Physical Sciences and Mathematics Commons^™

Interactions In The Cpsrp Dependent Targeting Of Light Harvesting Chlorophyll Binding Protein To The Thylakoid Membrane, Rory Henderson

Graduate Theses and Dissertations

Targeting of proteins is a critical component of cellular function. A universally conserved targeting system of the cytosol utilizes a signal recognition particle (SRP) to target many proteins contranslationally to the endoplasmic reticulum in eukaryotes or the inner membrane in prokaryotes. A homologous SRP system exists in the chloroplast that delivers light harvesting chlorophyll binding proteins (LHCP) to they thylakoid membrane. The chloroplast SRP (cpSRP) is a heterodimer composed of a novel 43 kDa subunit and a 54 kDa subunit homologous to a component of the SRP system, SRP54. Many details regarding the interactions between the proteins of the cpSRP …

Role Of The Inner Shell Architecture On The Various Blinking States And Decay Dynamics Of Core-Shell And Core-Multishell Quantum Dots, Pooja Bajwa

Graduate Theses and Dissertations

Colloidal semiconductor nanocrystals (quantum dots, QDs) have received much attention in recent years due to their uniquely size-tunable properties leading to a number of promising applications. Some of their most popular applications include their use as fluorescent probes in biology, as electro-optical components and in photovoltaic devices. CdSe-based QDs are particularly important because of their ease of synthesis, high photoluminescence quantum yields (PL QYs) across the whole visible spectrum and their photostabilty. Shelling of core QDs is usually carried out to improve their optical properties, minimize outer environmental effects on their properties, and avoid toxic element exposure to the environment. …

Bioorthogonal Reactions: Synthesis And Evaluation Of Different Ligands In Copper Catalyzed Azide-Alkyne1,3-Dipolar Cycloaddition (Cuaac), Zainab Abdullah Almansaf

Graduate Theses and Dissertations

The Copper CatalyzedAzide-Alkyne1,3-Dipolar Cycloaddition (CuAAC) reaction has unique features that qualify it to be one of the best click reactions. Its applications have been shown in different aspects and for multiple purposes. The oxidative degradation of biological systems (labile proteins and live cells) is, however, generally recognized as the major problem when using this reaction in living systems. Reactive oxidation species can be easily produced in the presence of copper(II), ascorbate and air, and this is the main cause of toxicity. However, the uses of ligands have shown a major impact on reducing copper toxicity, protecting Cu(I) from the redox …

Direct Attachment Of 4-Hydroxybenzoic Acid Polymers And Capture Agents To Flat Sheet And Microdialysis Membranes For Improved Mass Transport, Sarah Jane Phillips

Graduate Theses and Dissertations

Microdialysis (MD) sampling is a diffusion-based separation method which has the ability to sample any analyte that can diffuse across the semi-permeable membrane. However one challenge for MD is that for soluble proteins greater than 10 kDa, the relative recovery (RR) using a 100 kDa MD probe is between 1-5%.1 There are two major barriers that lead to these low recovery values - nonspecific adsorption (NSA) and poor solute mass transport. To overcome these two barriers, the modification of PES-based MD membranes has been initiated by laccase. Previous researchers have used laccase to modify PES flat sheet and hollow fiber …

Heparin-Peptide Interactions, Jacqueline Anastasia Morris

Graduate Theses and Dissertations

Heparin is a polydispersed sulfated molecule that is part of the family called glycosaminoglycans found in the extracellular matrix and cell surfaces. This molecule is extremely important for the activation of proteins and protein-receptor interactions that are responsible for downstream cell signaling pathways. Heparin has been isolated from porcine intestine and used as an anticoagulant for the prevention of embolisms, heart thrombosis, and clotting during heart surgeries. This so-called miracle drug was in use until 2008, when isolated batches were found to be contaminated with other glycosaminoglycans similar to heparin. From 2008, there has been a dire need for a …

Investigation Of The Interaction Of Dimeric Ruthenium Complexes With Cytochrome B5, Christopher Dain Rupar

