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Biochemistry > Final Exam Cumulative Material > Flashcards

Final Exam Cumulative Material Flashcards

1
Q

What are the characteristics of prokaryotes?

A

-simple cell architecture
-cell wall
-loosely organized genetic information

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2
Q

Define prokaryotes.

A

Unicellular organism without a nucleus. (bacteria & archaea)

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3
Q

What are the characteristics of eukaryotes?

A

-linear DNA organization
-membrane bound structures
-prokaryotic relics

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4
Q

Define eukaryotes.

A

Complex cellular organisms with membrane enclosed organelles that have specialized functions.

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5
Q

What is the biological polymer of an amino acid?

A

Polypeptide

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6
Q

What is the biological polymer of a monosaccharides?

A

Polysaccharide

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7
Q

What is the biological polymer of a nucleotides?

A

Nucleic Acid

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8
Q

How do you identify a monosaccharide structure?

A

Sugars have a ~1-1 ratio of carbon: oxygen.

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9
Q

How do identify a lipid structure?

A

Lipids have a high ratio of carbon to oxygen/nitrogen/phosphorus.

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10
Q

What are residues?

A

A residue is a monomer that has been incorporated into a polymer.

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11
Q

What is a protein?

A

A protein is a functional unit consisting of one or more polypeptides.

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12
Q

What kind of bond forms a polysaccharide?

A

Glycosidic bond.

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13
Q

What are the major roles of proteins?

A

Major Role:
1. Carry out Metabolic Reactions
2. Support Cellular Structures

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14
Q

What are the major roles of nucleic acids?

A

Major Role:
1. Encode Information

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15
Q

What are the major roles of polysaccharides?

A

Major Role:
1. Store Energy
2. Support Cellular Structures

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16
Q

If DeltaG is <0, then…

A

A process is ‘spontaneous’ or ‘favorable’ and products are favored

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17
Q

If DeltaG is >0, then…

A

A process is ‘non-spontaneous’ or ‘unfavorable’ and reactants are favored

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18
Q

What is catabolism?

A

Breaking down larger molecules

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19
Q

What is anabolism?

A

Building complex molecules at the expense of energy.

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20
Q

What is a Hydrogen bond?

A

Hydrogen bonds occur when an H atom in a molecule, bound to O, N, or F is attracted to the lone pairs in another molecule

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21
Q

What is amphipathic molecule?

A

A molecule with both polar & non-polar regions

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22
Q

What is the hydrophobic effect?

A

Nonpolar regions cluster together to maximize the entropy of the surrounding water molecules.

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23
Q

What is the order of strength of intermolecular forces?

A

Covalent bond > ion-ion > H-bonds > dipole-dipole > London dispersion

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24
Q

What is London dispersion forces?

A

At any given moment the electrons may shift more to one side which can influence the molecule next to it.

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25
Q

What causes a higher boiling point?

A

Stronger IM forces

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26
Q

What is the equation for pOH?

A

pOH = -log [OH]

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27
Q

What is the equation for pH using H+ concentration?

A

pH = - log [H+]

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28
Q

Does a strong acid have a smaller or big Ka value? pKa value?

A

Strong acids have larger Ka values, and smaller pKa values

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29
Q

When do we consider a buffer to be useful?

A

Within +- 1 pH of its pKa

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30
Q

What is acidosis?

A

A condition where blood pH is too low

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31
Q

What is alkalosis?

A

A condition where blood pH is too high.

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32
Q

How do kidneys help maintain blood pH?

A

Kidneys usually retain HCO3- while eliminating H+ to prevent acidosis

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33
Q

How do lungs help maintain blood pH?

A

Lungs breathe faster to raise blood pH and slow breathing to lower blood pH.

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34
Q

When should a solution be mostly unprotanated?

A

When pKa is above the pH.

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35
Q

What is the general structure of a purine and what are the types?

A

2 rings; Adenine & Guanine

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36
Q

What is a nucleotide?

A

A nucleoside with one to three phosphates attached.

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37
Q

What is the general structure of a pyrimidine and what are the types?

A

1 ring; Cytosine, Thymine, & Uracil

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38
Q

What is a nucleoside?

A

A nitrogenous base attached to a ribose sugar

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39
Q

What is the structure of DNA?

A

The two DNA strands are antiparallel and the resulting helix is right-handed.

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40
Q

What is the Tm?

A

Tm is the point where half of the DNA is completely separated

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41
Q

What increases Tm?

A

Higher GC content

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42
Q

What is Ion-Exchange Chromatography?

A

Separates proteins by containing charged groups that bind to proteins of the opposite charge.

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43
Q

How are bound proteins eluted in Ion-Exchange Chromatography?

A

Increasing salt concentration or by changing the pH of the buffer to alter the charge of the bound proteins

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44
Q

What is Size exclusion chromatography?

A

Separates proteins based on size by using small pores and channels in the beads that separate proteins by size and can vary in range to change the % of proteins that will explore each channel.

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45
Q

What is affinity chromatography?

A

Takes advantage of the natural binding properties of a protein or uses an engineered tag in order to make some proteins bind to ligands in a mixture and the rest of the proteins will elute.

