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Biochemistry > Biochem 2 Midterm 1 > Flashcards

Biochem 2 Midterm 1 Flashcards

1
Q

If △G°’ > 0 how can you make a reaction occur?

A

1) Change the concentrations of reactants and products: cascade of reactions in biological systems controls this, downstream rxn uses previous reaction, compartmentalization allows for this
2) Couple with another exergonic reaction so that △Gnet < 0

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2
Q

What is the benefit of pairing two reactions?

A

even though one reaction is energetically favorable it may have high activation energy or have alot of requirements to occur

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3
Q

What is catabolism?

A

degradation, energy production, carbs, lipids, proteins

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4
Q

What is anabolism?

A

biosynthesis, synthesis of macromolecules, muscle contraction, active ion transport, thermogenesis

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5
Q

What are the high energy bonds in ATP? How many are there?

A

phosphoanhydride bonds, one ATP molecule has 4

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6
Q

What are high energy bonds?

A
  • cleavage yields energy more negative than -25kj/mol
  • not bond energy
  • does not refer to the intrinsic stability of a molecule
  • only refers to the stability of the cleaved product being higher than that of the reactant
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7
Q

What ion is important for stabilizing ATP?

A
  • magnesium is essential for balancing out electrostatic repulsion
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8
Q

How do organisms save free energy?

A
  • organisms capture free energy in high energy compounds whose subsequent breakdown is used to power endergonic reactions
  • high energy compounds and reducing equivalents
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9
Q

Why is the hydrolysis of a phosphoanhydride bond so exergonic?

A

1) The resonance stabilization of a phosphoanhydride bond is less than that of its hydrolysis products
2) There is destabilizing effect of electrostatic repulsions of the charged groups of a phosphoanhydride
3) Smaller solvation energy of a phosphoanhydride compared to that of its hydrolysis products

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10
Q

How do catabolism and anabolism relate to redox?

A

Catabolism: reduced substrates to oxidized products
Anabolism: oxidized precursor to reduced products

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11
Q

What occurs in a redox reaction?

A
  • electrons move between atoms
  • reduction: gain electrons, oxidation number decreases
  • oxidation: lose electrons, oxidation number increases
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12
Q

What are the oxidation rules (carbon bonds)?

A

C - C = 0
C - H = -1
C - (O,N,S) = +1

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13
Q

What are the oxidized and reduced forms of NAD+/H2

A 
NAD+ = oxidized form
NADH = reduced form
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14
Q

What is NADH derived from?

A

Niacin or vitamin B3 (or Tryptophan)

- cant make it from our diet

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15
Q

What is pellagra?

A
  • rough skin caused by a lack of niacin (VB3) and tryptophan from diet
  • symptoms: dementia, diarrhea, dermatitis, and death
  • in mexico there are fewer cases because corn is usually cooked alkaline solution that helps release niacin from the bound state to get used by the human body
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16
Q

What is an enzyme that catalyzed oxidation of NADH to NAD+?

A
  • Lactate dehydrogenase

Pyruvate + NADH + H2O -> Lactate + NAD+ OH

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17
Q

What are three pathways through which Acetyl CoA can be produced?

A

Glucose -> Pyruvate -> Acetyl CoA
Fats/Lipids -> oxidized to Acetyl CoA
Proteins -> proteinolysis to amino acids -> Acetyl CoA

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18
Q

What is the reverse process of glycolysis?

A

gluconeogenesis

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19
Q

How does acetyl coA store energy?

A
  • thioester bond

- breaking this bond △G°’ = -31.5kj/mol

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20
Q

Why does a thioester bond have higher △G for hydrolysis than an oxygen ester?

A

Oxygen ester has more resonance stabilization

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21
Q

What is glucose catabolism called?

A

glycolysis

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22
Q

Where does glycolysis occur?

A

in the cytosol of most eukaryotic cells

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23
Q

What is the reaction of glycolysis?

A

Glucose + 2NAD+ + 2ADP + 2Pi –> 2 pyruvate + 2NADH +2ATP + 2H2O + 4H+

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24
Q

Glycolysis occurs without______

A

oxygen

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25
Q

What are the objectives of glycolysis?

A
  • produce energy

- produce precursors for biomass (critical intermediates in biosynthesis)

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26
Q

Why is phosphorylation important in glycolysis?

A

1) when glucose becomes phosphorylated it becomes negative and gets trapped inside of the cell (phosphorylated sugar cannot leave the cell)
2) adding a phosphate group onto glucose activates/destabilizes glucose
3) phosphates form complexes with Mg2+ ions in enzyme active sites

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27
Q

What is a kinase?

