Term
| What do you need to do to the membrane in order to isolate integral membrane proteins? Is this required for the isolation of peripheral membrane proteins? |
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Definition
| You must solubilize the membrane with a non-ionic detergent. No, it is not required for peripheral proteins. |
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Term
| Do all proteins undergo lateral diffusion? Explain |
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Definition
| No, if a protein is anchored to the cytoskeleton or has aggregated into a large complex it will not undergo diffusion. |
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Term
| What provides the energetic barrier to transport polar molecules and ions across membranes? What specifically do transporter proteins (permeases) do to compensate for this barrier? |
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Definition
| The energetic barrier is the energy needed to perform desolvation of polar molecules. Transformer proteins form bonds with the solute that replace the bonds it had with the water. |
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Term
| Transport proteins are said to act like enzymes. What are 2 ways in which they act like enzymes? |
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Definition
| They use binding energy and are specific for their substrate. |
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Term
| In fascilitated diffusion, molecules move down their concentration gradients until equal concentrations are present on either side (equilibrium). With this in mind explain how erythrocytes maintain a low intracellular glucose concentration such that glucose will continually enter the cell via fascilitated diffusion. |
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Definition
| It converts glucose into glucose-6-P to maintain a low concentration of glucose. |
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Term
| In addition to the P-type ATPase, there are also V-type and F-type. What substance is transported by these? What does this result in for the V-type? For the F-type? |
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Definition
| Protons are moved by both. The V-type acidifies the membrane. The F-type makes ATP. |
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Term
| Ion channels allow the influx of ions down their concentration gradient. They are not considered to be permeases. What are the ways in which they differ from permeases? |
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Definition
| They are faster and are not saturable. |
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Term
| When acetylcholine binds to its receptor on an ion channel, the channel opens thereby allowing the movement of Na+ ions. In what direction (in or out) do the Na+ ions move? What effect does this movement have on the polarization of the membrane? What 2 gradients drive the movement of Na+? |
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Definition
| The Na+ ions move into the cell. This depolarizes the membrane. The 2 gradients that drive this are the electrical and chemical gradients. |
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Term
| Polysaccharides can be branched or unbranched. What kind of glycosidic linkage is usually involved in the branching? |
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Definition
| The alpha (1-->6)glycosidic bond. |
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Term
| The bacterial cell wall is made up of polysaccharide heteropolymers cross-linked by short peptides. What is the name of the enzyme that degrades the cell wall and where does it "cut"? |
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Definition
Lysozyme- cuts at beta(1-->4) glycosidic bond. |
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Term
| Why might a bacterial species that has gained the ability to change surface glycolipids/glycoproteins be dangerous? |
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Definition
| Because they could invade our immune systems. |
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Term
| Starch and glycogen are important energy storage polysaccharides that are "packaged" as dense granules. What causes them to form granules? |
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Definition
| The alpha (1-->6) linked bond causes the molecule to take on a coiled helix shape. |
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Term
| What is the most stable conformation for cellulose and chitin (structural polysaccharides)? What kind of structure does this allow them to take on? |
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Definition
The most stable conformation is the beta (1-->4) linear conformation. This allows them to take on a tough, fibrous structure. |
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Term
| Glycoproteins often require the ability to recognize specific molecules. Why are carbohydrates good candidates for the "recognition" role? |
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Definition
| They are structurally complex, which allows a wide variety of forms that are needed for a high degree of specificity. |
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Term
| In considering the ribose sugar in nucleotides/nucleic acids, what is the significance of the 1',2' and 5' carbons? |
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Definition
1'-base
2'-RNA or DNA
5'-phosphate |
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Term
| Nucleotides can have functions other than being subunits of DNA and RNA. Give 3 of these other functions and give an example of each. |
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Definition
Energy storage- ATP
Components of cofactors- CoA
Signaling-cAMP |
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Term
| What 2 properties are responsible for providing the stability of the DNA double helix? Which one provides most of the energy for stabilization? |
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Definition
| Hydrophobic stacking of base pairs and H-bonding btwn base pairs. Of these, hydrophobic stacking of base pairs provides the most energy. |
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Term
| Considering the A, B and Z forms of nucleic acid helices, which is the Watson and Crick form of the DNA helix? Which structure is the most prominent form as an RNA helix? |
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Definition
Watson and Crick- B form
Most prominent- A form |
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Term
| RNA can have 1*,2* and 3* structures. Explain what is meant by each. |
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Definition
1*-linear 2*-stemloop 3*-Fully folded nucleic acids- involves long range interactions |
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Term
| For the following base pairs, give their nucleoside names: adenine, guanine, thymine, cytosine and uracil. |
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Definition
