Lectures 18-25, Enzymes, regulation, Citric Acid Cycle, Glycolysis + Gluconeogenesis Flashcards

1
Q

What is Sir Archibald Edward Garrod known for?

A

First to make a connection between
disease and fundamental errors in
biochemical reactions

• Coined term “inborn errors of
metabolism”
• Enzymes must be link
– Thus, mutations in enzymes can cause
disease by altering biochemical reactions

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2
Q

What: – Contains a unique microenvironment, usually void of water, and controls the proper
shape, pH and polarity for substrate binding and chemical reactivity

A

Active Site

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3
Q

Define: Transition state

A

– Intermediate structure that is not the substrate and not yet the product
• Unstable and highest free energy

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4
Q

Define: Apoenzyme

A

enzyme without its cofactor

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5
Q

Define: Haloenzyme

A

Cofactor bound and catalytically active

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6
Q

Coenzymes are small organic molecules often derived from _________

A

vitamins

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7
Q

When coenzymes are bound tightly they are called _______

A

prosthetic groups

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8
Q

Examples of cofactors

A

Metals [smallest cofactor], coenzymes (vitamins - Biotin)

Stabilize

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9
Q

In alcohol dehydrogenase:

______ is reduced to ______ in the conversion of ethanol to acetaldehyde

The cofactors _____ and _____ are in a specific arrangement for this catalysis

A

Slide 27 - hint hint might be on test with a couple of questions

NAD+, NADH

NAD+, Zinc

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10
Q

Which class of enzymes is associated with the this type of reaction:

Oxidation-reduction

  • transfering electrons from one molecule to another
A

Oxidoreductases (ex. Lactate dehydrogenase)

ex. Alcohol dehydrogenase - converts alcohols to aldyhydes or ketones - Alcohol is oxidized and NAD+ is reduced

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11
Q

Which class of enzymes is associated with the this type of reaction:

Group transfer

Donor molecule required

A

Transferases (ex. nucleoside monophosphate kinase)

Coenzyme A transfering Acytl groups

Kinase receptors - phosphorylate proteins and themselves

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12
Q

Which class of enzymes is associated with the this type of reaction:

Hydrolysis reactions (transfer of functional groups to water)

Enzyme that catalyzes the hydrolysis of covalent bonds

transfer of functional groups to water

A

Hydrolases (ex. Chymotrypsin)

Ex. Disaccharidases - cleave double sugars to single sugars

Ex. defects in lactase - lactose intolerance

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13
Q

Which class of enzymes is associated with the this type of reaction:

Addition or removal of groups to form double bonds

Unique active site that can transfer electrons to active site and move them around on the product. Normally one substrate becoming two products with the formation of a double bond.

A

Lyases (ex. Fumarase)

Ex. Alsolase

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14
Q

Which class of enzymes is associated with the this type of reaction:

Isomerization (intramolecular group transfer)

Intramolecular oxidation-reduction reaction (group transfer)

Don’t lose any products, just move a double bond

A

Isomerases (ex. triose phosphate isomerase)

**making an isomer

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15
Q

Which class of enzymes is associated with the this type of reaction:

Ligation of two substrates at the expense of ATP hydrolysis

Creating the covalent linkage of two substrates

A

Ligases (Aminoacyl-tRNA synthetase)

Ex. DNA ligase - joining two DNA molecules, two phosphodiester bonds between the two molecules.

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16
Q

T/F: enzymes are biocatalysts that follow classical chemical laws. They speed up the rate at which a chemical reaction reaches equilibrium and alter the final concentrations of the reactants at equilibrium

A

False: they do not alter the final concentrations

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17
Q

What is enzyme kinetics?

A

Enzyme kinetics is the study of biochemical
reactions that are catalyzed by enzymes. The
focus of which is the reaction rates of these
enzymatic reactions.

Enzymes affect reaction rates by lowering the 
activation energy (ΔG‡) for the reaction.
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18
Q

Steady-state kinetics assumptions:

A
  1. ES is in rapid equilibrium with E and S
  2. Rate of ES formation = rate of ES breakdown
    – Therefore [ES] is essentially constant
  3. [S] >>> [E]
    – Therefore [S] is essentially constant
  4. Initial velocity of reaction is measured from
    time = 0 (thus, V0)
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19
Q

KM is the substrate concentration that produces
______ for the catalyzed reaction.

