Bioorganic Chemistry and Biochemistry CHM3218 Summer C 2008 Dr. Lyons office hours...
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Transcript of Bioorganic Chemistry and Biochemistry CHM3218 Summer C 2008 Dr. Lyons office hours...
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/
Test Dates
May 27June 17July 11July 25
August 8
Biochemistry is more than organic chemistry
Medically importantToxic
Questionably essential
Cr24
Bulk
HydrogenCarbon
NitrogenOxygenSodium
MagnesiumPhosphorous
SulfurChlorine
PotassiumCalcium
ManganeseIron
CobaltNickel
CopperZinc
MolybdenumSelenium
Iodine
EssentialTrace
Other Elements
Boron
Silicon
Vanadium
Environment is the key to understanding biological systemsIron as a case study
Geochemical considerations are critical for life
Effect of O2 concentration on other elements
Effect of O2 concentration on other elements
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
Heterotrophic origin for lifeor
The Primordial Soup Hypothesis
Bioorganic molecules built up by a variety of reactions that precede metabolism
Urey-Miller
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
Deep Sea Vents as Models for Early Pre-Biotic Environments
Vent Effluent
CO2, CO, N2, H2O, H2S, CH4, and NH3
Plus plenty of metals
IRON!!!!!!!
What about outer space?
Comets– CO2, CO, H2O, CH3OH and NH3
– Stellar UV and cosmic rays
Prebiotic Synthesis of Biomonomers
Problems?
• High initial [ ]
• requires [HCN] = 0.01M
• requires [H2CO] = 0.01M
• Must evolve metabolism
before soup is depleted
• Adenine from cyanide
• Ribose from formaldehyde
• 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
What about an autotrophic origin?
Autotrophy = synthesizing complex organics from simple inorganic
molecules
Chemolithoautotrophs
Use inorganic molecules as an energy source
Beggiatoa oxidize sulfide to reduce carbon in the dark
Pyrite
HCO3- + Fe(II)S + H2S HCOO- + Fe(IV)S2 (pyrite) + H2O
∆G = -37.1 kJ mol-1
• Ethyne to ethane• Nitrate to ammonia
Importance of FeS clusters in central metabolism (aconitase, succinate
dehydrogenase, etc…)
The Iron/Sulfur World
Three extant ways of CO2 fixation
• Reverse TCA (bacteria)• Calvin cycle (plants, bacteria)• Acetyl-CoA synthase (bacteria)
After Chemical EvolutionWhat Next?
Replicators
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
A Replicator Replicates
X
X2X+
X
X
X
X
X
X
X
X2X
X
Fidelity
Must make accurate copies. Otherwise the copy will not have the properties
that made the original such as success
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
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.
Evolvability?
The ability to adapt to environmental changes
• 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
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
Ribonucleic AcidsCan fold into complex structures
RNA can act as an information molecule and an enzyme
Certain RNA molecules can
“edit” themselves by self-splicing mechanisms
Self-splicing
Template driven synthesis!
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
RNA could have independently replicated
itself
• RNA evolution can be demonstrated in vitro
The RNA World