Ubiquitin Lab Report

Ubiquitin Lab Report
 INTRODUCTION: Ubiquitin is a small protein that is found in almost all cellular tissues in humans and other
eukaryotic organisms, which helps to regulate the processes of other proteins in the body. Through a process known as
ubiquitination or ubiquitylation, an ubiquitin molecule can bind to a substrate protein, changing the way it functions.
This can lead to a number of different outcome. It is most widely recognised for its role in apoptosis of proteins, earning
it the title of the molecular "kiss of death" for proteins, although it also plays a major part in several other cellular
processes related to the regulation of proteins. Ubiquitin is a highly conserved 8.5 kDa protein that is abundant in all
types of cells and exists as a free molecule or ... Show more content on Helpwriting.net ...
Ubiquitination requires three types of enzyme: ubiquitin–activating enzymes, ubiquitin–conjugating enzymes, and
ubiquitin ligases, known as E1s, E2s, and E3s, respectively. The process consists of three main steps: o Activation:
Ubiquitin is activated in a two–step reaction by an E1 ubiquitin–activating enzyme, which is dependent on ATP. The
initial step involves production of a ubiquitin–adenylate intermediate. The E1 binds both ATP and ubiquitin and
catalyses the acyl–adenylation of the C–terminus of the ubiquitin molecule. The second step transfers ubiquitin to an
active site cysteine residue, with release of AMP. This step results in a thioester linkage between the C–terminal
carboxyl group of ubiquitin and the E1 cysteine sulfhydryl group. o Conjugation: E2 ubiquitin–conjugating enzymes
catalyze the transfer of ubiquitin from E1 to the active site cysteine of the E2 via a esterification reaction. In order to
perform this reaction, the E2 binds to both activated ubiquitin and the E1 enzyme. Humans possess 35 different E2
enzymes, whereas other eukaryotic organisms have between 16 and
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Functions of Ubiquitin Specific Proteases Essay
Eukaryotic cells rely on the ubiquitination of proteins for the proper control of their internal processes. Adding multiple
ubiquitin groups aids in the breakdown of proteins, whereas adding only one ubiquitin serves regulatory roles other than
degradation. The enzymatic activity of two protease classes frees ubiquitin groups from associated proteins: Ubiquitin
specific proteases (USP) and Ubiquitin C–terminal hydrolases (UCH). USPs are strongly involved in eukaryotic cellular
functions and are found in copious amounts. Certain protein ligases attach ubiquitin to proteins, which degrades them
and interferes with normal cellular functions. The discovery of a specific de–ubiquitinating enzyme (HAUSP/USP7)
found in humans was due to its ... Show more content on Helpwriting.net ...
The labels associated with the resulting proteins from previous steps were rinsed and removed. USP7 was purified and
utilized in sedimentation trials in varying concentrations. Absorbance analysis was carried out after the samples were
centrifuged. EBNA1 was purified, ubiquitinated, and combined with USP7, which was purified in previous steps. SDS–
PAGE was used to disrupt the protein interaction and separate them. The separated fragments were then used in a
western blot, and analyzed after probing. The affinity of USP7 for EBNA1 and p53 was tested using a stepwise
combination of titration, incubation, and fluorescence analysis. Lastly, amino acid residues of EBNA1and USP7 were
studied by gel filtration and size–exclusion chromatography. USP7 was found as hexahistidine fusion after being
inserted (through a vector) in insect cells. The de–ubiquitinating capacity of USP7 for conjugated ubiquitin groups was
observed on EBNA1, and was shown to an efficient process. The capacity of USP7 to de–ubiquitinate specific proteins
in various environments (acidity, presence of inhibitors, and salt concentration) was studied. As seen in figure 2, USP7
sensitivity to salt concentration and acidity showed a steep slope followed by a plateau at lower salt concentrations and
higher pH levels, while lower pH and higher salt concentrations rendered a steeper, less plateau–like graph. USP7 was
found to be a monomer with multiple domains, each involved

4. 1 Functional Classifications Of Functional Functions
4.1 Functional classification of dysregulated proteins
It was shown that MPS VII is characterized by accumulation of ubiquitin and neurofilament, but not PHF–τ, α–
synuclein or apoptosis [20]. Similarly, significant alterations in the ubiquitin–proteasome system (UPS), but not
proteins associated with apoptosis or PHF–τ and α–synuclein, were identified in this study. Previous transcriptomic and
proteomic analyses of MPS VII mouse brain identified many dysregulated proteins involved in metabolism and
cytoskeleton [21,22]. Additionally, these studies found that neuroinflammation is also upregulated, but not to a large
extent. Similar results were observed in this study, indicating the reliability of the proteomics approach. We also
examined ... Show more content on Helpwriting.net ...
Dysregulation of cytoskeletal genes has also been seen in MPS I mouse brains [4], MPS IIIB mouse brains [26] and
MPS VII dog hearts [27]. Additionally, low density lipoprotein–related protein 1B (LRP1B), dynamin–1 (DMN1) and
dynamin–related protein 1 (DNM1L), which are involved in the process of endocytosis, are downregulated. Vesicle
associated membrane protein 2 (VAMP2) is involved in the targeting and/or fusion of transport vesicles to their target
membrane [28]. These results further suggest impaired lysosomal membrane trafficking pathways in MPS VII.
Based on previous reports and results in this study, we hypothesize that GAG accumulation leads to alterations in the
cytoskeletal system and thereby impairs lysosomal membrane pathways including endocytosis, exocytosis, autophagy
and vesicle transport. Notably, endocytosis defects in brain endothelial cells may contribute to low transcytosis, making
enzyme replacement therapy more difficult to achieve neurological benefits. Therefore, targeting specific pathways
involved in transcytosis may be an effective strategy to enhance enzyme delivery to the brain in lysosomal diseases
including MPS VII.
4.1.2 Proteostasis
Many neurodegenerative diseases share a common molecular signature: disruption of proteostasis [29]. This often
manifests as an accumulation of ubiquitylated proteins, with evidence for a robust contribution to

Autophagy
Autophagy gives cells with oxidizable substrate when nutrients become deficient. It can give protection against aging
and a number of pathologies such as cancer, cardiac disease, diabetes, neurodegeneration, and infections. Autophagy
principally plays an adaptive character to save organisms against various pathologies, including infections, cancer, and
aging, neurodegeneration, and heart disease. A number of modern studies have stressed the importance of autophagy
and the ubiquitin–proteasome in the pathogenesis of muscle declining in different types of inherited muscle problems.
Some current studies have concentrated on autophagy in heart disease elicited by alters in hemodynamic load. Pressure
overuse stress evokes a robust autophagic reply in cardiomyocytes that is maladaptive, giving to disease progression.
Autophagy may develop an essential physiological reply to cardiac stresses such as ischemia or pressure overuse, which
are repeatedly encountered in patients with coronary artery disease, hypertension, and congestive heart failure. Cardiac
remodeling requires improved rates of cardiomyocyte cell death and antecedes heart collapse. At the same time,
appearing multiple features of failing hearts incorporate not only apoptosis and necrosis but also autophagy as ... Show
more content on Helpwriting.net ...
Usual liver function demands hepatocellular basal autophagy. Due to their high biosynthetic project and character in
protein turnover and carbohydrate depositary, hepatocytes may be especially dependent on basal autophagy for their
normal physiological tasks. Autophagy appears to play a major function not only in common liver physiology, but also
in the pathogenesis of liver problems such as nonalcoholic and alcoholic fatty liver, drug– affected liver damage,
protein conformational liver disorder, viral hepatitis, liver cancer, and liver ischemia–reperfusion

Ubiquitin-Proteasome System
Alzheimer's disease (AD) is an irreversible, age–related neurodegenerative disorder clinically characterized by
progressive loss of cognitive functions and behavioral disturbances. AD is associated with widespread accumulation of
amyloid beta (Aβ) plaques and neurofibrillary tangles that disrupt the homeostatic processes in the brain and result in
severe cognitive deterioration. Although the exact cause of AD is still unknown but preclinical studies have emphasized
that deficits in the functioning of the ubiquitin–proteasome system (UPS) is the major underlying factor for abnormal
accumulation of Aβ, and associated cognitive alterations. (PMID: – 24512022) To date, there are no effective disease–
modifying therapies for AD and existing drugs ... Show more content on Helpwriting.net ...
UPS is a major pathway that plays an integral role in abetting the clearance of damaged, misfolded and senescent
proteins from nucleus and cytoplasm to maintain tissue homeo–stasis. However, in the neurodegenerative disorders
(AD) aggregation of pathogenic proteins (Aβ) compromise UPS function and delay the degradation of proteasome
substrates. Many of these substrates are essential for supporting and regulating highly dynamic connections between
neurons that are necessary for cognitive functions, learning and memory. The improper functioning of UPS results in
inadvertent stabilization of these substrates resulting in loss of synaptic connections and diminished cognitive functions
in neurodegenerative disorders. Therefore to maintain cellular homeostasis it is essential to keep the ubiquitin–
dependent proteolysis operative as deficits in the UPS system result in accumulation of proteasome substrates. But, so
far there is no evidence whether UPS exert any control on the expression of proteins that regulate the transition from
proliferation to neural differentiation of stem/ progenitor cells. Further, the relationship between neurodevelopmental
pathways and UPS is poorly understood. Therefore, in an effort to limit the onset and progression of AD it is imperative
to understand the interdependence of UPS and neurogenesis so that the actual potential of gene regulatory networks
involved in the survival and maturation of neurons in the brain can be harnessed. Overall the proposed work will
provide a deep look into the cellular and molecular mechanisms responsible for maintaining the stemness characteristics
in NSCs and the generation of functional neurons and how they can be modulated to provide alternative therapeutic
targets to slow the cognitive impairment and behavioral disturbances associated with

