1
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Energy and Cellular Metabolism
Chapter 4
2About This Chapter
• Energy in biological systems
• Chemical reactions
• Enzymes
• Metabolism
© 2013 Pearson Education, Inc.
3Table 4.1 Properties of Living Organisms
4KEY
Transfer of radiantor heat energy
Transfer of energyin chemical bonds
Energy for work
Energy storedin biomolecules
H2O CO2
Respirationtakes place inhuman cells,
yielding:
Energy lostto environment
Heatenergy
Energy stored inbiomolecules
O2 ++++Photosynthesis
takes place inplant cells, yielding:
CO2
H2ON2
Radiantenergy
Sun
Figure 4.1 Energy transfer in the environment
5Energy: Capacity to Do Work
• Two principle forms of energy– Kinetic – the energy of movement– Potential – stored energy
• Energy can be used to do work:– that is, to move matter against opposing forces, such as gravity,
friction, electric repulsive force• Chemical work
– Making and breaking of chemical bonds• Transport work
– Moving ions, molecules, and larger particles– Useful for creating concentration gradients
• Mechanical work– Moving organelles, changing cell shape, beating flagella and cilia– Contracting muscles
6Energy Comes in Two Forms
• Kinetic energy– Energy of motion
– Work involves movement
• Potential energy– Stored energy
– In concentration gradients and chemical bonds
– Must be converted to kinetic energy to perform work– Transformation efficiency
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7Figure 4.2 The relationship between kinetic energy and potential energy
Work is used to push a ballup a ramp. Kinetic energy ofmovement up the ramp isbeing stored in the potentialenergy of the ball’s position.
The ball sitting at the top of theramp has potential energy, thepotential to do work.
The ball rolling down the rampis converting the potentialenergy to kinetic energy.However, the conversion is nottotally efficient, and someenergy is lost as heat due tofriction between the ball, ramp,and air.
8Thermodynamic Energy
• First law of thermodynamics– Total amount of energy in the universe is constant
– Energy cannot be created or destroyed
– Energy can be converted from one form to another
– The pathway of conversion is irrelevant, the energy change between identical initial and final states is equal
• Second law of thermodynamics– Processes move from state of order to randomness
or disorder (entropy)
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9Thermodynamic Energy
• Second law of thermodynamics– Processes move from state of order to randomness or
disorder (entropy)
– No conversion is 100% efficient.
– Total useful energy in a closed system decreases as conversions occur.
– Entropy – Measure of Disorder
– Closed systems tend to their highest state of disorder
– Entropy of the universe increases with every conversion
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10Chemical Reactions
• Bioenergetics is the study of energy flow through biological systems
• Chemical reactions– Reactants become products
– Reaction rate
• Activation energy
• Net free energy change of the reaction– Exergonic versus endergonic reactions
– Coupled reactions
– Reversible versus irreversible reactions
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11Table 4.2 Chemical Reactions
12Figure 4.3a Activation energy and exergonic and end ergonic reactions (1 of 3)
Activation energy is the “push” needed to start a reaction.
Reactants
Starting freeenergy level
Final free energy level
Products
Activationenergy
13Figure 4.3b Activation energy and exergonic and end ergonic reactions (2 of 3)
Exergonic reactions release energy because theproducts have less energy than the reactants.
Activationenergy
Time
A++++B
C++++D
Net freeenergychange
Fre
e en
ergy
of m
olec
ule
KEYReactants
Activationof reaction
Reaction process
Products
14Figure 4.3c Activation energy and exergonic and end ergonic reactions (3 of 3)
KEYReactants
Activationof reaction
Reaction process
Products
Endergonic reactions trap some activationenergy in the products, which then have morefree energy than the reactants.
Fre
e en
ergy
of m
olec
ule
E++++F
Activation energyG++++H
Net freeenergy change
Time
15Figure 4.4 Energy transfer and storage in biologica l reactions
Exergonic reactions releaseenergy.
Endergonic reactions will notoccur without input of energy.