Graduate Theses and Dissertations

Photoreactive complexes to study the kinetics of electron transfer of proteins have been in use for a long time. It has always been speculated that complexes bind near the heme or the electron transfer reaction would not occur. But it is unkown exactly how the complex interacts with the protein. The structural, thermodynamic, and kinetic properties of rat liver microsomal cytochrome b5 were investigated when bound to ruthenium dimer complexes. Heteronuclear Single Quantum Coherence studies support a dynamic binding model of a dimer Ru complex bound near the protein’s heme involving residues H39, E44, G42, V61, G62, and H63. The …

Studies In The Asymmetric Synthesis Of The C21-C34 Fragment Of The Natural Product, Antascomicin B, Brian Lee Walker

Graduate Theses and Dissertations

This dissertation describes studies in the asymmetric synthesis of the C21 – C34 fragment of the natural product, antascomicin B. Antascomicin B is structurally related to FK506, binds strongly to FKBP12, yet does not shown immunosuppressive activity. Small ligand FKBP12 binding complexes were shown to have potent neuroprotective and neuroregenerative properties in mouse models of Parkinson’s disease. The highlighted chemical reactions include an asymmetric transfer hydrogenation (ATH), Ireland-Claisen rearrangement (ICR), directed hydrogenation and allylic diazene rearrangement.

The Role Of Organic Matter In The Fate And Transport Of Antibiotic Resistance, Metals, And Nutrients In The Karst Of Northwest Arkansas, Victor Lee Roland Ii

Graduate Theses and Dissertations

Organic matter (OM) in the environment acts as a nutrient, but may also act as a transport vector for harmful chemical compounds and bacteria. Acetate is a labile form of OM produced during fermentation in anaerobic lagoons used to store animal fecal-waste from concentrated animal feeding operations (CAFOs). Dry and liquid fertilizers from CAFOs pose a threat to groundwater by introducing excessive amounts of nutrients (e.g. OM, nitrate and ammonia), metals, and antibiotic compounds. In the epikarst of Northern Arkansas in the Buffalo River watershed additional input of labile dissolved organic carbon (DOC) from liquid CAFO waste-fertilizers was hypothesized to …

Mechanism Of Rapid Electron Transfer Reactions Involving Cytochrome Bc1, Cytochrome C And Cytochrome Oxidase, Jeremy Erik Durchman

Graduate Theses and Dissertations

Electron transfer between mitochondrial proteins complexes represents the primary means by which living things acquire the requisite energy for survival. The coupling of electron transfer to proton translocation creates an electrochemical gradient that drives the synthesis of highly energetic compounds such as ATP. The purpose of these studies is to measure rates of electron transfer and elucidate the important governing factors in the redox events involving cytochrome bc1, cytochrome c and cytochrome oxidase. Using rapid initiation of redox events triggered by laser flash excitation of ruthenium compounds, and strategically monitoring unique spectral properties of these proteins in the visible region …

Two Studies: Stereoselective C-C Bond Formations Of N-Boc-Piperidines Using Selected Organolithiums And Visible-Light-Mediated Synthesis Of Fused Indolines Using Tethered Styrenes, Scott Alan Morris

Graduate Theses and Dissertations

Chemists worldwide have accepted the challenge of developing methods to access a variety of compounds as single enantiomers, including the use of enzymes, chiral auxiliaries, and resolutions. In particular, dynamic resolutions offer a unique way to access chiral compounds using a few controllable steps, including the variation of both time and temperature. Many groups have implemented this methodology to generate various polysubstituted pyrrolidines and piperidines, which are substructures ranking high on the list of nitrogen–containing pharmaceuticals.

