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ACS Biochemistry > ACS Exam 2022 > Flashcards

ACS Exam 2022 Flashcards

1
Q

Henderson-Hasselbach Equation

A

pH = pKa + log ([A-] / [HA])

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2
Q

FMOC Chemical Synthesis

A

Used in synthesis of a growing amino acid chain to a polystyrene bead. FMOC is used as a protecting group on the N-terminus.

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3
Q

Salting Out (Purification)

A

Changes soluble protein to solid precipitate. Protein precipitates when the charges on the protein match the charges in the solution.

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4
Q

Size-Exclusion Chromatography

A

Separates sample based on size with smaller molecules eluting later.

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5
Q

Ion-Exchange Chromatography

A

Separates sample based on charge. CM attracts +, DEAE attracts -. May have repulsion effect on like charges. Salt or acid used to remove stuck proteins.

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6
Q

Hydrophobic/Reverse Phase Chromatography

A

Beads are coated with a carbon chain. Hydrophobic proteins stick better. Elute with non-H-bonding solvent (acetonitrile).

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7
Q

Affinity Chromatography

A

Attach a ligand that binds a protein to a bead. Elute with harsh chemicals or similar ligand.

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8
Q

SDS-PAGE

A

Uses SDS. Gel is made from cross-linked polyacrylamide. Separates based off of mass with smaller molecules moving faster. Visualized with Coomassie blue.

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9
Q

SDS

A

Sodium dodecyl sulfate. Unfolds proteins and gives them uniform negative charge.

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10
Q

Isoelectric Focusing

A

Variation of gel electrophoresis where protein charge matters. Involves electrodes and pH gradient. Protein stops at their pI when neutral.

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11
Q

FDNB (1-fluoro-2,3-dinitrobenzene)

A

FDNB reacts with the N-terminus of the protein to produce a 2,4-dinitrophenol derivative that labels the first residue. Can repeat hydrolysis to determine sequential amino acids.

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12
Q

DTT (dithiothreitol)

A

Reduces disulfide bonds.

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13
Q

Iodoacetate

A

Adds carboxymethyl group on free -SH groups. Blocks disulfide bonding.

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14
Q

Homologs

A

Shares 25% identity with another gene

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15
Q

Orthologs

A

Similar genes in different organisms

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16
Q

Paralogs

A

Similar “paired” genes in the same organism

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17
Q

Ramachandran Plot

A

Shows favorable phi-psi angle combinations. 3 main “wells” for α-helices, ß-sheets, and left-handed α-helices.

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18
Q

Glycine Ramachandran Plot

A

Glycine can adopt more angles. (H’s for R-group).

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19
Q

Proline Ramachandran Plot

A

Proline adopts fewer angles. Amino group is incorporated into a ring.

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20
Q

α-helices

A

Ala is common, Gly & Pro are not very common. Side-chain interactions every 3 or 4 residues. Turns once every 3.6 residues. Distance between backbones is 5.4Å.

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21
Q

Helix Dipole

A

Formed from added dipole moments of all hydrogen bonds in an α-helix. N-terminus is δ+ and C-terminus is δ-.

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22
Q

ß-sheet

A

Either parallel or anti-parallel. Often twisted to increase strength.

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23
Q

Anti-parallel ß-sheet

A

Alternating sheet directions (C & N-termini don’t line-up). Has straight H-bonds.

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24
Q

Parallel ß-sheet

A

Same sheet directions (C & N-termini line up). Has angled H-bonds.

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25
Q

ß-turns

A

Tight u-turns with specific phi-psi angles. Must have gly at position 3. Proline may also be at ß-turn because it can have a cis-omega angle.

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26
Q

Loops

A

Not highly structured. Not necessary highly flexible, but can occasionally move. Very variable in sequence.

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27
Q

Circular Dichroism

A

Uses UV light to measure 2° structure. Can be used to measure destabilization.

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28
Q

Disulfide-bonds

A

Bonds between two -SH groups that form between 2° and 3° structure.

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29
Q

ß-mercaptoethanol

A

Breaks disulfide bonds.

