Download Integration of Metabolism

FUNDAMENTALS I 10:00-11:00
FRIDAY, SEPTEMBER 3, 2010
PRITCHARD
I.
INTEGRATION OF METABOLISM
Scribe: LOUISA WARREN
Proof: LAUREN MORRIS
Page 1 of 7
Integration of Metabolism [S1]:
a. What to study for the exam:
i. Look for the major message on each slide
ii. For example, learn which enzymes are allosterically regulated, what the small effector molecules are (ATP,
glucose, etc.), enzymes involved in these pathways, effect of high and low glucose on various pathways
iii. Won’t have to draw structures, identify structures, or know historical facts
b. Today: Integration of Metabolism
c. Metabolic pathways separated for teaching, but these different pathways are all going on at the same time
d. All of them involve ATP, but there is only one pool of ATP
i. So if one thing causes ATP to go up, it will affect all of the different pathways
e. This is a metabolic chart that looks complicated, but you know most of it
i. (Top yellow) glycolysis, (circular yellow) the citric acid cycle, (bottom yellow) electron transport chain
II. Integration of Metabolism [S2]
a. Sugar Metabolism, Amino Acid Metabolism, Lipid Metabolism shown on slide
b. Dentist story- final exam was to reproduce this chart from memory, we won’t have to do that
c. All of these different compounds are converted to nearby compounds by enzymes
III. Integration of Metabolism (dot and line figure) [S3]
a. Each dot represents a compound or an intermediate
b. Each line involves an enzyme converting a compound
c. The glycolysis pathway is the central pathway connecting all of these other pathways
i. Shows breaking glucose down to pyruvate, Acetyl CoA, citric acid cycle
d. Notice that the dots are just intermediates on the way to making something or breaking it down
i. Most are just connected by 2 different lines
ii. But some like pyruvate are connected to a dozen different places, and these are key compounds
IV. Integration of Metabolism (Table 14.1) [S4]
a. Most dots have 1 or 2 lines
i. If it has one line, it is the starting material or an end product
ii. Anything connected by two lines is just an intermediate on the way to making something else
b. The real key points are these compounds that are connected to multiple things
i. They are highly regulated to determine what is being made and what is being broken down
V. Enzymes in Cytosol or Membrane and Multienzyme Complexes [S5]
a. Many of the reactions we have been talking about occur in the cytosol
b. Some of these enzymes are just soluble enzymes with soluble substrates that are converted to an
intermediate to get to the final product
c. In other cases, enzymes are associated with each other in big multienzyme complexes (ex: pyruvate
dehydrogenase)
i. Sometimes present in the cytosol, sometimes in the membrane
VI. Catabolism and Anabolism [S6]
a. Metabolism involves making things or breaking them down
i. Catabolism is breaking things down
ii. Anabolism is making things
b. Anabolism and Catabolism are linked, basically through ATP and NADPH
i. When you break things down like carbohydrates, fats, and proteins, the final end products are water,
carbon dioxide and ammonia
ii. You make ATP and reducing equivalents in the form of NADPH, and these are used in the making of other
things
VII. 3 Stages of Catabolism [S7]
a. Proteins are broken down to amino acids, carbohydrates are broken down to glucose, lipids are broken down
to fatty acids and glycerol
b. Then all these breakdown products are converted to pyruvate and/or Acetyl CoA in the second stage
(glycolysis)
c. Acetyl CoA is run through the citric acid cycle to make CO2 and water
d. So all of these pathways have something in common- they all make Acetyl CoA and get energy out of it in the
citric acid cycle followed by oxidative phosphorylation
VIII. Metabolism [S8]
a. These pathways are enormously conserved, especially in glycolysis
i. Same thing in bacteria, humans, plants, mushrooms, etc
b. Enzymes that catalyze these reactions have very similar, sometimes identical sequences
FUNDAMENTALS I 10:00-11:00
Scribe: LOUISA WARREN
FRIDAY, SEPTEMBER 3, 2010
Proof: LAUREN MORRIS
PRITCHARD
INTEGRATION OF METABOLISM
Page 2 of 7
c. Catabolism involves oxidations while anabolism involves reductions, and they occur simultaneously
d. You may be breaking down glucose and making fat at the same time
e. You will not be breaking down glucose and making glucose at the same time because of regulatory
mechanisms
IX. Metabolism [S9]
a. An important key concept: pathways can often go one direction or the other, and they will be regulated
b. There has to be one step in the pathway that is different to be regulated (to make something or break
something down)
c. A hydride ion is Hi. You don’t actually get these in solution
ii. In the oxidation reaction, NAD+ is converted to NADH
1. You haven’t just added a hydrogen, but a hydrogen plus an electron (a hydride ion)
2. These are hydride ion transfers
X. NAD+ and NADP+ [S10]
a. Remember deficiency disease you get if you don’t have plenty of niacin
b. In the form of NAD+, niacin looks like (pink box) with an aromatic ring
c. When it is reduced, there is no longer a positive charge or aromatic ring but just had two double bonds (blue)
XI. Alcohol Dehydrogenase Reaction [S11]
a. When you drink alcohol, your body oxidizes it to Acetyl CoA which can be used in the citric acid cycle
b. What do you think happens to how fast you break down alcohol you have ingested depending on whether you
exercise or not?
