Ch 4: Energy and Cellular Metabolism Energy as it relates to Biology Energy as it relates to Biology...
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Transcript of Ch 4: Energy and Cellular Metabolism Energy as it relates to Biology Energy as it relates to Biology...
![Page 1: Ch 4: Energy and Cellular Metabolism Energy as it relates to Biology Energy as it relates to Biology Chemical reactions Chemical reactions Enzymes Enzymes.](https://reader036.fdocuments.us/reader036/viewer/2022081516/55159d54550346486b8b5cff/html5/thumbnails/1.jpg)
Ch 4: Energy and Cellular Ch 4: Energy and Cellular MetabolismMetabolism
Ch 4: Energy and Cellular Ch 4: Energy and Cellular MetabolismMetabolism
EnergyEnergy as it relates to Biology as it relates to Biology
Chemical reactionsChemical reactions
EnzymesEnzymes and how they speed rxs
MetabolismMetabolism and metabolic pathways and metabolic pathways CatabolismCatabolism (ATP production) (ATP production) AnabolismAnabolism ( (Synthesis of biologically
important molecules))
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Energy in Biological SystemsEnergy in Biological Systems
Review on your own!
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Chemical ReactionsChemical Reactions
1.1. Transfer energyTransfer energy
2.2. or use energy to do workor use energy to do work
Substrates / reactants Products
BioenergeticsBioenergetics: Study of energy flow through biol. systems
Reaction rate = speed of reaction
A + B A + B C + DC + D
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Activation Energy Starts ReactionActivation Energy Starts Reaction
Reversible (most biol. rxs.) vs. Reversible (most biol. rxs.) vs. irreversible reactionsirreversible reactions
Fig 4-3
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Endergonic vs. Exergonic ReactionsEndergonic vs. Exergonic Reactions
CouplingCoupling endergonic endergonic and exergoinic rxsand exergoinic rxs
DDirect coupling vs. irect coupling vs. indirect couplingindirect coupling
Which kind?
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Enzymes are Proteins acting as Enzymes are Proteins acting as Biological CatalystsBiological Catalysts
1.1. chemical reaction rate by lowering chemical reaction rate by lowering activation energyactivation energy
2.2. are are not changed themselves themselves
3.3. do not change nature of rx nor resultdo not change nature of rx nor result
4.4. are specificare specific
4 important characteristics of enzymes
Fig 4-8
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![Page 8: Ch 4: Energy and Cellular Metabolism Energy as it relates to Biology Energy as it relates to Biology Chemical reactions Chemical reactions Enzymes Enzymes.](https://reader036.fdocuments.us/reader036/viewer/2022081516/55159d54550346486b8b5cff/html5/thumbnails/8.jpg)
Enzymes lower activation energy:Enzymes lower activation energy:All chemical reactions in body must be conducted at body temp.!!
How do enzymes lower activation energy ?
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Enzymes bind to reactant molecules and Enzymes bind to reactant molecules and bring them together in best position for rx.bring them together in best position for rx.
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Small region of the complex Small region of the complex 3D structure is active (or 3D structure is active (or
binding) site.binding) site.
Enzymes bind to substrateEnzymes bind to substrate
Active Site:Active Site:
Old: Lock-and-key model / New: Induced-fit modelFig 2-16
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Enzyme-substrate interaction: Enzyme-substrate interaction: The old and the new modelThe old and the new model
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Naming of EnzymesNaming of Enzymes
KinaseKinase
PhosphatasePhosphatase
PeptidasePeptidase
DehydrogenaseDehydrogenase
mostly suffix mostly suffix -ase-asefirst part gives info on functionfirst part gives info on function
examples
Not in book
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IsozymesIsozymes == different models of same different models of same enzyme (differ in 1 or few aa)enzyme (differ in 1 or few aa)
ExamplesExamples::
1.1. AmylaseAmylase
2.2. LDH → LDH → importance in diagnostics
Catalize same reaction under Catalize same reaction under different conditions and in different conditions and in
different tissues/organsdifferent tissues/organs
Review Table 4-3
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Enzyme Activity Enzyme Activity depends on depends on
1. proteolytic activation (for some)(for some)
2. cofactors & coenzymes (for some)(for some)
3. temperature
4. pH
5. other molecules interacting with enzymeinteracting with enzyme
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1) Proteolytic 1) Proteolytic Activation Activation
Also 1. Pepsinogen Pepsin2. Trypsinogen Trypsin
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2) Cofactors & Coenzymes2) Cofactors & Coenzymes
structure:___________ molecules
(e.g. ?)