Cad101 Research Paper
For attention of: David Ward
Student ID: 225693
Student Name: Kathleen Sanderson
Unit Code: CAD101
Assessment Title: Task 4– Essay
Word Count: 1500
Academic Referencing Style (where appropriate):
APA
Please note: APA referencing style is required for all students commencing study in Semester 2, 2014 or later.
I declare that all material in this assignment is my own work except where there is clear acknowledgement or reference
to the work of others. I am aware that my assignment may be submitted to plagiarism detection software, and might be
retained on its database. I have read the University statement on Academic Misconduct (Plagiarism) on the University
website at www.utas.edu.au/plagiarism or in the Student Information Handbook.
Signed...K. Sanderson................................................. Date 17/5/2015...................................................
Note: if submitting ... Show more content on Helpwriting.net ...
and Chan, R.O., (2011). Frontotemporal dementia: Features, diagnosis and management. Australian family physician,
Vol. 40, No. 12. Retrieved 12/5/2015 from http://www.racgp.org.au/afp/2011/december/frontotemporal–dementia/
Eastern Cognitive Disorders Clinic. FTD toolkit 1. What is frontotemporal dementia? An Australian Government
initiative. Eastern Cognitive Disorders Clinic. Retrieved 11/5/2015 from http://ecdc.org.au/ftd–toolkit.htm
Josephs, K.A., (2008). Frontotemporal dementia and related disorders: Deciphering the enigma. Annals Of Neurology
[serial online]. July 2008; 64(1): 4–14. Retrieved 7/5/2015 from
http://eds.b.ebscohost.com.ezproxy.utas.edu.au/eds/detail/detail?vid=5&sid=dfeca149–610b–
4406b299b5969309beb8%40sessionmgr198hid=117bdata=JnNpdGU9ZWRzLWxpdmU%3d#db=c8h&AN=2010001272
Lawrence, J., (2015) Potential dementia treatment target identified using stem cell research. The Pharmaceutical
Journal. 2/1/2015. Retrieved 13/5/2015 from

The Importance Of Protein Degradation
The authors' goal in conducting this experiment was to establish a link between, among other things, protein
degradation through the ubiquitin–protease system (UPS) and the consolidation and reconsolidation of long–term fear
memories. This research was necessary because, while research had been done linking protein degradation to synaptic
plasticity, no study had been performed to analyze the role of UPS in the amygdala, where long–term fear memories are
believed to be stored. Additionally, prior research had led to conflicting reports of the importance of protein degradation
in consolidation as opposed to reconsolidation, which the authors intended to clarify. To obtain the desired information,
researchers tested male Long Evans rats' ... Show more content on Helpwriting.net ...
Most research findings confirmed what prior research indicated – protein degradation and synthesis are essential in
memory formation and memory formation relies on NMDA. However, the research indicated differences between the
memory processes used by the hippocampus and amygdala in that prior researchers had found little evidence that
protein degradation was a necessary part of the consolidation of memories in hippocampus. This led researchers to
conclude that the amygdala and hippocampus may be more similar with regard to reconsolidation of memories than
consolidation of memories.
Analysis:
Prior to reading the article, I had very little understanding of the importance of proteins in memory functions. I believed
them to be most important with regard to enzymatic functioning and structural composition. However, the article
indicates how incredibly important the minutiae of protein function are to a properly functioning memory. Based on
protein function, researchers were able to control if and how much the rats were able to remember. The data do seem to
support the authors' conclusions. Protein degradation was measured by the presence of ubiquitin, which was a fairly
accurate measurement tool. In addition, the researchers used an abundance of controlled groups in order to isolate the
desired variable – the combination of shock and auditory cue. Conclusions about the presence of elevated protein
degradation are supported by the collected data from the

Ubiquitin Lab Report
Cell homeostasis is a complex yet strictly regulated by many regulators. Different from big role–player such as enzymes
in many signaling pathways, the universal consensus of small regulator ubiquitin contributes a great length to the of the
complex post translational regulating protein system. Consisting of 76–residue protein, ubiquitin not only highly
expresses in cell for various signal transduction pathways, it also is one of the most resilience and packed protein that is
highly conserved among the eukaryotes[1]. Ubiquitin is firstly produced intracellularly as precursor fusion protein chain
consisting polyubiquitin or ubiquitin fused to amino–terminus of Ribosomal protein 40S and 60S units; the generation
of free ubiquitin from these precursor ... Show more content on Helpwriting.net ...
The de–ubiquitinase (DUB) will cleave this precursor into free monomer ubiquitin molecules and can be activated and
attached to the target protein through ATP dependent process called ubiquitination with the help of activating enzyme
E1, conjugating enzyme E2, and ligase E3. Through forming (iso)–peptide, thioester, or ester bond between carboxyl
groups of C–terminal glycine 76 on ubiquitin and the ε–amino group of the lysine, cysteine, serine/threonine on the
substrate, respectively, the poly–ubiquitin chain is formed [3]. Based on the different internal Lysine (Lys6, Lys11,
Lys27, Lys29, Lys33, Lys48, and Lys63) and on the proximal ubiquitin, the (iso)–peptide bond can be form with
another ubiquitin, distal mono–ubiquitin [4, 5]. Consequently, seven conventional poly–ubiquitin chains resulting in
different 3–dimentional shapes explaining its different characteristics inherited upon binding to the target protein [5, 6].
With ranging more than 500 putative E3 ligases exist in human, the E3 ligase will tag the poly–ubiquitin chain to the
target protein with high specificity

Turnover Mechanisms
Turnover mechanisms such as ubiquitination must be carefully regulated, as it is very significant in metabolic
regulation, and removing errors which arise during the transcription and translating process, as well as protein
activation and degradation which is necessary for some signalling pathways. Proteins that are targeted for degradation
use energy from ATP hydrolysis to form an isopeptide bond between the targeted protein and ubiquitin. In addition, the
activated carboxyl terminal glycine of ubiquitin is covalently bonded to the ε–amino groups in multiple Lys located in
the protein.
Ubiquitin is composed of 3 enzyme units, which facilitate the breakdown of proteins into amino acids, these are E1:
ubiquitin activating enzyme, E2: ubiquitin–conjugating enzyme and E3: ubiquitin–protein ligase. Once targeted proteins
are marked by ubiquitin for degradation, a proteasome will digest the protein and break it down into its constituent
amino acids, while the ubiquitin is cleaved off and recycled for future use. ... Show more content on Helpwriting.net ...
Proteins that are targeted for degradation use energy from ATP hydrolysis to form an isopeptide bond between the
targeted protein and ubiquitin. In addition, the activated carboxyl terminal glycine of ubiquitin is covalently bonded to
the ε–amino groups in multiple Lys located in the

Gfe3 Synthesis
In a recent study, researchers report a novel and easy way to hijack the brain's natural processes. This technique, which
involves the fusion protein GFE3, interferes with the inhibitory synapses between neurons resulting in an overall rise in
the brain's electrical activity.
The team, led by Don B. Arnold, professor of biological sciences at the University of Southern California, used GFE3
which is a fusion of two proteins: E3 ligase, which degrades proteins; and FingR, which recognizes and binds to
proteins in inhibitory synapses.
Arnold explains: "Rather than a cell deciding when a protein needs to be degraded, we sort of hijack the process."
Synapses can either be excitatory or inhibitory, depending on whether the postsynaptic neuron is ... Show more content
on Helpwriting.net ...
For this, they used the zebrafish as an animal model.
They created genetically modified zebrafish by injecting the zygotes with the GFE3 construct that was further modified
to be expressed only in the spine.
Consistent with their earlier results, imaging techniques show the absence of the inhibitory proteins in the spines of the
zebrafish. Interestingly, they also found that zebrafish injected with GFE3 had sharply reduced motor coordination
described by poor tail flicking motions.
Perhaps most remarkably, however, is that the team was able to show that the effects of GFE3 were reversible;
something that other similar techniques do not have. The team did this by further modifying GFE3 to be expressed only
when the chemical dox is present.
When they removed dox, the team observed that GFE3 disappeared and the inhibitory proteins returned.
This study represents one of the first few studies that have focused on a protein–centric approach to controlling neurons
and synapses. According to Arnold, further studies could contribute to therapies and drugs predicated on the ability to
finely tune the brain. This is especially useful in diseases caused by altered brain chemistry like schizophrenia and