i. Krebs gave a talk about giving people alcohol and measuring how fast they metabolize it with some on a
treadmill
ii. If you exercise vigorously, you don’t get rid of alcohol faster
XII. How would exercise affect breakdown of ingested alcohol? [S12]
a. The reason is because when you vigorously exercise, you use up your NAD+ because you are converting the
pyruvate from glycolysis into lactic acid
b. You need the NAD+ to oxidize the alcohol, so don’t try to work off alcohol
XIII. Activation of one mode accompanied by reciprocal inhibition of the other mode [S13]
a. In a pathway that can go both ways, the step that will be regulated is always the first committed step
i. It will be positively regulated
ii. There will almost always be inhibition of the opposing pathway
b. Seen in many pathways
XIV.
10 Main Building Blocks in Anabolism [S14]
a. Almost everything we make in biosynthesis is made from 10 common starting materials
b. Sugar phosphates, Keto acids, Acetyl CoA, and phosphoenolpyruvate
c. There are a few exceptions, but these are key compounds
XV. ATP has 2 metabolic roles [S15]
a. ATP has multiple roles
b. One role is to push reactions uphill
i. Can make things that are thermodynamically unfavorable to make
ii. By coupling the cleavage of ATP, you can make things that require a lot of energy
c. ATP is also a major allosteric effector molecule that can inhibit some reactions and activate others
d. We are making ATP all the time, and we make a lot of ATP because we make it and break it constantly
i. The average sedentary adult makes 200 lbs ATP/ day
ii. If you were a long-distance cyclist like Lance Armstrong, you would make a ton of ATP a day to use for
muscle contraction
XVI.
Allosteric Regulation of Enzyme Activity[S16]
a. Enzymes that are allosterically regulated behave like this (pink)
b. As you increase the substrate concentration, instead of getting the hyperbolic increase that levels out, you get
the S-shaped/ sigmoid curve that is characteristic of allosteric enzymes
XVII. Allosteric Regulation of Enzyme Activity [S17]
a. An allosteric enzyme almost always has 2 or more subunits- they are not monomers
b. Allosteric activators bind to the site that is distinct from active site- it may activate or inhibit the enzyme
c. Example that I gave you before:
i. Normally, Phosphorylase a in the liver is active, and it breaks down glycogen to make glucose
ii. When glucose levels in the blood go up, the glucose will bind to and inhibit this enzyme, causing it to
change from the relaxed state to the tense state, which is inactive
XVIII. Which pathway will be regulated [S18]
FUNDAMENTALS I 10:00-11:00
Scribe: LOUISA WARREN
FRIDAY, SEPTEMBER 3, 2010
Proof: LAUREN MORRIS
PRITCHARD
INTEGRATION OF METABOLISM
Page 3 of 7
a. Suppose a hypothetical pathway here- what step do you think would be regulated?
b. Suppose body needed E but no more H or I
i. You wouldn’t want to regulate the A to B step- say you downregulated it to get little conversion to B, you
wouldn’t get any E
c. You want to inhibit the first committed step to making a product
d. Not all possible answers are shown here
XIX.