Adenine- adenosine
Guanine-Guanosine
Thymine-Deoxythymidine
Cytosine-Cytidine
Uracil-Uridine |
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Term
| In the cell, DNA is present as chromatin. An uncondensed form of chromatin is often referred to as "beads on a string." What structure is represented by the "beads"? the "string"? |
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Definition
Beads- nucleosomes
String-linker DNA |
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Term
| During which phase of the cell cycle (interphase or mitosis) is the chromatin most condensed? |
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Definition
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Term
| ATP is a high energy molecule because the products of its hydrolysis (ADP and Pi)are more stable than the ATP reactant. What are 3 explanations for why this difference exists? What kind of bond is broken in the hydrolysis of ATP to ADP and Pi? |
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Definition
| 1)Greater degree of solvation in product 2)ADP ionizes 3)resonance stabilization of Pi The bond broken is a phosphoanhydride bond. |
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Term
| Does ATP usually provide energy as the result of a single or double step reaction? Explain. |
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Definition
| It is the result of a double step reaction. It involves a phosphorylated intermediate (Phosphate is lost in last step, only used as a good LG). |
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Term
| High energy phosphorylated compounds achieve their ^G by having products that are more stable than the reactants. ATP achieves this in part via the resonance stabilization of the released Pi. What is the major mode of stabilization of the products from hydrolysis of PEP? |
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Definition
| Tautomeric shift- goes from enol to more stable keto state. |
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Term
| What are the 3 major products of glycolysis? How many of each are made? |
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Definition
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Term
| Which step in glycolysis is the "committed" step? What is meant by "committed step"? What enzyme is involved? |
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Definition
Step 3-(Fruc-6-P ----> Fruc-1,6-bis P) once the F 1,6-b-P is formed, it is committed to go forward in the pathway. The enzyme involved is PFK. |
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Term
| Two reactions in glycolysis are a special kind of group transfer reaction called substrate level phosphorylation. What reactant is being phosphorylated in these reactions? What are the 2 reactions? |
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Definition
ADP is the reactant for both. The reactions are #7 and #10. |
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Term
| Draw a diagram (in your head) of an integral membrane protein with 5 membrane spanning domains. Indicate the hydrophobic regions. What sort of secondary structure is usually present? Does this protein require lipids for its activity? |
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Definition
| The hydrophobic region is within the lipid bilayer. The secondary structure is the alpha helix. No lipids are not required. |
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Term
| Bacterial cells do not contain cholesterol. How do they regulate the fluidity of their membranes? |
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Definition
| Lipid composition; increase in FAs increases fluidity |
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Term
For the reaction, what is being achieved chemically and what kind of rxn?
Glucose---(ATP-->ADP)--> Glucose |
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Definition
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Term
For the reaction, what is being achieved chemically and what kind of rxn?
G3P---(NAD+--->NADH)---> 1,3 bis PG |
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Definition
| Redox rxn. Harvests a pair of electrons from NADH. Generates a high energy 3C mc, an acyl phosphate |
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Term
For the reaction, what is being achieved chemically and what kind of rxn?
3PG--(PG mutase)->2PG |
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Definition
| Rearrangement rxn. Phosphate gets in a better position to become high energy phosphate bond |
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Term
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Definition
Glucose---(ATP->ADP)---> glucose-6-P ATP acivates glucose Group transfer rxn Hexokinase |
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Term
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Definition
Glu-6-P -------> Fruc-6-P
Rearrangement so it can pick up a Phos.
PG Isomerase |
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Term
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Definition
Fruc-6-P ----(ATP->ADP)----> Fruc-1,6-bis P Makes fully activated sugar (HIGHLY REG!) PFK group transfer committed step |
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Term
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Definition
Fruc-1,6-bis P <---------> DHAP & G3P
Splits into 2 reactive mcs
Aldolase
Cleavage rxn |
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Term
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Definition
DHAP <---> G3P
Triose phos. Isomerase
Isomerization, get 2G3P/ea. glucose
Rearrangement rxn |
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Term
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Definition
G3P --> 1,3 bis-PG Harvest e- from NADH Generate high E 3C mc make acyl phos. RedOx rxn |
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Term
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Definition
1,3-bis PG --(ADP->ATP)--> 3PG
transfer a phos. to ADP (make ATP)
PG kinase
Group transfer rxn (sub. level phos.) |
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Term
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Definition
3PG ---> 2PG
puts P in a better position to be in phos bond
PG mutase
Rearrangement rxn |
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Term
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Definition
2PG ---> PEP
Removal of water produces high E phos. bond
Enolase
Dehydration |
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Term
| What kind of bond connects nucleotides together? |
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Definition
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Term
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Definition
PEP --(pyruvate kinase)--> Pyruvate
2 ATP made
Group transfer- sub. level phosph. |
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Term
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Definition
| Produce isoprenoids --> --> synth. of vit a,k |
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