Exam 3 Review Flashcards

1
Q

In what organelle does glycosylation occur?

A

Glycosylation begins in the endoplasmic reticulum and continues in the Golgi apparatus

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2
Q

Which type of glycoproteins are more frequent: O-linked or N-linked?

A

N-linked are more frequent than O-linked

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3
Q

What is the consensus sequence?

A

Asn - X - Ser

where X is any AA except proline

This is the site of carbohydrate attachment to N-linked glycoproteins

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4
Q

Why is the oligosaccaride stem the same in many glycoproteins?

A

They are all generated from the same process in the endoplasmic reticulum

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5
Q

What is erythropoietin (EPO)?

A

A renal hormone that is stimulated by hypoxia

Stimulates red blood cell production (used for blood doping)

Has three major sugar moieties, which, if removed, decrease red blood cell production

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6
Q

In proteoglycans, which part is the functional part?

A

The sugar is the functional part unlike in glycoproteins

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7
Q

Describe the structure of proteoglycans in cartilage

A

proteoglycans bind to a central stem structure

G1 binds to the carbohydrate stem, hyaluronan

Disacharide structures (between G2 and G3) interact with H2O to form a gel like structure

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8
Q

After exiting the ER, where do vesicles transport proteins to?

A

The golgi aparatus

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9
Q

Describe the different components of the Golgi apparatus

A
  • cis* Golgi network (from ER)
  • cis* cisterna

medial cisterna

  • trans* cisterna
  • trans* Golgi network (towards plasma membrane)
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10
Q

What molecule addresses proteins to the lysosome?

A

Mann-6 P

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11
Q

What is the function of glycosyltransferases?

A

They catalyze the formation of glycosidic bonds

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12
Q

What is aglutination?

A

Red blood cells are clumping up

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13
Q

Which blood type is the universal receptor and which is the universal donor?

A

AB positive is the universal receptor

O negative is the universal donor

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14
Q

In A-type blood, what antigens are found?

A

anti-B antigens

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15
Q

What are Lectins?

A

Sugar binding proteins

Usually have a Ca2+ cofactor

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16
Q

What are the membrane glycoproteins associated with influenza virus?

A

Hemagglutinin (H) recognizes carbohydrates on the cell surface; useful for getting in

Neuraminidase (N): cuts glycosydic bonds with RNA release; useful for getting out

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17
Q

What do neuraminidase inhibitors do?

A

They trap the influenza virus within the cell that it infects

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18
Q

Do lipids form polymers?

A

No, lipids do not form polymers, they form together via hydrophobic interactions

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19
Q

What are the biological roles of lipids?

A
  1. Fuel
  2. Building blocks
  3. Thermal insulator
  4. Special tasks
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20
Q

Describe the difference between saturated and unsaturated fatty acids

A

Saturated have no double bonds, unsaturated have one or more double bonds

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21
Q

Describe the general structure of fats

A

fatty acid chains attach to a glycerol molecule

Phospholipids have 2 fatty acid chains and a phophate group attached to a glycerol

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22
Q

On which sides of membranes are glycolipids found?

A

They are only found on the extracellular side of the membrane

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23
Q

What are the functions of glycolipids?

A

Help protect membrane from harsh conditions

Charged glycolipids can influence electric field across membranes and ion concentration

Cell-cell recognition

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24
Q

Which membranes contain cholesterol?

A

All membranes except the inner mitochondrial membrane.

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25
Q

What role does cholesterol play in membranes?

A

It keeps fatty acids apart and prevents crystalization in low temperatures

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26
Q

How does saturation change how membrane lipids pack?

A

Saturated fatty acids are able to pack tighter into solids

Unsaturated fatty acids have lower melting points, are more fluid

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27
Q

What is a sphingosine?

A

An amino alcohol with a long hydrocarbon chain

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28
Q

What are the structural differences between triacylglycerol and sphingophospholipids?

A

The sphingophospholipid comes with a lipid chain as part of the sphingosine molecule

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29
Q

What type of bond is present in phosphoglycerides?

A

An ester bond between the phosphate group and the hydroxyl group of the alcohol

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30
Q

What molecule are glycolipids derived from?

A

Sphingosine

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31
Q

Explain how cholesterol fits into the membrane

A

The hydroxyl interacts with the phospholipid head groups and the nonpolar hydrocarbon tail fits between the lipid hydrocarbon tails

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32
Q

Describe the structure of a micelle

A

The hydrophobic tails all interact forming a sperical molecule with the polar heads all facing out interacting with water.