Which pathway will be regulated [S19]
a. The answer is B to C
b. If you inhibited B to F, you would get less H and less I- this wouldn’t make since if you wanted more I
c. Remember: you want to regulate the first committed step in a pathway
d. (Question at the end)
i. There may be a situation where you want to make more E but not H or I
1. You wouldn’t want to downregulate A to B because then you wouldn’t make any B, E, H or I
2. If you upregulated B to C, you would make more E but also more H and I
3. If you downregulated B to C, you would make less E
ii. You wouldn’t want to regulate B to F because that would prevent H and I even if you wanted more H but
not I
iii. You can look at pathways and predict which step will be regulated
1. In glycolysis, it is the conversion of G-6-P to G-1,6-BP with PFK
2. You wouldn’t want to regulate glucose to G-6-P because G-6-P is involved in so many different
pathways
iv. You regulate the first step that is committed to a certain final product
XX. Covalent Regulation of Enzyme Activity [S20]
a. There are regulatory cascades where a tiny amount of hormone, through various steps of amplification, can
lead to an enormous final result
i. You can activate formation of grams and grams of glucose (from breakdown of glycogen) with nanograms
of hormone
XXI.
Covalent Regulation of Enzyme Activity [S21]
a. Some of these steps are examples of regulatory mechanisms such as the activation of Protein Kinase A
XXII. Blank [S22]
XXIII. Modulator Proteins [S23]
a. Protein Kinase A is an example of a modulator protein
b. Normally, this enzyme has two catalytic sites bound to two regulatory sites
c. High levels of cAMP cause cAMP to bind to regulatory subunits with
i. 2 molecules of cAMP per subunit
ii. catalytic subunits dissociate and become active Protein Kinase A
XXIV. Hormonal Activation of Transcription [S24]
a. skipped
XXV. Control Sites of Major Metabolic Pathways [S25]
a. These are some metabolic pathways you’ve learned, now we will try to tie everything together
b. For the exam, learn where these different pathways take place
i. Glycolysis happens in the cytosol, -oxidation of fatty acids in the mitochondria, citric acid cycle in the
mitochondria, gluconeogenesis first step in the mitochondria and the rest in the cytosol- *typical exam
questions
XXVI. Glycolysis [S26]
a. The primary key step in glycolysis is the phosphofructokinase reaction where you turn fructose-6-phosphate
into fructose-1,6-bisphosphate
b. That step is allosterically activated by AMP and the regulatory molecule fructose-2,6-bisphosphate
c. When glucose levels are low
i. This regulatory molecule (F-2,6-BP) will be low
ii. You don’t want to break down glucose in glycolysis, so this step is not activated because F-2,6-BP is
absent
d. When glucose levels are high, you might as well use it
i. Break it down or store as glycogen
ii. This (F-2,6BP) regulatory molecule is high, and it activates this reaction to speed up glycolysis
iii. That is allosteric activation
XXVII. Gluconeogenesis [S27]
a. Occurs in liver and kidneys
b. First step occurs in the mitochondria, other steps in the cytosol
FUNDAMENTALS I 10:00-11:00
Scribe: LOUISA WARREN
FRIDAY, SEPTEMBER 3, 2010
Proof: LAUREN MORRIS
PRITCHARD
INTEGRATION OF METABOLISM
Page 4 of 7
c. With low glucose, you have low F-2,6-BP and the reverse when glucose is high
d. Study this diagram, all of these will make sense
XXVIII. Gluconeogenesis and Glycolysis [S28]
a. For example, if ATP is low you need to make more ATP, so it is important to activate glycolysis
i. When ATP is low, AMP will be high
ii. So AMP activates glycolysis (+ sign), which leads to making more ATP
b. You can sit and rationalize all of these things without memorizing
XXIX. Citric Acid Cycle [S29]
a. The citric acid cycle results in making a lot of ATP, especially when the two reducing compounds (NADH and
FADH2) go through the electron transport chain and oxidative phosphorylation
b. There is something called respiratory control
i. In order for the citric acid cycle to continue, you have to regenerate NAD and FAD in the mitochondria