Nucleotides captureand transfer energyand electrons
ENERGYreleased
ENERGYutilized
A++++B C++++D
E++++F G++++H
Heat energy
High-energyelectrons
ATP
NADPH
NADH
FADH2
16Figure 4.5 Some reactions have large activation ene rgies
C++++D
A++++B
KEYReactants
Activationof reaction
Reaction process
Products
Activation energy
Time
Net freeenergychange
Fre
e en
ergy
of m
olec
ule
17Enzymes: Overview
• Enzymes – Are proteins catalysts (not used up in the reaction)– speed up the rate of chemical reactions by lowering the activation
energy– They don’t change equilibrium! – With infinite time in a closed system, the same equilibrium
would be reached whether with enzymes or without. – Reactants are called substrates
• Isozymes– Catalyze same reaction, but under different conditions
• May be activated, inactivated, or modulated– Modulated by other enzymes: Phosphorylation (kinase)
/dephosphorylation (phosphatase)– Coenzymes → (e.g., vitamins)– Chemical modulators → temperature and pH
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18Figure 4.7 Enzymes lower the activation energy of re actions
KEYReactants
Activationof reaction
Reaction process
Products
C++++D
A++++B
Time
Fre
e en
ergy
of m
olec
ule
Activation energywithout enzyme
Lower activationenergy in presence
of enzyme
19Table 4.3 Diagnostically Important Enzymes
20Figure 4.6 Effect of pH on enzyme activity
If the pH falls from 8 to 7.4,what happens to the activityof the enzyme?
GRAPH QUESTION
Most enzymes in humans have optimal activitynear the body’s internal pH of 7.4.
Rat
e of
enz
yme
activ
ity
pH5 6 7 8 9
21Table 4.4 Classification of Enzymatic Reactions
22Metabolism
• All chemical reactions that take place in an organism
• Catabolism (break down/degrade) versus anabolism (build up/synthesize)
• Kilocalories are measures of energy released from or stored in chemical bonds
• Molecules in pathways are intermediates
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23Figure 4.8 A group of metabolic pathways resembles a road map
Section of road map Metabolic pathways drawn like a road map
Glucose
Fructose Fructose 1-phosphate
GlycerolDHAP
DHAP ==== dihydroxyacetone phosphate
Glucose 3-phosphate
Ribose 5-phosphateFructose 1,6-
biphosphate
Fructose 6-phosphate
Glucose 6-phosphate
Glycogen
24Cells Regulate Their Metabolic Pathways
1. Controlling enzyme concentrations1. Synthesis/degradation
2. Producing modulators that change reaction rates1. Ex. Feedback inhibition: negative feedback where
accumulation of product inhibits production of that product
3. Using different enzymes to catalyze reversible reactions
4. Compartmentalizing enzymes within organelles
5. Maintaining optimum ratio of ATP to ADP
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25Figure 4.9 Feedback inhibition
enzyme 1 enzyme 2 enzyme 3
Feedback inhibition
A B C Z
26Figure 4.10 The reversibility of metabolic reaction s is controlled by enzymes
FIGURE QUESTION
What is the differencebetween a kinase and aphosphatase? (Hint: SeeTable 4.4.)
Irreversible reactions lackthe enzyme for the reversedirection.
Reversible reactions requiringtwo enzymes allow morecontrol over the reaction.
Some reversible reactionsuse one enzyme for bothdirections.
Carbonic acid Glucose 6-phosphate Glucose 6-phosphate
carbonicanhydrase
carbonicanhydrase
hexokinase glucose 6-phosphatase
hexokinase
Glucose GlucoseCO2 H2O PO4 PO4
27ATP Transfers Energy Between Reactions
• High-energy phosphate bond
• ATP production– Aerobic metabolism (yeilds more ATP)
– Citric acid cycle– Electron transport chain
– Anaerobic metabolism– Glycolysis
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28Figure 4.11 ESSENTIALS – ATP Production
29Figure 4.12 ESSENTIALS – Glycolysis
30Figure 4.13 ESSENTIALS – Pyruvate, Acetyl CoA, and t he Citric Acid Cycle
31Figure 4.14 ESSENTIALS – The Electron Transport Syst em
32Figure 4.15 Summary of energy yields from catabolis m of one glucose molecule
1 Glucose
2 Pyruvate
2 Lactate
NADH FADH2 CO2ATP
24
−−−−2
−−−−2
2ATP
0NADH
TOTALS
AnaerobicMetabolism
AerobicMetabolism
2 Pyruvate
1 Glucose
GLYCOLYSIS
GLYCOLYSIS
NADH FADH2 CO2ATP
−−−−2
++++42*
2 2
2 26 4Citric acidcycle
High-energy electronsand H+6 O2
ELECTRONTRANSPORT
SYSTEM26-28
30-32ATP
6H2O
6CO2
2 Acetyl CoA
* Cytoplasmic NADH sometimes yields only1.5 ATP/NADH instead of 2.5 ATP/NADH.
