12/1/2009Biochemistry: Metabolism I General Metabolism Principles; Nutrition Andy Howard...
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Transcript of 12/1/2009Biochemistry: Metabolism I General Metabolism Principles; Nutrition Andy Howard...
12/1/2009Biochemistry: Metabolism I
General Metabolism Principles; Nutrition
Andy HowardIntroductory Biochemistry
1 December 2009
12/1/2009Biochemistry: Metabolism I
Page 2 of 50
Metabolism depends strongly on cofactors We’ll attend to the reality that a lot of the versatility of enzymes depends on their incorporation of cofactors; and most vitamins are precursors of cofactors
12/1/2009Biochemistry: Metabolism I
Page 3 of 50
What we’ll discuss Post-translational modification
Phosphorylation Other reversible PTMs
How pathways evolve Oxidation-Reduction Reactions: Quantitation
How we study metabolism (revisited)
Nutrition Macronutrients Micronutrients Specific cofactors and vitamins reconsidered
Fat soluble vitamins
Ascorbate
12/1/2009Biochemistry: Metabolism I
Page 4 of 50
Phosphorylation’s effects
Phosphorylation of an enzyme can either activate it or deactivate it
Usually catabolic enzymes are activated by phosphorylation and anabolic enzymes are inactivated
Example:glycogen phosphorylase is activated by phosphorylation; it’s a catabolic enzyme
12/1/2009Biochemistry: Metabolism I
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Amplification
Activation of a single molecule of a protein kinase can enable the activation (or inactivation) of many molecules per sec of target proteins
Thus a single activation event at the kinase level can trigger many events at the target level
12/1/2009Biochemistry: Metabolism I
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Other PTMs Are there other reversible post-translational modifications that regulate enzyme activity? Yes: Adenylation of Y ADP-ribosylation of R Uridylylation of Y Oxidation of cysteine pairs to cystine
Cis-trans isomerization of prolines
12/1/2009Biochemistry: Metabolism I
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Metabolism and evolution Metabolic pathways have evolved over hundreds of millions of years to work efficiently and with appropriate controls
12/1/2009Biochemistry: Metabolism I
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Evolution of Pathways:How have new pathways evolved? Add a step to an existing pathway Evolve a branch on an existing pathway
Backward evolution Duplication of existing pathway to create related reactions
Reversing an entire pathway
12/1/2009Biochemistry: Metabolism I
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Adding a step
A B C D E P
• When the organism makes lots of E, there’s good reason to evolve an enzyme E5 to make P from E.
• This is how asn and gln pathways (from asp & glu) work
E1 E2 E3 E4 E5
Original pathway
12/1/2009Biochemistry: Metabolism I
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Evolving a branch Original pathway: D A B C X
Fully evolved pathway: D A B C X
E1 E2E3
E3a
E3b
12/1/2009Biochemistry: Metabolism I
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Backward evolution Original system has lots of E P
E gets depleted over time; need to make it from D, so we evolve enzyme E4 to do that.
Then D gets depleted; need to make it from C, so we evolve E3 to do that
And so on
12/1/2009Biochemistry: Metabolism I
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Duplicated pathways
Homologous enzymes catalyze related reactions;this is how trp and his biosynthesis enzymes seem to have evolved
Variant: recruit some enzymes from another pathway without duplicating the whole thing (example: ubiquitination)
12/1/2009Biochemistry: Metabolism I
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Reversing a pathway
We’d like to think that lots of pathways are fully reversible
Usually at least one step in any pathway is irreversible (Go’ < -15 kJ mol-1)
Say CD is irreversible so E3 only works in the forward direction
Then D + ATP C + ADP + Pi allows us to reverse that one step with help
The other steps can be in common This is how glycolysis evolved from gluconeogenesis
12/1/2009Biochemistry: Metabolism I
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Oxidation-reduction reactions and Energy Oxidation-reduction reactions involve transfer of electrons, often along with other things
Generally compounds with many C-H bonds are high in energy because the carbons can be oxidized (can lose electrons)
12/1/2009Biochemistry: Metabolism I
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Reduction potential Reduction potential is a measure of thermodynamic activity in the context of movement of electrons
Described in terms of half-reactions
Each half-reaction has an electrical potential, measured in volts, associated with it because we can (in principle) measure it in an electrochemical cell
12/1/2009Biochemistry: Metabolism I
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So what is voltage, anyway? Electrical potential is available energy per unit charge:
1 volt = 1 Joule per coulomb 1 coulomb = 6.24*1018 electrons Therefore energy is equal to the potential multiplied by the number of electrons
12/1/2009Biochemistry: Metabolism I
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Electrical potential and energy
This can be expressed thus:Go’ = -nFEo’
n is the number of electrons transferred
F = fancy way of writing # of Coulombs (which is how we measure charge) in a mole (which is how we calibrate our energies) = 96.48 kJ V-1mol-1
12/1/2009Biochemistry: Metabolism I
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Oh yeah? Yes. 1 mole of electrons = 6.022 * 1023 e-
1 coulomb = 6.24*1018 e-
1 mole = 9.648*104 Coulomb 1 V = 1 J / Coulomb=10-3 kJ / Coulomb
Therefore the energy per mole associated with one volt is10-3 kJ / C * 9.648*104 C = 96.48 kJ
12/1/2009Biochemistry: Metabolism I
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What can we do with that? The relevant voltage is the difference in standard reduction potential between two half-reactions
Eo’ = Eo’acceptor - Eo’donor
Combined with free energy calc, we seeEo’ = (RT/nF ) lnKeq andE = Eo’ - (RT/nF ) ln [products]/[reactants]
This is the Nernst equation
12/1/2009Biochemistry: Metabolism I
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Free energy from electron transfer
We can examine tables of electrochemical half-reactions to get an idea of the yield or requirement for energy in redox reactions
Example:NADH + (1/2)O2 + H+ -> NAD+ + H2O;
We can break that up into half-reactions to determine the energies
12/1/2009Biochemistry: Metabolism I
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Half-reactions and energy NAD+ + 2H+ + 2e- NADH + H+,Eo’ = -0.32V
(1/2)O2 + 2H+ + 2e- H2O, Eo’ = 0.82V
Reverse the first reaction and add:NADH + (1/2)O2 + H+ NAD+ + H2O,Eo’ = 0.82+0.32V = 1.14 V.
