3 Cell Metabolism

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3 Cell Metabolism

• Chapter 3 Cell Metabolism - review
• Student Learning Outcomes
• Describe central role of enzymes as catalysts
• Vast array of chemical reactions
• Many enzymes are proteins
• Role of NAD/NADH coenzyme carrying electrons
• Explain how metabolic energy comes from breaking/
  rejoining covalent bonds ATP is energy currency
• Glycolysis, fermentation or aerobic respiration
• What goes into reactions, what comes out
• Briefly explain biosynthesis of cell constituents
  
• (requires energy)

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Fig 3.1 Energy diagrams for catalyzed and
uncatalyzed reactions

• Enzymes catalysts increase rate of chemical
  reactions in cells (lower activation energy)
• not consumed in reaction
• not alter chemical equilibrium between
  reactants and products
• Conversion of substrate (S) to product (P)

• Enzymes bind substrates to form enzyme-substrate
  complex (ES)
• S binds to active site of enzyme.
• S converted to product, released

Fig. 3.1
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Fig. 3.2 Enzymatic catalysis of reaction between
2 substrates

• Biochemical reactions often 2 or more
  substrates.
• ex peptide bond joins 2 amino acids
• Enzyme brings substrates together in proper
  orientation to favor transition state
• Active sites clefts or grooves from tertiary
  structure
• Substrates bind active site
• hydrogen bonds, ionic bonds, hydrophobic
  interactions.

Fig. 3.2
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Fig 3.3 Models of enzyme-substrate interaction

• Lock-and-key model
• substrate fits precisely active site.
• Induced fit
• modifies configurations
• of both enzyme and substrate

Specific side chains in active site may react
with substrate and form bonds with reaction
intermediates
Fig. 3.3
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Fig 3.4 Substrate binding by serine proteases

• Ex. Chymotrypsin digests proteins by catalyzing
  hydrolysis of peptide bonds
• Chymotrypsin digests adjacent to hydrophobic
  amino acids
• Trypsin digests next to basic amino acids
• Nature of active site
• pocket determines
• substrate specificity
• of different proteases
• Active site amino acids
• are involved in reaction

Fig. 3.4
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Fig 3.5 Catalytic mechanism of chymotrypsin
Chymotrypsin Substrate binding orients peptide
bond adjacent to serine in active site catalytic
reaction involves covalent join to serine.
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The Central Role of Enzymes as Biological
Catalysts

• Small molecules binding in active sites assist
  catalysis.
• Prosthetic groups small molecules bound to
  proteins - critical functional roles.
• Ex myoglobin and hemoglobin,
• prosthetic group is heme, which binds O2.
• Ex. metal ions (zinc, iron)
• Coenzymes low-molecular-weight organic molecules
  that work with enzymes to enhance reaction rates.
  
• Ex. NAD works with many enzyme (carries
  electrons)

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Fig 3.6 Role of NAD in oxidationreduction
reactions
Nicotinamide adenine dinucleotide (NAD) REDOX
coenzyme carries electrons in oxidation
reduction reactions
NAD accepts H and 2 e- from one substrate
?NADH. NADH donates these e- to second
substrate, re-forming NAD.
S1 (red) S2 (ox) -gt S1 (ox) S2 (red)
Fig. 3.6
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Enzymes and coenzymes
Some coenzymes are related to vitamins
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Fig 3.7 Feedback inhibition

• Enzyme activity is often regulated
• Ex. feedback inhibition, product of pathway
  inhibits an enzyme involved in its synthesis.

Fig. 3.7
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Fig 3.8 Allosteric regulation

• Feedback inhibition is example of allosteric
  regulation enzyme activity controlled by binding
  of small molecules to regulatory sites on enzyme
  (not at active site)
• changes conformation of enzyme and alters
  active site.

Fig. 3.8
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Fig 3.9 Protein phosphorylation
Enzyme activity can be modified by
phosphorylation addition of phosphate can
stimulate or inhibit activity of an enzyme.
Kinases add Phosphate (-OH of ser, thr,
tyr) Phosphatases remove Phosphate
Fig. 3.9 ex. phosphorylation activates enzyme
that degrades glycogen
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Metabolic Energy

• A large portion of cells activities is devoted
  to obtaining energy from environment, and using
  energy to drive energy-requiring reactions
• Many reactions in cells are energetically
  unfavorable, can proceed only with energy input
• (especially biosynthetic reactions)
• ATP and NADH provide energy and reducing material
  (e-) for coupled reactions

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Fig 3.10 ATP as a store of energy
Adenosine 5'-triphosphate (ATP) plays central
role in storing, using free energy in the cell
Energy currency.
Bonds between phosphates in ATP are high-energy
bonds Hydrolysis is accompanied by large
decrease in free energy powers coupled reactions.
Fig. 3.10
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Metabolic Energy

• Hydrolysis of ATP drives energy-requiring
  reactions
• Ex first step in glycolysis is unfavorable (?G'
  3.3)

ATP hydrolysis is energy yielding (?G ' 7.3
kcal/mol) Combined (coupled) reaction (?G'
-4.0) kcal/mol)
Energy-yielding reactions - coupled to ATP
synthesis Energy-requiring reactions - coupled
to ATP hydrolysis.
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Metabolic Energy
Energy-yielding reactions - coupled to ATP
synthesis Energy-requiring reactions - coupled
to ATP hydrolysis.

