Biochemistry Commons^™

Influence Of Physical Variability Of Highly Weathered Sedimentary Rock On Nitrate In Area 3 Of The Enigma Field Research Site At Y-12, Erin Kelly

Masters Theses

Uranium processing and waste storage in unlined waste ponds leached contaminants into the groundwater at Y-12, Oak Ridge, Tennessee, from the 1950s to 1980s. Groundwater wells near the S-3 ponds have had the highest nitrate concentrations of groundwater anywhere in the world (>10,000 mg/L). For reference, the maximum contaminant level for nitrate in drinking water set by the U.S. Environmental Protection Agency is 10 mg/L. Since 2012, the ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies) group has been characterizing, monitoring, and conducting field experiments to understand the interactions between contaminants, microbes, and the subsurface. The goals …

Comparison Of Activation Enthalpies For Aminoglycoside Modification Reactions, Brittany Sterling Soto

Masters Theses

At highly elevated temperatures, many biological reactions can proceed spontaneously from the ground state to the transition state. However, due to the long half-life of these reactions, catalysts are required to catalyze these reactions at modern day temperatures by lowering the activation energy. Wolfenden et al. has previously shown that catalysts enhance the rate of the reaction by reducing the enthalpy of activation. Therefore, the activation energies have been determined for three aminoglycoside modifying enzymes, APH(3’)-IIIa, AAC(3)-IIIb, and AAC(3)-VIa, to determine whether these three enzymes distinguish between the two classes of aminoglycoside antibiotics by reducing the enthalpy of activation during …

Determination Of Structural Stabilities Of Metal-Free Porphyrin Cytochrome C, Zinc Cytochrome C, And Cobalt Cytochrome C, Usha K. Tottempudi

Masters Theses

No abstract provided.

Design And Synthesis Of Boronic Acid-Based Sensors For Microarray Analysis And Fret-Detection To Study Carbohydrates, Yilin Wang

Masters Theses

Carbohydrates play significant roles in various biological and pathological processes such as cancer metastasis and inflammation. They participate in various signaling pathways and are able to bind to a litany of biological receptors such as proteins and viruses. Biologists have known for decades that the structure of glycans changes with the onset of cancer and inflammation. Due to these important activities, carbohydrate sensing has long been a focus of research. One example of such a carbohydrate sensor is boronic acid-based sensors. Boronic acid-based sensors are of particular interest due to their selectivity for 1,2- or 1,3-diols. A variety of techniques …

Non-Thermal Plasma Inactivation Of Bacillus Amyloliquefaciens Spores, Yaohua Huang

Masters Theses

Bacterial spores have remarkable resistance to a variety of harsh conditions, causing spoilage in food industry and becoming the primary bacterial agent in biowarfare and bioterrorism. In this study, inactivation mechanisms of Bacillus amyloliquefaciens (BA) spores by non-thermal plasma (NTP) were investigated by using Fourier-transform infrared spectroscopy (FTIR) as a major tool to exam spores after NTP treatment. Chemometric techniques, such as multivariate classification models based on soft independent modeling of Class Analogy (SIMCA) and Principal Component Analysis (PCA), were employed to identify functional group changes in FTIR spectra. The IR absorbance bands correlated to dipicolinic acid (DPA) decreased after …

Investigating The Allosteric Behavior Of Malate Dehydrogenase From Escherichia Coli, Eman M. Ghanem

Masters Theses

Regulatory mechanisms of malate dehydrogenase from E.coli (eMDH) involving NADH as an allosteric effector were investigated. The reaction was studied in both directions: malate oxidation and oxaloacetate reduction. When malate was the variable substrate, a plot of rate against substrate concentration was sigmoidal in the presence of 0.065 mM NADH, which indicates the presence of an allosteric site for NADH on the enzyme. Binding of NADH at the allosteric site causes conformational changes in the active site and, thereby, changes the catalytic activity of the enzyme. An increase in K_m value, from 1.3 to 3.9 mM malate was observed, …

Mechanistic Studies On Malate Dehydrogenase From Escherichia Coli, S. Kirk Wright

Masters Theses

Kinetic studies and chemical modification studies were performed on malate dehydrogenase from Escherichia coli (eMDH). Chemical modification studies using diethylpyrocarbonate and iodoacetic acid, along with log V/K profiles indicate that one ionizing group with a pK_a between 7.9 and 8.5 acts as a general acid/base in the catalytic mechanism. Log V profiles suggest that malate binds to the correctly protonated form of the enzyme. These results imply that a histidine residue is required for catalysis.

A primary deuterium kinetic isotope effect of 1.43 (±0.14) was observed on V/K using malate-2-d, while no isotope effect was measured on V_{max …}

Analysis Of The Surface Polysaccharides Of R. Trifolii Su843 And Its Sym Plasmid Alterated Mutants, Jauh-Lin Duh

Masters Theses

The Rhizobium trifolii polysaccharides from SU843 and mutants--HC843(pBR1AN), HC843, 8002--in which the sym plasmid is replaced, absent, or mutated by transposon Tn5 were isolated. The surface polysaccharides of genetically altered mutants were compared quantitatively and qualitatively with one another and with the parent strain. The interpretation of these results is discussed in relation to the function of Rhizobium surface polysaccharides in the symbiotic process. The symbiotic ability of SU843 and mutant strains is as follows: (a) SU843, nod⁺, fix⁺; (b) mutant 8002, roa⁺ (still attaches to root hair), hac^-, nod^-; (c) …