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46
Q

What is SDS-PAGE?

A

Assesses what is in a protein sample by unfolding proteins and putting them in a gel well in order to measure their size.

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47
Q

What is the primary structure of a protein?

A

The sequence of amino acid residues.

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48
Q

What is the secondary structure of a protein?

A

The localized conformation of the polypeptide backbone.

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49
Q

What is the tertiary structure of a protein?

A

The 3D structure of an entire polypeptide, including all of it’s side chains.

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50
Q

What is a quaternary structure of a protein?

A

The spatial arrangement of polypeptide chains in a protein with multiple subunits.

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51
Q

What is a domain?

A

Regions of a polypeptide that fold independently and have their own functions.

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52
Q

What does the dissociation constant mean?

A

Indicates how tightly bound a molecule is. A smaller Kd value shows higher affinity

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53
Q

What is myoglobin?

A

Favors oxygen moving from the blood to the muscle cell

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54
Q

What is the oxygen carrier in blood?

A

Hemoglobin

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55
Q

What does it mean when a ligand is cooperative?

A

The binding of one molecule will influence the binding of other molecules.

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56
Q

What are the 2 conformational states that hemoglobin can exist in?

A

The T state has low affinity for O2 while the R state has high affinity for O2.

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57
Q

Why is the T-state favored in the absence of O2?

A

Due to the formation of salt bridges involving the C-term residues of the a and b subunits.

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58
Q

Why does oxygenated hemoglobin favor the R-state?

A

Formation of the Fe-O2 bond is favorable and pulls the Fe2+ into the plane of the porphyrin ring, which shortens the Fe-N bond giving a lower free energy.

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59
Q

Why are intermediate conformations between R-state and T-state disfavored?

A

Due to steric clashes

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60
Q

What is the Bohr Effect?

A

Hemoglobin binding H+ favors unloading O2 to the tissue that needs O2 the most.

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61
Q

Why does muscle metabolism favor the T-state of hemoglobin?

A

Muscle metabolism causes a pH drop in surrounding tissues, the increase [H+] protonates the hemoglobin which favors salt-bridge formation that stabilizes the T-state.

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62
Q

How does the presence of BPG affect oxygen binding to hemoglobin?

A

BPG binds in the central cavity of T-state hemoglobin and contributes to further salt-bridge formation.

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63
Q

What is special about fetal hemoglobin?

A

Fetal hemoglobin doesn’t have beta subunits so it binds BPG poorly and therefore has a stronger affinity for O2 and favors movement of O2 across the placental membrane.

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64
Q

How does BPG affect oxygenation at higher altitudes?

A

An incr. in BPG decr. the affinity for O2 helps in lower O2 environments because it means hemoglobin doesn’t hold onto O2 as tight in the blood so more oxygen is releases and reach body tissue.

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65
Q

What is sickle cell anemia?

What subunit is the mutation on?

A

Sickle cell anemia is a mutation arising from a Glu6Val mutation on hemoglobin b. Sickled cells may block small blood vessels, limiting O2 delivery.

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66
Q

What is the biochemical basis for sickle cell anemia?

A

A hydrophobic pocket is exposed on the b-subunit when hemoglobin is in the T-state. This pocket bind the exposed Val on a neighboring hemoglobin and aggregation produces long, rigid strands of hemoglobin which deform the cell into a sickle shape.

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67
Q

What are the classes of cytoskeletal fiber?

A

Actin microfilaments, Intermediate filaments, Microtubules

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68
Q

What is the structure of hemoglobin?

A

Hemoglobin is composed of 2 alpha chains and 2 beta chains.

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69
Q

How do actin monomers form microfilaments?

A

Actin monomers (G-actin) polymerize to form ‘F-actin’ microfilaments because the negative charges on the cleft are attracted to the positive charges of other actin monomers.

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70
Q

What are the steps of the contraction cycle?

A

Myosin head bound to an actin subunit of the thin filament. ATP binds and myosin releases actin.
Hydrolysis of ATP to ADP + Pi rotates the myosin lever and increases the affinity of myosin for actin.
Myosin binds to an actin subunit farther along.
Binding to actin causes Pi + ADP to be released. The myosin lever returns to its original position. The thin filament moves (power stroke).

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71
Q

What is the structure of keratin?

A

Two long helices forming a coiled-coil. Each helix has a repeating 7 amino acid sequence where the 1st and 4th residues of each repeat are hydrophobic.

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72
Q

What is activation energy?

A

The energy to go from the ground state to the transition state.

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73
Q

How do catalysts increase the rate of a reaction?

A

Catalysts increase the rate of reaction by lowering the activation energy for both the forward and reverse reaction.

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74
Q

How do enzymes bind substrates specifically?

A

Substrate binding occurs in a pocket or cleft on the surface of the enzyme.

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75
Q

What type of reaction is catalyzed using an Transferase enzyme?

A

Transferases swap a functional group between substrates.

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76
Q

What type of reaction is catalyzed using an Oxidoreductase enzyme?