Exosomes As A Whole Has Gained Momentum Through The Area...
The interest and research invested into the area of exosome biogenesis and the topic of exosomes as a whole has gained
momentum in the last decade (Urbanelli, L. et al. 2013). Their discovery in 1983, detailed in two papers published in
JCB (Harding et al) and in Cell (Pan and Johnstone), showed that the nomenclature had been prescribed wrongly to a
broad range of membrane vesicles that bud directly from the plasma membrane (Clifford V. Harding. et al. 2013). When
in fact the term 'exosome' more accurately describes small vesicles, ranging from 30–100nm in diameter (Urbanelli, L.
et al. 2013), that originate via a different mechanism of budding than apoptotic bodies and microvesicles, (Yu, S. et al.
2015).
Exosome function was initially ... Show more content on Helpwriting.net ...
Whilst exosomes have been retrieved in many body fluids, for example; blood, urine, saliva and cerebrospinal fluid
(Urbanelli, L. et al. 2013). They are recently thought to be present in all biological fluids.
Exosome Biogenesis
Exosomes are exceptional from other types of vesicles based on a number of factors; including their size (relatively
small in comparison), morphology, cargo composition and most distinctly, their endosomal origin (Théry C. 2002).
Familiar types of vesicles such as microvesicles are formed at the cell surface, budding directly from the plasma
membrane (Alenquer, M. et al. 2015). Exosome biogenesis follows an alternative method that begins in the early
endosome (Huotari, J and Helemius, A. 2011), whereby the ultimate result is the formation of intraluminal vesicles
(IVL's) inside the lumen of the endosome, this aggregate body is known as the multivesicular body (MVB) or the
multivesicular endosome (MVE).
Initially the early endosomal membrane, tube–like in shape (Beach, A. et al, 2014), buds inwards via intraluminal
invagination (Lopez–Verrilli, M and Court, F. 2013), randomly engulfing sections of the cytosol contents such as the
peripheral and transmembrane proteins. This formation of the IVL's noticeably augments as the endosomes mature
(Huotari, J and Helemius, A. 2011) and after transformation the late endosome is more spherical in shape (Beach, A. et
al. 2014). It is known

A Short Note On Receptor And Its Effect On The Body
Introduction CD36, which stands for cluster of differentiation 36 and is also known as SR–B2 (scavenger receptor b2),
is a transmembrane protein that is part of the class b scavenger receptors. This is a protein that has many functions
throughout the body. CD36 is typically involved in the binding of lipid–related ligands like oxidized LDL particles,
long–chain fatty acids, collagens, thrombospondin–I, and others. With its versatility, CD36 can elicit a large variety of
responses in the body such as different immune responses, waste removal, angiogenesis regulation, roles in taste
reception etc. CD36 is also important to skeletal and cardiac muscle because it plays a key role in the utilization of long
chain fatty acids which is used in the formation of energy (Luiken, JJ. 2016). Deletion or reduction of CD36 can cause a
myriad of issues in an organism, whether that is a mouse or a human because of its role in dietary lipid use. In mice,
there was reduction in the uptake of long–chain fatty acids by different types of muscle (cardiac, skeletal), a loss of
preference for foods high in lipids, and a decrease in orosensory–mediated responses in digestive secretions. In humans,
CD36 gene variants are susceptible to many issues such as abnormalities in lipid and glucose metabolism, metabolic
syndrome, and diabetes–associated coronary disease (Tran, TTT. 2011). CD36 is a transmembrane protein that consists
of two membrane–spanning regions surrounding a larger loop on the

Muscle Atrophy Research Paper
Cellular and Molecular Mechanisms of Muscle Atrophy
The Ubiquitin–Proteasome System The ubiquitin–proteasome system is needed to rid muscles of sarcomeric proteins
when there are muscle changes. "A decrease in muscle mass is associated with: (1) An increased conjugation of
ubiquitin to muscle proteins; (2) an increased proteasomal ATP–dependent activity; (3) increased protein breakdown
that can be efficiently blocked by proteasome inhibitors; and (4) upregulation of transcripts encoding ubiquitin, some
ubiquitin–conjugating enzymes (E2), a few ubiquitin– protein ligases (E3) and several proteasome subunits" (Lecker et
al., 2006, p. 25). Muscle atrophy is best defined as an active process that is controlled by a specific set of signaling
pathways ... Show more content on Helpwriting.net ...
A., Bedard, N., Baracos, V., Attaix, D. and Wing, S. S.
(2005). USP19 is a ubiquitin–specific protease regulated in rat skeletal muscle during catabolic states. Am. J. Physiol.
Endocrinology and Metabolism. 288, E693–E700.
Judge, A. R., Koncarevic, A., Hunter, R. B., Liou, H. C., Jackman, R. W. and
Kandarian, S. C. (2007). Role for IkappaBalpha, but not c–Rel, in skeletal muscle atrophy. American Journal of
Physiology: Cell Physiology. 292, C372–C382.
Lecker, S. H., Goldberg, A. L. and Mitch, W. E. (2006). Protein degradation by the ubiquitin–proteasome pathway in
normal and disease states. Journal of the American Society of Nephrology. 17,1807–1819.
Mittal, A., Bhatnagar, S., Kumar, A., Lach–Trifilieff, E., Wauters, S., Li, H.,
Makonchuk, D. Y., Glass, D. J. and Kumar, A. (2010). The TWEAK–Fn14 system is a critical regulator of denervation–
induced skeletal muscle atrophy in mice. The Journal of Cell Biology. 188, 833–849.
Mizushima, N., Levine, B., Cuervo, A. M. and Klionsky, D. J. (2008). Autophagy fights disease through cellular self–
digestion. Nature. 451, 1069–1075.
Narendra, D. P. and Youle, R. J. (2011). Targeting mitochondrial dysfunction: role for
PINK1 and Parkin in mitochondrial quality control. Antioxidants and Redox Signaling. 14,

Klhl3 Gene Essay
The KLHL3 gene (Kelch like family member 3) creates a protein that works in conjunction with proteasomes to
degrade unwanted proteins via an ubiquitin–proteasome system. KLHL3 is mainly expressed in the cerebellum and the
distal collecting tubule in the kidneys (3). is Though expressed in the KLHL3 protein has a N–terminal BTB domain, a
C–terminal that has Ketch–like repeats, and a BACK domain, forming a conformation that is a bladed beta propeller
structure (1). The protein produced by this gene is part of a complex (E3 ubiquitin ligase), which functions to indicate
damaged and additional proteins by labelling these with ubiquitin, which is the tag later recognized by proteasomes for
breakdown (4). This labelling is possible with the ... Show more content on Helpwriting.net ...
Mutations for KLHL3 that cause disease all involve missense mutations, resulting in a different amino acid, again
noting the inability to interact with substrates (7). One mutation, for example, resulted in a cytosine to thymine
nucleotide change at codon 410, changing from a serine to a leucine amino acid. This change in polarity, moving from a
polar to nonpolar amino acid, disrupts regular formation of the E3 complex, not allowing for ubiquitin attachment.
These missense mutations often inhibit the ability of the KLHL3 protein to form the E3 ubiquitin ligase complex, and
so this prevents the normal function of identifying extraneous and damaged proteins, resulting in an excess of WNK4,
due to no protein degradation as a result of the inability to tag these excess proteins. This inability to form the complex
in some mutations is a result of the cluster of serine residues that were affected by the mutation, building up on the
propeller domains, disrupting interactions with substrate and/or altering protein structure, though it is more common to
see one or the other (6). This leads to high blood pressure, due to no control over WNK4 concentrations in the blood. It
was commented on that the majority of mutations affected the ability of the KLHL3 to associate with the rest of the
complex, therefore unable to