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33
Q

Describe the structure of a lipid bilayer

A

It has a hydrophobic interior that acts as a permeability barrier

It is formed spontaneusly because of hydrophobic interactions and can develop into cells w/ a large diameter

This conformation is favored over micelle

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34
Q

Which molecules are able to pass through the membrane and which cannot?

A

Small molecules can freely pass through the membrane, but large molecules and ions cannot

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35
Q

What type of amino acids make up transmembrane regions of membrane proteins?

A

Mostly nonpolar amino acid residues

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36
Q

Describe the structure of a pore

A

The outside surface is nonpolar and the inside surface is polar.

They have a hydrophilic channel through the middle, allowing for substrates to pass through

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37
Q

How are integral membrane classified?

A

Type I through VI are distringuished by which end sticks out and in which direction

Type III: one protein with many transmembrane domains

Type IV: many proteins grouped together each with a transmembrane domains

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38
Q

What is Prostaglandin H2 synthase-1?

A

I membrane protein with a hydrophobic channel.

This channel is blocked by aspirin to aleviate headaches

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39
Q

How many amino acid residues does it take for an alpha helix to span the membrane?

A

About 20 amino acid residues will span the membrane

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40
Q

What is a hydrophobicity plot?

A

A plot of the free energy of transfer to water in a shifting window along the primary sequence of a protein.

Peaks with values greater than +84 kJ/mol have a high chance of being part of an alpha helix, and thus in a transmembrane domain

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41
Q

How does the viscosity of the membrane compare to that of H2O?

A

It is ~100x higher

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42
Q

What are the three ways that lipids can move throughout a membrane?

A

They can rotate in place or diffuse laterally

Can also flip-flop (but very rare)

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43
Q

What enzyme catalyzes the flip-flop movement of lipids?

A

flipases

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44
Q

What is the function of a scramblase enzyme?

A

They allow the bilayer to grow evenly by translocating lipids from the inner membrane to the outer membrane (or vice versa)

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45
Q

What factors increase membrane fluidity?

A

More cis double bonds

Shorter hydrocarbon chains

Less cholesterol

Higher temperature

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46
Q

How does cholesterol help with temperature regulation?

A

The amount of cholesterol in the membrane changes to help deal with temperature changes

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47
Q

How do charged ions usually get through the membrane?

A

Through channels or transporters

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48
Q

Describe the relative concentrations of Na+ and K+ inside and outside of the cell

A

The ICF has low Na+ and high K+ compared to the ECF

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49
Q

Describe the electrochemical gradient

A

The difference in the concentration of the solute between the two sides of the membrane

The charge or valence of the solute molecule

The difference in voltage between the two sides of the membrane

**Membrane potential can be opposite direction of chemical gradient.

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50
Q

What is the equation for diffusion of ions across the cell membrane?

A

ΔG = RT ln(c2/c1) + zFΔV

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51
Q

How are primary and secondary active transport related?

A

Secondary active transport requires gradients created by primary active transporters

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52
Q

What are the three types of ATP pumps?

A

P-type

F-type

ABC transporter

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53
Q

What is a P-type ATP pump?

A

The actual protein is phosphorylated

Couples free energy of ATP hydrolyses to an interconversion between two conformations, allowing a substrate to pass through

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54
Q

What is an F-type proton pump?

A

The pump is phosphorylated, but it uses ATP

ex: in lysosomes

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55
Q

What is an ABC transporter?

A

ABC = ATP binding casettes

Plays an important role in resistance to antibiotics

When cells are exposed to a drug, these pumps remove the drug out before the drug can exert its effect

56
Q

What type of pump is the Ca2+ pump in the sacroplasmic reticulum?

A

A P-type pump

The conformational change creates/destroys the binding site

57
Q

What are E1 and E2 of the sarcoplasmic Ca2+ pump ?

A

They are the two distinct enzyme conformations (Eversion States)

58
Q

What is the effect of digitalis?

A

It inhibits the Na+/K+ pump by preventing dephosphorylation

59
Q

Describe the mechanism for ABC Transporters

A

1) No ATP or substrate bound
2) Substrate enters central cavity which causes a conformational change that increases ATP affinity
3) ATP binds to ABCs
4) Conformational change
5) Hydrolysis of ATP resets the protein

60
Q

What is the major difference in tertiary structure between the Na channel and the K channel?

A

The Na channel is made up of 4 repetitive domains all from the same protein whereas the K channel is a homotetramer made from 4 identical proteins

61
Q

Why isn’t Na able to pass through the K channel?