A

Oxidation-reduction reactions

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77
Q

What type of reaction is catalyzed using an Hydrolase enzyme?

A

Hydrolases use water to break a bond or condense to eliminate water.

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78
Q

What type of reaction is catalyzed using an Lysase enzyme?

A

Lyases break bonds without the use of redox activity or water and produce an extra double bond (or ring) in the products.

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79
Q

What type of reaction is catalyzed using an Isomerase enzyme?

A

Isomerases rearrange functional groups within a substrate, but keep the chemical formula the same.

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80
Q

What type of reaction is catalyzed using an Ligase enzyme?

A

Ligases use ATP energy to connect 2 other substrates.

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81
Q

What is a coenzyme?

A

Coenzymes are organic cofactors.

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82
Q

What are cosubstrates?

A

Cosubstrates are coenzymes that transiently associate with the enzyme.

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83
Q

What is a holoenzyme?

A

An active enzyme with its required cofactors.

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84
Q

What is an apoenzyme?

A

An inactive enzyme without its required cofactors.

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85
Q

What is a cofactor?

A

A cofactor is a small organic molecule or metal ion that is required for enzymatic activity.

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86
Q

What is acid-base catalysis?

A

In acid-base catalysis, a H+ is transferred between an enzyme and the substrate.

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87
Q

What amino acids may participate in acid-base catalysis?

A

Charged amino acids, Cys, His, Ser, Tyr

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88
Q

What are the ways a metal ion aids catalysis?

A
  1. Stabilize negative charges that form in the transition state
  2. Shield charges that might repel the attacking group
  3. Promote nucleophilic attacks through the ionization of water
  4. Participate in redox reactions
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89
Q

How does the proximity and orientation of substrates affect catalysis?

A

An enzyme can speed up a reaction by positioning the reactants properly.

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90
Q

What is chymotrypsin?

A

An intestinal protease that helps you digest proteins by breaking peptide bonds.

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91
Q

How does the chymotrypsin recognize which peptide bond to break?

A

The specificity pocket only binds amino acids that it is complementary too, which position the peptide bond for cleavage.

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92
Q

What are zymogens?

A

Inactive precursors of proteases.

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93
Q

What is a protease?

A

An enzyme which breaks down proteins and peptides.

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94
Q

Why don’t proteases destroy the small intestine where they are made?

A

Zymogens are secreted into the small intestine and cleaved by other proteases so that they acquire a conformation where the specificity pocket and oxyanion hole are available for catalysis. However, inhibitors in the blood stream and pancreas bind the protease to inhibit any proteases that are active outside the small intestine.

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95
Q

How do you know if an enzyme is more optimized for substrate or transition state binding?

A

The more tightly an enzyme binds to the transition state form, relative to the substrate, the greater the rate of the catalyzed reaction.

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96
Q

What are the criteria for the Michaelias-Menten kinetics being valid?

A
  1. Measurements are made before much product has formed.
  2. There is only one substrate.
  3. The reaction occurs in a single step.
  4. Binding is non-cooperative.
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97
Q

What is an irreversible inhibitor?

A

A molecule that permanently binds to an enzyme and prevents it from working.

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98
Q

What is pure competitive inhibition?

A

A pure competitive inhibitor can only bind to an enzyme if the substrate isn’t there because it competes with the substrate at the enzyme’s active site.

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99
Q

What is the KI?

A

The inhibitor constant, a low KI indicates a good inhibitor that binds tightly.

100
Q

How does a competitive inhibitor affect a reciprocal plot?

A

Competitive inhibition:
-Vmax stays the same
-KM increases by a factor of a

101
Q

What is pure uncompetitive inhibtion?

A

Pure uncompetitive inhibitors only bind to enzymes when the substrate is present.

102
Q

How does an uncompetitive inhibitor affect the reciprocal plot?

A

Lowers the Km and the Vmax by the same factor of a’

103
Q

How do you determine Vmax from a Lineweaver-Burk plot?

A

Vmax = 1 / y-int

104
Q

How do you determine Km from a Lineweaver-Burk plot?

A

Km = slope x Vmax

105
Q

What is mixed inhibition?

A

A mixture of competitive and uncompetitive inhibition affects both Vmax and Km.

106
Q

How can you tell a noncompetitive inhibitor from the Lineweaver-Burk plot?

A

Meets at same X-intercept, but with steeper slope

107
Q

The ______ side of the plasma membrane frequently has glycosylated ______?

A

Extracellular; lipids & proteins

108
Q

How can you tell an uncompetitive inhibitor from the Lineweaver-Burk plot?

A

Same slope, but increase y-int.

109
Q

What is Km?

What indicates a high affinity?

A

A measure of affinity, a smaller Km indicates that the substrate is more tightly bound.

110
Q

What is divergent evolution?

A

Common ancestor but leads to different structures

111
Q

What is convergent evolution?

A

Different ancestors leads to different structures, but converge to find same solutions

112
Q

What is pure noncompetitive inhibition?

A

A pure noncompetitive inhibitor binds away from the enzyme active site and does not affect the substrate binding.

113
Q

What is allosteric regulation?