A

an enzyme that transfers phosphate groups from ATP

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28
Q

Why is glucose used to store energy?

A

1) it was likely available as fuel for primitive organisms

2) has low tendency to glycate proteins

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29
Q

List the first 5 enzymes of glycolysis in order.

A

1) Hexokinase
2) Phosphoglucose Isomerase (PGI)
3) Phosphofructokinase 1 (PFK-1)
4) Aldolase
5) Triose Phosphate Isomerase

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30
Q

Describe the first stage of glycolysis.

A
  • no electron transfer
  • one molecule of glucose to two molecules of GAP
  • 2 ATP consumed
  • (energy investment stage)
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31
Q

Describe the thermodynamics of the hexokinase reaction. (Step 1)

A
  • reaction of glucose + phosphate (to form G6P) is thermodynamically unfavorable
  • coupled to exergonic cleavage of ATP
  • overall reaction is thermodynamically favorable
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32
Q

What occurs when glucose binds to hexokinase? (Step 1 Glycolysis)

A
  • glucose induces a large conformational change in hexokinase
  • movement excludes water from the active site, and prevent hydrolysis of ATP
  • this functions to bring the reactants together
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33
Q

Describe the PFK-1 reaction. (Step 3 Glycolysis)

A
  • F6P to FBP
  • PFK-1 reaction is very similar to hexokinase reaction
  • PFK is an important reaction because it catalyzes one of the pathways rate-determining steps
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34
Q

Describe the structure of PFK-1. How is this reaction regulated? (Step 3 Glycolysis)

A
  • PFK-1 is a tetramer with four identical subunits
  • These subunits act cooperatively with each other
  • R and T states
  • Regulated allosterically
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35
Q

Describe the allosteric regulation of PFK-1. (Step 3)

A
  • PFK-1 subunits have two conformers: R & T
  • R (active) and T (inactive) bind ATP equally in the substrate site
  • Only T binds ATP in the regulatory site
  • When ATP is high it drives the equation to the T state
  • Only R state binds substrate (F6P)
  • Another Mechanism: AMP, ADP, and F2, 6 bisphosphate binding facilitates the R state (this process overrides ATP allosteric binding)
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36
Q

What is Tarui disease?

A
  • Patients experience exercise induced muscle cramps and weakness and myoglobinuria, can cause hemolytic anemia
  • caused by PFK-1 deficiency
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37
Q

What mechanism does aldolase proceed through? (Step 4 Glycolysis)

A

retro-aldol condensation

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38
Q

Describe the triose phosphate isomerase enzyme. (Step 5 Glycolysis)

A
  • essential residues: Glu, His, Lys (Glu abstracts proton, his protonates carbonyl, lys stabilizes negative transition state)
  • TIM is an alpha/beta barrel protein (TIM barrel); 8 parallel beta strands surrounded by 8 parallel alpha helices
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39
Q

What is unique about triose phosphate isomerase (Step 5)

A
  • TIM is a catalytically perfect enzyme - rate is diffusion controlled
  • GAP and DGAP are interconverted so efficiently that concentrations are maintained at equilibrium value; GAP consumed before DHAP by glycolytic flux
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40
Q

What is the enzyme in step 6 of glycolysis and how does it function?

A
  • GAPDH couples aldehyde oxidation (exergonic reaction) to the synthesis of high energy 1,3-BPG
  • GAPDH can be thought of as catalyzing two reactions
  • GAPDH forms a high energy thioester intermediate
  • Thiol group from cysteine residue -S-H
  • NAD+ alters the chemical reactivity and polarizes decreasing the pKa of the thiol group from 8 to 3.5, making it easier for deprotonated thiol to form
41
Q

What is phosphoryl transfer potential? When is it relevant?

A
  • the amount of energy released when a phosphorylated compound transfers its phosphoryl group to water
  • GAPDH produces the first “high-energy” intermediate in glycolysis
  • 1,3 BPG has a greater phosphoryl transfer potential than ATP (Acyl Phosphate)
42
Q

GAPDH is _______

A
  • GAPDH is a dehydrogenase, not a kinase

- It is a double displacement reaction

43
Q

What are the two types of biochemical reactions?

A
  • single displacement reactions (sequential)

- double displacement reactions (ping-pong)

44
Q

What is a single displacement reaction?

A
  • all substrates must combine with the enzyme before a reaction occurs and products are released
45
Q

What is a double displacement reaction?