A Research Study On Cultured And Handled At 20. C Using...
Nematodes were cultured and handled at 20 °C using standard methods (Brenner, 1974). C. elegans strains used in this
study are as follows: N2 Bristol and MR156: rrIs01[Pelt–2::GFP; unc–119(+)] X, which were used as wild type.
CB3514: lin–23(e1883)/dpy–10(e128) II, YHS47: lin–23(e1883)/dpy–10(e128) II; rrIs01[Pelt–2::GFP + unc–119(+)]
X, DH2: zyg–11(b2) II. DS97: mat–2(ax76) II, EU593: mel–26(or184) I, EU640: cul–2(or209) III, UP63: mat–
3(ku233) III, NJ582: cul–1(e1756)/unc–69(e587) III, VC141: zif–1(gk117) III, VC370: rfp–1(ok572)/eT1 III; +/eT1 V,
VC562: rbx–1(ok782) V/nT1[qls51] (IV;V), VC684: rbpl–1(ok907) I/hT2[bli–4(e937)let–?(q782)gls48] (I;III), VC954:
rnf–113(ok1401) III/hT2[bli–4(e937) let–?(q782)qls48] (I;III), VC1241: skr–1(ok1696) I, VC1439: skr–2(ok1938)
I/hT2[bli–4(e937) let–?(q782)qls48] (I;III), YHS171: rfp–1(ok572) III/hT2[bli–4(e937)let–?(q782)gls48] (I;III);
rrIs01[Pelt–2::GFP + unc–119(+)] X, YHS161: rbx–1(ok782) V/nT1[qls51] (IV;V); rrIs01[Pelt–2::GFP + unc–119(+)]
X, and YHS163: skr–1(ok1696) I; rrIs01[Pelt–2::GFP + unc–119(+)] X.
Quantification of intestinal nuclei and microscopy
To examine the number of intestinal nuclei marked by GFP using an elt–2::GFP transgene, worms were transferred to
0.2 mM tetramisole in M9 buffer on a poly–L–lysine–coated slide glass, covered with a coverslip and observed using a
fluorescence microscope (Zeiss Axioskop 2, Carl Zeiss, Germany). Otherwise, DNA of some strains, whose intestine is
not marked with intestinal

Angelman Syndrome Research Paper
Angelman Syndrome is a rare disease that affects one in every 20,000 children. The disease used to be known as "happy
puppet syndrome" because children that have it have happy moods and their gestures look like a puppets. However, the
only name that is used for the disease today is Angelman Syndrome or AS. This disease is caused by a mutation in
chromosome fifteen. It is disease that should be taken very seriously.
Angelman Syndrome is neurons in the brain that lack the expression of a non–functional UBE3A. UBE3A is Ubiquitin–
protein ligase and E3A is an enzyme that is encoded in humans by the UBE3A gene. This enzyme includes targeting
protein that declines inside cells. Angelman Syndrome is affected by problems with a gene in chromosome fifteen
which is called Ubiquitin–protein ligase E3A (UBE3A). Symptoms are usually noticed during six to twelve months of
age in a child. A lack of crawling or babbling, having a frequent smile, laughter, and a happy, excitable personality are
early symptoms of the disease. As a person gets older they have minimal or no speech and have an inability to walk,
move or balance well, which is also called ataxia. They display jerking movements, tongue thrusting, bursts of laughter
and have epilepsy. ... Show more content on Helpwriting.net ...
The tests that are done check for developmental delays, small head size and flatness on the back of the head. If the
disease is found in someone there is no cure for it. Researchers are focusing on how to treat the specific gene. There
isn't a lot that you can do for the disease, but you can do some treatments that can help with symptoms. Some people
have to take anti–seizure medication. Others go to communication, behavior and physical therapy to help with walking
or balance issues. Seizures are recurrent in people that have Angelman Syndrome and those reoccurring seizures can
make their symptoms

Membrane Proteins And Non Membrane Bound Organelles
Chapter 4: Membrane Bound Organelles and Non–Membrane Bound Organelles
Membrane Bound Organelles: are contained within an isolated environment surrounded by a membrane. The
composition of these organelles differ in composition, shape and enzyme inclusion. Members of Membrane Bound
Organelle Systems include the Endoplasmic Reticulum, Golgi Apparatus, Lysosomes, Mitochondria and Peroxisomes.
Endoplasmic Reticulum (ER): is a continuous membrane system which forms flattened sacs within the cytoplasm of
Eukaryotic cells and acts a barrier between Cytosol and fluid with the structure. The Endoplasmic Reticulum plays a
variety of different roles including the synthesis, folding, modification and transport of proteins. There are two different
... Show more content on Helpwriting.net ...
Lysosomes: contain hydrolytic enzymes which aid in the digestion of particles and disintegration of cells. Formed by
the Golgi Apparatus, Lysosomes are surrounded by a membrane–bound cell organelle which contain acidic enzyme
material, because of their small sac–like appearance and the digestive acidic material contained within, Lysosomes are
often referred to as "suicide sacs" or "suicide bags".
Mitochondria: are oblong in appearance and contain a double membrane. Present in the cytoplasm of nearly all
Eukaryotic cells, the primary function of Mitochondria is in the creation of energy. Commonly referred to as "The
Powerhouse of the Cell", Mitochondria is responsible for most of the cell 's supply of Adenosine Triphosphate (ATP).
Other vital roles include cell growth, cycle and death, signaling and cellular differentiation.
Peroxisomes: are membrane–bound organelles similar in appearance to Lysosomes, yet they are smaller in comparison.
Peroxisomes contain catalese, peroxidase and oxidative enzymes which aid in metabolic function, specifically in the
beta–oxidation of fatty acid and the conversion of hydrogen peroxide into water and oxygen.
Non–Membrane Bound Organelles: are organized structures which are not bound by a membrane. Members of Non–
Membrane Bound Organelles are Centrosome, Cytoskelaton, Ribosomes and Proteasomes.
Centrosome: are usually located near

Sequence And Sequence Of Proteins
Sequence Information of Proteins
Just as members in the same family often resemble each other, similarly structured molecules are often grouped in the
same category. There are several methods of comparing amino acid sequencing and determining how closely they are
related. A simple example is the sequence–comparison method. Sequence databases are searched for a specific amino
acid sequence of unknown characteristics. A set of molecules that are similar in structure can give insight into the
properties of the unknown sequence of amino acids.
To determine the similarity between 2 amino acid sequences, one can apply sequence alignment. This method aligns the
2 sequences and slides them past each other one amino acid at a time and calculates what position has the greatest
amount of matched residues. However, there is a drawback to this method in that it does not show all of the possible
alignments. To counteract this, one can induce a gap in one of the sequences to increase the total possibilities of
matches. The gap will compensate for the insertions of deletions of sequences in a gene that is absent in the second
sequence.
However, simply comparing the identities of amino acids cannot account for everything. To increase the accuracy in the
comparing two sequences there are 2 kinds of substitutions that can be made to further progress the determination of
amino acids. The first is a conservative substitution which substitutes one amino acid with another amino acid that is

Angelman Syndrome
There are many diseases and syndromes that occur in the developmental stage of human development. One of the many
syndromes is Angelman syndrome. When this syndrome was first discovered by Harry Angelman, it was known as
"happy puppet syndrome". This syndrome is not typically diagnosed at birth, but can also be diagnosed from the ages of
one to six. This syndrome is a neuro–genetic disorder that occurs in one in 15,000 people. Because of its rareness, this
syndrome is often misdiagnosed as autism or cerebral palsy. Make thesis– Angelman syndrome is caused by a defect in
the UBE3A gene, has various symptoms, that can be misdiagnosed, and patients will live with lifelong treatment. The
are various causes of Angelman syndrome, but the main cause ... Show more content on Helpwriting.net ...
Angelman syndrome can be diagnosed within the first year of the life if the abnormalities are noticed and investigated,
but the disorder is more often diagnosed between 1 and 4 years of age as the child's abnormalities become more
clinically apparent (Bevinetto). In order to confirm the diagnosis, a blood test must be done to look at the child's
genetics (Angelman). Then, a combination of genetic test can reveal the chromosome defects. There are three different
defect tests may reveal: parental DNA pattern, missing chromosome, or gene mutation. Parental DNA pattern test
screens for three of the four genetic defaults that cause this syndrome. To find out if the chromosome is missing either a
fluorescence in situ hybridization (FISH) test or a comparative genomic hybridization test (CGH) can show if portions
of chromosomes are missing. It is rare if Angelman syndrome occurs with only a gene mutation. This happens when the
UBE3A gene is present and active, but mutated. A UBE3A gene sequencing test is used to look for maternal mutation
(Mayo). After the diagnosis is complete, treatments are discussed with the patient and their