A

½ Vmax

• KM has units of molarity (M)
• KM is independent of enzyme amount and purity
• KM is dependent on assay conditions such as pH,
presence of inhibitors or activators, temperature,
and ionic strength. This is because that KM is
constructed purely of rate constants.

Km is called Michaelis constant

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20
Q

____ is the maximum velocity - at which enzyme is
saturated with substrate.

A

Vmax

• Vmax has units of μmol/min
• Vmax is dependent on amount of enzyme used.
• Vmax is the highest reaction rate that can be
attained because all of the enzyme is
saturated with substrate.

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21
Q

kcat =

A

Vmax/[Etotal]

kcat is called either the catalytic constant or turnover number

• If kcat = 1000 sec-1, the enzyme can convert 1000 molecules of substrate into product each second at saturating [S]

**number of molecules that can be converted to product per second.

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22
Q

On a Lineweaver Burk Plot the y intercept =

A

1/Vmax

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23
Q

On a Lineweaver-Burk Plot the x-intercept =

A

-1/Km

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24
Q

On a lineweaver burk plot the slope =

A

Km/Vmax

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25
Q

A low Km means what about the affinity of the active site?

A

high affinity at active site.

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26
Q

What is the name of the concentration at which half the active sites are filled?

A

Km

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27
Q

What is the measure of catalytic efficiency?

A

kcat/Km

higher the kcat/Km value the more efficient te enzyme (limits - 10^9. Cannot be more efficient than standard diffusion)

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28
Q

How is the lineweaver burke plot derived?

A

it is the reciprocal of michaelis-menton

michaelis menton: Vo= Vmax*[S]/(Km+[S])

lineweaver burke: 1/Vo = Km/ (Vmax*[S]) + 1/Vmax

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29
Q

** Look at tables of Lineweaver Burke, be able to get Km and Vmax, etc.

A
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30
Q

What type of reaction:

All substrates bind to the enzyme before any product
is released

A

Sequential reactions

both substrates form some product. ex. NADH binds first, then creates better binding site for pyruvate, then lactate is formed and NAD+ is released

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31
Q

What type of reaction:

One of the products is released before a second
substrate binds

A

Double-displacement (ping-pong) reactions

One substate binds, a product is released, then a second substrate comes in and binds and a second product is released.

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32
Q

Where is Sirt1 found in the cell?

A

In the nucleus

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33
Q

Where is Sirt3 found in the cell?

A

in the mitochondria

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34
Q

Define: Reversible Inhibition

A

bind to enzymes with non-covalent interactions such as H+ bonds, hydrophobic interactions and ionic bonds and do not undergo chemical reactions when
bound to the enzyme and can be easily removed by dilution or dialysis.

Mimics the substrates
– EXAMPLE: HIV protease inhibitors: mimics the enzymes’ substrates

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35
Q

Define: Irreversible Inhibition

A
**covalently modifies an enzyme**, and **inhibition cannot therefore be reversed**. These inhibitors aregenerally specific for one class of enzyme and do not 
inactivate all proteins; they do not function by destroying 
protein structure but by specifically altering the active site of 
their target 

“kills the enzyme”
– Example: FFR-CK (Phenlalanine-phenelalanine-arginine
chloromethylketone) covalently binds to the active site serine in
plasmin.

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36
Q

What are the Three kinds of Reversible Inhibition and what are their effects?

A
  1. Competetive - **Increase effective Km **(More substrate needed because active site are filled by inhibitors). Inhibits at the active site.
  2. Uncompetetive - Binds only to the enzyme-substrte complex. Both Km and Vmax are altered. DOES NOT inhibit at the active site.
  3. Non-competitive - Affects only the Vmax. can bind with both the enzyme and enzyme substrate complex.

LOOK AT GRAPHS FOR EACH!!!!! Be able to indentify!

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37
Q

How does pH effect enzyme activity?

A

pH can denature and change effectivness (kcat)

Changes in pH may denature enzymes by
altering the enzyme’s charge

altering the ionic bonds of the enzyme that
contribute to its functional shape

Enzymes have an optimal pH that helps
maintain their 3D shape

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38
Q

What two outcomes happen with Allosteric regulation?

A

allosteric inhibition stabilizes the enzyme in it’s low affinity form resulting in little or no activity

OR

stabilizes it in high affinity form, resulting in enzyme activity

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39
Q

Review slide 30

ATCase is what type of enzyme modification?