TOTALS
33Figure 4.16 Pyruvate is the branch point between ae robic and anaerobic metabolism of glucose
==== Carbon
==== Oxygen
==== Coenzyme A
H and –OH not shown
PyruvateLactate
Pyruvate
NADHNAD+
AnaerobicAerobic
Cytosol
Mitochondrialmatrix
CoA
Acetyl CoACoA
Acyl unit
CITRIC ACIDCYCLE
34Central dogma of molecular biology
• Transfer of sequence information between biopolymers
• 3 General transfers of sequence information– Transcription (same language, different format)
– DNA sequence to mRNA sequence
– RNA polymerase synthesizes RNA from DNA
– Translation (different language)– mRNA sequence to Polypeptide sequence
– Ribosomes synthesize polypeptides from mRNA
– Replication (same language, same format)– DNA sequence to DNA sequence
– DNA polymerase synthesizes new DNA from a DNA template
35Protein synthesis
• Proteins are composed of 20 naturally occurring amino acids (chemical synthesis can produce many many more)
• The amino acid sequence (primary structure) of proteins is determined by the genetic code stored in DNA
• Sections of DNA that produce a particular polypeptide (or its variant) are known as genes
– One gene-one polypeptide hypothesis (doesn’t account for alternative splicing
• Genetic code is comprised of 4 different nucleotides
• To encode 20 amino acids with 4 “letters,” the minimum length of a code for amino acids is 3
– 42=16; 43=64
– One triplet of nucleotides is known as a codon
36Figure 4.17 The genetic code as it appears in the c odons of mRNA
Second base of codon
Firs
t bas
e of
cod
on
Third base of codon
Phe
Leu
Leu
Ile
Met
Val
Ser
Pro
Thr
Ala
Tyr
His
Gln
Asn
Lys
Asp
Glu
Cys
Trp
Arg
Ser
Arg
Gly
Start
Stop Stop
37Figure 4.18 ESSENTIALS – Overview of Protein Synthes is
38Figure 4.18 ESSENTIALS – Overview of Protein Synthes is
GENE ACTIVATION
Induction Repression
Regulatedactivity
Constitutivelyactive
Gene Regulatory proteins
Cytosol
Nucleus
Slide 1
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39Figure 4.18 ESSENTIALS – Overview of Protein Synthes is
GENE ACTIVATION
TRANSCRIPTION(See Fig. 4.19)
mRNA
Induction Repression
Regulatedactivity
Constitutivelyactive
Gene Regulatory proteins
Cytosol
Nucleus
Slide 2
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40Figure 4.18 ESSENTIALS – Overview of Protein Synthes is
GENE ACTIVATION
TRANSCRIPTION(See Fig. 4.19)
mRNA PROCESSING(See Fig. 4.20)
Cytosol
Nucleus
ProcessedmRNA
Alternativesplicing Interference
mRNA “silenced”
si RNAmRNA
Induction Repression
Regulatedactivity
Constitutivelyactive
Gene Regulatory proteins
Slide 3
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41Figure 4.18 ESSENTIALS – Overview of Protein Synthes is
GENE ACTIVATION
TRANSCRIPTION(See Fig. 4.19)
mRNA PROCESSING(See Fig. 4.20)
TRANSLATION(See Fig. 4.21)
Cytosol
Nucleus
• rRNA in ribosomes• tRNA• Amino acids
ProcessedmRNA
Alternativesplicing Interference
mRNA “silenced”
si RNAmRNA
Induction Repression
Regulatedactivity
Constitutivelyactive
Gene Regulatory proteins
Protein chain
Slide 4
© 2013 Pearson Education, Inc.
42Figure 4.18 ESSENTIALS – Overview of Protein Synthes is
GENE ACTIVATION
TRANSCRIPTION(See Fig. 4.19)
mRNA PROCESSING(See Fig. 4.20)
TRANSLATION(See Fig. 4.21)
POST-TRANSLATIONALMODIFICATION Folding and
cross-linksCleavage into
smaller peptidesAssembly into
polymeric proteinsAddition of groups:
• sugars• lipids• -CH3• phosphate
Cytosol
Nucleus
• rRNA in ribosomes• tRNA• Amino acids
ProcessedmRNA
Alternativesplicing Interference
mRNA “silenced”
si RNAmRNA
Induction Repression
Regulatedactivity
Constitutivelyactive
Gene Regulatory proteins
Protein chain
Slide 5
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43RNA Synthesis
• RNA polymerase
• Promoter
• Transcription factors
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44
RNA polymerase binds toDNA.
The section of DNA thatcontains the gene unwinds.