Essay On Proteasome
Recent findings have focused on developing effective proteasome inhibitors as anti–proliferative agents because
previous reports strongly suggest that abnormal or impaired functions of proteasome aggravate the accumulation of
aberrant proteins in cells, which consequently stimulate apoptosis in cells (Chhangani et al., 2013; Chhangani and
Mishra, 2013; Huang and Figueiredo–Pereira, 2010). Although, the role of proteasome is well–established in clearance
of misfolded aggregation of proteins linked with neurodegeneration and aging,still critical examination of previous
studies suggest that inhibition of proteasome activities can be auseful therapeutic strategy to induce apoptosis in cancer
cells, due to their high metabolic demands and ... Show more content on Helpwriting.net ...
Mitochondrial Membrane Potential Detection JC–1 Kit (BDTMMitoScreen) and FITC Annexin–V–Apoptosis
Detection Kit I (BD PharmingenTM) were obtained from BD Biosciences. Lipofectamine® 2000, OptiMEM, and JC–1
(5,5', 6,6'– tetrachloro–1,1',3,3'tetraethylbenzimidazolocarbocyanine iodide) were purchased from Life Technologies
and Molecular Probes respectively. TUNEL assay kit, Dual luciferase reporter gene assay kit and Proteasome–GloTM
assay reagents were obtained from Promega. Anti–ubiquitin, anti–GFP, anti–20S proteasome, anti–p53, anti–p27, anti–
p21, anti–Bax, anti–IkB–α, anti–β–actin and anti–HA antibodies were purchased from Santa Cruz Biotechnology.
Horseradish peroxidase–conjugated anti–rabbit–IgG and anti–mouse IgG; anti–rabbit, and anti–mouse (IgG fluorescein
isothiocyanate and IgG–rhodamine) were obtained from Vector Laboratories. Plasmid pcDNA™ 3.1 was purchased
from Life Technologies. pcDNA3–EGFP (Addgene 13031), pRK5–HA–Ubiquitin–WT (Addgene plasmid 17608),
pEGFP–Hsp70 (Addgene plasmid 15215) and Luciferase–pcDNA3 (Addgene plasmid 18964) plasmids were purchased
from Addgene.
2.2. Cell Culture, Transfection, Reporter Gene And Cell Viability Assays
COS–7 and A549 cell lines were maintained at 37°C, 5% CO2 in Dulbecco's modified Eagle medium (DMEM)
supplemented with 10% fetal bovine serum (FBS) and 1% (v/v) streptomycin/penicillin (Gibco, Invitrogen). For various
transfection and treatment experiments, cells

The Pros And Cons Of Misfolded Protein
Introduction
The central dogma of molecular biology conveys the idea that genetic information passes from DNA to RNA before
'culminating in protein synthesis' (Bandyra & Luisi, 2015). In essence, our genetic information is mainly used to code
for specific proteins. There are 20 amino acids that can be bonded together in many different orders to form a number in
excess of 10 million proteins across all biological organisms (Innovateus, 2015). Proteins have many different uses and
functions, as well as modifications. Examples of these differences include glycoproteins with carbohydrates attached to
be used in the cell membrane and phosphorylated serine molecules that act as metabolites. For the protein to be able to
carry out its specific function, it must fold in the correct way. A precise path must be followed to allow the correct shape
to be formed and if there is an error in this process, the misfolded protein could lead to dangerous diseases forming.
The ... Show more content on Helpwriting.net ...
The point of using this molecule is to reduce the risk of proteins folding into non–functioning shapes and aggregating
(Saibil, 2006). Protein aggregation is the accumulation of misfolded proteins and they can form insoluble plaques
known as amyloids. The pathway to aggregation is, perhaps; an alternative to the innate pathway and that the
aggregation pathway favours interactions within the molecules rather than between them (Stefani, 2004). There are
specific and non–specific forms of chaperones and it is thought that their existence was a product of evolution.
Therefore, protein misfolding is likely to have been a prominent feature of life, encouraging the eventual production of
quality–control molecules. A mutation to the chaperones can render them obsolete and in some cases they are not
present at all. Some diseases are caused by a mutation to the chaperone or an absence of the protein altogether
(Reynaud,

How Does Diabetes Mellitus Affect The Individual 's...
Metabolism is a sequence of biochemical reactions that take place in every single cell and organ to maintain the
organism growth, reproduction, damage repair, and adaptation to the surrounding environment. These reactions involve
catabolism and anabolism using the major sources of energy: proteins, lipids, and carbohydrates. Furthermore, any
disruption in the regulation of the metabolic processes affects the individual's morbidity and mortality [1]. Accordingly,
in this chapter, we are going to discuss diabetes mellitus, which is one of the main metabolic disorders.
1.1.1 Pancreatic regulation of Blood Glucose
The regulation of the cornerstone of the whole body energy, glucose, in blood stream by the pancreas, specifically the
islets of Langerhans, is very critical through the secretion of insulin and glucagon. Insulin, which is secreted from beta
cells of the islets of Langerhans in response to high blood glucose levels, has an anabolic effect via its stimulation of
glucose uptake in peripheral, skeletal muscle, as well as central, brain, tissues to be stored in the form of glycogen and
fat [2]. On the other hand, low glucose levels enhance pancreatic alpha cells secretion of Glucagon that plays the
catabolic role through stimulation of stored glycogen breakdown and formation of glucose from non–carbohydrate
sources via glycogenolysis and hepatic gluconeogenesis, respectively [2]. This mechanism is well controlled through
the opposite secretion of these hormones in response

The Formation Of Cellulose Fibrils Essay
Other genes like chvA, chvB, pscA and att regulate the formation of cellulose fibrils which are required for the first step
of weak and reversible attachment. Cellulose fibrils help the bacteria to attach to the wounded parts of the plant and also
anchoring to each other forming a microcolony.
VirD4 protein and 11 VirB proteins make up type IV secretion system for the transfer of T–DNA and several other Vir
proteins like VirE2, VirF etc to the host cell. VirD4 also promotes interaction of the processed T–DNA/VirD2 complex.
As discussed earlier the T–DNA/VirD2 complex in turn transforms into the T–strand that is then transferred into the
plant cell. Most VirB proteins help either in forming the membrane channel or serve as ATPase to provide energy. T–
pilus is then formed by VirB2 ,VirB5, VirB7, VirB2 as they are the major pilin protein.
So the first major step in the transfer of T strand is the formation of a long flexious appendage known as the T–pilus
(Bulgakov, 2000) . The detection of presence of acetosyringone and other substances activates the expression of 11
genes in VirB operon which are responsible for the formation of the T–pilus. Other products of VirB genes like VirB6,
VirB7 etc are used to transfer other subunits across the plasma memebrane.
Now the T–DNA is delivered as a single stranded DNA molecule coupled with the VirD2 protein in the plant cell. The
T–DNA is then integrated into the plant chromosome and are expressed by plants transcriptional machinery.

The Von Hippel-Lindau (VHL) Gene
The Von Hippel–Lindau (VHL) gene was first discovered as a tumor suppressor gene in 1993 by Latif, et al. (1). The
gene was identified in an attempt to determine the driver of tumorigenesis in Von Hippel–Lindau Disease. VHL disease
is an autosomal dominant hereditary cancer syndrome that is characterized by tumor and cyst formation throughout the
body, with those infected especially predisposed to hemangioblastomas of the central nervous system, eyes, pancreas,
and kidney. Latif, et al. were able to match the gene region to chromosome 3p.25–26 by positional cloning and created a
map of the region using pulsed–field gel electrophoresis in order to isolate the prospective genes. The DNA of 221 VHL
patients was then probed using specified plasmids to determine that there were 28 rearrangements present, with three
large non–overlapping deletions detected in the hypothesized VHL gene segment. This sequence was conserved across
different species, with implications of its necessity for normal cellular function, pointing to its role as a tumor
suppressor. Since part of the sequence of the protein product (pVHL) also matched (48%) to that of a surface membrane
protein sequence in Trypanosoma brucei, pVHL is thought to have some role in signal transduction or cell adhesion as
well.
The VHL gene itself is made of three exon segments located on chromosome 3p25. Patients with VHL syndrome are
heterozygotes of the VHL gene, with one allele that is a mutated or inactivated copy of the