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30
Q

α-keratin

A

formed from 2 α-helices twisted around each other. “Coiled coil”. Cross-linked by disulfide bonds.

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31
Q

Collagen

A

Repeating sequence of Gly-X-Pro. 3 stranded “coiled coil”. Contains gly core.

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32
Q

Myoglobin 4° Structure

A

Symmetric homodimer,

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33
Q

Hemoglobin 4° Structure

A

Tetramer. Dimer of dimers. α2ß2 tetramer.

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34
Q

α/ß Protein Folding

A

Less distinct areas of α and ß folding.

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35
Q

α+ß Protein Folding

A

Two distinct areas of α and ß folding.

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36
Q

Mechanism of Denaturants

A

Highly soluble, H-binding molecules. Stabilize protein backbone in water. Allows denatured state to be stabilized.

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37
Q

Temperature Denaturation of Protein

A

Midpoint of reaction is Tm.

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38
Q

Cooperative Protein Folding

A

Folding transition is sharp. More reversible.

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39
Q

Folding Funnel

A

Shows 3D version of 2D energy states. Lowest energy is stable protein. Rough funnel is less cooperative.

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40
Q

Protein-Protein Interfaces

A

Core and “fringe” of the interfaces. Core is more hydrophobic and is on the inside when interfaced. Fringe is more hydrophilic.

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41
Q

π-π Ring Stacking

A

Weird interaction where aromatic rings stack on each other in positive interaction.

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42
Q

σ-hole

A

Methyl group has area of diminished electron density in center; attracts electronegative groups

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43
Q

Fe Binding of O2

A

Fe2+ binds to O2 reversible. Fe3+ has an additional + charge and binds to O2 irreversibly. Fe3+ rusts in O2 rich environments.

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44
Q

Ka for Binding

A

Ka = [PL] / [P][L]

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45
Q

ϴ-value in Binding

A

ϴ = (bound / total)x100%

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46
Q

Kd for binding

A

Kd = [L] when 50% bound to protein.

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47
Q

High-Spin Fe

A

Electrons are “spread out” and result in larger atom.

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48
Q

Low-Spin Fe

A

Electrons are less “spread out” and are compacted by electron rich porphyrin ring.

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49
Q

T-State

A

Heme is in high-spin state. H2O is bound to heme.

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50
Q

R-State

A

Heme is in low-spin state. O2 is bound to heme.

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51
Q

O2 Binding Event

A

O2 binds to T-state and changes the heme to R-state. Causes a 0.4Å movement of the iron.

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52
Q

Hemoglobin Binding Curve

A

4 subunits present in hemoglobin that can be either T or R -state. Cooperative binding leads to a sigmoidal curve.

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53
Q

Binding Cooperativity

A

When one subunit of hemoglobin changes from T to R-state the other sites are more likely to change to R-state as well. Leads to sigmoidal graph.

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54
Q

Homotropic Regulation of Binding

A

Where a regulatory molecule is also the enzyme’s substrate.

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55
Q

Heterotropic Regulation of Binding

A

Where an allosteric regulator is present that is not the enzyme’s substrate.

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56
Q

Hill Plot

A

Turns sigmoid into straight lines. Slope = n (# of binding sites). Allows measurement of binding sites that are cooperative.

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57
Q

pH and Binding Affinity (Bohr Affect)

A

As [H+] increases, Histidine group in hemoglobin becomes more protonated and protein shifts to T-state. O2 binding affinity decreases.

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58
Q

CO2 binding in Hemoglobin

A

Forms carbonic acid that shifts hemoglobin to T-state. O2 binding affinity decreases. Used in the peripheral tissues.

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59
Q

BPG (2,3-bisphosphoglycerate)

A

Greatly reduces hemoglobin’s affinity for O2 by binding allosterically. Stabilizes T-state. Transfer of O2 can improve because increased delivery in tissues can outweigh decreased binding in the lungs.