RNA bases bind to DNA,creating a single strand ofmRNA.
DNA
Templatestrand Site of
nucleotide assembly
mRNAtranscript
RNApolymerase
RNApolymerase
RNA bases
LengtheningmRNA strand
RNApolymerasemRNA strand
released
Leaves nucleusafter processing
mRNA and the RNA polymerasedetach from DNA, and themRNA goes to the cytosol afterprocessing.
Figure 4.19 Transcription
45Figure 4.20 mRNA processing
Gene
Templatestrand
DNA
Promoter Transcribed section
TRANSCRIPTION
UnprocessedmRNA
mRNA Processingmay produce twoproteins from one
gene byalternative splicing.
Introns removedIntrons removed
Exons for protein #1 Exons for protein #2
a b c d e f g h i
A
A
B
B
C
C
D
D
E
E
F
F
G
G
H
H
I
I
C
D H
E
46Figure 4.21 Translation
Transcription
mRNAprocessing
Attachment ofribosomal subunits
Translation
Termination
DNA
RNApolymerase
Nuclearmembrane
Amino acid
tRNA
mRNA
Ribosomalsubunits
Completedpeptide
Growing peptidechain
Incoming tRNAbound to anamino acid
Anticodon
Outgoing“empty” tRNA
Ribosome
Each tRNA molecule attaches at one end to a specifi c amino acid.The anticodon of the tRNA molecule pairs with the a ppropriatecodon on the mRNA, allowing amino acids to be linke d in theorder specified by the mRNA code.
mRNA
47Figure 4.21 Translation
RNApolymerase
Nuclearmembrane
DNA
Transcription
Slide 1
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48Figure 4.21 Translation
RNApolymerase
Nuclearmembrane
DNA
Transcription
mRNAprocessing
Slide 2
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49Figure 4.21 Translation
RNApolymerase
Nuclearmembrane
DNA
Transcription
mRNAprocessing
Attachment ofribosomal subunits
Slide 3
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50Figure 4.21 Translation
RNApolymerase
Nuclearmembrane
DNA
Transcription
mRNAprocessing
Attachment ofribosomal subunits
Translation
Amino acid
tRNA
mRNA
Outgoing“empty” tRNA
Growing peptidechain
Ribosome
Anticodon
Incoming tRNAbound to anamino acid
Asp
Phe Trp
Lys
Each tRNA molecule attaches at one end to a specifi camino acid. The anticodon of the tRNA molecule pair swith the appropriate codon on the mRNA, allowing am inoacids to be linked in the order specified by the mR NA code.
Slide 4
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51Figure 4.21 Translation
RNApolymerase
Nuclearmembrane
DNA
Transcription
mRNAprocessing
Attachment ofribosomal subunits
Translation
Amino acid
tRNA
mRNATermination
Ribosomalsubunits
Completedpeptide
mRNA
Outgoing“empty” tRNA
Growing peptidechain
Ribosome
Anticodon
Incoming tRNAbound to anamino acid
Asp
Phe Trp
Lys
Each tRNA molecule attaches at one end to a specifi camino acid. The anticodon of the tRNA molecule pair swith the appropriate codon on the mRNA, allowing am inoacids to be linked in the order specified by the mR NA code.
Slide 5
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52Protein Synthesis
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BioFlixTM: Protein Synthesis
53Protein Sorting Directs Proteins to Their Destination
• Signal sequence
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54Proteins Undergo Post-Translational Modification
• Protein folding
• Cross-linkage
• Cleavage
• Addition of other molecules or groups
• Assembly into polymeric proteins
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55Summary
• Energy in biological systems
• Chemical reactions
• Enzymes
• Metabolism
• ATP production
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56Summary
• Chemical reactions– Reactants
– Products
– Reaction rate
• Free energy
• Activation energy
• Exergonic versus endergonic reactions
• Reversible versus irreversible reactions
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57Summary
• Enzymes and substrates
• Cofactors versus coenzymes
• Classification of reactions– Oxidation-reduction
– Hydrolysis-dehydration
– Addition-subtraction-exchange
– Ligation
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58Summary
• Metabolism– Catabolic versus anabolic reactions
• Control of metabolic pathways
• Aerobic versus anaerobic pathways
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59Summary
• ATP production– Glycolysis
– Citric acid cycle
– Electron transport chain
• Glycogen, protein, and lipid metabolism
• Aerobic versus anaerobic metabolism
• Gene transcription and alternative mRNA splicing
• Translation and transfer and ribosomal RNA
• Post-translational modifications
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