ii. If you have enough ATP, the mitochondria won’t be making more, so NADH and FADH2 build up, and the
citric acid cycle, which needs the oxidized forms, really slows down
XXX. Pentose Phosphate Pathway [S30]
a. Takes place in the cytosol
b. First committed step is the oxidation of Glucose-6-phosphate
c. That is activated when NADP+ is high (remember pentose phosphate pathway makes NADPH)
i. When NADPH is low, NADP+ will be high
ii. That activates the first step
XXXI. Glycogen Synthesis and Degradation [S31]
a. Regulated at a couple of different levels
b. Hormonal regulation happens through reversible phosphorylation
i. Phosphorylation activates phosphorylase, the key molecule in breaking down glycogen
ii. Phosphorylation inactivates synthase
c. Allosteric regulation occurs on top of hormonal regulation
i. AMP activates muscle but not liver phosphorylase
ii. High glucose levels inactivate liver phosphorylase
XXXII. Fatty Acid Synthesis [S32]
a. First step occurs in cytosol and is the conversion of Acetyl CoA to Malonyl CoA
b. Inhibited by palmitoyl CoA, the end product of fatty acid biosynthesis (if you have a lot of it, don’t need to
make more)
c. It is almost always the first committed step that is regulated
XXXIII. Fatty Acid Degradation [S33]
a. Breakdown of fatty acids is -oxidation, which takes place in the mitochondria
b. In order to get the fatty acids in, the carrier molecule carnitine is acylated
i. Acyl carnitine is transported into the mitochondria
ii. Acylation inhibited by malonyl CoA (the first product of making fatty acids)
1. Malonyl CoA first product of making fatty acids
2. If you are making fatty acid, you don’t want to simultaneously break down, so inhibition makes sense
XXXIV. Camels [S34]
a. Camels go a long time without drinking water
b. They don’t carry water in their humps- they carry fat
c. Much better to carry fat than water because you can convert 4 gallons of fat to 26 gallons of water
i. Because water weighs 7x more than fat
ii. The extra mass comes from the air
iii. The fat supplies the hydrogen, and the oxygen comes from the air
XXXV. Table 23.2 [S35]
a. By breaking down fat, you make a lot of water
b. From the full breakdown of one fat molecule (palmitoyl CoA) you get 123 molecules water
XXXVI. Killer Whale [S36]
a. Killer whale does the same thing- doesn’t drink sea water, makes water needed for metabolism from breaking
down fat from seals he ate
XXXVII. Key Junctions [S37]
a. Metabolic map again with key points circled: Glycose-6-phosphate, pyruvate, and acetyl CoA
XXXVIII.
Glucose-6-Phosphate Pathways [S38]
a. Glucose can go in a lot of different directions
b. Glucose goes into a cell and gets phosphorylated to G-6-P
FUNDAMENTALS I 10:00-11:00
Scribe: LOUISA WARREN
FRIDAY, SEPTEMBER 3, 2010
Proof: LAUREN MORRIS
PRITCHARD
INTEGRATION OF METABOLISM
Page 5 of 7
c. If a lot of ATP present, G-6-P converted to glycogen (after converting G-6-P to G-1-P with
phosphoglucomutase)
d. If ATP low, run G-6-P through glycolysis to make pyruvate, which makes ATP
e. If the cell needs NADPH or pentose phosphates for making DNA and RNA, the pentose phosphate pathway
will be used and G-6-P will be oxidized to 6-phosphogluconate
f. So what happens in the cell depends on what the cell needs
XXXIX. Pyruvate and Acetyl CoA [S39]
a. This illustrates the same thing
XL. Fuel Storage [S40]
a. The major fuel storage for animals and people is fat, stored in adipose tissues
b. We store far more fat than carbohydrate (we store some carbohydrate as glycogen)
c. Protein not considered a fuel storage, but it can be used if we are starving
d. So the order of breakdown is glycogen first- fat takes longer because it needs oxygen, and protein only
breaks down if you absolutely need it
e. The brain and kidneys need a lot of glucose
i. You can’t form glucose from fat
ii. If there is no glucose in your diet, you have to break down your muscle to amino acids, which can be
broken down into compounds and converted to sugar in gluconeogenesis
XLI.