A

The channel maximizes its interactions with the K+ ion. Because the Na+ ion has a smaller ionic radius, it is not large enough to be properly stabilized, so it cannot pass through.

62
Q

Explain how the K+ ions pass through the K+ channel

A

They enter the vestibule and align into ‘single file’

Repulsion between individual ions push them through the channel and out the other side.

63
Q

Explain how the voltage gated potassium channel works

A

The S4 region acts like a valve, turning to open the channel when it is depolarized

Important for propagation of action potentials

64
Q

What is the ball-and-chain model?

A

Explains the inactivation of the K+ channel

There is an inactivation domain that acts as a stopper. It is rapidly pulled up into the channel to block it once the channel is open.

Three distinct phases of channel: closed, open, inactivated

65
Q

What are the differences between gap junctions and other membrane channels?

A

They traverse two membranes rather than one

They connect cytoplasm to cytoplasm, instead of to ECF or lumen of an organelle

The connexons forming them are synthesized by different cells

66
Q

What are the two general types of pathways involved with metabolism?

A

Catabolic pathways (breakdown of food)

Anabolic pathways (building new molecules)

67
Q

What is the only ATP producing pathway that can occur in the absesnce of O2?

A

Glycolysis

68
Q

What cells in the body rely exclusively on glycolysis for energy?

A

Red blood cells and neurons

69
Q

What are Coupling Reactions?

A

Using ATP to drive anabolic reactions that are energetically unfavorable

The overall free energy change for a chemically coupled series of reactions is equal to the sum of the free energy changes of the individual steps.

70
Q

Fill in the blank:

_______ drives ________ in a process we call metabolism

A

Catabolism drives anabolism in the process we call metabolism

71
Q

What factors cause the high transfer potential of ATP?

A

Resonance stabilization

Electrostatic repulsion

Stabilization due to hydration

72
Q

What energy charge is maintained throughout the body?

A

About 0.8-0.9

73
Q

Is ATP hydrolysis exergonic or endergonic?

A

Exergonic

74
Q

What is the importance of a combined intermediate?

A

It physically connects the 2 reactions, allowing for the reaction to occur using energy of hydrolysis (for example)

75
Q

Is substrate level phosphorylation dependent on oxygen levels?

A

No. It is independent of O2

76
Q

Why is it important that ATP have a intermediate phosphoryl transfer potential?

A

It enables ATP to function efficiently as a carrier of phosphoryl groups.

Allows ADP to be phosphorylated by other groups with higher phosphoryl transfer potential to form ATP

77
Q

When ATP reacts with hexokinase, is ATP hydrolyzed?

A

No. In many metabolic reactions, ATP is not hydrolyzed because it reacts with enzymes that prevent H2O from entering the active site.

This allows the energy to be used for coupled reactions

78
Q

What are the 2 ways that ATP can be formed?

A

Substrate level phosphorylation

Oxidative phosphorylation

79
Q

What percent of the ATP is produced by oxidative phosphorylation?

A

90%

80
Q

Describe the sources of ATP during exercise.

A

Available ATP is immediately used up

Then Creatine phosphate can combine with ADP to make useable ATP

Anaerobic metabolism begins to produce ATP after minutes, and aerobic metabolism begins after ~1 hour

81
Q

Describe the mechanism of Glyceraldehyde 3-phosphate dehydrogenase

A

A thioester bond is formed between glyceraldehyde 3-phosphate and the active site of the enzyme.

NAD+ is protonated to NADH during the formation of the thioester bond.

The molecule is then phosphorylated by an inorganic phosphate, crerating 1,3 BPG

82
Q

What are the three types of activated carriers of electrons?

A
  1. Activated carriers of electrons for fuel (NAD+, FAD)
  2. Activated carriers of electrons for reductive biosynthesis (NADPH)
  3. Activated carrier of two carbon fragments (AcetylCoA)
83
Q

What is the significance of adding a second phosphoryl group to G3P in glycolysis?

A

The product, 1,3 BPG has a very high transfer potential, which allows it to donate a phosphoryl group to ADP to produce ATP in the next step.

84
Q

Describe the pH in the mitochondria, and its significance for ATP generation.

A

There is a higher pH in the matrix, which means that there is a proton gradient. This gradient is used in order to form ATP molecules in the mitochondria.

85
Q

Does regulation occur by modifying the reactants, the enzymes, or the products in the glycolysis pathway?

A

Pathways are regulated by controlling the enzyme activities

86
Q

What type of pathway can NAD+ be found in? What about NADP?