Liddle's Syndrome
4.2.0 Mutations: As was previously outlined, the cause of Liddle's syndrome is from ENaC over presenting in the
ASDN due to a mutation to the channel is the cause of Liddle's syndrome. It has been shown that mutations on the
gamma and beta subunits are responsible for the gain of function in the ENaC. No mutation has been observed yet for
the alpha subunit. Mutations occur at the level of the gene for the beta and gamma subunit and cause either missense,
nonsense or frameshift mutations in the mRNA of the PY motif for ENaC(ref). This results in either a truncated protein
or elimination of some amino acids from the PY motif, which interfere with the binding ability of Nedd4 ligase and
inhibit Nedd4 ligase binding, respectively. Overall, this either decreases or eliminates the possibility of Nedd4–2
ligases' ability to tag and degrade the ENaC. With the inability to control ENaC surface expression at the kidney, its
reabsorption of sodium will be markedly increased due to ... Show more content on Helpwriting.net ...
As has been discussed, an inheritable mutation in genes coding for the beta and gamma subunits of the ENaC, causing
deletion or truncation of the PY motif leads to a disruption in ENaC ubiquitination. Ubiquitination itself is the process
of tagging a protein with a series of glycosyl subunits, signalling its degradation at the proteasome, destroying the
channel. With this inhibition in ubiquitination, ENaC is expected to and is seen to have a much larger surface expression
and channel open probability, leading to an overall increase in sodium reabsorption which causes the characteristic
symptoms of Liddle's syndrome. Through understanding the two major regulatory mechanisms at the levels of protein
trafficking of the ion channel and protein–protein interactions with the channel itself, better methods of control and a
better understanding of Liddle's syndrome can be

Essay on Biology Case Study
Advanced Cell Biology II Step 1: How will you identify the "vital" cellular protein that the virus targets for
degradation? (Hint: think proteomics). (3 pts.) First, since we know the viral RNA sequence and its targeting protein,
we can investigate it in bioinformatics database, and can acquire some clues or hints about the target proteins. From the
bioinformatics database, we might be able to find its structure, similarity with other proteins, functions, and binding
domains. In other words, we can get some partial or complete amino sequences of the targeting proteins or information
about likeness. Second, in order to further confirm the information about characteristics and function of the targeting
protein that we have ... Show more content on Helpwriting.net ...
Since we have already known the amino sequence of the protein in previous step, we can narrow down the targeting
ubiquitin ligase based on existing research data such as papers, NCBI data. There are many types of ubiquitin ligases in
cells. However, we can make some candidate groups of targeting E3 based on the bioinformatics database. We will use
antibodies which specifically bind to each type of ubiquitin ligase and impede its function. For example, the antibodies
may covalently bind to the targeting ubiquitin ligase, and therefore, impede its function. Then, we will measure the
amount of targeting protein. If we find that the amount of targeting protein is not changed in a cell, we can identify the
target ubiquitin ligase. This is because only when the function of the target ubiquitin ligase is impeded, the degradation
of the targeting protein will not be occurred. Step 3: What protein will be your drug target? What property of that
protein will you target? Design an assay/approach to identify an antidote for "degron". (4 pts.) Since "degron" targets a
vital cellular protein for ubiquitin–dependent degradation, if we block its process of degradation, we can effectively turn
off its effect. As mentioned earlier, ubiquitin ligase brings specificity. Since we have already known which ubiquitin
ligase is

Ubiquitin Specific Protease 7 Case Study
Introduction:
The ongoing search for new anticancer and antiviral treatments has led to many new discoveries. Ubiquitin–specific
protease 7 (USP7) is an example of a protein involved in different cancer development pathways and is also a target of
many viruses belonging to the Herpesviridae family. While ubiquitin proteins play an essential role in signaling
cascades and protein degradation, deubiquinating enzymes like USP7 interfere in these processes by cleaving the bond
between the substrate and ubiquitin. USP7 has a variety of targets including p53 (a tumor suppressing gene), different
transcription factors, and ICP0 – a protein that forms an integral part of the herpes simplex virus–1. The aim of this
study is to investigate the ... Show more content on Helpwriting.net ...
Lentiviruses that expressed shRNA were used to to infect HFF–1 cells, either in the presence of USP7 or GFP (used as a
control). These cells were then infected with HSV–1 and stained in order to compare viral growth rates. The results
showcased a 100–fold decrease in viral growth in cells that lacked USP7 compared to those lacking GFP. Another set of
experiments were done in order to specifically determine which UBL domains played a central role in the USPL–ICP0
interaction. For this, different UBL domains were isolated and labelled using radioactive nitrogen. These domains were
then titrated with ICP0 and an NMR spectra was used to look at binding–induced changes at the peaks. The results
showcased no changes for UBL1 and UBL3 domains, but changes in the intensities and positions of many peaks in the
labelled UBL12 spectrum. Taking the movement of the peaks into account, it was noted that the UBL12 domain plays a
pivotal role in the USPL–ICP0 interaction and the process is slow on the NMR time scale. To further locate the
UBL12–ICP0 binding site, the 1H– 15N HSQC spectra of free and ICP0–bound UBL12 were compared. While the two
spectra were similar, there were many residues missing in the free UBL12 spectra that only appeared after the binding
of ICP0. This helped reveal the various conformational changes associated with the binding of USPL with its substrate.
Discussion:
While previous studies had already characterized the structures

Gardner 's Respiratory Virus ( Grv )
Gardner's Respiratory Virus (GRV) is an enveloped, single–stranded RNA (ssRNA) virus that has been shown to cause
both upper and lower respiratory tract infections. This virus is an intracellular virus capable of replicating free within
the cytoplasm of host cells. Spread through small, airborne viral droplets, GRV invades the physical barrier that is the
mucosal surface lining the lungs and respiratory tract. The cells that line this surface are mostly epithelial cells, and
GRV enters these cells by being transported across their membranes through receptor mediated endocytosis. Once
inside the host cell, GRV replicates and begins its cytopathic effects on the host cells; the infected epithelial cells
undergo structural changes that lead to irritation, inflammation, and eventual lysis that can weaken these mucosal
surfaces, making the host more susceptible to further pathogenic attack. As with similar viruses, once the first line of
defense is breached and GRV is transported into the host cells, the immune response, involving both the innate and
adaptive branches of the immune system is initiated and attempts to remove the virus as well as prevent future infection.
GRV however, is highly evolved and possesses various evasion mechanisms that prevent the immune system from
accomplishing its job; luckily, a drug does exist to help eliminate the virus.
Expected Immune Response The innate immune response is meant to prevent further invasion and replication of the
pathogen

Role Of Phosphorylation Of Second Messenger Dependent On...
1. What is the role of the phosphorylation of GPCRs in the process known as "receptor desensitization?" First describe
the process, or what is meant, by the term "receptor desensitization." What does it mean when we say that the receptor
is "uncoupled" versus "down–regulation" of the receptor? Define and contrast the roles of the "second messenger–
dependent" protein kinases versus the "G protein–coupled receptor" kinases in the process of receptor desensitization.
What do the terms "homologous" versus "heterologous" desensitization refer to? (Ferguson, Pharmacological Reviews
53:1–24, 2001; Gainetdinov et al., Annual Review of Neuroscience 27:107–144, 2004; Vasudevan et al., Cell Cycle
10:3684–3691, 2011).
Receptor desensitization: ... Show more content on Helpwriting.net ...
This process called the "uncoupled". "Down regulation" means the receptor mRNA and protein synthesis decrease and
the preexisting receptor degradation. The "uncouple" and "down regulation" are both involved in the receptor
desensitization, but in different steps. These steps are following described. First, the receptor uncouple from
heterotrimeric G proteins; Second, cell surface receptors internalize into intracellular membranous compartments;
Third, receptor mRNA and protein synthesis decrease result in the down regulation of the total cellular complement of
receptors, as well as both the lysosomal and plasma membrane degradation of pre–existing receptors. There are two
generally kinases which are G protein coupled receptor kinase GRKs and second messenger–dependent protein
kinases(e.g., PKA and PKC). The G protein coupled receptor kinase only act on the phosphorylate agonist activate
receptor. For example, GRK family members work on activated receptors, and then promote the binding of cytosolic
arrestins, which sterically uncouple the receptor from heterotrimeric G protein. In contrast, second messenger–
dependent proteins kinases act on both phosphorylate agonist–activated GPCRs and other phosphorylates receptors that
have not been exposed to agonist. Thus, agonist–independent phosphorylation can only happen with the second
messenger–dependent protein kinases, but GRKs cannot do it. When we recognize the

Neurodegeneration
Neurodegeneration is a name used for a variety of conditions that have an effect on neurons that are within the brain.
Neurons are a major component of the nervous system which is made up of the brain and spinal cord. If the neurons
become damaged the body can not replace them.
There are many neurogenerative diseases which include Alzheimer's,Parkinson's and Huntington's disease. Most of the
diseases are not yet curable so in the result of this, the brain's neurons start to die because of this an individual will start
to develop symptoms of a Neurodegenerative disease.
As research progresses there have been many similarities that have been found within these three diseases. The most
common similarity that links Alzheimer's, Parkinson's and ... Show more content on Helpwriting.net ...
The alpha–synuclein within the Lewy body is usually modified in some way, for example, it may be bound to ubiquitin
this tags a protein in the cell for destruction by the proteasome.
In Alzheimer's the misfolding protein is due to abnormal accumulation of a beta and tau which are proteins within the
brain. These proteins produce aggregates that form around the cells nucleus which makes it become clogged.
In Huntington's disease
The symptoms of the three diseases are a little bit similar in terms of that they all have an effect on the individuals
coordination and memory.
Alzheimer's and Huntington's disease both have very similar symptoms like jerky movement this is to do with
involuntary movement and It can have an effect on the face, hands and legs.
Parkinson's and Huntington disease both have a few symptoms in common like rigidity which is stiffness of limbs,
making the individual not able to swing or move their arms when walking because their muscles are tight.
Parkinson's can make the muscles in the jaw and face weaker, which affects chewing and