A

Transferase

condensation reaction joining two molecules with loss of a small molecule

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40
Q

ATCase is found in what two distinct conformational states?

textbook example of allosteric modification (products inhibit upstream reactions)

A

T state (less active - favored by CTP binding - inhibits the enzyme) and R state (more active - relaxed/open - ** Favored by substrate binding**)

Zinc is a cofactor in ATCase

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41
Q

Why do you have the multiphasic curve in the formation of N-carbamoylaspartate (ATCase)?

A

Combination of T and R state curves. - Sigmoidal curve

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42
Q

Serine proteases use what for the active site?

A

Use active site serine for peptide cleavage

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43
Q

Cleavage of peptide backbone in serine proteases occurs in which step?

A

3rd.

Go over slide 52

Acyl-anzyme intermediate created via the serine

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44
Q

Where is Pepsin synthesized?

A

Stomach

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45
Q

Where is Chymotrypsin, Trypsin, Carboxypeptidase, and Elastase synthesized?

A

Pancrease

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46
Q

Anabolic are:

A

those that require inputs of energy to proceed

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47
Q

____ Is the Universal Currency of Free Energy in
Biological Systems

A

ATP

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48
Q

In aerobic organisms, the ultimate electron acceptor in the
oxidation of carbon is ____
and the oxidation product is _____
.

A

O2, CO2

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49
Q

Which of the following has the most energy released during oxidation?

A. Methane

B. Methanol

C. Formaldehyde

D. Formic Acid

E. Carbon Dioxide

A

A. Methane

A->E is most to least amount of energy, Slide 10

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50
Q

Oxidation of 2-carbon units to produce

A

 2 CO2 molecules
 1 GTP
 Electrons in the form of NADH and FADH2

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51
Q

3 ways metabolic processes are regulated:

A

1) Controlling the amounts of enzymes
 Transcription/signaling
2) Controlling catalytic activity
 Feedback inhibition – conformation/modification
3) Controlling the accessibility of substrates
 Compartmentalization of pathway

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52
Q

Citric acid cycle general characteristics:

A

Take place in mitochondria matrix, etc…

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53
Q

Under anaerobic conditions pyruvate
is converted to __________

A

lactate or ethanol

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54
Q

State the Prosthetic group, Reaction catalyzed, and # of chains:

  1. E1
  2. E2
  3. E3
A
  1. 24 chains, TPP, Oxidative decarboxylation of pyruvate
  2. 24 chains, Lipoamide, Transfer of acetyl group to CoA
  3. 12 chains, FAD, Regeneration of the oxidized form of lipoamide

Slide 28 table

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55
Q

First step in Citric Acid cycle is what?

A

Generation of Acetyl CoA

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56
Q

Pyruvate is fromed via what process?

A

Glycolysis

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57
Q

Draw out and go over slide 39!!

A
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58
Q

T/F: Prosthetic groups are modified and put back into the origional form for each step of the reaction?

A

True

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59
Q

How can pyruvate dehydrogenase be regulated?

A

Allosterically and by reverse phosphorylation

Slide 47

high Acetyl CoA inhibits E2

Products also increase phosphorylation of PDH E2

Accumulation of ADP and pyruvate activate phosphatases

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60
Q

The citric acid cycle occurs under ______ conditions and
produces _____ energy from glucose than glycolysis

A

aerobic, more

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61
Q

What is the function of PDH?

A
Pyruvate dehydrogenase (PDH) links glycolysis to the 
citric acid cycle
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62
Q

PDH contains ___ enzymes and uses ____ cofactors to
generate acetyl CoA for entry into the citric acid cycle

A

3, 5

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63
Q

The Citric acid cycle starts with what 2 carbon molecule?

A

Acytl CoA

64
Q

The first step of the TCA is to generate:

and the enzyme used is:

and what is condensed?

A

Citric Acid (Citrate)

Citrate synthase

4-carbon oxaloacetate is condensed with 2-carbon of acetyl CoA

65
Q

Which binds first Ozaloacetate or Acetyl CoA?

A

Oxaloacetate, wont bind unless enough oxaloacetate is around

66
Q

T/F: The first step of TCA cycle exhibits sequential, ordered kinetics

A

True

67
Q

The second step of the TCA uses what enzyme/substrate, and produces what?