The Gawley group revealed a catalytic dynamic resolution (CDR) of N–Boc–piperidine using a chiral ligand. Impressively, the chemistry was tolerant of a variety of …

[3+2] Annulation Of Cyclopropylanilines With Alkynes Under Photocatalysis, Theresa Ha Nguyen

Graduate Theses and Dissertations

Over the past decade, pharmaceutical industries have prioritized their focus on discovering new innovative drugs, yet the syntheses are often either inefficient or the approach of environmental sustainability presents a great deal of concern. Moreover, the methodology developments for amine syntheses have continued to flourish due to their important role and wide use in pharmaceutics. Yet their syntheses often lack sustainability and efficiency. Synthetic chemists have continued to explore potential innovative avenues for conducting chemical reactions more effectively and efficiently. One of the most abundant, renewable natural resources is solar energy and to harvest, use, and store it directly is …

The Large-Scale Synthesis And Asymmetric Hydrosilylations Of Cuiphet, A C2-Symmetric N-Heterocyclic Carbene, Elizabeth Suzanne Spahn

Graduate Theses and Dissertations

CuIPhEt is a C2-symmetric N-heterocyclic carbene catalyst used in the asymmetric hydrosilylation of a variety of prochiral ketones with good yields and selectivities. The large-scale, five-step synthesis of this carbene has been devised. The second step of the synthetic plan includes a double asymmetric hydrogenation of a 1,1-diaryl alkene—a traditionally difficult transformation. The procedure for the use of CuIPhEt in asymmetric hydrosilylations has been optimized and used on both the originally published substrate scope and new compounds. This protocol for the hydrosilylation has been applied in a 10 g reduction to create an intermediate for use toward the total synthesis …

Regulation Of The Reaction Between Cytochrome C And Cytochrome Oxidase, Jennifer Silva-Nash

Chemistry & Biochemistry Undergraduate Honors Theses

Irreversible brain damage is commonly seen in patients that have suffered strokes, cardiac arrest, or other brain ischemia events. The hypoxic conditions result in neuron death, and previous studies have shown that additional damage occurs when blood flow is restored. It is thought that the lack of energy production during post-ischemia events also causes severe brain damage, as the brain heavily depends on oxidative phosphorylation. Cytochrome c (Cyt c) plays a crucial role in this energy production by means of the electron transport chain (ETC), transferring electrons between complexes ΙΙΙ (cytochrome bc1) and ΙV (cytochrome c oxidase, CcO). Mitochondrial …

Microdialysis Studies Using Porcine Pancreatic Elastase To Guide Mathematical Modeling Of Microdialysis Sampling For In Vivo Measurements., Mason W. Young

Biomedical Engineering Undergraduate Honors Theses

Microdialysis sampling uses a semi-permeable membrane to allow solute collection by diffusion. When used in conjunction with other instruments, analytes in question can be quantified. Matrix Metalloproteinases (MMPs) are enzymes involved in numerous biological processes where they serve the role of degrading extracellular matrix. Microdialysis sampling, in coordination with further analysis methods, can be used in order to measure the activity of these enzymes in a region of the body instantaneously. The intention of this project is to determine ways of measuring in vitro activity of elastase from porcine pancreas using determined activity values and the collection of elastase products. …

Synthesis Of Microgel Polymers As Catalysts, Hannah N. Miller

Chemistry & Biochemistry Undergraduate Honors Theses

New developments in organic synthesis show promise in achieving the best catalytic properties for the hydrolysis of glycosidic bonds through microgel polymers and transition metal complexes. A monomer mix of ethylene glycol dimethacrylate, butyl acrylate, and styrene form miniemulsion polymers after sonication and exposure to UV light. Gravimetrical analysis is used to determine the most suitable polymerization conditions by performing experiments at varying pH values, temperatures, monomer amounts, initiator amounts, and lamp heights. The final data show that the best polymerization conditions are a pH of 10.50 at 0°C with a high monomer ratio, 20% initiator amount, and a lamp …

Improving Photocatalytic Activity By Appending A Quinone To Ruthenium Polypyridyl Complex, Amy N. James

Chemistry & Biochemistry Undergraduate Honors Theses

By converting natural light energy into chemical energy, chemists are studying ways to take advantage of clean energy. The rising precedence of “green chemistry” has led to academic interest in the activity of photocatalysts and harnessing visible light in an efficient, accessible, and safe manner. Photochemistry is an upcoming and fascinating field of study that has made significant progress, but also has great potential for future work. By utilizing light as a natural energy source, many reaction processes in chemistry can be viewed with a new perspective. Ru(bpy)₃²⁺ is one of the most widely used photocatalysts. An efficient …