A

NAD+ is found in catabolic pathways

NADP is found in anabolic pathways

87
Q

What type of high energy bond is found in Acetyl CoA?

A

A high energy thioester bond is found in Acetyl CoA

88
Q

How are most activated carriers produced in the body?

A

They cannot be synthesized, and therefore must be ingested through vitamins

89
Q

What are the 6 types of chemical reactions that occur in metabolism?

A
  1. Oxidation-reduction
  2. Ligation requiring ATP cleavage
  3. Isomerization
  4. Group transfer
  5. Hydrolytic
  6. Addition or removal of functional groups
90
Q

How are metabolic processes regulated?

A
  1. Controlling the amount of enzyme (transcriptional regulation)
  2. Controlling catalytic activity (allosteric regulation, feedback, covalent modifications)
  3. Controlling accessibility of substrates (Compartmentalization)
91
Q

What quantity regulates every pathway in the cells?

A

The energy charge

= (ATP + 1/2 ADP)/ (ATP +ADP + AMP)

92
Q

What is phosphorylation potential?

A

Phosphorylation potential of the mitochondria is the free energy storage available from ATP

= [ATP] / ([ADP] + [Pi])

93
Q

How is AMP produced ?

A

2 ADP molecules can combine to form 1 ATP and 1 AMP

94
Q

As the energy charge increases, what happens to the relative rates of the ATP generating pathway and the ATP utilizing pathway?

A

As Energy charge moves from 0 to 1:

ATP generating pathway slows down

ATP utilizing pathway speeds up

95
Q

Describe the general process of Glycolysis

A

Glucose (a 6 C ring) is broken down into 2 molecules of pyruvate (a 3-C compound)

Energy must be put in in order to break apart the stable glucose ring

96
Q

What is stage 1 of glycolysis?

A

The investment phase: glucose is trapped in the cell and is formed into a compound that can readily be cleaved into phosphorylated 3-C units

No ATP is generated

97
Q

What is stage 2 of glycolysis?

A

Numerous small molecules are degraded to a few simple units that play a central role in metabolism

98
Q

What is stage 3 of glycolysis?

A

ATP produced from complete oxidation of acetyl CoA (TCA cycle and oxidative phosphorylation)

99
Q

What enzyme catalyzes the first reaction of glycolysis?

A

Hexokinase

Phosphorylates Glucose to Glucose-6-Phosphate

100
Q

Describe the conformational change of hexokinase

A

When glucose binds to the enzyme, the environment around glucose becomes more nonpolar, which favors the reaction between the hydrophilic hydroxyl group of glucose and the terminal phosphoryl group of ATP.

The conformational change enables the kinase to discriminate agains H2O as a substrate.

101
Q

What cofactor is needed for hexokinase activity?

A

Mg2+ (or Mn2+)

102
Q

Describe the glycolytic reaction that converts an aldose into a ketose

A

Phosphoglucose Isomerase catalyzes the conversion of G6P into F6P

The glucose ring is broken open, the groups are moved, and then the ring is closed into a 5 membered fructose ring.

103
Q

What is the key enzyme or pacemaker of glycolysis? What does it do?

A

Phosphofructokinase (PFK)

It uses ATP to phosphorylate F-6P to F-1,6-BP

104
Q

What is the significance of breaking a 6C unit into 2 3C units?

A

This step allows for all downstream steps to happen two times simultaneously (in parallel)

Aldolase creates DHAP and GAP, and then DHAP is converted into GAP, resulting in 2GAP molecules

105
Q

What enzyme converts DHAP into GAP?

A

Triose phoosphate isomerase

106
Q

What 2 amino acids are found in the active site of triose phosphate isomerase?

A

Glutamate (H+ donor)

Histidine (Base)

107
Q

What is the only oxidation reaction that occurs in glycolysis?

A

Glyceraldehyde 3-phosphate dehydrogenase catalyzes the oxidation reaction from GAP to 1,3 BPG

2 processes:

Oxidation of aldehyde to carboxylic acid by NAD+

Joining of carboxylic acid and orthophosphate

108
Q

What glycolytic enzyme has a peroxidative cysteine in the active site?

A

Glyceraldehyde 3-phosphate dehydrogenase

The cysteine forms a thioester intermediate

109
Q

What molecule is the limiting factor for the reactoin catalyzed by glyceraldehyde 3 phosphate dehydrogenase?

A

The availability of NAD+ limits this reaction

Electrons must be siphoned off for reaction to occur

110
Q

What is unique about the enzyme phophoglycerate mutase?