A
  • first the substrate transfers a functional group to the enzyme, then a second substrate displaces it to yield the product
46
Q

Describe glycolysis in cancer.

A
  • cancer cells grow faster - results in hypoxia
  • glycolysis is 10x faster in cancer cells
  • GAPDH is overexpressed in many cancers including melanoma and colon cancer
47
Q

Describe Phosphoglycerate Kinase (Step 7 Glycolysis)

A
  • has an induced fit model similar to hexokinase
  • functions as a reverse kinase - reverse process is phosphorylation
  • GAPDH and PGK reactions are coupled, 1,3 BPG consumption pulls GAPDH reaction forward
48
Q

Describe Phosphoglycerate mutase (Step 8 Glycolysis)

A
  • phosphate is the same group just moved to a different location on the molecule
  • 2,3 BPG Enzyme Complex is formed
  • PGM has a phosphorylated histidine in the active site
49
Q

Describe Enolase (Step 9 Glycolysis)

A
  • Forms complex with two Mg2+ ions
  • Fluoride ions inhibit glycolysis by blocking enolase, blocks substrate binding by forming a complex with Mg2+ at the active site and preventing binding of 2PG
  • Forms high energy intermediate: PEP
50
Q

Describe Pyruvate Kinase (Step 10 Glycolysis)

A
  • Couples free energy of PEP cleavage to the synthesis of ATP during the formation of pyruvate
  • PK reaction requires monovalent K+ and divalent Mg2+
51
Q

How is glycolysis regulated?

A
  • the steps with the largest changes in △G are might tightly regulated
  • 1, (hexokinase), 3 (PFK-1), and 10 (PK)
52
Q

What are three ways a reaction may be regulated?

A
  • metabolic effectors - changing the concentrations of metabolites (allosteric -> most rapid response, fastest) (ms)
  • second messengers - hormones (seconds)
  • genes - turning on and off - slowest regulation (hours)
53
Q

What are the three fates of pyruvate?

A
  • under aerobic conditions, pyruvate is completely oxidized via the citric acid cycle
  • under anaerobic conditions, pyruvate must be converted to a reduced end product in order to reoxidize the NADH produced by GAPDH: reduced to lactate, or decarboxylated to ethanol
54
Q

Describe homolactic fermentation.

A
  • in muscle during vigorous activity (ATP demand is high, oxygen is limited); ATP is synthesized via anaerobic glycolysis
  • lactate dehydrogenase catalyzes the oxidation of NADH by pyruvate to yield NAD+ and lactate
  • this reaction is freely reversible, so pyruvate and lactate concentrations are readily equilibrated
55
Q

Describe alcoholic fermentation (yeast).

A
  • pyruvate is converted to ethanol and carbon dioxide

- occurs in two steps catalyzed by pyruvate decarboxylase and yeast alcohol dehydrogenase

56
Q

What is required for pyruvate decarboxylase to function?

A
  • contains thiamine pyrophosphate (TPP) which is synthesized from thiamin (vitamin B1)
  • TPP is used to diffuse negative charge formed during the reaction
57
Q

What is the pentose phosphate pathway?

A
  • generates NADPH
  • NAD+/NADH favors metabolic oxidation
  • NADP+/NADPH favors reductive biosynthesis
58
Q

What is gluconeogenesis?

A
  • synthesizing glucose from pyruvate
  • mainly occurs in liver
  • closely regulates blood sugar
  • liver makes new glucose and releases it into the blood
  • occurs in mitochondria, cytosol, and ER
59
Q

What two enzymes catalyze the first step of gluconeogenesis (reverse of step 10 of glycolysis)?

A

pyruvate carboxylase - (oxyloacetate) -PEPCK

60
Q

What does pyruvate carboxylase require and how is it regulated?

A
  • requires biotin cofactor

- activated allosterically by acetyl CoA

61
Q

What are the two routes used in gluconeogenesis?

A
  • may start from lactate or pyruvate
62
Q

What are the 3rd and 4th enzymes that catalyze gluconeogenesis?

A
  • Fructose 1,6 bisphosphatase and glucose-6-phosphatase
63
Q

Glycolysis and gluconeogenesis are ____

A

independently regulated

64
Q

Why is hyperglycemia bad?

A
  • organs dont have the ability to restrict uptake of glucose (peripheral nerves, kidneys, and retina) so they act as sponges and absorb excess glucose
  • over absorption of glucose generates superoxides that activate poly ADP-ribose polymerase (PARP) which ribosylates GAPDH
  • GAPDH - cysteine residue, which forms thioester bond is damaged in diabetes and inhibits glycolysis
65
Q

What is the function of the Schiff base in the aldolase reaction?

