| It involves a substrate enzyme covalent intermediate. Aids in catalysis when Ea2 + Ea3< Ea1 (dont know how to explain rxn) |
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Term
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Definition
| Can help orient a substrate through ionic interactions. Can also mediate RedOx rxns |
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Term
| Mechanisms of Chymotrypsin |
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Definition
Acylation- formation of a covalent acyl enzymes intermediate and cleavage of a peptide bond
Deacylation- Regenerates enzyme and releases another part of the protein |
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Term
| Michaelis-Menten kinetics: |
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Definition
| Single substrate, enzyme catalyzed rxns. kM is the M'n'M constant |
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Term
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Definition
| Measurement of an enzymes affinity for it's substrate; kM=K-1/k1= dissoc./assoc. |
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Term
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Definition
High kM, low affinity Low kM, high affinity |
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Term
| How does the Kcat number compare with the rate? |
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Definition
| The higher the Kcat number, the higher the rate will be |
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Term
| What are the units of Kcat numbers? |
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Definition
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Term
| What are the units of the rate? |
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Definition
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Term
| What are the units of kM? |
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Definition
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Term
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Definition
| The maximum rate of an enzymes activity (Saturation velocity) |
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Term
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Definition
| Looks like substrate and competes for binding at active site. |
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Term
| Uncompetitive inhibition: |
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Definition
| Inhibitor binds to separate site than S, only binds ES complex |
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Term
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Definition
| Binds to site distant from active site |
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Term
| What are the 2 types of glycerides? |
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Definition
| Triglycerides and phosphogylcerides |
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Term
| Name the structural component common to sterols and steroids |
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Definition
| Steroid nucleus (three 6c, one 5 c) |
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Term
| What differs between steroids and sterols? |
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Definition
| The R group can be polar or non-polar |
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Term
| From what compound are eicosanoids derived? Isoprenoids? |
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Definition
| Eicosanoids are derived from Arachidonic acid. Isoprenoids are derived from Isoprene. |
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Term
| Name the 5 major structural groups of lipids: |
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Definition
| Glycerides, Sphingosine derivatives, sterols/steroids, Eicosanoids, Isoprenoids |
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Term
| T/F: All fatty acids are equally insoluble |
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Definition
| False; the degree of insolubility depends on the hydrocarbon chain |
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Term
| Give an example of a type of catalysis performed at an enzyme's active site. Describe what the enzyme's functional group does. |
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Definition
Covalent catalysis;
A-B + X ---> A-X +B ---> A+B+X |
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Term
| Describe what is happening at the top of the graph (levels off at the top) |
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Definition
| The reaction is at it's equilibrium |
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Term
| Write the equation showing the relationship between the rate constants involved under conditions where the rate for reaching the transition state is limiting for the rxn. |
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Definition
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Term
| What kind of reaction occurs when glycerol and FAs come together to form triglycerides? What kind of linkage holds the FAs onto glycerol? Is the resulting triglyceride more or less polar? |
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Definition
| It is a condensation rxn. Ester linkages hold the FAs onto the glycerol. The resulting triglyceride will be less polar |
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Term
| What kinds of lipids are derivatives of Phosphatidic acid? |
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Definition
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Term
| Name 2 eicosanoids and describe a function of each: |
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Definition
Thromboxanes: blood clot formation
Leukotrienes: bronchiole constrictions |
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Term
| What are 2 functions of isoprenoids? |
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Definition
Terpenes-poison for plants
Pigments-night vision |
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Term
| What kind of structure forms when you add phospholipids to water? when you add fatty acids to water? |
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Definition
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Term
| What is the description of cholesterol? |
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Definition
| It is absent from E. Coli membrane and is important for mediating extremes in fluidity |
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Term
| What is the description of glycolipids? |
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Definition
| Abundant in the plasma membrane, absent from many molecular membranes |
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Term
| What is the description of phospholipids? |
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Definition
| Most abundant lipid in the membrane |
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Term
| What do flipases do? Do they act on proteins or lipids? |
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Definition
| They flip the phospholipid into the other leaflet. They act on lipids. |
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Term
| What are the 3 types of movement through a membrane? |
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Definition
| Lateral diffusion, thermal flexing, flip flopping |
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Term
| How are peripheral membrane proteins held on to the membrane? Describe a method used for removing a peripheral protein. |
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Definition
| They are held together by weak interactions. Peripheral proteins can be removed by changing the pH. |
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Term
| Define reversible inhibition: |
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Definition
| Comes on and off the enyzme |
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Term
| Give an example of reversible covalent modification. How does this modification affect the enzyme? |
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Definition
| Phosphorylation- adds a phosphate group, turns enzyme on or off |
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Term
| How does a change in pH affect hemoglobin's affinity for O2? |
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Definition
| If the pH decreases, so does the affinity for O2 |
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