A

Allosteric regulators affect the activity of multisubunit enzymes by stabilizing the R-state or T-state

114
Q

How does HIV infect cells?

A

The virus attaches to the CD4 cell and uses reverse transcription to imbed itself in the DNA.

115
Q

How do we design an inhibitor for the HIV reverse transciptase?

A

The error-prone nature of HIV reverse transcriptase means it may incorporate chain-terminator nucleotide drugs.

116
Q

What are the 2 ends of a fatty acid?

A
117
Q

What is the difference between saturated and unsaturated fatty acids?

A

Unsaturated fatty acids have at least one double bond in the hydrocarbon tail.

118
Q

What happens to the melting point of fatty acids as the chain length increases?

A

The melting point increases because temperature must increase to overcome the greater van der Waals interactions.

119
Q

Why is the melting point of saturated fatty acids higher?

A

The packing of fatty acid chains is disrupted by the presence of cis double bonds which lowers the VDW forces and decreases melting point.

120
Q

What is the role of Vitamin A? What does a deficiency result in?

Is it fat soluable or water soluable?

A

A fat soluble vitamin that is important for visual perception. A deficiency results in night blindness.

121
Q

What is cholesterol?

A

Cholesterol is a major component of animal membranes that helps maintain fluidity and integrity. Cholesterol also serves as a precursor for steroid hormones, Vitamin D, and bile salts.

122
Q

What is the role of Vitamin D? What does a deficiency result in?

A

A fat soluble vitamin that is important for calcium homeostasis. A deficiency results in rickets, a disease characterized by deformed bones and stunted growth.

123
Q

What is the role of Vitamin E?

A

A fat soluble vitamin that has antioxidant activity.

124
Q

What is the role of Vitamin K? What does a deficiency result in?

A

A fat soluble vitamin that is a cofactor for an enzyme that modifies glutamate residues on blood clotting proteins. A deficiency results in excessive bleeding.

125
Q

What is the main component of lipid bilayers?

A

Glycerophospholipids

126
Q

What is the advantage of two-tailed amphipathic lipids in membrane formation?

A

A two-tailed lipid gives the correct geometry to stack correctly without forming voids.

127
Q

What are integral membrane proteins?

A

Integral membrane proteins have hydrophobic regions embedded in the lipid bilayer and these proteins require strong detergents to isolate.

128
Q

What are peripheral membrane proteins?

How can you isolate these proteins?

A

Peripheral membrane proteins associate with the polar head groups of membrane lipids. These proteins may be isolated with mild salt solutions.

129
Q

What is a lipid-linked protein?

A

Lipid-linked proteins insert a hydrophobic anchor into the membrane.

130
Q

What is the fluid mosaic model?

A

Proposes that lipids and proteins may freely move laterally but cannot flip-flop through the layer by themselves.

131
Q

Are both sides of a membrane the same?

A

Membranes have a polarity. The inside of a membrane is different, in both lipid and protein composition, from the outside.

132
Q

Does sodium have a higher concentration inside or outside of the cell?

A

Outside

133
Q

Does potassium have a higher concentration inside or outside of the cell?

A

Inside

134
Q

What are the steps of the action potential?

A
  1. Stimulus opens Na+ channels in the membrane
  2. Influx of Na+ causes depolarization, which triggers the opening of the VGPC.
  3. Efflux of K+ restores resting membrane potential.
  4. Initial depolarization also triggers opening of additional Na+ channels farther down the axon.
135
Q

What are porins?

A

Porins are proteins that form an open channel in the membrane of bacteria and certain organelles to allow the passage of small solutes.

136
Q

What happens when K+ moves into the selectivity filter?

A

When K+ moves into the filter, it loses favorable interactions with water, but gains favorable interactions with the residues lining the filter.

137
Q

What is an aquaporin?Why doesn’t it allow H+ to pass through?

A

A channel that allows water to pass through, but not H+ because the size of the channel is optimized for a single chain of H2O and a positively charged Arg residue disfavors entry of H3O+.

138
Q

What is an antiporter?

A

Antiporters move two different substances across the membrane in opposite directions.

139
Q

What is a symporter?

A

Move two different substances across the membrane in the same direction.

140
Q

What is primary active transport?

A

The use of ATP to drive transport

141
Q

What is secondary active transport?

A

Using the favorable movement of an ion down its gradient to move another substance across the membrane.

142
Q

What is a uniporter?

A

Uniporters move a single substance across the membrane.

143
Q

What is facilitated diffusion?

A

Using a protein to bind and move a molecule or ion across the membrane.

144
Q

How does the glucose transporter work?

A

Glucose binding changes the conformation, so that the transporter opens on the opposite side of the membrane.

145
Q

How does exocytosis work?

A
  1. When an action potential reached the axon terminus, it causes VGCC to open
  2. An incr. in Ca2+ triggers the fusion of synaptic vesicles with the plasma membrane and release NT into the synaptic cleft
146
Q

How do SNARE proteins help mediate exocytosis?

A

The favorable formation of a four-helix coiled-coil pulls the vesicle into the target membrane

147
Q

What are the steps of GPCR transmitting the ligand binding signal?

