metabolism • enzymes - professor welday's weebly...

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© 2013 Pearson Education, Inc.

Energy and Cellular Metabolism

Chapter 4

2About This Chapter

• Energy in biological systems

• Chemical reactions

• Enzymes

• Metabolism


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


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)


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


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


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


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


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


18Figure 4.7 Enzymes lower the activation energy of re actions

KEYReactants


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


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


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


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


GENE ACTIVATION

Induction Repression

Regulatedactivity

Constitutivelyactive

Gene Regulatory proteins

Cytosol

Nucleus

Slide 1



GENE ACTIVATION

TRANSCRIPTION(See Fig. 4.19)

mRNA


Regulatedactivity



Cytosol

Nucleus

Slide 2



GENE ACTIVATION


mRNA PROCESSING(See Fig. 4.20)

Cytosol

Nucleus

ProcessedmRNA

Alternativesplicing Interference

mRNA “silenced”

si RNAmRNA


Regulatedactivity



Slide 3



GENE ACTIVATION



TRANSLATION(See Fig. 4.21)

Cytosol

Nucleus

• rRNA in ribosomes• tRNA• Amino acids

ProcessedmRNA


mRNA “silenced”

si RNAmRNA


Regulatedactivity



Protein chain

Slide 4



GENE ACTIVATION



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


mRNA “silenced”

si RNAmRNA


Regulatedactivity



Protein chain

Slide 5


43RNA Synthesis

• RNA polymerase

• Promoter

• Transcription factors


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


RNApolymerase

Nuclearmembrane

DNA

Transcription

Slide 1



RNApolymerase

Nuclearmembrane

DNA

Transcription

mRNAprocessing

Slide 2



RNApolymerase

Nuclearmembrane

DNA

Transcription

mRNAprocessing


Slide 3



RNApolymerase

Nuclearmembrane

DNA

Transcription

mRNAprocessing


Translation

Amino acid

tRNA

mRNA



Ribosome

Anticodon


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



RNApolymerase

Nuclearmembrane

DNA

Transcription

mRNAprocessing


Translation

Amino acid

tRNA

mRNATermination

Ribosomalsubunits

Completedpeptide

mRNA



Ribosome

Anticodon


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


52Protein Synthesis


BioFlixTM: Protein Synthesis

53Protein Sorting Directs Proteins to Their Destination

• Signal sequence


54Proteins Undergo Post-Translational Modification

• Protein folding

• Cross-linkage

• Cleavage

• Addition of other molecules or groups

• Assembly into polymeric proteins


55Summary

• Energy in biological systems

• Chemical reactions

• Enzymes

• Metabolism

• ATP production


56Summary

• Chemical reactions– Reactants

– Products

– Reaction rate

• Free energy

• Activation energy

• Exergonic versus endergonic reactions

• Reversible versus irreversible reactions


57Summary

• Enzymes and substrates

• Cofactors versus coenzymes

• Classification of reactions– Oxidation-reduction

– Hydrolysis-dehydration

– Addition-subtraction-exchange

– Ligation


58Summary

• Metabolism– Catabolic versus anabolic reactions

• Control of metabolic pathways

• Aerobic versus anaerobic pathways


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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