Go’ = -nFEo’ = -2*(96.48 kJ V-1mol-1)(1.14V) = -220 kJ mol-1; that’s a lot!
12/1/2009Biochemistry: Metabolism I
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How to detect NAD reactions
NAD+ and NADH(and NADP+ and NADPH)have extended aromatic systems
But the nicotinamide ring absorbs strongly at 340 only in the reduced(NADH, NADPH) forms
Spectrum is almost pH-independent, too!
So we can monitor NAD and NADP-dependent reactions by appearance or disappearance of absorption at 340 nm
NAD+
NADH
Absorbance
Wavelength
340 nm
12/1/2009Biochemistry: Metabolism I
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Classical metabolism studies
Add substrate to a prep and look for intermediates and end products
If substrate is radiolabeled (3H, 14C) it’s easier, but even nonradioactive isotopes can be used for mass spectrometry and NMR
NMR on protons, 13C, 15N, 31P Reproduce reactions using isolated substrates and enzymes
12/1/2009Biochemistry: Metabolism I
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Next level of sophistication… Look at metabolite concentrations in intact cell or organism under relevant physiological conditions
Note that Km is often ~ [S].If that isn’t true, maybe you’re looking at the non-physiological substrate!
Think about what’s really present in the cell.
12/1/2009Biochemistry: Metabolism I
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Mutations in single genes
If we observe or create a mutation in a single gene of an organism, we can find out what the effects on viability and metabolism are
In humans we can observe genetic diseases and tease out the defective gene and its protein or tRNA product
Sometimes there are compensating enzyme systems that take over when one enzyme is dead or operating incorrectly
12/1/2009Biochemistry: Metabolism I
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Deliberate manipulations Bacteria and yeast:
Irradiation or exposure to chemical mutagens
Site-directed mutagenesis Higher organisms:We can delete or nullify some genes;thus knockout mice
Introduce inhibitors to pathways and see what accumulates and what fails to be synthesized
12/1/2009Biochemistry: Metabolism I
Page 27 of 50
Nutrition Lots of nonsense,some sense on this subject
Skepticism among MDs as to its relevance
Fair view is that nutrition matters in many conditions, but it’s not the only determinant of health
12/1/2009Biochemistry: Metabolism I
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Macronutrients
Proteins Carbohydrates Lipids Fiber
12/1/2009Biochemistry: Metabolism I
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Protein as food
Source of essential amino acids Source of non-essential aa Fuel (often via interconversion to a-ketoacids and incorporation into TCA)
All of the essential amino acids must be supplied in adequate quantities
12/1/2009Biochemistry: Metabolism I
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Which amino acids are essential?
At one level, that’s an easy question to answer: they’re the ones for which we lack a biosynthetic pathway: KMTVLIFWH
That shifts the question to:why have some of those pathways survived and not all?
Answer: pathways that are complex or require more than ~30 ATP / aa are absent (except R,Y)
12/1/2009Biochemistry: Metabolism I
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The human list
AA molesessen- ATPtial?