• Ex. complete oxidative breakdown of glucose
• to CO2 and H2O yields large amount of free
  energy ?G' 686 kcal/mol.

To harness this energy, glucose is oxidized in a
series of steps coupled to ATP synthesis Glycolysi
s, citric acid cycle, e- transport chain
(Krebs cycle), (oxidative
phosphorylation)
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Metabolic Energy

• Glycolysis common to all cells does not require
  O2
• Anaerobic organisms, can provide all metabolic
  energy (ex. E. coli, Streptococcus, yeast).
• Aerobic cells, only 1st stage in glucose
  degradation
• Glycolysis
• Breakdown of glucose -gt 2 pyruvate, net gain 2
  ATP
• Enzymes that catalyze reactions are regulatory
  points
• if adequate supply of ATP, glycolysis is
  inhibited
• Also converts 2 molecules of NAD to NADH
• NADH must be recycled by donating e- for other
  oxidationreduction reactions.
• .

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Figure 3.11 Reactions of glycolysis

• Glycolysis 1 glucose ? 2 pyruvate, net gain of
  2 ATP
• First part of pathway consumes energy (2 ATP)
• Second part generates energy (4 ATP)
• Also converts 2 molecules of NAD to NADH
• NAD is oxidizing agent that accepts e-
• NADH must be recycled by donating e- for other
  REDOX

Fig. 3.11
pyruvate
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Metabolic Energy

• In eukaryotic cells, glycolysis in cytosol.
• NADH must be recycled, donate e- for other REDOX
• Anaerobic conditions, NADH reoxidized to NAD by
  conversion of pyruvate to lactate or ethanol
  (fermentation)
• Wasteful process reduces pyruvate, low ATP gain
• Aerobic conditions, NADH donates e- to electron
  transport chain (oxidative respiration) (lot of
  ATP)
• Pyruvate is transported into mitochondria, for
  complete oxidation (Krebs electron transport
  chain)
• (citric acid cycle)

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Fig 3.12 Oxidative decarboxylation of pyruvate
Pyruvate oxidative decarboxylation with coenzyme
A (CoA-SH) forms acetyl CoA and more NADH.
Fig. 3.12
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Fig 3.13 The citric acid cycle

• Acetyl CoA enters citric acid cycle (Krebs cycle)
• 2-C acetyl group oxaloacetate (4-C) yields
  citrate (6-C).
• 2 C of citrate are completely oxidized to CO2
• oxaloacetate is regenerated.

Citric acid cycle completes oxidation of
glucose to 6 CO2 Each Acetyl-CoA yields 2 CO2, 1
GTP, 3 NADH, 1 flavin adenine dinucleotide
(FADH2), (another e- carrier.
Fig. 3.13
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Oxidative phosphorylation summary

• Oxidative phosphorylation electrons of NADH,
  FADH2 combine with O2 energy released drives
  synthesis of ATP.
• Passage of e- through carriers electron
  transport chain, inner mitochondrial membrane of
  eukaryotes
• (inner plasma membrane of prokaryotes)
• H are pumped out ? electrochemical gradient
• H back in through ATP synthase makes ATP
  (3/NADH)

Fig. 21.1 Lieberman Marks, Basic Medical
Biochemistry
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Metabolic Energy

• Glucose breakdown (O2) to CO2, H2O ? 36-38 ATP
• Breakdown of other organic molecules yields
  energy
• Nucleotides and polysaccharides are broken down
  to sugars which enter glycolytic pathway
• Amino acids are degraded via citric acid cycle.
• Fats (triacylglycerols) broken to glycerol and
  free fatty acids.
• fatty acid joins to coenzyme A, yields fatty
  acyl-CoA
• fatty acids degraded stepwise process, two C at a
  time
• Yield 1 Acetyl CoA, 1 NADH, 1 FADH2 each cycle
• 130 ATPs per molecule of 16-carbon fatty acid.

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Fig 3.15 Oxidation of fatty acids
Each round of fatty acid oxidation yields one
NADH, one FADH2. Acetyl CoA enters citric acid
cycle (for complete oxidation). Net gain 130
ATPs per molecule of 16-carbon fatty acid (net
gain of 38 ATPs per molecule of glucose with 6
C).
Fig. 3.15
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Photosynthesis brief

• Photosynthesis converts energy of sunlight to
  usable form of chemical energy.
• ultimate source of all metabolic energy in
  biological systems.