function:conformational change
of active site
structure:Organic molecules (vitamin derivatives, FADH2 ....)
function:act as receptors & carriers for atoms or functional groups that are removed from substrate
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5) Molecules interacting with enzyme: 5) Molecules interacting with enzyme:
Allosteric Modulators bind to enzyme away bind to enzyme away from active site changing shape of active site for better or for from active site changing shape of active site for better or for worseworse
Allosteric Activator
Allosteric Inhibitor
Fig 2-20
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5) Molecules interacting with enzyme cont.5) Molecules interacting with enzyme cont.
Competitive inhibitorsCompetitive inhibitors::
reversible binding to reversible binding to active site active site
block active siteblock active site
Also possible: irreversible binding via covalent bonds, e.g.:• Penicillin • Cyanide
Fig 2-19Fig 2-19
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Reversible Reactions follow the Reversible Reactions follow the Law of Mass ActionLaw of Mass Action
Fig 4-9
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Three Major Types of Enzymatic Three Major Types of Enzymatic Reactions:Reactions:
1. Oxydation - Reduction reactions(transfer of ?)(transfer of ?)
2.2. Hydrolysis - Hydrolysis - Dehydration reactions(breakdown & synthesis of ?)(breakdown & synthesis of ?)
3.3. Addition-Subtraction-Exchange Addition-Subtraction-Exchange reactionsreactions
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?
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MetabolismMetabolism
Catabolism Anabolism
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Metabolism definition: ___________Metabolism definition: ___________
Metabolic pathways = network of Metabolic pathways = network of linked reactions linked reactions
Cells regulate metabolic pathways viaCells regulate metabolic pathways via1. Control of enzyme concentration2. Modulator production (allosteric
modulators, feedback inhibition, Fig 4-11)
3. Different enzymes for reversible rxs, Fig 4-12)
4. Compartmentation of enzymes
5. ATP / ADP ratio
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Metabolic pathways: Network of Metabolic pathways: Network of interconnected chemical reactionsinterconnected chemical reactionsLinear pathway
Circular pathway
Branched pathway
Intermediates
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= end product inhibitionSpecial case:
Fig 4-11
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Catabolic Pathways: Catabolic Pathways: ATP-Production-Production
Amount of ATP produced reflects on usefulness of metabolic pathways:
Aerobic pathways
Anaerobic pathways
Different biomolecules enter pathway at different points
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ATP Cycle
ATP = Energy Carrier of Cell ATP = Energy Carrier of Cell (not very useful (not very useful for energy storage) for energy storage)
ATP : ADP ratio determines status of ATP synthesis reactions
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GlycolysisGlycolysis From 1 glucose to 2 From 1 glucose to 2
pyruvate moleculespyruvate molecules
Main catabolic pathway of Main catabolic pathway of cytoplasmcytoplasm
Does not require ODoes not require O2 2 part part of _________ and of _________ and ____________ catabolism____________ catabolism
Starts with Starts with phosphorylation phosphorylation (“Before (“Before doubling your money you first doubling your money you first have to invest!”)have to invest!”)
Fig 4-13
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Anaerobic catabolism: Pyruvate
lactate
Aerobic catabolism: Pyruvate
Citric Acid Cycle
Pyruvate has 2 Possible Fates Pyruvate has 2 Possible Fates
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Citric Acid CycleCitric Acid Cycle
Other names ?Other names ?
Takes place in ?Takes place in ?
