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)
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
S  E  ES  E  P
Fig. 3.1
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
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
Fig 3.4 Substrate binding by serine proteases
Ex. Chymotrypsin digests proteins by catalyzing
hydrolysis of peptide bonds
Protein  H 2O  Peptide1  Peptide2
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
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.
2
1
3
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)
Fig 3.6 Role of NAD+ in oxidation–reduction 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) -> S1 (ox) + S2 (red)
Fig. 3.6
Enzymes and coenzymes
Some coenzymes are related to vitamins
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
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
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
Metabolic Energy
• A large portion of cell’s 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
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 highenergy bonds:
Hydrolysis is
accompanied by
large decrease in
free energy:
powers coupled
reactions.
Fig. 3.10
Metabolic Energy
Hydrolysis of ATP drives energy-requiring reactions
Ex: first step in glycolysis is unfavorable (ΔG°′ = +3.3)
glucose  HPO42  glucose6 phosphate  H 2O
ATP hydrolysis is energy yielding: (ΔG °′ = –7.3 kcal/mol):
ATP  H 2O  ADP  HPO42
Combined (coupled) reaction : (ΔG°′ = -4.0) kcal/mol)
glucose  ATP  glucose6 phosphate  ADP
Energy-yielding reactions - coupled to ATP synthesis
Energy-requiring reactions - coupled to ATP hydrolysis.
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:
ΔG°′ = –686 kcal/mol.
C6 H12O6  O2  6CO2  6 H 2O
To harness this energy, glucose is oxidized in a series
of steps coupled to ATP synthesis
Glycolysis, citric acid cycle, e- transport chain
(Krebs cycle), (oxidative phosphorylation)
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 -> 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
oxidation–reduction reactions.
.
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
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)
Fig 3.12 Oxidative decarboxylation of pyruvate
Pyruvate oxidative decarboxylation with coenzyme A
(CoA-SH): forms acetyl CoA and more NADH.
Fig. 3.12
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
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
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.
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
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:
6CO2  6 H 2O 
 C6 H12O6  6O2
light
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
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
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
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
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
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
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
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
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
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.
Ribonucleotides
are converted to
deoxyribonucleotides,
building blocks of DNA
Fig. 3.24
Fig 3.25 Synthesis of polynucleotides
Nucleic acid synthesis requires energy;
NTPs are activated precursors.
Fig. 3.25
Review
Review Questions:
1. Binding pocket of trypsin contains Asp residue. How would
changing this aa to Lys affect enzyme’s activity?
4. 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?