Essay On Indomethacin
Our preliminary results suggest the possible interaction of indomethacin with proteasome subunits. To test whether this
interaction can affect proteasome functions, we measured various proteasome activities in indomethacin treated cells at
different concentrations (Fig 2A and 2B) and time intervals (Fig 2C and 2D). As shown in Fig 2A and Fig 2C, exposure
of cells with indomethacin suppresses chymotrypsin–like activity and similar effect of indomethacin was observed for
peptidylglutamyl peptide hydrolyzing (PGPH)–like activity(Fig 2B and 2D). To further examine the potential impact of
indomethacin on proteasomal functions, we sought to directly map the activities of proteasome in a cell–free assay. To
do so, we incubated purified proteasome ... Show more content on Helpwriting.net ...
Our above results suggest that indomethacin induces aggregation of aberrant proteins, which may be associated with
impaired proteasomal functions. To understand how indomethacin contributes in accumulation of aggregate–prone
proteins via proteasomal dysfunction, we treated cells with indomethacin and MG132 with or without nocodazole and
immunofluorescence analysis was performed with anti–ubiquitin and γ–tubulin antibodies, as represented in Fig 3F.
These findings indicate that use of indomethacin disturbs proteasomal functions and most likely accelerates the
accumulation of aggregate–prone proteins in cells.
3.3. Indomethacin increases ubiquitylated proteins aggregation and consequently generates aggresomes in cells.
In our previous experiments, we examined the proteasome dysfunctions in indomethacin–treated cells. To further
determine the role of indomethacin on proteasome homeostasis, we decided to observe the sequential effects of
proteasome impairment in the presence of indomethacin. Cells were treated with indomethacin in time dependent
manner; post–treated cell lysates were used for immunoblot analysis and blots were developed with ubiquitin and β–
actin antibodies. Notably, we re–examined that inhibition of proteasome functions mediated by indomethacin treatment
results in increased levels of the ubiquitylated higher molecular weight conjugates due to their enhanced aggregation
(Fig.

Research Paper On Friedreich's Ataxia
Friedreich's ataxia (FRDA) is an inherited disease named after Nikolaus Friedreich, who first described the disease in
1863 (National Ataxia Foundation, 2013). FRDA is autosomal recessive, meaning an individual only develops
symptoms if there is a deficiency in both Frataxin genes. An individual with a deficiency in only one Frataxin gene is
said to be a carrier and will not exhibit symptoms. FRDA affects the coordination of human's movements. The disease
affects the central nervous system, mainly the spinal cord and nerves that control muscle movement in the arms and
legs. The disease is caused by a deficiency in the frataxin expression (Medline Plus, 2014). Symptoms of this disease
normally occur between the ages of 5 and 15; and include difficulty walking, muscle weakness, speech problems,
involuntary eye movements, scoliosis, and heart palpations. Individuals with this disease eventually have to use a
wheelchair. At this point in time there is no cure for FRDA, except for treatment with medicines, braces, surgery, and
physical therapy. The cause of Friedreich's ataxia has been linked to a ... Show more content on Helpwriting.net ...
There is ongoing research aimed at reducing mitochondrial dysfunction and detecting molecules that increase frataxin
expression. Human frataxin is synthesized as a 210 amino acid precursor targeted for the mitochondrion (Rufini et al.,
2010). As soon as the frataxin precursor enters into the mitochondria, it is mediated by the mitochondrial processing
peptidase as it undergoes a two–step proteolytic–process, resulting in a mature frataxin that resides in the mitochondrial
matrix. The mature frataxin, which is a globular polypeptide, is involved in the iron–sulfur cluster assembly that occurs
in the matrix. The frataxin reduces the activity of Iron–Sulfur Cluster (ISC)– containing enzymes, more specifically,
aconitase, which leads to defective ATP

Regulation and Functions of the p53 Protein
p53 gene, also known as tumor protein 53 (TP53), encodes for a tumor suppressor protein which regulates the cell cycle
and apoptosis. The p53 protein has been described as the guardian of the genome (1) because of its role in preventing
genetic mutation. It belongs to a protein family which includes p53, p63 and p73 and these are structurally and
functionally related to each other. However, p53 seems to have evolved as a tumor suppressor in higher organisms,
while p63 and p73 play a role in normal developmental biology (2).
Structure of p53
P53 functions primarily as a transcription factor, and is biologically active as a homo–tetramer comprising of 4 X 393
amino acid residues. Each monomer comprises of several functional domains:
1. An acidic N–terminus transcription–activating domain 1 and 2 (TAD1/2) – This region interacts with various
transcription factors
2. Proline–rich region (PRR) – This plays a role in p53 stability
3. Central DNA binding domain (DBD) – required for binding to specific sites on the DNA.
4. Tetramerization domain (OD) – required for the assembly of the functional tetramer.
5. Carboxyl terminus domain (CTD) – which is bound to DNA binding domain and is involved in negative modulation
of DNA binding domain.
The central DNA binding domain is the most highly conserved region of p53, when compared to its other family
members, p63 and p73. Loss of tumor suppressor function of p53, as seen in most cancers, results from missense
mutations in the DNA

Ea-OTU ) Case Study
Abstract
Emeria acervulina ovarian tumor (Ea–OTU) belongs to OTU domain class of cysteine protease deubiquitinating
enzymes. We show here that Ea–OTU is highly linkage–specific, cleaving Lys48(K48)–、Lys63(K63)–、Lys6(K6)–
linked diubiquitin but not K29–、K33、K11–linked diubiquitin. Recombinant Ea–OTU but not a catalytic–site mutant
Ea–OTU (C229A、H359A) exhibited activity against diubiquitin. The activity was selective for diubiquitin chains with
preference for specific lysine linkages (K6 >K48>K63). The K48– and K63– polyubiquitin linkage modifications were
found to be present in E. acervulina, where they exhibited differential levels in the each stage of E. acervulina. Ea–OTU
removed ubiquitin from the K48– linked ubiquitinated E. acervulina ... Show more content on Helpwriting.net ...
acervulina remains unclear.
Protein ubiquitination regulates cellular processes by influencing the stability and function of modified proteins. The
ubiquitin (Ub) protein is highly conserved in all eukaryotes and composed of 76 amino acids. A single Ub protein or Ub
oligomers can modify single or multiple lysine residues of the protein. Ubiquitin forms covalent chains through each of
its seven lysine residues (Lys6, Lys11, Lys27, Lys29, Lys33, Lys48 or Lys63) or its N terminus and the type of Ub
chains determines the functional outcome of the modification. Modification by a K48–linked chain directs modified
proteins to the 26S proteasome for subsequent degradation[22]. In contrast, modification by K63–linked chains
modulates the function of the modified protein, such as its role in DNA damage repair or genome stability[23]. Lys11–
linked chains constitute an alternative degradation signal used during cell cycle progression[24]. K6–linked Ub chain–
modified parkin participates the translocation of parkin and then regulates mitophagy and mitochondrial integrity. USP8
can preferentially remove K6–linked Ub chains from parkin to promote parkin turnover, which is necessary for
mitophagy to proceed efficiently[25][26]. The roles of proteins modified by other types of linked Ub chains remain
unclear. Ub or Ub chains can be removed by deubiquitinases (DUBs). DUBs consist of five main subfamilies: the Ub–
specific protease (USP) superfamily, the OTU superfamily, the

