Biochemistry Commons^™

Functional Characterization Of The Newly Discovered Type V Crispr-Cas Protein Cas12a2, Dylan J. Keiser

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Similarly to people, bacteria are under the treat of infection by viruses. To circumvent these threats, bacteria evolve complex immune systems. Our understanding of some of these immune systems has led to many advancements in the field of Biotechnology including tools that made expressing proteins for study in a lab easier, tools that revolutionized the feasibility of gene editing, and tools that could change the way we think about viral diagnostics and cancer therapeutics. A certain type of immune system that bacteria use to fight virus is called a CRISPR system. Presented here is work to understand the function of …

Utah Tick Surveillance An Animated Public Service Announcement, Keith Wilson

Undergraduate Honors Capstone Projects

As the United States’ population grows, we develop more land into housing and recreate farther into wilderness areas, consequentially encountering ticks with increasing frequency. As the climate continues to change, tick population distributions are also changing, influencing our population’s exposure to tick-borne diseases. Lyme disease, a tick-borne disease named after Lyme, Connecticut, is one of the fastest growing emerging diseases in North America, and the most prevalent vector-borne infection in the United States. There are two species of tick in North America, Ixodes scapularis and Ixodes pacificus, known to be carriers of the causative agent of Lyme disease, a …

Determination Of The Structure, Function, And Mechanism Of Type Iv Crispr-Cas Prokaryotic Defense Systems, Hannah Nicole Taylor

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Bacteria are under constant threat of invasion by bacteriophage (viruses which infect bacteria). To prevent bacteriophage from entering and overtaking the bacteria, bacteria utilize defense systems to identify and destroy foreign elements. One method of defense is called CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats – CRISPR-Associated). Many different bacteria and most archaea use CRISPR-Cas systems. There are many diverse types of CRISPR-Cas systems, each of which provides defense in a slightly different way. One such CRISPR-Cas type is called type IV. The type IV CRISPR-Cas system is poorly understood and there are very few studies published on type IV …

Investigations Of Substrate Reduction By Nitrogenase: Light Powered Substrate Reduction By A Cds:Femoco System And Understanding Dinitrogen Inhibition Of Electron Transfer, Hayden Kallas

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Nitrogen fixation is a key step of the nitrogen cycle which makes biologically inert N₂ gas available for organisms to use in the form of ammonia. Nitrogen fixing microorganisms all contain the same enzyme called nitrogenase which catalyzes the six electron transfers to N₂ required for conversion into ammonia. Nitrogenase is a two-component enzyme that contains a cofactor composed of iron and sulfur as well as heavier metals whose identity can be molybdenum, vanadium, or an additional iron atom depending on the variant. The two components of nitrogenase are the MFe protein and the Fe protein. The Fe …

Utilizing Earth's Microbiology To Develop The Framework For A Manufactured Martian Nitrogen Cycle, Kyle Valgardson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

History has shown us that space travel is a complicated activity not to be taken lightly. Extended missions such as those that would accompany a manned mission to Mars are guaranteed to have increased complexity and require creative solutions to problems we likely take for granted. One such issue is how to supply the necessary amount of nitrogen to the astronauts to keep them alive. Nitrogen is an essential component to life on Earth as most biological molecules, such as protein and DNA, contain a significant amount of it. Most organisms have to get it from what they eat, but …

Innovative Biological Solutions For Nitrogen Fixation, Mathangi Soundararajan

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Nitrogen is an important part of biological molecules like proteins and DNA and hence is essential for life as we know it. The most commonly found form of nitrogen is dinitrogen gas (N₂) in the atmosphere, which is not accessible to most organisms. Conversion of N₂ into a usable form (ammonia), occurs through an energy-demanding reaction called nitrogen fixation. As we think about sending humans to Mars, there is a need to develop technologies for nitrogen fixation to produce fertilizer and other valuable compounds to support life in those harsh conditions.