Table 30.3 Fuel Sources for Muscle Contraction [S41]
a. The purpose of this slide is to give you a feel for how much energy you can get from different things
b. There is a certain amount of ATP in your muscles right now- gives you 223 mmol
c. Creatine phosphate can very rapidly regenerate ATP, and you get twice as much energy (446)
i. Takes a little longer, but still fast
d. Anaerobic glycolysis converting muscle glycogen to lactic acid is slower, but you can get a lot of energy out of
it
e. If you aerobically convert glycogen all the way to CO2 you can get loads of energy
f. But nothing compared to the amount of energy you can get from breaking down fat
i. Fat is a high density fuel storage depot, but it is slower
XLII.
Fuel Use During Exercise [S42]
a. How fast somebody can run basically ends up depending on how much ATP they can make because ATP is
essential for muscle contraction
b. A 100m sprint takes about 10s and is powered mainly by ATP stored in the muscle, creatine phosphate, and
some anaerobic glycolysis
c. A whole kilometer takes longer, you can’t run as fast, and you rapidly deplete creatine phosphate
i. Anaerobic glycolysis starts becoming a problem because you start building up lactic acid
ii. You will get some ATP from oxidative phosphorylation, but you can’t get it as fast, so you can’t run as fast
XLIII. Running a Marathon [S43]
a. Running a marathon takes a long time and totally depletes your body of glycogen supply
i. The body is constantly trying to make glycogen during that time, but it is depleted
b. Marathon runners get their energy by consuming about equal amounts of fatty acids and glycogen
XLIV. Contribution of Various Energy Sources During Mild Exercise [S44]
a. This illustrates the contribution of different energy sources during exercise (schematic)
b. ATP that is there originally is rapidly reduced
c. You are making more ATP from these other processes
i. Phosphocreatine regenerates ATP so you get energy from that
ii. Anaerobic metabolism allows you to last longer
iii. Aerobic metabolism can go on for a long time
1. With prolonged exercise, aerobic metabolism primarily contributes to ATP energy
XLV. Brain [S45]
a. Uses a lot of glucose and oxidizes it with a lot of oxygen
i. It is only 2% of body mass, but it uses 20% of the oxygen that the body normally uses (muscles use more if
you are rigorously exercising)
b. Brain uses so much oxygen to maintain electric potentials of the neurons, which requires a lot of ATP
c. Normal fuel is glucose, but the brain can use ketone bodies
i. Ketone bodies (a stupid name) - acetone, -hydroxy-butyrate, and acetoacetate
1. Don’t know why “bodies”, and -hydroxy-butyrate is not a ketone
2. Small molecules that can pass the blood-brain barrier
a. Muscles can use fatty acids, but fatty acids are carried on albumin
b. Albumin a large molecule and can’t pass the blood brain barrier
FUNDAMENTALS I 10:00-11:00
Scribe: LOUISA WARREN
FRIDAY, SEPTEMBER 3, 2010
Proof: LAUREN MORRIS
PRITCHARD
INTEGRATION OF METABOLISM
Page 6 of 7
XLVI. Muscle [S46]
a. Resting muscles use fatty acids, but they can also use glucose and ketone bodies
b. Phosphocreatine gives you enough energy to replenish ATP for about 4 seconds (so doesn’t last very long)
XLVII. Cori Cycle [S47]
a. Anaerobic glycolysis occurring in vigorous exercise can result in lactic acid
b. Lactate in the blood supply flows through the bloodstream to the liver, the liver reconverts it to pyruvate and
then converts it to glucose through gluconeogenesis
c. Glucose returns to the blood and travels back to the muscle, this cycle is called the Cori cycle
d. In addition to converting the pyruvate to lactate, it can also make alanine if it is transaminated, and that
alanine can pass through the same cycle to the liver and back to the muscle
XLVIII. Phosphocreatine Serves as a Reservoir of ATP-Synthesizing Potential [S48]
a. Phosphocreatine is an interesting small molecule- some athletes take creatine supplements
b. Creatine levels actually do go up when you take these
i. This is very strange because concentration of most compounds is tightly regulated
ii. They only last about 4 seconds, so it depends what sort of athlete you are
1. Helpful for weightlifters (a few seconds of intense exertion)
