bioorganic chemistry and biochemistry chm3218 summer c 2008 dr. lyons office hours...
TRANSCRIPT
![Page 1: Bioorganic Chemistry and Biochemistry CHM3218 Summer C 2008 Dr. Lyons office hours lyons@chem.ufl.edu 846-3392 T,W 3-4 PM, R 9-10 AM Class website lyons](https://reader036.vdocuments.site/reader036/viewer/2022081512/5697bf7c1a28abf838c8407b/html5/thumbnails/1.jpg)
Bioorganic Chemistry and Biochemistry
CHM3218 Summer C 2008
Dr. Lyons office hours
846-3392
T,W 3-4 PM, R 9-10 AM
Class website http://www.chem.ufl.edu/~lyons/
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Test Dates
May 27June 17July 11July 25
August 8
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Biochemistry is more than organic chemistry
Medically importantToxic
Questionably essential
Cr24
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Bulk
HydrogenCarbon
NitrogenOxygenSodium
MagnesiumPhosphorous
SulfurChlorine
PotassiumCalcium
ManganeseIron
CobaltNickel
CopperZinc
MolybdenumSelenium
Iodine
EssentialTrace
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Other Elements
Boron
Silicon
Vanadium
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Environment is the key to understanding biological systemsIron as a case study
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Geochemical considerations are critical for life
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Effect of O2 concentration on other elements
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Effect of O2 concentration on other elements
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Iron as a Case Study
Fe(H2O)63+ ---> Fe(OH)3 + 3H+ + 3H2O
Ksp = [Fe3+][OH-]3 ≈ 10-38 M[Fe3+] = 10-38/[OH-]3
At pH 7.0, [Fe3+] = 10-38/(10-7)3 = 10-17 M
Fe(H2O)62+ ---> Fe(OH)2 + 3H+ + 3H2O
Ksp = [Fe2+][OH-]2 ≈ 10-15 M[Fe2+] = 10-15/[OH-]2
At pH 7.0, [Fe2+] = 10-15/(10-7)2 = 0.08 M
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Heterotrophic origin for lifeor
The Primordial Soup Hypothesis
Bioorganic molecules built up by a variety of reactions that precede metabolism
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Urey-Miller
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Urey-Miller used a reducing atmosphere
• Strongly Reducing– H2O, CH4, NH3 and H2
• Mildly Reducing (Cosmic rays)– CO, N2, H2O and H2
• Oxidizing– CO2, CO, N2, H2O, CH4, and H2
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Deep Sea Vents as Models for Early Pre-Biotic Environments
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Vent Effluent
CO2, CO, N2, H2O, H2S, CH4, and NH3
Plus plenty of metals
IRON!!!!!!!
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What about outer space?
Comets– CO2, CO, H2O, CH3OH and NH3
– Stellar UV and cosmic rays
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Prebiotic Synthesis of Biomonomers
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Problems?
• High initial [ ]
• requires [HCN] = 0.01M
• requires [H2CO] = 0.01M
• Must evolve metabolism
before soup is depleted
• Adenine from cyanide
• Ribose from formaldehyde
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• We don’t know the composition of the early atmosphere
• Many important compounds have not YET been synthesized under simulated conditions
• Many ancient life forms (by phylogeny) are autotrophic and hyperthermophilic
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What about an autotrophic origin?
Autotrophy = synthesizing complex organics from simple inorganic
molecules
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Chemolithoautotrophs
Use inorganic molecules as an energy source
Beggiatoa oxidize sulfide to reduce carbon in the dark
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Pyrite
HCO3- + Fe(II)S + H2S HCOO- + Fe(IV)S2 (pyrite) + H2O
∆G = -37.1 kJ mol-1
• Ethyne to ethane• Nitrate to ammonia
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Importance of FeS clusters in central metabolism (aconitase, succinate
dehydrogenase, etc…)
The Iron/Sulfur World
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Three extant ways of CO2 fixation
• Reverse TCA (bacteria)• Calvin cycle (plants, bacteria)• Acetyl-CoA synthase (bacteria)
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After Chemical EvolutionWhat Next?
Replicators
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A Replicator Replicates
• It recognizes its components and uses them to makes copies of itself
• It is subject to the laws of natural selection and must compete with other replicators for resources
• Success is governed by its– Fidelity– Fecundity– Longevity– Evolvability
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A Replicator Replicates
X
X2X+
X
X
X
X
X
X
X
X2X
X
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Fidelity
Must make accurate copies. Otherwise the copy will not have the properties
that made the original such as success
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Fecundity
Must replicate at a high enough rate so that it can out-breed its competitors.
Replication is a constant competition with other replicators for limited
building blocks
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Longevity
A replicator must be stable and long-lived enough so that it has a chance to replicate. Unstable replicators are
unlikely to be able to compete.
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Evolvability?
The ability to adapt to environmental changes
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• Pre-cellular replicator would need to catalyze its own replication
• Need a molecule that:– Act as a biochemical catalyst to make starting material– Act as a template to replicate itself
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What about RNA?
BASE
O
OHOH
HH
HH
HO
Guanine
UracilAdenine
Cytosine
PURINES PYRIMIDINES
N
N
N
N N
NN
O
O
Ribose
Ribose
H
H
H
N
N
N
O
N
N
N
N O
NRibose
Ribose
H
H
H
H
H
Can recognize itself
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Ribonucleic AcidsCan fold into complex structures
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RNA can act as an information molecule and an enzyme
Certain RNA molecules can
“edit” themselves by self-splicing mechanisms
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Self-splicing
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Template driven synthesis!
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RNA molecules have been selected that catalyze many
reactions• RNA cleavage• RNA ligation
• RNA phosphorylation• Phosphodiester cleavage
• Cyclic PO4 hydrolysis• Amino acid activation
• tRNA charging• Template driven RNA polymerization
• Porphyrin metallation• Glycosidic bond formation
• Peptide bond formation
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RNA could have independently replicated
itself
• RNA evolution can be demonstrated in vitro
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The RNA World