A
  1. Ligand binds
  2. Conformation change in GPCR
  3. Ga releases GDP and binds GTP
  4. Ga-GTP dissociates from the Gby subunits
  5. Ga has intrinsic GTPase activity and hydrolyzes GTP back to GDP to turn off
  6. Ga-GDP reassociates with the Gby subunits
148
Q

How does the hormone epinephrine initiate the fight or flight response?

A

Epinephrine is an agonist for a GPCR which activates adenyly cyclase to produce cAMP. cAMP activates PKA which phosphorylates multiple proteins involved in fuel metabolism.

149
Q

How are signaling pathways turned off?

What do phosphatases, phosphodiesterases, and Arrestin do?

A
  • Phosphatases hydrolyze (turn off) the phosphate group from proteins that have been modified by kinases
  • Phosphodiesterases hydrolyze cAMP to turn off PKA
  • Arrestin binds the GPCR and prevents further activation
150
Q

How do receptor tyrosine kinases transmit a ligand binding signal?

A

Ligand binding to the extracellular domain of RTK induces a conformation change so that the cytosolic domain of one monomer moves close enough to the cytosolic domain of other monomer to phosphorylate Tyr residues and turn the receptor on. RTK activation induces a kinase cascade.

151
Q

How do Ras proteins mediate growth factor signaling?

A
  1. Ras is a G-protein that is activated by adapter proteins once RTK is auto-phosphoylated with a growth factor ligand bound.
  2. Ras exchanges GDP for GTP and initiates a kinase cascade that regulates the expression of genes that are important for cell growth and division.
152
Q

How does the body initiate the pain and inflammation response?

What enzyme cleaves it?

A
  1. Phospholipases cleave a 20-carbon fatty acid (arachidonated) from the membrane
  2. Cyclooxygenase enzymes the convert the arachidonate to prostaglandins that promote a pain and inflammation response
153
Q

How do certain drugs like Aspirin and Ibuprofen limit pain and inflammation?

A

Aspirin and ibuprofen inhibit both COX-1 and COX-2

154
Q

How do you distinguish an L from a D enantiomer?

A

A D-sugar has the -OH group to the right of the furthest carbon
An L-Sugar has the -OH group to the left of the furthest carbon

155
Q

What is a b-anomer in a D-sugar?

A

Anomeric hydroxyl above the ring

156
Q

What is an b-anomer in a L-sugar?

A

Anomeric hydroxyl below the ring

157
Q

What is the structure of amylose?

A

An unbranched polymer made up of only a1-4 linkages

158
Q

What is the structure of amylopectin?

A

A branched polymer that has a1-4 linkages along with a1-6 branch points every ~30 residues

159
Q

How do animals store glucose? What is the structure?

A

Glycogen - similar structure to amylopectin, but the branch points are every 8 to 12 residues

160
Q

What is cellulose? What is its’ structure?

A

Cellulose is the primary component of plant cell walls. B1-4 linkage.

161
Q

What is a N-linked protein?

A

Oligosaccharide is attached to an Asn side chain

162
Q

What is an O-linked protein?

A

Oligosaccharide is attached to a Ser or Thr side chain

163
Q

What blood types have a sugar being added and why?

A

Differences in a few active site residues of a glycosyltransferase result in a different sugar being added to the O antigen in A- and B-type individuals.

164
Q

Why is the structure of glycosaminoglycans useful in connective tissue?

A

The polar groups on glycosaminoglycans attract H2O to help lubricate tissue, while negative charges repel each other upon compression to act as shock absorbers.

165
Q

How are proteins degraded outside cells?

A

The lysosome is an organelle containing degradative enzymes that primarily breaks down extracellular or membrane proteins.

166
Q

What is the proteasome?

A

The proteasome is a multisubunit protease that targets intracellular proteins.

167
Q

How does the proteasome know which proteins to degrade?

A

Ubiquitin ligase transfers a small protein, called ubiquitin, to a Lys residue of the target protein. Once 4 ubiquitins have been added, the end cap subunits of the proteasome recognize the target protein for degradation.

168
Q

What is the role of Vitamin C in the body?

A

Vitamin C is an antioxidant and acts as a cofactor for the enzyme important for collagen.

169
Q

What is the role of Vitamin B1 in the body?

A

Thiamine (precursor for B1) is a cofactor for the pyruvate dehydrogenase complex and a-ketoglutarate dehydrogenase.

170
Q

What is the role of Vitamin B3 in the body?

A

Niacin is a precursor for NAD(P)+/NAD(P)H.

171
Q

What is Ubiquinone/ Coenzyme Q?

A

A lipid soluble electron carrier used as redox cofactor to conserve energy. A mobile electron carrier that often receives electrons from an FADH2 prosthetic group.

172
Q

What are flavins?

A

Flavins are prosthetic groups that can carry 1 or 2 electrons.

173
Q

What is an irreversible step in a metabolic pathway?

A

An irreversible step occurs early in a metabolic pathway to commit a metabolite to the pathway. (DG far from zero).

174
Q

What is the net yield of glycolysis?