Staphylococcal Nuclease And Ubiquitin Local Folding Energies And Rates Using Peps-Hdx-Esi-Ms, Julie Rhee

Chemistry & Biochemistry Undergraduate Honors Theses

In this study, Protein Equilibrium Population Snapshot Hydrogen-Deuterium Exchange Electrospray Ionization Mass Spectrometry (PEPS-HDX-ESI-MS) was applied to study the local regions of model proteins, staphylococcal nuclease and ubiquitin. The hydrogen deuterium exchange (HDX) has become a key technique for studying the structural and dynamic aspects of proteins in solution. This technique creates a rapid exchange between all of the exchangeable hydrogen ions with deuterium when the protein is exposed to a solvent. The PEPS method is an equilibrium-based method used to determine the populations of the closed native and open denatured states of a protein. By combining the applications of …

Influence Of Cholesterol On Single Arginine-Containing Transmembrane Helical Peptides, Jordana K. Thibado

Chemistry & Biochemistry Undergraduate Honors Theses

An essential component of animal cells, cholesterol exerts significant influence on the physical properties of the cell membrane and in turn, its constituents. One such category of constituents, the membrane proteins, are responsible for diverse and essential biological functions and often contain polar amino acids. Although sparse within the hydrophobic interior of lipid-bilayer membranes, polar amino acid residues are highly conserved and may play pivotal roles in determining specific structural and functional properties of key proteins. To gain greater understanding of the lipid membrane environment, and more broadly, cellular function, a model peptide framework termed “GWALP23” (acetyl-GGALWLALALAL¹²AL^{14 …}

Development Of Electrochemical Sensors Suitable For In Vivo Detection For Neurotransmitters, Mengjia Hu

Graduate Theses and Dissertations

The electrochemical method of redox cycling was exploited to achieve new discoveries in neurotransmitter detection and to advance its suitability toward in vivo use. Redox cycling has advantages in signal amplification, selectivity of species based on their electrochemical reaction mechanisms, and limited or no background subtraction. Distinction of dopamine from norepinephrine in a mixture with an electrochemical method at unmodified electrodes was demonstrated for the first time in vitro. This ability resulted from a series of fundamental studies of redox cycling behavior of the catecholamines (dopamine, norepinephrine and epinephrine) using different electrode configurations. Taking advantage of the ECC’ mechanism associated …

A Bond Length – Bond Valence Relationship For Carbon – Nitrogen Bonds, C. Harris, F. D. Hardcastle

Journal of the Arkansas Academy of Science

In a recent study, Pauling’s relationship between bond length and valence was derived along with a definition for his fitting parameter b that incorporates the orbital exponents for each atom contributing to the bond of interest. The values of b for various bonds, including C-N bonds, were calculated using the orbital exponent data. In this study, Pauling’s correlation between bond length and bond valence, as well as his valence sum rule, were used with the recently-derived definition for b in order to produce a relationship specifically applicable to C-N bonds. The resulting equation was checked against published x-ray diffraction data …

A General Valence-Length Correlation For Determining Bond Orders: Application To Carbon-Carbon And Carbon-Hydrogen Chemical Bonds, F. D. Hardcastle

Journal of the Arkansas Academy of Science

A quantum-mechanical LCAO approach was used to derive Pauling’s popular empirical bond valencelength relationship s = exp((R₀-R)/b), where s is the bond order or bond valence associated with bond length R, and R₀ and b are fitting parameters. An expression for the b “empirical” fitting parameter is derived in terms of atomic orbital exponents. The b parameters calculated from the atomic orbital exponents are consistent with optimized b parameters. In general, atomic orbital exponents may be used to determine bond valence-length relationships for any chemical bond regardless of valence state, oxidation number, physical or chemical environment. In this study, almost …