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60
Q

Michaelis-Menton Equation

A

V0 = (Vmax[S]) / (Km + [S])

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61
Q

Km in Michaelis-Menton

A

Km = [S] when V0 = 0.5(Vmax)

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62
Q

Lineweaver-Burke Graph

A

Slope = Km/Vmax

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63
Q

Lineweaver-Burke Equation

A

Found by taking the reciprocal of the Michaelis-Menton Equation.

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64
Q

Kcat

A

Rate-limiting step in any enzyme-catalyzed reaction at saturation. Known as the “turn-over number”. Kcat = Vmax/Et

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65
Q

Chymotripsin

A

Cleaves proteins on C-terminal endof Phe, Trp, and Tyr

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66
Q

Competitive Inhibition Graph

A

Slope changes by factor of α. Slope becomes αKm/Vmax.

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67
Q

Uncompetitive Inhibition Graph

A

Does not change slope.

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68
Q

Mixed Inhibition Graph

A

Allosteric inhibitor that binds either E or ES.

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69
Q

Non-Competitive Inhibition Graph

A

Form of mixed inhibition where the pivot point is on the x-axis. Only happens when K1 is equal to K1’.

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70
Q

Ionophore

A

Hydrophobic molecule that binds to ions and carries them through cell membranes. Disrupts concentration gradients.

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71
Q

ΔGtransport Equation

A

ΔGtransport = RTln([S]out / [S]in) + ZFΔΨ

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72
Q

Pyranose vs. Furanose

A

Pyranose is a 6-membered ring.

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73
Q

Mutarotation

A

Conversion from α to ß forms of the sugar at the anomeric carbon.

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74
Q

Anomeric Carbon

A

Carbon that is cyclized. Always the same as the aldo or keto carbon in the linear form.

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75
Q

α vs. ß sugars

A

α form has -OR/OH group opposite from the -CH2OH group.

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76
Q

Starch

A

Found in plants. D-glucose polysaccharide. “Amylose chain”. Unbranched. Has reducing and non-reducing end.

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77
Q

Amylose Chain

A

Has α-1,4-linkages that produce a coiled helix similar to an α-helix. Has a reducing and non-reducing end.

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78
Q

Amylopectin

A

Has α-1,4-linkages. Has periodic α-1,6-linkages that cause branching. Branched every 24-30 residues. Has reducing and non-reducing end.

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79
Q

Reducing Sugar

A

Free aldehydes can reduce FeIII or CuIII. Aldehyde end is the “reducing” end.

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80
Q

Glycogen

A

Found in animals. Branched every 8-12 residues and compact. Used as storage of saccharides in animals.

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81
Q

Cellulose

A

Comes from plants. Poly D-glucose. Formed from ß-1,4-linkage. Form sheets due to equatorial -OH groups that H-bond with other chains.

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82
Q

Chitin

A

Homopolymer of N-acetyl-ß-D-glucosamine. Have ß-1,4-linkages. Found in lobsters, squid beaks, beetle shells, etc.

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83
Q

Glycoproteins

A

Carbohydrates attached to a protein. Common outside of the cell. Attached at Ser, Thr, or Asn residues.

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84
Q

Membrane Translayer Flip-Flop

A

Typically slow, but can be sped up with Flippase, Floppase, or Scramblase.

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85
Q

Membrance Fluidity

A

Membrane must be fluid. Cis fats increase fluidity, trans fats decrease fluidity.

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86
Q

Type I Integral Membrane Protein

A

Membrane protein with C-terminus inside and N-terminus outside

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87
Q

Type II Integral Membrane Protein

A

Membrane protein with N-terminus inside and C-terminus outside

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88
Q

Type III Integral Membrane Protein

A

Membrane protein that contains connected protein helices

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89
Q

Type IV Integral Membrane Protein

A

Membrane protein that contains unconnected protein helices

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90
Q

Bacteriorhodopsin

A

Type III integral membrane protein with 7 connected helices.

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91
Q

ß-Barrel Membrane Protein

A

Can act as a large door. Whole proteins can fit inside.

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92
Q

α-hemolysin

A

Secreted as a monomer. Assembles to punch holes in membranes.