A

Citrate (from the end of the 1st step)

Aconitase is the enzyme (contains iron sulfur complex)

Isocitrate is produced

68
Q

** First major regulatory step: 3rd step:

What substrate, enzyme, product

First of 4 redox reactions

A

Isocitrate

Isocitrate dehydrogenase

a-Ketoglutarate

loss of electrons in form of NADH

69
Q

What is the rate limiting step of the TCA?

A

3rd step

That 5 carbon’s best path is to remain in the cycle, isocitrate could go back to acetyl CoA if energy is not needed

70
Q

What allosterically regulates the 3rd step of TCA?

A

ADP

71
Q

a-ketoglutarate dehydrogenase complex is very similar to what?

A

pyruvate dehydrogenase

72
Q

4th step of TCA substrate, enzyme, product

A

a-Ketoglutarate,

a-Ketoglutarate dehydrogenase complex,

succinyl CoA

73
Q

5th step of TCA, substrate, enzyme, product

A

Succinyl CoA

Succinyl CoA synthetase

Succinate

only step that directly yeilds GTP formed

74
Q

6th step of TCA substrate, enzyme, product

A

Succinate

Succinate dehydrogenase

Fumarate

FADH2 formed

75
Q

7th step of TCA substrate, enzyme, product

A

Fumarate

Fumarase

Malate

76
Q

8th step of TCA substrate, enzyme, product

A

Malate

Malate dehydrogenase

Oxaloacetate!

77
Q

Which reaction of the TCA yields GTP?

A

Succinyl CoA synthase

78
Q

Which amino acid transfers the phosphate group in the succinyl CoA synthase reaction?

A

Histidine

79
Q

How many redox reactions are there from Succinate to Oxaloacetate?

A

2 (final state of cycle), 2 steps of oxidation

80
Q

electrons from FADH2 are transferred directly to what?

A

Coenzyme Q of electron transport chain,

16 mins into lecture

81
Q

______________ catalyzes formation of fumarate
while generating FADH2

A

Succinate dehydrogenase

82
Q

If Acetyl CoA is not needed for energy it is transformed into:

A

Lipids

83
Q

We have a high level of Acetyl CoA, is PDH on or off?

A

On

84
Q

Low energy charge means we have a lot of ADP or little ADP

A

a lot

85
Q

review slide 81!!!

A
86
Q

Accumulation of NAD means what?

A

we need more energy

drives the reaction (a substrate for PDH)

87
Q

Phophatases can also be stimulated by what ion to increase muscle contraction?

A

Ca2+

88
Q

T/F: Insulin can stimulate fatty acid synthesis by activating phosphatases

A

True

slide 83

89
Q

α-ketogluturate dehydrogenase is Allosterically inhibited by its products,
_________________

A

succinyl CoA and NADH

90
Q

α-ketoglutarate that builds up
from enzyme inhibition can be used
for synthesis of ___________

A

amino acids and purine bases

91
Q

Oxaloactetate is
replenished by ________

A

pyruvate

92
Q

____________ are a source for citric acid cycle
intermediates

A

Branch chain amino acids

slide 89

93
Q

definition: Anaplerotic reactions

A

Using our building blocks to create energy (intermediates)

we have low energy, not enough substrates to create intermediates, ATP production is sustained.

94
Q

Which is faster, anaerobic ATP generation or aerobic ATP generation

A

anaerobic

95
Q

Glycolysis is..

A

Sequence of reactions that metabolizes one molecule of glucose to two molecules of pyruvate and generates the net production of two molecules of ATP

  1. This is an anaerobic process (no O2)
  2. Pyruvate can be completely oxidized under aerobic conditions, generating much more ATP
96
Q

What occurs in the Hexokinase step of glycolysis?

A

Formation of glucose 6-phosphate

Phosphorylation traps glucose in cell

Irreversible step with hexokinase

97
Q

What occurs in the Phosphoglucose

step of glycolysis?

A

Isomerization of glucose 6-phosphate to fructose 6-phosphate (F6P) (from an aldose to a ketose)

**Readily reversible **

Phosphoglucose isomerase used

98
Q

What occurs in the Phosphofructokinase step of glycolysis?