The Haber-Bosch process is used in …

Investigation Of The Molecular Mechanisms Of The Shigella Type Iii Secretion System Tip Complex, Abram R. Bernard

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Shigella are bacteria that are responsible for millions of infections and hundreds of thousands of deaths every year. The emergence of antibiotic resistant Shigella adds to the potentially devastating effect that these bacteria can have on human health. Shigella flexneri utilize specialized molecular machinery called the Type III secretion system to infect humans and cause disease. Research of this machinery promises to provide the knowledge, tools, and direction for the development of new avenues to combat shigellosis. This dissertation presents studies of two Shigella proteins, invasion plasmid antigens C and D (IpaC and IpaD). These proteins are part of a …

Electron Flow And Management In Living Systems: Advancing Understanding Of Electron Transfer To Nitrogenase, Rhesa N. Ledbetter

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Nitrogen is a critical nutrient for growth and reproduction in living organisms. Although the Earth's atmosphere is composed of ~80% nitrogen gas (N₂), it is inaccessible to most living organisms in that form. Biological nitrogen fixation, however, can be performed by microbes that harbor the enzyme nitrogenase. This enzyme converts N₂ into bioavailable ammonia (NH₃) and accounts for at least half of the "fixed" nitrogen on the planet. The other major contributor to ammonia production is the industrial Haber-Bosch process. While the Haber-Bosch process has made significant advances in sustaining the global food supply through …

First-Row Transition Metal Sulfides And Phosphides As Competent Electrocatalysts For Water Splitting, Nan Jiang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Solar energy is a carbon-neutral and renewable energy resource. Its nature of intermittence and unequal distribution requires efficient solar energy capture, conversion, and storage. Solar-driven water splitting to produce hydrogen and oxygen is widely considered as an appealing approach to meet this goal, in which hydrogen acts as a green energy carrier. Water splitting consists of two redox half reactions: hydrogen evolution reaction (HER) and oxygen evolution reaction (OER). Both reactions involve the transfer of multiple electrons and protons and possess high energy barriers to proceed at appreciable rates, hence catalysts are needed.

A large number of HER and OER …

Mechanism Of Substrate Reduction By Nitrogenase, Nimesh Khadka

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Nitrogen (N) is a vital element of life and the main component of chemical fertilizer. The industrial Haber-Bosch process fulfills the demands of today’s nitrogen need and is therefore considered as one of the major scientific breakthroughs of the last century. However, the Haber-Bosch process operates at very high temperature and pressure, and requires fossils fuels to drive the reaction, making it an energy expensive process. The energy demand for this process accounts for almost 3% of the total global energy consumption. In addition, the rapid population growth, economic development and depletion of limited non-renewable fossil fuels have already created …

Conservative Tryptophan Mutations In Protein Tyrosine Phosphatase Ptp1b And Its Effect On Catalytic Rate And Chemical Reaction, Teisha Richan

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Protein-tyrosine phosphatases (PTPs) catalyze the hydrolysis of phosphorylated tyrosines by a 2-step mechanism involving nucleophilic attack by cysteine and general acid catalysis by aspartic acid. In most PTPs the aspartic acid resides on a flexible protein loop, consisting of about a dozen residues, called the WPD loop. PTP catalysis rates span several orders of magnitude, and differences in WPD loop dynamics have recently been show to correlate with the rate of enzymatic catalysis. The rate of WPD loop motion could possibly be related to a widely conserved tryptophan residue on the WPD loop. Therefore, point mutants were made in PTP1B …

Characterization Of The Substrate Interactions And Regulation Of Protein Arginine Methyltransferase, Yalemi Morales

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Protein arginine methylation is a posttranslational modification catalyzed by the family of proteins known as the protein arginine methyltransferases (PRMTs). Thousands of methylated arginines have been found in mammalian cells. Many targets of arginine regulation are involved in important cellular processes like transcription, RNA transport and processing, translation, cellular signaling, and DNA repair. Since PRMT dysregulation has been linked to a variety of disease states, understanding how the activity of the PRMTs is regulated is of paramount importance. PRMT1 is the predominant PRMT, responsible for about 85% of all arginine methylation in cells, but very little is known about how …