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93
Q

Cardiolipin

A

Lipid staple that ties two proteins (or complexes) together in a membrane. Formed from two phosphoglycerols.

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94
Q

Hydrolysis of Nucleotides

A

Base hydrolyzes RNA, but not DNA. DNA is stable in base because of 2’ deoxy position.

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95
Q

Chargaff’s Rule

A

Ratio of A:T and G:C are always equal or close to 1

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96
Q

DNA Double-Helix

A

Opposite strand direction. 3.4Å distance between complementary bases. 36Å for one complete turn.

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97
Q

A-form DNA

A

Condensed form of DNA. Deeper major groove and shallower minor groove.

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98
Q

B-form DNA

A

Watson-Crick model DNA. Deep, wide major groove.

99
Q

Z-form DNA

A

Left-handed helical form of DNA

100
Q

Inverted Repeat in DNA

A

Found in double-strands.

101
Q

Mirror Repeat in DNA/RNA

A

Found in single-strands.

102
Q

DNA UV Absorbtion

A

Absorbs UV light at 260nm.

103
Q

Restriction Enzyme

A

Cuts DNA at specific restriction sites.

104
Q

DNA Base-paring

A

G-C base pairs have 3 H-bonds

105
Q

GPCR (G-protein coupled receptor)

A

α-helical integral membrane proteins. Is a αßɣ heterotrimer.

106
Q

ß-adrenergic receptor

A

Prototype for all GPCR’s. Bind adrenaline/epinephrine to stimulate breakdown of glycogen.

107
Q

Step 1 of Epinephrine Signal Transduction

A

Epinephrine binds to its specific receptor

108
Q

Step 2 of Epinephrine Signal Transduction

A

Hormone complex causes GDP bound to α-subunit to be replaced by GTP, activating α-subunit

109
Q

Step 3 of Epinephrine Signal Transduction

A

Activated α-subunit separates from ßɣ-complex and moves to adenylyl cyclase, activating it.

110
Q

Step 4 of Epinephrine Signal Transduction

A

Adenylyl cyclase catalyzes the formation of cAMP from ATP

111
Q

Step 5 of Epinephrine Signal Transduction

A

cAMP phosphorylates PKA, activating it

112
Q

Step 6 of Epinephrine Signal Transduction

A

Phosphorylated PKA causes an enzyme cascade causing response to epinephrine

113
Q

Step 7 of Epinephrine Signal Transduction

A

cAMP is degraded, reversing activation of PKA. α-subunit hydrolyzes GTP to GDP and becomes inactivated.

114
Q

cAMP

A

Secondary messenger in GPCR signalling. Formed from ATP by adenylyl cyclase. Activates PKA (protein kinase A).

115
Q

AKAP

A

Anchoring protein that binds to PKA, GPCR, and adenylyl cyclase.

116
Q

GAPs (GTPase activator proteins)

A

Increase activity of GTPase activity in α-subunit of GPCR.

117
Q

ßARK and ßarr

A

Used in desensitization. ßARK phosphorylates receptors and ßarr draws receptor into the cell via endocytosis

118
Q

RTKs (Receptor Tyrosine Kinases)

A

Have tyrosine kinase activity that phosphorylates a tyrosine residue in target proteins

119
Q

INSR (Insulin Receptor Protein)

A

Form of RTK. Catalytic domains undergo auto-phosphorylation.

120
Q

INSR signalling cascade

A

INSR phosphorlates IRS-1 that causes a kinase cascade.

121
Q

INSR cross-talk

A

INSR causes a kinase cascade that alters gene expression and phosphorlates ß-adrenergic receptor causing its endocytosis.

122
Q

FADH2

A

Single-electron transfer

123
Q

FMN

A

Single electron transfer.

124
Q

Step 1 of Glycolysis

A

Glucose –> Glucose 6-phosphate.

125
Q

Step 2 of Glycolysis

A

Glucose 6-phosphate <–> Fructose 6-phosphate

126
Q

Step 3 of Glycolysis

A

Fructose 6-phosphate –> Fructose 1,6-bisphosphate

127
Q

First Committed Step of Glycolysis

A

Step 3 of Glycolysis.