A

Net yield = 2 ATP + 2 NADH

175
Q

What happens in Step 1 of glycolysis? What are the enzymes, reactant, and products?

A

Step 1: Hexokinase Phosphorylates Glucose
-irreversible
-phosphorylating glucose prevents the sugars from leaving the cell and reduces intracellular [glucose] so that the gradient favors import.
- enzyme: hexokinase
- reactants: Glucose, ATP
- products: G6P, ADP, H+

176
Q

What happens in Step 2 of glycolysis? What are the enzymes, reactants, and products?

A

Step 2: Phosphoglucose Isomerase
-reversible
-enzyme: Phosphoglucose Isomerase
-reactants: G6P
-products: F6P

177
Q

What happens in Step 3 of glycolysis? What are the enzymes, reactants, and products?

A

Step 3: Phosphofructokinase-1 phosphorylates F6P
-enzyme: Phosphofructokinase-1
-reactants: F6P, ATP
-products: F1,6-Bisphosphate, ADP, H+

178
Q

What happens in Step 7 of glycolysis? What are the enzymes, reactants, and products?

A

Step 7:
-enzyme: phosphoglycerate kinase
-reactants: 1,3 BPG, ADP
-products: 3-phosphoglycerate, ATP

179
Q

What happens in Step 9 of glycolysis? What are the enzymes, reactants, and products?

A

Step 9:
-enzyme: Enolase
-reactants: 2-phosphoglycerate
-products: Phosphoenolpyruvate, H20

180
Q

What happens in Step 10 of glycolysis? What are the enzymes, reactants, and products?

A

-enzyme: Pyruvate kinase
-reactants: phosphoenol pyruvate, ADP, H+
-products: Pyruvate, ATP

181
Q

What happens in Step 8 of glycolysis? What are the enzymes, reactants, and products?

A

-enzyme: phosphoglycerate mutase
-reactants: 3-phosphoglycerate
-products: 2-phosphoglycerate

182
Q

What happens in Step 6 of glycolysis? What are the enzymes, reactants, and products?

A

-enzyme: Glyceraldehyde-3-Phosphate Dehydrogenase
-reactants: Glyceraldehyde-3-Phosphate, NAD+, Pi
-products: 1,3-Bisphosphate, H+, NADH

183
Q

What happens in Step 5 of glycolysis? What are the enzymes, reactants, and products?

A

-enzyme: Triose Phosphate Isomerase
-reactants: Dihydroxyacetone Phosphate
-products: Glyceraldehyde-3-Phosphate

184
Q

What happens in Step 4 of glycolysis? What are the enzymes, reactants, and products?

A

In step 4, F1,6-P is split into 2.
-enzyme: aldolase
-reactants: F1,6-P, OH-
-products: Glyceraldehyde-3-Phosphate, Dihydroxyacetone Phospohate

185
Q

What evidence suggests aldolase uses a Schiff base mechanism in Step 4?

A

In alanine screening, the gene for a protein is modified to test the importance of a specific residue. Lys is essential to form the Schiff base.

186
Q

How do we metabolize ethanol?

A

convert ethanol to acetaldehyde using alcohol dehydrogenase and NAD+ and then convert that to acetate using acetaldehyde dehydrogenase, OH-, and NAD+

187
Q

What is gluconeogenesis? What does it cost?

A

The synthesis of glucose which occurs primarily in the liver.
4ATP + 2GTP + 2NADH

188
Q

How is glycolysis regulated?

What products inhibit and what products activate glycolysis?

A

High concentrations of glycolytic products such as ATP and PEP inhibit further glycolysis, while molecules that indicate low energy in the cell such as AMP and ADP activate glycolysis.

189
Q

What are the steps for glycogen synthesis?

A
  1. Phosphoglucomutase converts G6P to G1P
  2. G1P is activated by UTP to form UDP-glucose and PPi.
  3. Glycogen synthase links glucose units via a1-4
190
Q

How is glycogen broken down?

A

Glycogen phosphorylase use phosphorolysis to break bonds and produce G1P monomers.

191
Q

What is the oxidative path in creating the ribose sugar for nucleotides and/or NADPH?

A

The oxidative path. Irreversible.
Produces NADPH and ribulose-5-phosphate which may be reversibly converted to ribose-5-phosphate.

192
Q

What is the carbon rearrangement path in creating the ribose sugar for nucleotides and/or NADPH?

A

The carbon rearrangement.
2 F6P + 1 GAP are rearranged through a series of reversible reactions to ribulose-5-phosphate.

193
Q

What is Path 3 in creating the ribose sugar for nucleotides and/or NADPH?

A

Path 3: If the cell needs NADPH but not ribose, then G6P may be converted to ribulose-5-phosphate through the oxidative path and then converted to GAP and F6P by reversing the carbon rearrangement path.

194
Q

How can we treat cancer by targeting glucose metabolism?

A

Cancer cells have rates of glycolysis 10x more than normal cells so inhibiting glycolysis harms cancer cells more than regular cells.

195
Q

What is pyruvate dehydrogenase complex?