A

A different phosphate molecule is on the enzyme after each reaction occurs

111
Q

Explain why phosphoenolpyruvate (PEP) has a large phosphoryl transfer potential

A

There is a large driving force for the subsequent enol-ketone conversion of pyruvate

The enol form of pyruvate is energetically unstable, but the ketone form is stable

112
Q

What are the possible fates of pyruvate?

A

1) Ethanol: alcoholic fermentation
2) Lactate: lactic acid fermentation
3) TCA cycle: aerobic respiration ending with electron transport chain

113
Q

How many molecules of pyruvate are formed from each glucose molecule?

A

2 pyruvate for each glucose

114
Q

Why is hexokinase not a major enzyme for regulation of glycolysis?

A

It is involved in too many other bodily functions to regulate, so we regulate glycolysis using PFK

115
Q

Is ATP a substrate or a regulator of PFK?

A

BOTH

ATP binds to 2 different sites on PFK: the active site and the regulatory site

116
Q

Does PFK show a sigmoidal reaction kinetic curve?

A

Yes. At low [ATP] it appears nearly hyperbolic, but at high [ATP] the sigmoidal shape is apparent

117
Q

What is the primary control of glycolysis in the muscles?

A

The energy charge

PFK activity increases when the ATP/AMP ratio is lowered

118
Q

Describe the role of negative feedback in glycolysis in relaxed muscle fibers

A

If G6P accumulates, hexokinase is inhibited, lowering the rate of G6P production

High energy charge (high ATP/AMP) will downregulate the action of PFK and Pyruvate kinase in order to prevent accumulation of toxic intermediates

119
Q

What molecule activates PFK in the liver?

A

Fructose 2,6-biphosphate activates PFK in the liver

120
Q

What effect does citrate have on PFK function?

A

citrate inhibits the action of PFK

121
Q

What is unique about PFK-2?

A

PFK-2 is both a kinase and a phosphatase

If it is phophorylated, it acts as a phosphatase

If it is dephosphorylated, it acts as a kinase

122
Q

What is the last enzyme in the glycolytic pathway?

A

Pyruvate kinase converts phosphoenolpyruvate into pyruvate

123
Q

Many of the glycolytic steps have ΔGo close to zero. Why is this relevant?

A

These are the steps that can occur in either direction based on concentrations of products and reactants, and are therefore involved in both glycolysis and gluconeogenesis

124
Q

What is the general conversion that takes place in gluconeogenesis?

A

Pyruvate is converted into Glucose

125
Q

What are the major noncarbohydrate precursors of gluconeogenesis?

A

Lactate, amino acids, and glycerol

126
Q

What is the purpose of gluconeogenesis?

A

It maintains the glucose level in the blood so that the brain and muscle can extract sufficient glucose from it to meet their metabolic demands

127
Q

What organs does gluconeogenesis take place in?

A

The liver and the kidney

128
Q

How many steps are in glycolysis? What about gluconeogenesis?

A

Glycolysis has 10

Gluconeogenesis has 11

129
Q

Which steps differ between glycolysis and gluconeogenesis?

A

The irreversible steps (1, 3, and 10) of glycolysis are different in gluconeogenesis

Phosphatases perform reverse role of kinases

The pyruvate to PEP step is 2 reactions in gluconeogenesis, catalyzed by Pyruvate Carboxylase and then PEP carboxykinase

130
Q

In gluconeogenesis, what molecule is pyruvate first converted into before it is converted to PEP?

A

Oxaloacetate is formed in the mitochondrial matrix

131
Q

How does oxaloacetate exit the mitochondria?

A

It is reduced to malate by the oxidation of NADH. Upon exiting the mitochondria, it is oxidized back to oxaloacetate before the next step of gluconeogenesis

132
Q

Describe reciprocal regulation of glycolysis and gluconeogenesis

A

Both pathways are not active at the same time in the same cells.

They are regulated in order to prevent the accumulation of toxic intermediates.

133
Q

If glucose concentrations are high, what hormone responds?

A

Insulin acts via cAMP to increase the rate of glycolysis

134
Q

What hormone has the opposite effect on metabolism as insulin?

A

Glucagon

135
Q

What is the cori cycle?

A

In contracting skeletal muscle, the formation and release of lactate lets the muscle generate ATP in the absence of oxygen and shifts the burden of metabolizing lactate from muscle to other organs

lactate produced by anaerobic glycolysis in the muscles moves to the liver and is converted to glucose, which then returns to the muscles and is converted back to lactate

136
Q

What molecule does the Alanine cycle function to get rid of?

A

The alanine cycle gets rid of NH2 by excreting urea