128
Q

Step 4 of Glycolysis

A

Fructose 1,6-bisphosphate <–> dihydroxyacetone + glyceraldehyde 3-phosphate.

129
Q

Step 5 of Glycolysis

A

Dihydroxyacetonephosphate <–> glyceraldehyde 3-phosphate

130
Q

Step 6 of Glycolysis

A

Glyceraldehyde 3-Phosphate + Pi <–> 1,3-biphosphoglycerate.

131
Q

First Energy Yielding Step of Glycolysis

A

Step 6 of Glycolysis.

132
Q

Step 7 of Glycolysis

A

1,3-bisphosphoglycerate + ADP <–> 3-phosphoglycerate + ATP

133
Q

First ATP Yielding Step of Glycolysis

A

Step 7 of Glycolysis.

134
Q

Step 8 of Glycolysis

A

3-phosphoglycerate <–> 2-phosphoglycerate

135
Q

Step 9 of Glycolysis

A

2-phosphoglycerate <–> Phosphoenolpyruvate (PEP)

136
Q

Step 10 of Glycolysis

A

PEP + ADP –> Pyruvate + ATP

137
Q

ATP Consuming Steps of Glycolysis

A

Step 1 and 3.

138
Q

ATP Producing Steps of Glycolysis

A

Steps 7 and 10.

139
Q

NADH Producing Step of Glycolysis

A

Step 6

140
Q

Total Energy Produced by Glycolysis

A

2NADH + 4 ATP

141
Q

Lactic Acid Fermentation

A

Pyruvate –> L-Lactate

142
Q

Ethanol Fermentation

A

Pyruvate –> Acetalaldehyde –> Ethanol

143
Q

TPP Cofactor

A

Common acetaldehyde carrier. Used in pyruvate decarboxylase, pyruvate dehydrogenase, α-ketoglutarate dehydrogenase, and transketolase

144
Q

Bypass Reactions in Gluconeogenesis

A

Steps 1,3, and 10 must be bypassed.

145
Q

Gluconeogenic Bypass of Step 10

A

Bicarbonate + Pyruvate –> Oxaloacetate

146
Q

Gluconeogenic Bypass of Step 3

A

Fructose 1,6-bisphosphate + H2O –> Fructose 6-phosphate + Pi

147
Q

Gluconeogenic Bypass of Step 1

A

Glucose 6-phosphate + H2O –> Glucose + Pi

148
Q

Cost of Gluconeogenesis

A

4 ATP, 2 GTP, and 2 NADH

149
Q

Oxidative Pentose Phosphate Pathway

A

Uses glucose 6-phosphate to produce 2 NADPH and ribose 5-phosphate used for biosynthesis

150
Q

Non-Oxidative Pentose Phosphate Pathway

A

Regenerates glucose 6-phosphate from ribose 5-phosphate.

151
Q

Transketolase

A

Transfers a two-carbon keto group

152
Q

Transaldolase

A

Transfers a three-carbon aldo group

153
Q

Enzyme Km and Substrate Concentration

A

Most enzymes have a Km that is near the concentration of the substrate.

154
Q

Fructose 2,6-bisphosphate

A

Not a glycolytic intermediate. Interconverts between fructose 2,6-bisphosphate and fructose 6-phosphate using PFK-2 and FBPase-2

155
Q

Regulation with fructose 2,6-bisphosphate

A

Activates PFK-1 encouraging glycolysis. Inhibits FBPase-1 discouraging gluconeogenesis

156
Q

Regulation of Pyruvate Kinase

A

Inhibited by ATP, Acetyl-Coa, Alanine, long-chain FA’s.

157
Q

PDH (Pyruvate Dehydrogenase Complex)

A

Large complex that converts pyruvate + Coa –> Acetyl-Coa + CO2

158
Q

Pyruvate Dehydrogenase

A

E1 domain of the PDH complex. Contains TPP cofactor. Releases CO2.