Asp 21 noAsn 22-24 noLys 50-51 yesMet 44 yesThr 31 yesAla 20 noVal 39 yesLeu 47 yesIle 55
yesGlu 30 noGln 31 no
AA moles essen-ATP
tial?Arg 44 noPro 39 noSer 18 noGly 12 noCys 19 noPhe 65 yesTyr 62 no*Trp 78 yesHis 42 yes
12/1/2009Biochemistry: Metabolism I
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Carbohydrates as food
Generally recommended to be more than half of caloric intake
Complex carbohydrates are hydrolyzed to glucose-1-P and stored as glycogen or interconverted into other metabolites
12/1/2009Biochemistry: Metabolism I
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Lipids as food You’ll see in 402 that the energy content of a lipid is ~ 2x that of carbohydrates simply because they’re more reduced
They’re also more efficient food storage entities than carbs because they don’t require as much water around them
Certain fatty acids are not synthesizable; by convention we don’t call those vitamins
12/1/2009Biochemistry: Metabolism I
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Vitamins Vitamins are necessary micronutrients A molecule that is a vitamin in one organism isn’t necessarily a vitamin in another
E.coli can make all necessary metabolites given sources of water, nitrogen, and carbon
Most eukaryotic chemoautotrophs find it more efficient to rely on diet to make complex metabolites
We’ll discuss lipid vitamins first,then water-soluble vitamins
12/1/2009Biochemistry: Metabolism I
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Why wouldn’t organisms make everything?
Complex metabolites require energy for synthesis
Control of their synthesis is also metabolically expensive
Cheaper in the long run to derive these nutrients from diet
12/1/2009Biochemistry: Metabolism I
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Vitamins: broad classifications Water-soluble vitamins
Coenzymes or coenzyme precursors Non-coenzymic metabolites
Fat-soluble vitamins Antioxidants Other lipidic vitamins
12/1/2009Biochemistry: Metabolism I
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Are all nutrients that we can’t synthesize considered vitamins? No: If it’s required in large quantities,it’s not a vitamin
By convention, essential fatty acids like arachidonate aren’t considered vitamins
12/1/2009Biochemistry: Metabolism I
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Lipid vitamins Contain rings & long aliphatic sidechains
At least one polar group in each
Absorbed in intestine, carried via bile salts
Hard to study Most are formally built from isoprene units, as are steroids
12/1/2009Biochemistry: Metabolism I
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Vitamin A (retinol) 3 forms varying in terminal polar group
Involved in signaling and receptors -carotene is nonpolar dimer
12/1/2009Biochemistry: Metabolism I
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Vitamin A deficiency
Produces night blindness because the retina and cornea dry out
Most common cause: nursing infants whose mothers have vitamin A deficiency in their diet
12/1/2009Biochemistry: Metabolism I
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Vitamin D
Several related forms
Hormones involved in Ca2+ regulation
Figure courtesyCyberlipid
(cholecalciferol)
12/1/2009Biochemistry: Metabolism I
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Vitamin D deficiency Rickets in children:Bone disease, restlessness, slow growth
One form of vitamin D is actually synthesizable from cholesterol given adequate sunlight;
Therefore rickets is most common in densely settled urban environments
12/1/2009Biochemistry: Metabolism I
Page 43 of 50
Vitamin E (-tocopherol)
Phenol can undergo 1e- oxidation to moderately stable free radical
Antioxidant activity prevents damage to fatty acids in membranes
Fig. CourtesyUIC pharmacy program
phenol
12/1/2009Biochemistry: Metabolism I
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Vitamin K (phylloquinone)
Involved in synthesis of proteins involved in blood coagulation
Reduced form involved as reducing agent in carboxylation reaction on glu sidechainsFigure courtesy
Cyberlipid
12/1/2009Biochemistry: Metabolism I
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Vitamin overdoses?
It’s difficult to overdose on water-soluble vitamins: excess is simply excreted
Fat-soluble vitamins are stored in adipose tissue and can accumulate to high concentrations
May be toxic even dietarily Therefore: don’t eat polar bear liver
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
12/1/2009Biochemistry: Metabolism I
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Ascorbate
The only common water-soluble vitamin that is not a coenzyme or coenzyme precursor
Vitamin in primates, some rodents Synthesizable in most other vertebrates
Involved in collagen Reduced form acts as reducing agent during hydroxylation of collagen
Deficiency gives rise to inadequate collagen - scurvy
12/1/2009Biochemistry: Metabolism I
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PTM role of ascorbate
Proline + O2 + -ketoglutarate + ascorbate 4-hydroxyproline + succinate + CO2 + dehydroascorbate
This is a post-translational modification that occurs to prolines within collagen
The hydroxylated prolines help stabilize the collagen triple helix
Hydroxylysine found in collagen too
12/1/2009Biochemistry: Metabolism I
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Dietary deficiency of ascorbate Primary sources of ascorbate are fruits, particularly citrus, and green vegetables
Ascorbate deficiency’s first symptom involves collagen degradation, leading to scurvy
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
Image courtesy U.Cincinnati Medical School
12/1/2009Biochemistry: Metabolism I
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Scurvy in history Shortage of green vegetables
in sailors’ diets meant scurvy was rampant on shipboard until the 18th century
Success of English navy over French 1760-1800 was partly due to the introduction of limes in English sailors’ diets 50 years before the French caught on
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
12/1/2009Biochemistry: Metabolism I
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Megadoses of ascorbate Linus Pauling (2-time Nobel laureate) became convinced late in his life that very high doses of ascorbate (> 1 g /day) were beneficial as a preventative
His assertions were met with skepticism from the established medical community
I would say the jury is still out!
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
Linus PaulingImage courtesy Oregon State U.