• Overall equation for photosynthesis
• Process takes place in two stages
• Light reactions sunlight energy drives
  synthesis of ATP and NADPH, coupled to oxidation
  of H2O to O2.
• Dark reactions ATP and NADPH drive synthesis
  of carbohydrates from CO2
• 18 ATP and 12 NADPH required for each glucose

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Photosynthesis
Photosynthetic pigments absorb photons of light
shifts electrons into higher energy orbitals,
convert energy from sunlight to chemical energy
in ATP, and also NADPH In eukaryotic cells,
reactions occur in chloroplasts In
prokaryotic cells, reactions occur on plasma
membrane Chlorophylls major pigments other
pigments absorb different wavelengths of light
Fig. 3.16
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Fig 3.18 The Calvin cycle

• Light reactions energy from light converts H2O
  to O2.
• High-energy electrons enter electron transport
  chain transfer through series of carriers is
  coupled to synthesis of ATP.
• Dark reactions ATP and NADPH drive synthesis of
  carbohydrates from CO2 and H2O.
• One molecule of CO2 added each cycle of
  reactions, Calvin cycle, that forms carbohydrates.

Fig. 3.17,18
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The Biosynthesis of Cell Constituents

• Biosynthesis of cell constuents
• Energy derived from breakdown of organic
  molecules (catabolism) drives synthesis of other
  components of cell.
• Biosynthetic (anabolic) pathways use ATP and
  reducing power (usually NADPH) to produce new
  organic compounds.
• Animal cells glucose synthesis (gluconeogenesis)
  usually starts with lactate (from anaerobic
  glycolysis), amino acids (breakdown of proteins),
  or glycerol (breakdown of lipids)
• pyruvate is converted to glucose
• not just reversal of glycolysis requires more
  energy for biosynthesis of glucose than get from
  breakdown

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Fig 3.20 Synthesis of polysaccharides

• Glucose is stored as starch and glycogen.
• Synthesis of polysaccharides requires energy.
• Dehydration reaction joining sugars is
  unfavorable, couples to energy-yielding reaction
  nucleotide sugar intermediates.
• Glucose phosphorylated, reacts with UTP ?
  UDP-glucose.
• UDP-glucose (activated intermediate) donates
  glucose to growing polysaccharide chain.

Fig. 3.20
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The Biosynthesis of Cell Constituents

• Lipids are important energy storage molecules and
  major constituent of cell membranes.
• Fatty acids are synthesized from acetyl CoA,
  (from the breakdown of carbohydrates), in
  reactions that resemble reverse of fatty acid
  oxidation.
• Requires ATP, NADPH

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Fig 3.22 Biosynthesis of amino acids

• Amino acids are derived from diet (some are
  essential), or formed from citric acid
  intermediates
• NH3 is incorporated during synthesis of Glu and
  Gln
• These amino acids donate NH3 to form other amino
  acids,
• (derived from intermediates in glycolysis,
  citric acid cycle)
• Many bacteria and plants can synthesize all 20 aa

Fig. 3.22
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Molecular Medicine 3.1 Phenylketonuria
Abnormal metabolism of phenylalanine in patients
with phenylketonuria
Errors in amino acid metabolism can have large
impacts Ex. phenylketonuria is deficiency of
phenylalanine hydroxylase, which converts
phenylalanine to tyrosine. Phenylalanine and
metabolites accumulate and cause mental
retardation. Newborns tested, special diet
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The Biosynthesis of Cell Constituents

• Synthesis of proteins
• Amino acids are incorporated into proteins in
  order specified by nucleotide bases in gene
• mRNA is template for protein synthesis on
  ribosome
• Each amino acid is attached to specific transfer
  RNA (tRNA) molecule in reaction coupled to ATP
  hydrolysis (charging on 3 position)
• Aminoacyl-tRNAs align on mRNA bound on ribosome
• Peptide chain joins to new tRNA-aa, coupled to
  hydrolysis of GTP

Fig. 3.23
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Fig 3.24 Biosynthesis of purine and pyrimidine
nucleotides
Nucleotides can be synthesized from carbohydrates
and amino acids, or reused following nucleic acid
breakdown. Ribose-5-phosphate is starting point
for nucleotide synthesis. Different pathways for
synthesis of purine and pyrimidine. Ribonucleotid
es are converted to deoxyribonucleotides,
building blocks of DNA
Fig. 3.24
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Fig 3.25 Synthesis of polynucleotides
Nucleic acid synthesis requires energy NTPs are
activated precursors.
Fig. 3.25
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Review

• Review Questions
• Binding pocket of trypsin contains Asp residue.
  How would changing this aa to Lys affect enzymes
  activity?
• Many biochemical reactions (synthesis of
  macromolecules) are energetically unfavorable
  under physiological conditions. How does cell
  carry out these reactions?
• 8. Yeast can grow anaerobic or aerobic. For every
  molecule of glucose consumed, compare number of
  ATP generated in anaerobic versus aerobic
  conditions.
• 10. How do organisms growing under anaerobic
  conditions regenerate NAD from NADH produced
  during glycolysis?