159
Q

Dihydrolipoyl Transacetylase

A

E2 domain of the PDH complex. Catalyzes formation of Acetyl-CoA. Has oxidized, acyl, and reduced lipoyllysine.

160
Q

Dihydrolipyl Dehydrogenase

A

E3 domain of the PDH complex. Catalyzes regeneration of the lipoyllysine using FAD –> FADH2

161
Q

Step 1 of the Citric Acid Cycle

A

Acetyl-CoA + Oxaloacetate –> Citrate

162
Q

Rate-limiting Step of the Citric Acid Cycle

A

Step 1

163
Q

Step 2 of the Citric Acid Cycle

A

Citrate <–> Isocitrate

164
Q

Step 3 of the Citric Acid Cycle

A

Isocitrate –> α-ketoglutarate

165
Q

Step 4 of the Citric Acid Cycle

A

α-ketoglutarate –> succinyl-CoA

166
Q

Step 5 of the Citric Acid Cycle

A

Succinyl-CoA <–> Succinate

167
Q

Step 6 of the Citric Acid Cycle

A

Succinate <–> Fumarate

168
Q

Step 7 of the Citric Acid Cycle

A

Fumarate <–> L-Malate

169
Q

Step 8 of the Citric Acid Cycle

A

L-Malate <–> Oxaloacetate

170
Q

Net Energy Gain of the Citric Acid Cycle

A

3 NADH, FADH2, and GTP

171
Q

NADH Producing Steps of the Citric Acid Cycle

A

Steps 3, 4, and 8.

172
Q

FADH2 Producing Steps of the Citric Acid Cycle

A

Step 6

173
Q

GTP/ATP Producing Steps of the Citric Acid Cycle

A

Step 5

174
Q

CO2 Producing Steps of the Citric Acid Cycle

A

Steps 3 and 4

175
Q

Biotin Function

A

Prosthetic group that serves as a CO2 carrier to separate active sites on an enzyme

176
Q

Regulation of the Citric Acid Cycle

A

Regulation occurs at Steps 1, 2, 4, and 5.

177
Q

Glyoxylate Cycle

A

Found in plants. Produces succinate from 2 acetyl-CoA. Allows oxaloacetate in the CAC to be used in gluconeogenesis. Uses 3 steps from the CAC.

178
Q

Different Steps in the Glyoxylate Cycle

A

Isocitrate –> Glyoxylate (+ succinate)

179
Q

Step 1 of ß-oxidation

A

Fatty acyl-CoA –> trans-Δ2-enoyl-CoA

180
Q

Step 2 of ß-oxidation

A

trans-Δ2-enoyl-CoA (+ H2O) –> L-ß-hydroxy-acyl-CoA

181
Q

TFP (Trifunctional Protein)

A

Protein complex that catalyzes the last three reactions of ß-oxidation.

182
Q

Step 3 of ß-oxidation

A

L-ß-hydroxy-acyl-CoA –> ß-ketoacyl-CoA

183
Q

Oxidation of Odd-numbered FA’s

A

Results in propionyl-CoA formation. Propionyl-CoA can be converted to succinyl-CoA and used in the CAC

184
Q

Step 4 of ß-oxidation

A

ß-ketoacyl-CoA (+ CoA) –> Fatty acyl-Coa (shorter)

185
Q

ß-oxidation in plants

A

Electrons are passed directly to molecular oxygen releasing heat and H2O2 instead of the respiratory chain.

186
Q

ω-oxidation

A

Similar to ß-oxidation but occurs simultaneously on both ends of the molecule.

187
Q

α-oxidation

A

Form of oxidation of branched FA’s. Produced propionyl-CoA that must be converted to succinyl-CoA for use in the CAC

188
Q

Ketone bodies

A

Consists of Acetoacetate, Acetone, and D-ß-hydroxybutryate.

189
Q

Zymogen

A

An inactive precursor of an enzyme, activated by various methods (acid hydrolysis, cleavage by another enzyme, etc.)