Structural And Biochemical Characterization Of The Frequency-Interacting Rna Helicase Frh, Jacqueline M. Johnson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Cells function through a variety of regulatory pathways intricately communicating with one another. These pathways ensure that cellular functions happen at the appropriate times and keep the natural balance within the cell. When pathways do not communicate appropriately, this can lead to disease states and cell death. Two such connected pathways in Neurospora crassa involve the regulation of RNA levels and the circadian rhythms essential for these cells to maintain homeostasis. These pathways are connected by a unique helicase called the Frequency-interacting RNA Helicase (FRH), named for its discovery with the frequency protein involved in the circadian oscillation of the …

Quantum Mechanical Studies Of Charge Assisted Hydrogen And Halogen Bonds, Binod Nepal

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Like cement bridges one brick to another, noncovalent forces also bridge two or more molecules together to form a molecular crystal or molecular cluster. Although weaker than the covalent bond, the existence of noncovalent forces can be seen everywhere from liquid water to construction of complex biomolecules like DNA, RNA, proteins etc. An introduction of suitable charge; positive or negative, on the binding units can increase the strength of noncovalent interaction by several orders of magnitude. The primary aim of this dissertation is to explore some fundamental properties of such charge assisted noncovalent interactions which will be helpful for the …

Spa47 Is An Oligomerization - Activated Type Three Secretion System (T3ss) Atpase From Shigella Flexneri, Jamie Lee Kingsford

Undergraduate Honors Capstone Projects

Gram-negative pathogens often use conserved type three secretion systems (T3SS) for virulence. The Shigella type three secretion apparatus (T3SA) penetrates the host cell membrane and provides a unidirectional conduit for injection of effectors into host cells. The protein Spa4 7 localizes to the base of the apparatus and is speculated to be an ATPase that provides the energy for T3SA formation and secretion. Here, we developed an expression and purification protocol, producing active Spa47 and providing the first direct evidence that Spa47 is a bona fide ATPase. Additionally, size exclusion chromatography and analytical ultracentrifugation identified multiple oligomeric species of Spa47 …

The Effect Of Pure Infrared Light On The Growth Of Rhodospirrilum Rubrum, Jordan Lee Wilkes

Undergraduate Honors Capstone Projects

Scientists who study aquatic ecosystems quickly notice a diversity of pathways that different microbes and organisms can use to metabolize nutrients found in common ponds or pools. Competition for vital resources, such as light and inorganic minerals, allow only certain organisms to grow in certain niches within these ecosystems. Rhodospirillum rubrum is a gram negative, photosynthetic bacteria that competes for light within aquatic ecosystems in order to survive. R. rubrum is believed to specifically absorb light for photosynthesis at wavelengths in the range of infrared light. It was found that R. rubrum indeed can grow in "dark", anaerobic environments by …

Binding Interactions Of (R)- And (S)-Hydroxypropyl-Com Dehydrogenases And The Zinc Knuckle Proteins Air1 And Air2, Jeremy W. Bakelar

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

A thorough understanding of protein function requires knowledge of how proteins interact with their substrates and with other proteins. The work entailed in this dissertation describes the binding interactions of proteins from two different model systems: (1) the dehydrogenase enzymes R- and S-HPCDH and (2) the zinc knuckle proteins Air1 and Air2.

R- and S-HPCDH are highly similar enzymes (42% identical) that function in a unique metabolic pathway found in the soil bacterium Xanthobacter autotrophicus. The bacterium produces R- and S-HPCDH simultaneously to facilitate the transformation of two different forms of the organic …

Dna Methylation In Lung Tissues Of Mouse Offspring Exposed In Utero To Polycyclic Aromatic Hydrocarbons, Trevor J. Fish

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Polycyclic aromatic hydrocarbons (PAHs) comprise an important class of environmental pollutants that are known to cause lung cancer in animals and suspected lung carcinogens in humans. PAHs are also known to cause cancer in offspring when provided to a pregnant mouse. Some evidence from cell-based studies points to PAHs as modulators of the epigenome, that is modifications to DNA structure that control the expression of genes. Inappropriate changes to the epigenome and consequently expression of cancer-critical genes are often characteristic of cancer cells. The objective of this thesis research was to determine the impact of transplacental exposure to two model …