A

1) The “commited step”, reversible up to this point
2) second phosphorylation, formation of formation of fructose 1,6-bisphosphate (F-1,6-BP)

Phosphofructokinase is a key enzyme in the regulation and integration of much of metabolism

99
Q

Stage 2: Aldose step, involves?

A

Cleavage of 6-carbon F-1,6-BP into two 3-carbon phosphate compounds

readily reversible

100
Q

Stage 2: Triose phosphate isomerase step of glycolysis involves?

A

Interconversion of DHAP and G3P

Equilibrium is 96% DHAP and 4% G3P, but metabolism of G3P in remaining steps of glycolysis pulls reaction toward G3P

c. Reaction is reversible

101
Q

Which of the following enzymes catalyzes the committed step in glycolysis?

A. Glucokinase

B. Hexokinase

C. Phosphofructokinase 1

D. Phosphofructokinase 2

E. Pyruvate kinase

A

C. Phosphofructokinase 1

102
Q

•What is the difference between aerobic and anaerobic glycolysis?

A
103
Q

•What is the difference between allosteric and covalent regulation?

A
104
Q

•What is the role of fructose 2,6-bisphosphate in regulating glycolysis?

A
105
Q

•Why is glucose 6-phosphate “trapped” in most cells?

A

it is phosphorylated

106
Q

•What are the “by-pass” reactions of gluconeogenesis?

A
107
Q

•What is the role of the malate shuttle in gluconeogenesis?

A
108
Q

•How is glucose 6-phosphate dephosphorylated?

A
109
Q

•How are glycolysis and gluconeogenesis reciprocally regulated?

A
110
Q

Which of these enzymes is used in gluconeogenesis to by-pass one of the irreversible steps in glycolysis?

A. Glucokinase

B. Glyceraldehyde 3-phosphate dehydrogenase

C. Pyruvate carboxylase

D. Pyruvate kinase

E. Phosphofructokinase 2

A

C. Pyruvate carboxylase

111
Q

What three reactions in glycolysis are irreversible?

A

Hexokinase

Phosphofructokinase

Pyrovate kinase step

112
Q

In the liver, during gluconeogenesis, what enzyme is used instead of hexokinase?

A

Glucose 6-phosphatase

113
Q

In the liver, during gluconeogenesis, what enzyme is used instead of phosphofructokinase?

A

Fructose 1,6-biphosphatase

114
Q

In the liver, during glycolysis, what enzyme is used instead of hexokinase?

A

glucokinase

115
Q

Gluconeogenesis uses all of the following EXCEPT:

A. Lactate

B. Fatty Acids

C. Amino Acids

D. Glycerol

A

B. Fatty Acids

116
Q

Gluconeogenesis converts ______ into ________

A

pyruvate, glucose

117
Q

T/F: Gluconeogenesis is the reversal of glycolysis

A

F.

118
Q

Which 3 steps in gluconeogenesis require ATP/GTP?

A

pyruvate->oxaloacetate

Oxaloacetate-> phosphoenolpyruvate

3-phosphoglycerate-> 1,3-Bisphosphoglucerate

119
Q

About how many ATP does it take to convert 2 pyruvates to 1 glucose molecule?

A

6 ATP (3 for each pyruvate, gluconeogenesis has 3 steps that require ATP input)

120
Q

In gluconeogenesis, Oxaloacetate is transported from the mitochondria to the cytoplasm via:

A

malate shuttle

Oxaloacetate is actually converted to Malate, transferred across the membrane, and then back to Oxaloacetate

121
Q

Where in the liver cell is glucose-6-phosphatase (almost like a membrane protein) located?

A

ER lumen

SO

When you dephosphorlyate G6P in liver cells, this happens in the ER. The glucose is then transported out of the ER.

122
Q

What determines whether gluconeogenesis or glycolysis will be most active?

A

Energy charge (ATP/ADP ratio)

123
Q

When ATP levels are high, would you get glycolysis or gluconeogenesis in the liver?

A

gluconeogenesis

124
Q

What is the shuttle for pyruvate into the liver?

A

Alanine

used when muscle cells metabolize amino acids for fuel and have pyruvate as a by product. This pyruvate is then transported as Alanine to the liver.