190
Q

Amidotransferase

A

Uses a PLP group to transfer amino group from an amino acid to α-ketoglutarate to form L-glutamate and an α-ketoglutarate.

191
Q

Ammonia (NH4+) Transportation

A

L-glutamate is converted to L-glutamine via glutamine synthetase.

192
Q

Glucose-Alanine Cycle

A

Pyruvate can be converted into Alanine via alanine aminotransferase (PLP). Adds a NH4+ group from glutamate to pyruvate. Alanine can travel to the liver and be reconverted back into pyruvate needed for gluconeogenesis.

193
Q

Production of carbamoyl-phosphate

A

NH4+ –> Carbamoyl Phosphate

194
Q

Step 1 of the Urea Cycle

A

Ornithine (+ carbamoyl phosphate) –> citrulline

195
Q

Step 2 of the Urea Cycle

A

Citrulline –> Arginosuccinate

196
Q

Step 3 of the Urea Cycle

A

Arginosuccinate –> Argininine

197
Q

Step 4 of the Urea Cycle

A

Arginine –> Ornithine

198
Q

N-acetylglutamate

A

Upregulates the production of carbamoyl phosphate and the urea cycle. Formed from acetyl-CoA and glutamate.

199
Q

PCR (Protein Chain Reaction)

A

Process by which DNA is replicated. Has melting step, annealing step, replication step.

200
Q

pKa of Arginine R-group

A

12.5

201
Q

pKa of Aspartate R-group

A

3.9

202
Q

pKa of Cysteine R-group

A

8

203
Q

pKa of Glutamate R-group

A

4

204
Q

pKa of Histidine R-group

A

6.1

205
Q

pKa of Lysine R-group

A

10.5

206
Q

pKa of Tyrosne R-group

A

10

207
Q

Q (Ubiquinone/Coenzyme Q) Function

A

Lipid soluble electron carrier. Carries 2 electrons with 2 H+.

208
Q

ETC (Electron Transport Chain)

A

Consists of 4 functional protein complexes.

209
Q

Complex I in the ETC

A

Accepts two electrons from NADH via an FMN cofactor. Transfers 4H+ to Pside and 2H+ to Q

210
Q

Complex II in the ETC

A

Succinate dehydrogenase. Accepts two electrons electrons from succinate via an FAD group. Q –> QH2

211
Q

Complex III in the ETC

A

Transfers two electrons from QH2 to cytochrome c via the Q-cycle. Transfers 4H+ to Pside.

212
Q

Complex IV in the ETC

A

Transfers electrons from cytochrome c to O2. Four electrons are used to reduce on O2 into two H2O molecules. Transfers 4H+ to Pside

213
Q

Mitochondrial ATP Synthase

A

Consists of F1 and F0 domains

214
Q

F1 Domain of Mitochondrial ATP Synthase

A

Hexamer of 3 αß dimers. Catalyze ADP + Pi –> ATP via binding-change model

215
Q

F0 Domain of Mitochondrial ATP Synthase

A

Causes rotation of γ-subunit via a half channel and H+ gradient

216
Q

Malate-Aspartate Shuttle

A

Used to maintain gradient of NADH inside of the mitochondria. Involves transport of malate or aspartate; aspartate aminotransferase; and malate dehydrogenase.

217
Q

RuBisCo (Ribulose 1,5-bisphosphate carboxylase/oxygenase)

A

Incorporates CO2 into ribulose 1,5-bisphosphate and cleaves the 6C intermediate into 2 3-phosphoglycerate.

218
Q

Stage 1 of the Calvin Cycle

A

3 ribulose 1-5-bisphosphate + 3 CO2 –> 6 3-phosphoglycerate.

219
Q

Mg2+ in Rubisco

A

Stabilizes negative charge in intermediate and held by Glu, Asp, and carbamoylated Lysine residue

220
Q

Rubisco Activase

A

Triggers removal of ribulose 1,5-bisphosphate or 2-carboxyaarabinitol 1-phosphate so Lys can be carbamoylated.

221
Q

2-carboxyarabinitol 1-phosphate

A

inhibits carbamoylated rubisco. Synthesized in the dark and is broken down by rubisco activase or light.