Dna Synthesis Case Study
To achieve accuracy of DNA replication after the unwinding of DNA, the DNA must be synthesized. DNA synthesis, in
the case, the two strands are disconnected and then turned into single–stranded DNA. This is called replication fork.
The replication fork acts as a model for DNA synthesis. However, the site of impaired or mutated DNA can cause a
lower rate pf success for DNA synthesis. Impaired DNA can also lead to unprocessed and unligated okazaki fragments.
Okazaki frgaments are small DNA fragments that are linked to the lagging strand of DNA. The research article suggest
that okazaki fragemts should be tracked for the benefit of cancer patients. For instamce, the lack of DNA ligase 1 is
caused by the delay of okazaki frgaments. DNA ligase 1 ... Show more content on Helpwriting.net ...
An ubiquitin can change the way a cell functions or even where the call is located. The researchers then use a cdc9 with
a wild–type of DNA ligase 1 to determine whether PCNA ubiquitination happens because of the nicked DNA or
because of the lack of PCNA–DNA ligase interaction. While reviewing this, they noticed that the cdc9 mutants come to
a halt during the later phases of the cell cycle and they collect unligated okazaki fragments. THis proves that PCNA
ubiquitination occurs because of the nicked DNA. The nicks are left behind for repairin the last phase of the cell cycle,
G2. Although they discovered this, they alos discovered that breaks in the DNA were present in the cdc9 mutants. They
caused the replication forks to be held up. These breaks need to be repair via HR. To repair the breaks they suggest
RAD52 to be used. Unfortunately, RAD52 was unsuccessful and did not interact with the mutant. They then test if
RAD59 can be used to repair the breaks. THey recognize that RAD59 played an important role in supporting the kinase
needed for checkpoint activation of the cell cycle, known s Mec1. However, RAD59instead deactivated Mec1 by
restraining a protein coding gene called

Ubiquitination: An Unneeded Protein Analysis
You are a frustrated student who has a big biochemistry test tomorrow, but no time to look over material because he
have to work at Kroger tonight until closing because you used up all your sick days. Your annoying boss tells you there
is a shipment of new milk and meat products coming in and the old, expired products must be removed. He gives you
bright green stickers to stick onto the expired products that need to be removed from the shelves. As you are doing this,
you start to think about your test and try to apply biochemistry to real–life situations, but to no avail. You get more
frustrated and contemplate quitting your job right there. Suddenly, you think about the word 'quit' and realize you have
to know about ubiquitin for tomorrow's test. You remember one of ubiquitin's many roles is to tag an unneeded protein
for its destruction. Then you start realizing that labeling stickers on expired products so they can be removed in a
supermarket is like ubiquitin labeling old, outdated proteins in our cells so they can be removed for the proteins still
needed ... Show more content on Helpwriting.net ...
The protein usually targets old, dysfunctional proteins from the cell cycle, which makes sense for controlled cell
division. The ubiquitination mechanism was originally obscure, but made more clear in the mid–1980's by Aaron
Ciechhanover, Avram Hershko, and Irwin Rose, which helped them win the Nobel Prize for Chemistry in 2004 (Nobel
Prize website). Initially, the process was looked at as proteolytic system utilizing ATP. Many ATP–dependent
proteolysis factor 1 (APF–1) molecules linked with a substrates that were later found to be deteriorated with free APF–1
in the cellular extract (Ciechhanover, 2012). APF–1 was called ubiquitin and it uses its C–terminal glycine to conjugate
to the substrate's

Applying Autophagy and Apoptosis for Strategies to improve...
The pathways controlling autophagy and apoptosis should be targeted as the strategies to improve treatment of
glioblastoma. The proteins to be targeted are Beclin, p62 and EGFR.
Survival related or anti–apoptotic protein such as Bcl2 were found to be upregulated in glioblastomas whereas
autophagy proteins like Beclin were found to be downregulated. The autohagy (Atg) proteins function at several
discrete but continuous steps in autophagy which include induction or selection/packaging of cargo, vesicle nucleation,
vesicle elongation, vesicle docking and fusion with lysosomes, and degradation of vesicular contents. There is
significant evidence showing overlap between these two pathways. Hence, we choose to target these pathways and ...
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p62 is an autophagy selective substrate and it accumulates when autophagy activity is reduced. Indeed, the level of p62
is often used as an indicator of autophagy activity. Interestingly, p62 levels are commonly upregulated in human tumors
and genetic ablation of p62 in various tumor models has been shown to reduce the tumorigenesis occurring because of
autophagy‐deficiency.
EGFR: The most common genetic mutations / alterations seen in gliomas are the amplification of EGFR, expression of
EGFR VIII mutant and homozygous / hemizygous deletion of PTEN and NF–1. The aberrant signals that result from
these mutations interact with the PI3KAkt– mTOR pathway and are responsible for promoting survival and
chemoresistance in gliomas. Therefore targeting the receptor tyrosine kinases (RTKs) with either monoclonal antibodies
or small molecule inhibitors emerged as a promising therapeutic strategy . Clinical studies with small molecule
inhibitors of EGFR, such as erlotinib and gefitinib, have been disappointing in gliomas. Similarly, monoclonal
antibodies against EGFR, cetuximab and panitumumab, have only a cytostatic effect in glioma cell lines. The
abundance of multiple types of RTKs along with the frequent deletion of PTEN in gliomas may account for the lack of
effectiveness of single agent tyrosine kinase inhibitors.
In

Cystic Fibrosis Analysis
To understand the effects that Cystic Fibrosis has, it is important to discuss CFTR synthesis and trafficking. Mutations
in the CFTR results in protein misfolding, causing a defect in cellular processing and trafficking that targets the protein
for degradation and reduces the quantity of CFTR at the cell surface [56]. In order for the CFTR to function correctly,
then it must be synthesized, folded, and transported to the apical membrane of the cell without problem. The CFTR
passes through quality control systems to get rid of misfolded proteins that would not function properly or that could
become damaged [16]. It is apparent that only 33% of CFTR folds correctly and is allowed to leave the endoplasmic
reticulum [8]. The nucleus is the site ... Show more content on Helpwriting.net ...
One system detects defects in the cytosolic parts of the CFTR while the other detects defects within the endoplasmic
reticulum membrane. It is apparent that ubiquitylating proteins work with specific factors in order to detect misfolding.
For example, Hsp70 detects mutations in the cytosolic regions of the CFTR. It is suspected that Hsp70 keeps the CFTR
soluble until the E3 ligase CHIP binds with it. The complex that forms between these two redirects the CFTR to the
degradation pathway. Derlin–1 is involved with detecting defects in the endoplasmic reticulum membrane and is
involved in the retro–translocation of CFTR from the endoplasmic reticulum so that it can be send to the proteasome for
degradation [20]. If the CFTR protein is folded correctly within the endoplasmic reticulum, then it is sent to the Golgi
apparatus. The coat protein complex II (COPII), which is found within the ER membrane, helps to maintain the correct
CFTR structure and location, conformation, and protein–protein interactions as this occurs. Final processing for the
CFTR is carried out within the Golgi, as the CFTR replaces a mannose–enriched side chain with a mature complex
oligosaccharide side chain. After this is completed, the CFTR is moved to the apical membrane where it has a half–life
of 12 to 24 hours. If a CFTR is functioning poorly within the membrane, then it can be recognized by Hsc70 and then

The role of autophagy poses as a highly conserved...
The role of autophagy poses as a highly conserved catabolic phenomena where cells undergoing stress develop a
cytoplasmic crescent shaped phagophore that matures into an autophagosome. The autophagosome is involved in
engulfing damaged organelles and long lived proteins in order to replenish the cellular energy content and building
blocks for biosynthesis. The autophagy phenomenon always occurs to maintain the cellular homeostasis. But, under
stress there is triggering of this autophagy event beyond its basal level. The most important breakthrough in our
understanding of the molecular pathway of autophagy came from yeast genetic analysis where 35 Atg (Autophagy–
related) genes were identified. Various types of Cellular stress sparks an ... Show more content on Helpwriting.net ...
Ultimately, PI3P plays a crucial localization response to facilitate fusion at the last step of double–membrane
autophagosome synthesis. Binding between Vps34 and Beclin–1 is enhanced by Ambra–1 (activating molecule in
Beclin1–regulated autophagy protein–1), Bif–1 (Bax interacting factor–1), and UVRAG (ultraviolet radiation
resistance–associated gene) whereas Bcl–XL, Bcl–2 and Rubicon (Run domain Beclin–1 interacting cysteine–rich
containing protein) inhibits this interaction. Another stress induced transmembrane protein is vacuole membrane protein
1(VMP1) which interacts with Beclin–1 to induce autophagy. A couple of ubiquitin–like conjugation system gets
involved during autophagosome elongation through a chain of events. Atg 12 interacts with Atg 7 (E1 ubiquitin–like
activating enzyme), following which Atg12 binds to Atg10 (E2–like ubiquitin carrier), thereby linking Atg12 to Atg5;
then, Atg16 dimers gets attached to this complex resulting in phagophore expansion. The Atg5–Atg12–Atg16 complex
helps in the growth of the nascent edges of the phagophore. This trimeric conjugation drops out when the phagophore
finally matures into the autophagosome. A second ubiquitin– like system is involved in microtubule associated protein
light chain 3 (LC3, mammalian homolog of yeast Atg8) processing.Atg4 cleaves LC3 to an active intermediate LC3I by
conjugating with E1–like Atg7 through an ATP dependent

Ubiquitin Lab Report

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