125
Q

Fructose 2,6 bisphosphate activates _______ and inhibits _______

A

phosphofructokinase, fuctose 1,6 biphosphatase

126
Q

Glucagon stimulates ____ when blood glucose is rare. This causes an ______ of gluconeogenesis and a _____ of glycolysis

A

Protein kinase A, stimulation, inhibition

127
Q

At high blood glucose levels, High levels of fructose 6-phosphate stimulate ______, which in turn ______ glycolysis and _______ gluconeogenesis.

A

phosphoprotein phosphatase, stimulates, inhibits

128
Q

The Cori cycle, involves what?

A

converting lactate that was produced in skeletal muscle and RBCs back to pyruvate in the liver

129
Q

Glycogen is stored in liver, muscle, and other tissues as _______

A

granules

granules comprised of glycogen and enzymes required for metabolism.

130
Q

Glycogen degradation is also called

A

glycogenolysis

131
Q

Glucose phosphorylase continues to break down glycogen into glucose 1-phosphate until it gets to ___ residues from the branch point.

A

4

132
Q

When is vitamin B6 used as a cofactor?

A

Glycogen phosphorylase step

133
Q

What is the enzyme that transfers glucose from the branch point to the core chain?

A

Transferase

134
Q

what enzyme breaks the branch point, (named for the name of the link)

A

alpha-1,6 glucosidase

135
Q

What enzyme converts glucose 1 phosphate to glucose 6 phosphate?

A

Phosphoglucomutase

136
Q

What does branching of glycogen do?

A

increases solubility, increases rate at which glycogen can be synthesized and degraded.

137
Q

branching enzyme breaks _____ bonds and forms _____ bonds by transfering ____ glucoses

A

Alpha 1,4

Alpha 1,6

7-8

138
Q

The primer of glycogen is formed using glucose residues and what enzyme?

A

glycogenin

139
Q

What enzyme forms alpha 1,4 bonds onto existing glycogen chains

A

glycogen synthase

140
Q

Which enzyme combines UTP and glucose 1-phosphate to form UDP-glucose?

A

UDP-glucose pyrophosphorylase step

141
Q

phosphorylation of glycogen phosphorylase increase or decreases activity?

A

increases activity

142
Q

phosphorylation of glycogen synthase increases or decreases activity?

A

decrease

143
Q

Insulin triggers phorphorylation or dephosphorylation in liver and muscle tissue?

A

dephosphorylation

144
Q

Epinephrine triggers phosphorylation or dephosphorylation?

A

phosphorylation

145
Q

Glucagon triggers _______ in the liver

A

phosphorylation in the liver

146
Q

What is signal transduction?

A

the formation/release of a second messenger in response to binding of hormones (first messenger)

147
Q

cAMP is promoted by:______

cAMP activates:________ which activates __________

A

Epinephrine and glucagon.

Protein kinase A

Phosphorylase kinase and glycogen phosphorylase

EXAMPLE OF BIOCHEMICAL AMPLIFICATION

148
Q

Exercise:

cAMP (increases or decreases)

Protein Kinase A (active/inactive)

Phosphorylase kinase (active/inactive)

glycogen synthase (active -a/inactive - b)

phorphorylase (active-a/inactive b)

A

cAMP: increases

PKA - active

phorphorylase kinase - active

glycogen synthase - inactive

phorphorylase - active

149
Q

Insulin activates ______

A

Phosphoprotein phosphatase 1

which, dephosphorylates

1) glycogen synthase (activates)
2) phosphorylase kinase (deactivting phosphorylase a)
3) glycogen phosphorylase (deactivate)

150
Q

Phosphorylase kinase is activated by what ion in skeletal muscle?

A

Calcium - which breaks down more glycogen to provide a inflow of energy

151
Q

IN THE LIVER, high levels of glucose 6 phosphate activate ______ even when it is phosphorylated

A

glycogen synthase

152
Q

IN MUSCLE, glycogen phorphorylase is activated by ___ and inhibited ATP and G6P

A

AMP

153
Q

Blood glucose levels are maintained primarily through the storage, synthesis, and release of glucose by _______

A

the liver

154
Q

What organ releases both insulin and glucagon?

A

pancreas

155
Q

Which of the following directly activates glycogen phosphorylase?

A. Adenylate cyclase

B. cAMP

C. Protein kinase

D. Phosphorylase kinase

E. Phosphoprotein phosphatase

A

D. Phosphorylase kinase

156
Q

Does insulin or glucagon take part in allosteric regulation?

A

No, signal transduction

157
Q
A