Energy Produced:Energy Produced:1 ATP1 ATP3 NADH 3 NADH 1 FADH1 FADH22
Waste – 2 COWaste – 2 CO22
Fig. 4-16
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NADH
NADHNADH
FADH2
Energy Yield of Krebs Cycle
Compare to Fig. 4-16
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Final step:Final step: Electron Transport System Electron Transport System
Chemiosmotic theory / oxydative phosphorylation
Transfers energy from NADH and FADHTransfers energy from NADH and FADH22 to ATP to ATP (via e(via e- - donation and Hdonation and H++ transport) transport)
Mechanism:Mechanism: Energy released by movement Energy released by movement of eof e-- trough transport system is stored trough transport system is stored temporarily in Htemporarily in H++ gradient gradient
NADH produces a maximum of 2.5 ATP NADH produces a maximum of 2.5 ATP FADHFADH22 produces a maximum of 1.5 ATP produces a maximum of 1.5 ATP
1 ATP formed per 3H+ shuttled through ATP Synthase
Fig 4-17
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Cellular Cellular RespirationRespiration
Maximum potential yield for aerobic glucose metabolism: 30-32 ATP synthesized from ADP
H2O is a byproduct
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Synthetic PathwaysSynthetic Pathways
Unit molecules Macromolecules
PolysaccharidesLipidsDNA
Protein
nutrients & energy required
Anabolic rxs synthesize large biomoleculesAnabolic rxs synthesize large biomolecules
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Glycogen SynthesisGlycogen SynthesisMade from glucoseMade from glucose
Stored in all cells but especially inStored in all cells but especially in Liver Liver (keeps 4h glycogen reserve for between meals)(keeps 4h glycogen reserve for between meals)
Skeletal Muscle Skeletal Muscle muscle contractionmuscle contraction
GluconeogenesisGluconeogenesisGlycolysis in reverse Glycolysis in reverse
From glycerol, aa and lactateFrom glycerol, aa and lactate
All cells can make G-6-P, only liver All cells can make G-6-P, only liver and Kidney can make glucoseand Kidney can make glucose
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Proteins are the key to cell function → Proteins are the key to cell function → necessary for all cell functionsnecessary for all cell functions
Protein synthesis is under nuclear direction Protein synthesis is under nuclear direction DNA specifies ProteinsDNA specifies Proteins
Protein SynthesisProtein Synthesis
DNA DNA mRNA mRNA Protein Protein? ?
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How can only 4 bases in DNA How can only 4 bases in DNA encode > 20 different aa in protein?encode > 20 different aa in protein?
1 letter word: 1 base = 1 aa 1 letter word: 1 base = 1 aa how many possibilitieshow many possibilities??
2 letter word: 2 bases = 1 aa2 letter word: 2 bases = 1 aa how many possibilitieshow many possibilities??
3 letter word:3 letter word: 3 bases = 1 aa 3 bases = 1 aa how many possibilitieshow many possibilities??
3 letter words3 letter words = = base triplets base triplets or or codonscodons
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1 start codon 1 start codon (AUG = Met)(AUG = Met)
3 stop codons3 stop codons
60 other 60 other codons for codons for 19 aa19 aa
Redundancy of Genetic Code
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TranscriptionTranscription
DNADNA is transcribed into is transcribed into complementary complementary mRNAmRNA
byRNA PolymeraseRNA Polymerase
+ nucleotides+ Mg2+ ( = ?)
+ ?
Gene = elementary unit of inheritance
Compare to Fig. 4-25 and review Fig 4-26
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TranslationTranslationmRNA is translated into string of aa mRNA is translated into string of aa (= polypeptide)(= polypeptide)
mRNA + ribosomes + tRNA meet in cytoplasm
Anticodon pairs with mRNA codon aa determined
Amino acids are linked via
______________ bond.
2 important components ??
Fig 4-27
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Protein SortingProtein Sorting
Due to signal/targeting sequence Due to signal/targeting sequence No targeting sequence No targeting sequence protein stays in cytoplasmprotein stays in cytoplasm
Targeting sequence Targeting sequence protein destined for protein destined for translocation into organelles or for export from celltranslocation into organelles or for export from cell
Post – Translational protein modifications: Folding, cleavage, additions glyco- , lipo- proteins
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For “export proteins”: Signal sequence For “export proteins”: Signal sequence leads growing polypeptide chain across ER leads growing polypeptide chain across ER membrane into ER lumenmembrane into ER lumen
Modifications in ERModifications in ER
Transition vesicles toTransition vesicles to
Golgi apparatus for further modificationsGolgi apparatus for further modifications
Transport vesicles to cell membraneTransport vesicles to cell membrane Compare to Fig 4-28
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DNA Replication DNA Replication
Semi- Semi- conservativeconservative
DNA DNA polymerasepolymerase
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Running problem: Tay-Sachs Disease