222
Q

Stage 2 of the Calvin Cycle

A

3-phosphoglycerate –> glyceraldehyde 3-phosphate

223
Q

Stage 3 of the Calvin Cycle

A

Glyceraldehyde 3-phosphate –> Ribulose 1,5-bisphosphate

224
Q

Energy Consumption of the Calvin Cycle

A

9 ATP molecules and 6 NADPH molecules for every 3 CO2 molecules that are fixated.

225
Q

Pi-Triose Phosphate Anti-porter

A

Maintains Pi balance in cytosol/chloroplast due to G3P export to the cytosol.

226
Q

Oxygenase Activity in Rubisco

A

O2 competes with CO2 and reacts to form 2-phosphoglycerate

227
Q

Glycolate Cycle

A

Process of converting 2-phosphoglycerate to 3-phosphoglycerate in chloroplast, peroxisome, and mitochondria.

228
Q

C4 Plants

A

Fix CO2 into PEP to form oxaloacetate (via PEP carboxykinase) that is then converted to malate that carries CO2 to rubisco. Bypasses O2 binding.

229
Q

CAM plants

A

Fix CO2 into PEP to form oxaloacetate (via PEP carboxykinase) that is converted to malate at night and stored until the day time.

230
Q

Malonyl-CoA

A

Formed from Acetyl-CoA and HCO3 via the Acetyl-CoA carboxylase (ACC). Serves as a regulator of FA catabolism and precursor in FA synthesis.

231
Q

ACC (acetyl-CoA carboxylase) Regulation

A

Inhibited by PKA in glucagon chain and activated by pjhosphatase in INSR chain.

232
Q

FAS (Fatty-acid Synthetase)

A

Catalyzes condensation, reduction, dehydration, and reduction of growing fatty acid chain. Requires activation by acetyl-CoA or malonyl-CoA

233
Q

Additional Cost of FAS in Eukaryotes

A

Acetyl-CoA for lipid synthesis is made in mitochondria and must be transferred into the cytosol via citrate transporter. Costs 2 ATP.

234
Q

Cost of FAS in Eukaryotes

A

3 ATP’s per 2 carbon unit added.

235
Q

Phosphatidic Acid

A

Common precursor to TAGs and phospholipids. Consists of a glycerol 3-phosphate with two acyl groups that are attached via acyl transferases.

236
Q

TAGs (Triacylglycerols)

A

Made from phosphatidic acid by removing phosphate with phosphatase and adding an acyl group with acyl transferase.

237
Q

Cholesterol Synthesis

A

Synthesized from 15 acetyl-CoA through a number of intermediates.

238
Q

HMG-CoA Reductase

A

Enzyme that converts ß-hydroxy-ß-methyl glutaryl-CoA to mevalonate in cholesterol metabolism.

239
Q

Regulation of HMG-CoA Reductase

A

Inhibited by AMPK (AMP dependent kinase), glucagon, and oxysterol.

240
Q

Ribonucleotide Reductase

A

Contains two types of allosteric regulatory sites for activity and specificity. Converts ribonucleotides to deoxyribonucleotides.

241
Q

Nitrogenase Complex

A

Uses ATP hydrolysis and ATP binding to overcome activation energy. Has a FeMo cofactor. Is an α2ß2 homodimer. Fixes N2 into NH4+

242
Q

Anaerobic Ammonia Oxidation (Anammox)

A

Ability of some bacteria to oxidize NH4+ and NO2- into N2. “Short-circuits” the nitrogen cycle.

243
Q

Glutamine Synthetase Regulation in Nitrogen Metabolism

A

Catalyzes conversion of glutamate to glutamine. Inhibited by Gly, Ala, and endpoints of glutamine metabolism. Additive effectors.

244
Q

Glutamine amidotransferase

A

Enzyme that catalyzes the transfer of the amino group from glutamine to an amino group acceptor. Forms glutamate. Used in biosynthetic pathways.

ACS Biochemistry (3 decks)

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