A

A multienzyme that links glycolysis to the citric acid cycle

196
Q

What happens at site 1 in pyruvate dehydrogenase?

A

Decarboxylation of pyruvate and transfer of the acetyl group to lipoamide.

197
Q

What happens at site 2 in pyruvate dehydrogenase?

A

Transfer of the acetyl group to CoA.

198
Q

What happens at site 3 in pyruvate dehydrogenase?

A

Dihydrolipoamide is reoxidized using NAD+ and FAD.

199
Q

What are the advantages of a multienzyme?

A
  1. The product of one active site quickly moves to the next active site
  2. Easier to regulate all enzymes together
  3. Minimizes side reactions
200
Q

Where do the citric acid cycle and the pyruvate dehydrogenase complex take place?

A

The mitochondrial matrix contains the pyruvate dehydrogenase complex and most of the enzymes of the citric acid cycle.

201
Q

What does the citric acid cycle do?

A

The goal is to make energy for the cell using reduced cofactors.

202
Q

Why is the citric acid cycle considered to be a central metabolic pathway?

A

Intermediates of the citric acid cycle serve as precursors for a variety of anabolic pathways through cataplerotic reactions.

203
Q

What happens in oxidative phosphorylation?

A

In oxidative phosphorylation reduced cofactors donate electrons to an electron transport chain that generates a H+ gradient. This gradient is used to generate ATP.

204
Q

What does reduction potential tell you about where electrons will go?

A

Electrons flow spontaneously from the substance with the lower reduction potential to the substance with the higher reduction potential.

205
Q

Where does oxidative phosphorylation occur?

A

The inner membrane of mitochondria contains all of the complexes for oxidative phosphorylation.

206
Q

What is the Malate-Asparatate Shuttle System?

A

NADH produced from glycolysis is in the cytosol but needs to move into the matrix, but it is too large to be transported. The shuttle system transfers the electrons from cytosolic NADH to malate which puts it back on to matrix NADH. Malate is then converted to asparate and transferred out.

207
Q

How are ADP and ATP moved across the mitochondrial inner membrane?

A

ATP is produced in the matrix, so it must be exported to the cytosol while ADP is imported into the matrix in order to make more ATP. ATP and ADP are moved using an antiporter driven by the inner membrane potential.

208
Q

How is Pi imported into the matrix?

A

Pi is imported into the matrix in order to make more ATP. Pi is imported along with a H+ using a symporter driven by the H+ gradient.

209
Q

How many protons are translocated in Complex 1?

A

Complex 1 (NADH dehydrogenase), translocates 4 H+ into the inter membrane space for every 2e- that pass through

210
Q

How do electrons pass through Complex 1?

A

In complex 1, a H- ion is transferred from NADH to FMN. FMN then passes the electrons one at a time to a series of iron-sulfur clusters until they reach Q.

211
Q

What happens at Complex III in the electron transport chain?

How many protons are translocated?

A

QH2 donates 2 electrons to complex III (cytochrome C) to reduce it. Cyt C can only carry 1 electron at a time. 4 H+ are translocated into the intermembrane space for every 2 e- that pass.

212
Q

What happens in complex IV in the electron transport chain?

How many protons are translocated?

A

2 Cyt C proteins each donate 1 electron to complex 4, ultimately reducing the terminal electron acceptor O2. 2 H+ are translocated into the intermembrane space for every 2 e- that pass.

213
Q

What is the chemiosmotic model?

A

A combination of the H+ imbalance (due to e- transport), and the negative charges on the matrix side of the membrane, results in a electrochemical gradient that favors H+ moving into the matrix.

214
Q

What is the structure of the ATP synthase?

Hint: Counting up as you go into the cell.

A

F1 soluble portion in the matrix includes 3a and 3b subunits. Each of the B subunits has ATP synthase activity.
The F0 membrane-spanning portion includes the a subunit, where H+ enter and exit, and a c-ring. The c-ring consists of subunits that each bind an H+ to help rotate the ring.

215
Q

What does the y subunit in the ATP synthase do?

A

The y subunit extends from F0 to F1 and rotates 120* once enough strain has built up from the c-ring rotation. 120* rotation of the y subunit forces the B subunits into one of 3 conformations, 1 full rotation of the y subunit produces 3 ATP.

216
Q

How much ATP is generated in the electron transport chain?

A

1 ATP produced for every 4 H+ translocated.

217
Q

Where does photosynthesis occur?

A

Chloroplasts have an inner membrane that surrounds the stroma. Within the stroma, there are flattened vesicles called thylakoids.

218
Q

How is an electron promoted to a higher state?

A

Absorbing a photon promotes an electron to a higher energy level.

219
Q

How are photons captured?

A

Photosynthetic organisms have light-harvesting complexes consisting of pigments bound to proteins.

220
Q

How is light energy transferred?

A

Antenna chlorophyll surround a reaction center and pass the energy of an absorbed photon from chlorophyll to chlorophyll until the energy is trapped by the reaction center because it has a lower excited state.

221
Q

How do plants generate ATP?

A

An electron transport chain generates a H+ gradient that drives ATP synthase.