2. Doesn’t help a soccer player (rapidly depleted)
XLIX. Heart [S49]
a. The heart is completely aerobic- anaerobic glycolysis is not carried out in the heart
b. A lot of mitochondria in the heart
c. Mitochondria carry out the citric acid cycle with Acetyl CoA from glycolysis
d. There are low levels of glycogen and hardly any phosphocreatine in the heart
e. But the heart can also use glucose and ketone bodies if it needs to
L. Adipose Tissue [S50]
a. Fat/ fatty tissue/ adipose tissue
b. Some people store a large amount of fat, which can last a long time as energy storage
c. Free fatty acid is made in the liver and binds to albumin to travel to the cell (storage depots for fat)
LI. Adipose Cell [S51]
a. Fatty acids made in the liver and transported
LII. Kidneys [S52]
a. Major function is to make urine by filtering out most of the molecules in blood and reabsorbing what is needed
b. Reabsorption requires ATP, so kidneys use a lot of ATP
c. Kidneys only about 0.5% of the mass but use 10% of the oxygen
LIII. Liver [S53]
a. A key organ because it makes the fuel for almost all other organs
b. Plays a central role in carbohydrate, lipid, and amino acid metabolism
c. Most of the glucose in our diets is converted by liver to G-6-P, which can then be used for glycolysis,
glycogen formation, or the pentose phosphate pathway
LIV.
Role of Liver in Lipid Metabolism [S54]
a. In the fasted state, liver converts fatty acids into ketone bodies
i. Remember ketone bodies can be used to substitute for fuel in brain (can partially substitute glucose by
about 30%)
b. Regulation of fatty acid breakdown by inhibiting formation of acyl carnitine
LV. Role of Liver in Amino Acid Metabolism [S55]
a. We eat a lot more protein than we need to make new protein
b. So we take off amino groups as ammonia and use the carbon skeletons either as fuel or intermediates to
make something else (ex: made into glucose)
c. Ammonia taken off is eventually converted to urea, which is excreted
d. When you take ammonia off of an amino acid, you get an -ketoacid
i. This is the primary fuel of the liver
ii. Good exam question: what is the primary fuel of liver? - ketoacids
LVI.
Table 22.1 Energy Metabolism In Major Vertebrate Organs [S56]
a. Summarizing what I have already said
LVII.
Energy Charge [S57]
a. A way of measuring the energy status of a cell is called energy charge
b. Processes are breaking things down to make ATP, and other processes are using ATP to make something at
the same time
i. They all depend on the concentration of ATP, which has to be tightly regulated
c. Energy charge is basically telling you what percent of the adenosine nucleotides are ATP
FUNDAMENTALS I 10:00-11:00
Scribe: LOUISA WARREN
FRIDAY, SEPTEMBER 3, 2010
Proof: LAUREN MORRIS
PRITCHARD
INTEGRATION OF METABOLISM
Page 7 of 7
d. EC= ½((2[ATP]+[ADP])/([ATP]+[ADP]+[AMP]))
LVIII. Energy Charge Graph [S58]
a. If you had 100 % ATP (which you never do- this diagram is theoretical) you would have an energy charge of 1
b. If all ATP were used up, you would have an energy charge of 0 (also theoretical- this never happens)
LIX.
Responses of Regulatory Enzymes to Variation in Energy Charge [S59]
a. You can group enzymes into ATP-generating enzymes
i. At high levels of ATP and as energy charge approaches 1, you want to downregulate enzymes that make
ATP
ii. If you don’t need ATP, you don’t want enzymes functioning to make more ATP
b. Other enzymes use ATP for reactions
i. If you have very little ATP, you don’t want to use it up
ii. If you have a lot of ATP, these reactions will go very fast
c. Notice where these groups converge
LX. Energy Charge Oscillates About a Steady-State Value [S60]
a. There is a steady state- usually the energy charge in normal cells is 0.85
b. This energy charge is very steady in different types of cells- bacterial, mushroom, human, plant cells
c. If it ever gets too low, the cell dies
d. You can see how this would be regulated
i. If it starts to go up, reactions take place to push it back
ii. If it starts to go down, reactions take place to make more ATP
e. A lot of metabolic processes are regulated this way, and this is a key idea that ties together a lot about
metabolism
[End 49:56 mins]