Microbial-Derived Oils And Value-Added Products: Biosynthesis And Applications For Biofuel Production, Alex T. Mccurdy

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Efforts are being made to replace petroleum-derived fuels with biofuels in a cost competitive manner. It is apparent that the continued use of petroleum is futile as population and technological growth put increasing pressure on the demand for cheap energy and chemicals. Diminishing resources, civil unrest in the Middle East, and the impact of using petrochemicals on the environment are critical driving forces for research in generating renewable petroleum replacements that can be produced with a limited carbon-footprint. Today, biofuels are derived mostly from land-based plants, but their potential for displacing petroleum is limited due to the competition with available …

Cloning And Expression For The Future Characterization Of The Air2 Protein, Emily Sue Frampton

Undergraduate Honors Capstone Projects

Air2 is a eukaryotic protein involved in multiple biological processes including protein-protein interactions as well as RNA binding. Air2 plays a critical role in RNA quality control and also helps regulate post-translational modification of various proteins. Although previous studies have revealed information regarding Air2's roles within a cell, the molecular and structural basis for Air2 function is unclear. Using a codon-optimized version of the Air2 gene, various constructs were created that improved the expression and solubility of Air2. Additionally a co-expression complex of Air2 with a PRMTI mutant, K13S, was made to obtain the Air2 protein with a native binding …

Pop2: A Potential Regulator Of Hmt1-Catalyzed Arginine Methylation In Yeast, Celeste Excell

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Protein arginine methylation is an important post-translational modification that is vital in regulating various cellular processes such as gene transcription, cell signaling, and RNA processing. Protein arginine methyltransferases (PRMTs) are responsible for performing this important modification. PRMT1 (protein arginine methyltransferase 1) and Hmt1 (hnRNP methyltransferase 1) are the predominant PRMTs in humans and yeast, respectively. Despite growing momentum in this field, relatively little is understood about PRMT regulation. Further work discovering how PRMTs are regulated will greatly advance our understanding of diseases where PRMTs have been implicated, such as heart disease, viral pathogenesis, and cancer.

It has been discovered that …

Electron Transfer And Substrate Reduction In Nitrogenase, Karamatullah Danyal

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The reduction of nitrogen to ammonia by the industrial Haber-Bosch process is considered one of the major scientific breakthroughs of the last century. It is considered to be responsible for approximately one third of the world's current population. This growth over the past 50 or so years accompanied by the changes in dietary habits due to economic growth have markedly increased the demand for fixed nitrogen in the form of fertilizer. The Haber-Bosch process and biological nitrogen fixation has been able to fulfil this demand. However, this industrial process is costly due to its high temperature and pressure requirements. Every …

Quantum Mechanical Study Of Weak Molecular Interactions, Upendra Adhikari

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Molecular interactions play key role in the existence of biomolecules like proteins and nucleic acids, and various materials. Molecular interactions are weak forces that hold different molecules or different fragments of the same molecule together, and are often referred to as noncovalent interactions. Due to the complexity in biomolecules, these interactions are still poorly understood. This dissertation presents results from quantum mechanical simulations of various types of noncovalent interactions, which are extremely important for the structure and functions of biomolecules and materials.

A new sort of noncovalent interaction is identified. This new sort of interaction originates from a direct interaction …

Investigating The Importance Of The N-Terminal Negative Residues In Human Prmt1, Brooke Siler

Undergraduate Honors Capstone Projects

Many essential physiological pathways, such as cell proliferation, gene expression, and cardiovascular health are regulated by Protein Arginine Methyltransferases (PRMTs) through methylation of arginine residues in protein substrates. Understanding how PRMTs interact with their substrates is pivotal to understanding the biological role of these enzymes, and fundamental to the goal of identifying possible sites to be inhibited through drug therapy. Natural variations in the N-terminus of the PRMTl enzymes and data collected in our lab suggest that the N-terminus is important for activity and/or the binding of protein substrates. Preliminary data collected had led us to hypothesize that the negatively …

The Phosphoramidase Competency Of Prototypical Phosphatase Catalytic Motifs, Mark P. Haney

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Phosphorylation of proteins is ubiquitous. Phosphorylation can activate proteins, deactivate proteins, assist in signaling, or serve other roles depending upon the biochemical pathway. Attaching phosphate to proteins is accomplished by enzymes called kinases; removing phosphate from proteins is accomplished by enzymes called phosphatases. Cells must regulate their biochemical pathways, and the antipodal roles of kinases and phosphatases represent the yin-yang of phosphorylation.

