On the relations between error rates in DNA replication and elementary chemical rate constants

1982 ◽  
Vol 94 (3) ◽  
pp. 607-632 ◽  
Author(s):  
Jean Durup
2017 ◽  
Author(s):  
Ben Newsome ◽  
Mat Evans

Abstract. Chemical rate constants determine the composition of the atmosphere and how this composition has changed over time. They are central to our understanding of climate change and air quality degradation. Atmospheric chemistry models, whether online or offline, box, regional or global use these rate constants. Expert panels synthesise laboratory measurements, making recommendations for the rate constants that should be used. This results in very similar or identical rate constants being used by all models. The inherent uncertainties in these recommendations are, in general, therefore ignored. We explore the impact of these uncertainties on the composition of the troposphere using the GEOS-Chem chemistry transport model. Based on the JPL and IUPAC evaluations we assess 50 mainly inorganic rate constants and 10 photolysis rates, through simulations where we increase the rate of the reactions to the 1σ upper value recommended by the expert panels. We assess the impact on 4 standard metrics: annual mean tropospheric ozone burden, surface ozone and tropospheric OH concentrations, and tropospheric methane lifetime. Uncertainty in the rate constants for NO2 + OH    M →  HNO3, OH + CH4 → CH3O2 + H2O and O3 + NO → NO2 + O2 are the three largest source of uncertainty in these metrics. We investigate two methods of assessing these uncertainties, addition in quadrature and a Monte Carlo approach, and conclude they give similar outcomes. Combining the uncertainties across the 60 reactions, gives overall uncertainties on the annual mean tropospheric ozone burden, surface ozone and tropospheric OH concentrations, and tropospheric methane lifetime of 11, 12, 17 and 17 % respectively. These are larger than the spread between models in recent model inter-comparisons. Remote regions such as the tropics, poles, and upper troposphere are most uncertain. This chemical uncertainty is sufficiently large to suggest that rate constant uncertainty should be considered when model results disagree with measurement. Calculations for the pre-industrial allow a tropospheric ozone radiative forcing to be calculated of 0.412 ± 0.062 Wm−2. This uncertainty (15 %) is comparable to the inter-model spread in ozone radiative forcing found in previous model-model inter-comparison studies where the rate constants used in the models are all identical or very similar. Thus the uncertainty of tropospheric ozone radiative forcing should expanded to include this additional source of uncertainty. These rate constant uncertainties are significant and suggest that refinement of supposedly well known chemical rate constants should be considered alongside other improvements to enhance our understanding of atmospheric processes.


2002 ◽  
Vol 2 ◽  
pp. 275-281 ◽  
Author(s):  
Igor V. Shevelev ◽  
Kristijan Ramadan ◽  
Ulrich Hubscher

Proofreading function by the 3′→ 5′ exonuclease of DNA polymerase δ (pol δ) is consistent with the observation that deficiency of the associated exonuclease can lead to a strong mutation phenotype, high error rates during DNA replication, and ultimately cancer. We have isolated pol δdfrom isotonic (pol δi) and detergent (pol δd) calf thymus extracts. Pol δdhad a 20-fold higher ratio of exonuclease to DNA polymerase than pol δi. This was due to the physical association of the TREX2 exonuclease to pol δd, which was missing from pol δi. Pol δdwas fivefold more accurate than pol δiunder error-prone conditions (1 μM dGTP and 20 dATP, dCTP, and dTTP) in a M13mp2 DNA forward mutation assay, and fourfold more accurate in an M13mp2T90 reversion assay. Under error-free conditions (20 μM each of the four dNTPs), however, both polymerases showed equal fidelity. Our data suggested that autonomous 3′→ 5′ exonucleases, such as TREX2, through its association with pol I can guarantee high fidelity under difficult conditions in the cell (e.g., imbalance of dNTPs) and can add to the accuracy of the DNA replication machinery, thus preventing mutagenesis.


1997 ◽  
Author(s):  
Naoual Belouaggadia ◽  
Raymond Brun ◽  
Naoual Belouaggadia ◽  
Raymond Brun

2013 ◽  
Vol 135 (4) ◽  
Author(s):  
Mohammad Janbozorgi ◽  
M. Reza H. Sheikhi ◽  
Hameed Metghalchi

The principle of detailed balance is shown to be a sufficient condition for the second law of thermodynamics in thermally equilibrated elementary chemical reactions. For an elementary reaction, the principle of detailed balance relates the forward and the reverse rate constants through the reaction equilibrium constant. It is shown that, in addition to the long known thermodynamic inconsistency at chemical equilibrium state, departure from this principle introduces an extra source/sink of entropy in the entropy balance for an elementary chemical reaction. The departure results in the wrong final chemical equilibrium state and, depending on the choice of the reverse rate constants, may lead to negative entropy productions during kinetic transients.


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