A

Because of its positive charge, protonated Schiff base is a better electron withdrawing group than carbonyl oxygen

66
Q

What is the role of TPP in pyruvate decarboxylase?

A
  • TPP is an electron sink of the transition site, it diffused negative charge formed during the reaction
  • synthesized from vitamin B1
67
Q

How does the liver buffer blood glucose level?

A
  • Cells in pancreas release hormones
  • Alpha cells -> glucagon -> increase [CAMP]+ -> protein kinase A
  • Beta cells -> insulin -> phosphoprotein phosphatase
68
Q

How is pyruvate carboxylase regulated?

A
  • activated allosterically by acetyl CoA
69
Q

How is PEPCK regulated?

A
  • regulation is more transcriptionally controlled
  • insulin increases activity
  • glucagon decreases activity
70
Q

Explain F26BP.

A
  • potent activator of PFK
  • inhibitor of FBPase
  • synthesized by PFK2 - activated by PP1
  • degraded by FBPase2 - activated by PKA
71
Q

Which reaction is F26BP at play in?

A

3rd reaction of glycolysis - activates PFK

72
Q

What is glycogen?

A

storage form of glucose as a polymer

73
Q

What does glycogen level indicate?

A

sugar storage

74
Q

How do liver and muscle buffer blood sugar?

A
  • liver - uptake and release

- muscle - uptake only

75
Q

Why do we have glycogen?

A

1) Glycogenolysis is faster than fatty acid release and degradation
2) fat cant be metabolized into glucose, necessary for brain
3) fats cannot be used without O2

76
Q

What is glycogen structure?

A
  • a (1-4) linear

- a (1-6) branched

77
Q

What is the purpose of branching of glycogen?

A

1) increases solubility

2) creates more sites of action for enzymes

78
Q

Which glycogen enzymes are faster?

A

a (1-4) (linear) are faster than a (1-6) (branched)

79
Q

What are the three glycogen break down enzymes?

A

1) glycogen phosphorylase
2) debranching enzyme
3) Phosphoglucomutase

80
Q

What are problems with glycogen synthase?

A
  • need branching - branching enzyme

- need primer - glycogenin

81
Q

What is glycogenin and what does it do?

A
  • glycogenin attaches a glucose residue donated by UDPG to the OH group of its Tyr 194
  • then it extends the chain by up to 7 residues to form a small glycogen so that glycogen synthase can commence synthesis
82
Q

What molecules are responsible for regulating the flux of glycogen synthesis and glycogenolysis?

A
  • glycogen phosphorylase

- glycogen synthase

83
Q

What are PTMS?

A

post translational modification

84
Q

Where do PTMs occur?

A

Ser, Thr, Tyr

85
Q

What does a protein kinase do?

A

add Pi from ATP to a molecule

86
Q

What does a protein phosphatase do?

A

removes a Pi from a molecule (H20) to Pi

87
Q

How can phosphorylation affect a protein?

A

1) conformational change

2) affects electrostatic interactions

88
Q

What enzymes activate and deactivate glycogen phosphorylase and glycogen synthase?

A

phosphorylase kinase and phosphoprotein phosphatase

89
Q

What activates phosphorylase kinase?

A
  • maximally activated by Ca2+ (muscle contraction)

- phosphorylation by PKA

90
Q

What activates PKA?

A

cAMP

91
Q

The citric acid cycle is a _____ process

A

amphibolic (catabolic and anabolic functions)

92
Q

What are the catabolic and anabolic processes of TCA?

A
  • catabolic - production of reducing equivalents (NADH and GTP)
  • anabolic - production of metabolites important for synthesis
93
Q

What is catapleurosis?

A

pull out metabolites to make other things

94
Q

What is anapleurosis?

A

refill metabolites into the TCA

95
Q

What must happen before pyruvate can enter the TCA?

A

pyruvate dehydrogenase complex turns pyruvate into Acetyl-CoA

96
Q

In addition to metabolic effectors, second messengers, and genes what else regulates flux through glycolysis and gluconeogenesis?

A

Substrate cycling

97
Q

What is substrate cycling?

A

for non-equilibrium reactions 2 different enzymes catalyze forward and reverse reactions a set of opposing reactions known as a substrate cycle

98
Q

What is a phosphatase?

A

an enzyme that removes phosphate groups from proteins

Biochemistry (12 decks)

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