222
Q

How are electrons transferred from H2O (high E) to pheophytin (low E) in photosystem II?

A

Photosystem II has a P680 reaction center that is excited by photon energy, lowering the P680 reduction potential so that is can transfer an electron to pheophytin.

223
Q

What are the steps for transferring electrons in Photosystem II?

A

P680 is excited by a proton and reduces pheophytin. Pheo- then passes an e- to a PQa. PQa transfers an electron to the mobile PQb.The steps repeat so that a 2nd electron fully reduces PQb- to PQbH2.

224
Q

How is P680 restored to it’s normal state?

A

P680+ has a high enough reduction potential that it is spontaneously reduced back to P680 by H2O.

225
Q

What happens when PQbH2 is fully reduced?

A

PQbH2 carriers 2 e- away from PSII and toward cytochrome b6f

226
Q

What happens in the Z-scheme?

How do electrons move to PSI?

How many protons are translocated?

A

the movement of 4 e- through cytochrome b6f translocates 8 H+ and reduces 4 plastocyanins (a mobile electron carrier). Plastocyanin carrys an electron to PS1. Electrons move through PS1 and reduce the mobile e- carrier ferredoxin.

227
Q

How is free energy conserved by photosystem 1? Non cyclic vs. cyclic

A

Free energy can be conserved by reducing NADP+ –> NADPH (noncyclic) or in the H+ gradient by transferring the e - back to cyctochrome b6f (cyclic e- flow).

228
Q

When is rubisco activated?

A

When light reactions are occurring, the stroma pH increases to activate rubisco. Otherwise rubisco is inactive to allow the cell to conserve ATP and NADPH.

229
Q

What happens in the Calvin cycle?

A

Rubisco fixes CO2 to form GAP at the expense of ATP and NADPH. GAP is converted to Ru5P. Ru5P is then phosphorylated by ATP to get the Rubisco substrate RuBP.

230
Q

How are carbons rearranged in the Calvin cycle?

A

For every 6 GAP produced, one is removed from the cycle to serve as a precursor for various biomolecules. The other 5 GAPs have their carbons rearranged to form 3 5-carbon ribulose sugars.

231
Q

How are lipids transported from the intestine to the liver and adipose tissue?

A

Chylomicrons transport dietary triacylglycerols from the intestine to adipose tissue and transport cholesterol to the liver.

232
Q

What do very low density lipoproteins (VLDL) do?

A

Transport triacylglycerols from the liver to other tissues.

233
Q

What do intermediate density lipoproteins (IDL) do?

A

Form as VLDLs lose triacylglycerols

234
Q

What do low density lipoproteins (LDL) do? What are high levels of LDL associated with?

A

LDL transport cholesterol to various tissues. High LDL levels are associated with an increased risk of atherosclerosis.

235
Q

What do high density lipoproteins (HDL) do?

A

HDL transport excess cholesterol back to the liver.

236
Q

What are the compositions of lipoproteins?

A

Lipoproteins have a highly hydrophobic core of triacylglycerols and cholesteryl esters surrounded by proteins and amphipathic lipids.

237
Q

How does acyl-CoA generated in the cytosol produce acyl-CoA in the matrix?

A

Acyl-CoA is too large to move into the matrix. Instead, the acyl group is esterified to carnitine for import to the mitochondrial matrix from the cytosol.

238
Q

How are fatty acids oxidized?

A

Each round of B-oxidation removes 2 carbons, and produces 1 QH2, 1 NADH, 1 Acetyl CoA. The last round produces 2 Acetyl CoA.

239
Q

What is the energy yield for each round of B-oxidation?

A
240
Q

What are the steps for fatty acid synthesis?

A
  1. Acetyl-CoA is carboxylated in the cytosol by acetyl-CoA carboxylase (ACC) to form malonyl-CoA.
  2. Acetyl-CoA is extended, 2 carbons at a time by the fatty acid synthase multifunctional enzyme
  3. Fatty acid synthase uses substrate channeling: the acyl carrier protein swings intermediates between active sites
241
Q

Where are fatty acids synthesized?

A

Fatty acid synthesis occurs in the cytosol.

242
Q

What inhibits and activates fatty acid synthesis?

Glucagon/Epinephrine vs. Insulin

What do they phosphorylate or dephosphorylate?

A

-Glucagon/epinephrine signaling inhibits by phosphorylating ACC
-Insulin signaling activated by dephosphorylating ACC

243
Q

How is fatty acid metabolism regulated?

What is the primary regulation point?

A
  1. Aceteyl-CoA carboxylase (ACC) is the primary regulation point for FA metabolism
    - activated by citrate
    - inhibited by fatty acids
    - inhibited by malonyl-CoA
244
Q

How are ketone bodies synthesized?

A

Ketogenesis occurs when blood glucose is low and glycogen is depleted. The liver responds by generating glucose through gluconeogenesis and using Acetyl-CoA to make the ketone bodies which are converted back in the central nervous system for energy.

245
Q

How is cholesterol synthesized?

A

Cholesterol is assembled from acetyl-CoA units.

Biochemistry (6 decks)

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