Phosphorylation of proteins is known to occur on serine, threonine, and tyrosine. This creates a phosphoester bond. Phosphoester bonds have a phosphorus-oxygen (P-O) bond. The ability of phosphatases to cleave such phosphoester bonds is well studied. Phosphorylation of …

Characterization Of The Product Specificity And Kinetic Mechanism Of Protein Arginine Methyltransferase 1, Shanying Gui

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Protein enzymes perform a vast array of functions within living organisms, catalyzing various metabolic reactions including DNA replication, DNA repair, protein synthesis, etc. In order to maintain proper cellular functions, enzymes need to be accurately regulated under different circumstances. Specifically, enzymes can be modified after their creation to give them additional functions. These modifications can do a variety of things including activating (turning on) or inactivating (turning off) an enzyme, changing what proteins or molecules can interact with the enzyme, changing the enzyme’s location in the cell, and/or targeting the enzyme for destruction. This dissertation focuses on a single class …

Investigation Of The Oxidation/Reduction Of Prmt1, Substrate Interaction With Prmt1, And The Role Of Arginine Methylation In Rna Surveillance, Damon V. Nitzel

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Enzymes are the machines of our cells. Just like machines, it takes a lot of energy to create them, and they then serve only the function they were created for. If we want to change the function of a machine, we need to modify it. Similarly, enzymes can be modified after their creation to give them additional function. These modifications can do a variety of things including activating (on) or inactivating (off) an enzyme, changing the enzyme’s location in the cell, and targeting the enzyme for destruction. This thesis focuses on a single class of enzymes, protein arginine methyltransferases (PRMTs), …

Increased Production And Extraction Efficiency Of Triacylglycerides From Microorganisms And An Enhanced Understanding Of The Pathways Involved In The Production Of Triacylglycerides And Fatty Alcohols, Robert M. Willis

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The continued increase in the demand for fossil fuels combined with their ever dwindling supply has prompted the search for a suitable alternative fuel. The research contained within this dissertation seeks to increase the lipid (fat) content of cellular feedstocks, improve extraction efficiencies of lipids, and to understand the pathways involved in the production of fatty alcohols and triacylglycerides, compounds commonly used in many industrial processes, from microbial feedstocks. This work has been done in an attempt to increase the overall economic viability of microbial biofuels production.

The production of biofuels from microalgae used as a feedstock allows for the …

Caehnorhabditis Elegans: A Low-Cost In Vivo Animal Model For Efficacy Studies Of Novel Antibiotics, Rylee Ann Gregory

Undergraduate Honors Capstone Projects

Since the 1940s, antibiotics have greatly reduced the adverse effects of infectious diseases caused by microbes. However, due to excessive, and often incorrect, use of known antibiotics, many organisms have adapted antibiotic resistance. Currently, over 70% of known infectious bacteria are resistant to at least one antibiotic. In the U.S. , 90,000 deaths occur each year due to infection by bacteria resistant to antibiotics. This number has increased by nearly 75,000 in the last 20 years. It is necessary, therefore, to continue developing new antibiotics in an effort to keep up with increasing antibiotic resistance. Traditional in vitro and whole …

Structural And Mechanistic Investigations Of Phosphothreonine Lyase Class Of Enzymes, Alok Gopalkrishna Shenoy

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Phosphorylation and dephosphorylation are a highly pervasive mechanism in biology that is used by the cell to modulate enzymes and proteins. The presence of a phosphate group can activate or deactivate an enzyme. The phosphate group is linked to a protein by a phosphoester bond that is known to be highly stable in cytoplasmic pH range. Thus the breaking and formation of these bonds need to be effected by enzymes.

Recent discovery of the activity carried out by certain virulence related proteins (OspF released by Shigella and SpvC released by Salmonella) have resulted in a necessity to create a new …