Functions Of Protein Gamma Secretase Essay

Functions Of Protein Gamma Secretase Essay
Introduction
Proteins are linear polymers that consist of monomer units called amino acids. These amino acids are linked end to end by peptide bonds (M. Berg,
2015). The linear, unbranched chain of amino acids will fold into one or a few closely similar three–dimensional structures known as conformations.
Conformations of the proteins and the chemical properties of side chain amino acids, determine the function of the protein. Proteins can have functions
that are essential for life within the cell. Without these functions, the cells wouldn't be able to function properly (Lodish, 2016). Sometimes proteins can
have mutations (change within the base sequence) within them causing their three–dimensional shape to change. The protein gamma–secretase is an
example of this. This protein can have a mutation within one of its main components which can have an important role in Alzheimer's disease (Lodish,
2016). Proteins have four different structures: primary, secondary, tertiary and quaternary. These different structures will have different roles in the
protein folding into its specific three–dimensional shape.
Primary Structure:
The primary structure is the linear sequence of amino acids (Lodish, 2016). These amino acids can be arranged in different orders to form different
proteins. The 3D structure of a protein is determined by the primary structure as this influences the intramolecular forces that form between the amino
acids. Also, depending on the properties of the amino
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DNA: A Double Helix Structure Of Protein
Hereditary material in humans is contained in our DNA. DNA is a double helix structure of deoxyribonucleic acid comprised of four chemical bases:
adenine (A), guanine (G), cytosine (C), and thymine (T). Adenine forms hydrogen bonds with thymine and cytosine forms hydrogen bonds with
guanine. The polypeptide strand is held together by covalent bonds. RNA is ribonucleic acid, a nucleic acid essential to coding, decoding, and
regulation of gene expression as well as protein synthesis. RNA is so vital to these functions because, unlike DNA, it can leave the nuclear envelope.
Like DNA, RNA is comprised of four chemical bases: adenine (A), uracil (U), guanine (G) and cytosine (C). In addition to one base being different,
RNA and DNA contain different sugar molecules. RNA is comprised of ribose and DNA is comprised of deoxyribose, hence the names. RNA is
transcribed from DNA. DNA and RNA are essential in the production of protein. Proteins are distinctly folded amino acid sequences dictated by the
nucleotide sequences of its genetic material. Proteins carry out specific functions within the cell such as catalyzing chemical reactions, receptors and
offering structure in the form of collagen or elastin for example. ... Show more content on Helpwriting.net ...
Once genetic information has been embedded in a protein it cannot be removed. This is a multi–step process in which genetic information from the
nucleus in DNA moves to RNA and then to protein which will ultimately perform a specific

Protein Structure And Proteins : Proteins
Introduction:
Protein Structure
When first discussing the protein itself we should understand the components of a protein by structure and function. Proteins are considered biological,
organic polymers made of amino acids. Amino acids which are connected by peptide bonds to create a polypeptide chain. One or more polypeptide
chains can become twined into a 3–D shape forming a protein. Proteins have many complex shapes that comprise of many loops, curves, and folds.
Folding in proteins usually happens in a spontaneous manner. Chemical bonding consists of portions of the polypeptide chain holding the protein in one
and giving it its shape. There are two general classes of protein molecules: globular proteins and fibrous proteins. Globular proteins are usually soluble,
spherical in shape, and compact. Fibrous proteins are mostly elongated and insoluble. Globular and fibrous proteins may display one or more of four
types of protein structure. These structured orders are called primary, secondary, tertiary, and quaternary structures. The 4 levels of protein structure are
distinguished from one another by the degree of complexity in the polypeptide chain. A single protein molecule may include one or more of the protein
structure types. The primary structure is best described as the unique order in which amino acids are joined together to form a protein. Proteins are
constructed from a set of twenty amino acids.
Method
The alpha carbon bonds to the four groups: A hydrogen atom

Ap2 Lab Report
Discussion
HEPN dimerization
Due to the HEPN domains property of dimerizing, sacsin's interaction with JIP3 cannot be confirmed to act through though HEPN. Performing a
pulldown assay with a mutated hepen construct which retains the property of binding but is unable to dimerize would indicate that HEPN interacts with
JIP3. A mutated construct of HEPN construct called ARSACS Asn–4549 mutation exists, which disrupts the HEPN dimer interface due to the
replacement of an asparagine with aspartic acid in the α4–α5 loop near the edge of the HEPN dimer interface. However, this construct destabilizes
HEPN folding through the introduction of a charge at the dimer interface and loss of two polar contacts. Furthermore, the expression of this HEPN ...
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Furthermroe, due to the expression if all of these cosntructs ina abacterial system, post translational modifications are lost which may have an effect on
the these constructs three dimensional structre. Expressing these constructs in in a mammalian system such as in human neurons would allow for the
study of the effect of post translational modification on influencing JIP3 interaction.
Sacsin is involved in lysosomal transport
Overexpression of the HEPN domain in HeLa cells results in abnormal lysosomal positioning under both starved and nutrient deficient conditions. This
indicates that sacsin is involved in lysosomal transport due to the drastic increase in perinuclear lysosomal clustering when HPN is overexpressed.
HEPN's property of dimerizing with full–length sacsin may be disrupting its function by preventing endogenous sacsin from dimerizing within the cell
which may be essential to its function, particularly for binding JIP3 which is necessary for lysosomal transport6??6.
The abnormal perinuclear lysosomal clustering phenotype observed under unstarved conditions suggests a novel role of sacsin in lysosomal transport.
Particularly, in anterograde transport due to the reduction in peripheral lysosomes, suggesting that the majority of lysosomes have migrated toward the
center and are unable to redistribute throughout the cell. Additionally, increased lysosomal scattering is observed following three hours of starvation,
which

Essay On Protein Structure Assurance
Protein structure assurance by NMR techniques includes reconciliation of a wide range of programming apparatuses. The heterogeneous exhibit of
programming instruments utilized as a part of the procedure of protein NMR structure assurance presents authoritative difficulties in the structure
assurance and approval forms, and makes an expectation to absorb information that constrains the more extensive utilization of protein NMR in
science. It also shows a coordinated arrangement of computational strategies for protein NMR limitation investigation and structure quality evaluation,
relabeling of prochiral iotas with remedy IUPAC names, and additionally numerous techniques for examination of the consistency of nuclear positions
showed by their ... Show more content on Helpwriting.net ...
Specifically, the test and significance of protein NMR structure approval has been the subject of the ongoing project work and the research conducted
by the students. In any case, the heterogeneous programming condition of protein NMR spectroscopes keeps on bewildering and back off the endeavors
of amateurs and specialists alike, and challenges endeavors to institutionalize protein NMR structure assurance and evaluation. In this lab students have
mostly focused on definite depiction of the PDBStat programming, and feature a few of its significant computational capacities.
One of the difficulties of working in the heterogenous programming condition that the students have found in the lab, which has advanced in the protein
NMR people group, is that the naming traditions and arrangements for nuclear directions are distinctive for different vital programming apparatuses.
The most widely recognized utilization of PDBStat by the students is for changing over between XPLOR/CNS, CYANA, and Rosetta directions and
restrictions. PDBStat can read nuclear arrangement and restriction records in any of these configurations and change over them to standard PDB design
organize documents, with redress prochiral hydrogen names, and a relating limitation document steady with these PDB

Proposed Genetic Algorithm Of Protein Tertiary Structure...
In the next subsections, the proposed genetic algorithm of protein tertiary structure prediction will be described. i) The Proposed Genetic Algorithm
Genetic Algorithms (GA) primarily motivated by the biological theory of evolution, and it was originally developed by J. Holland in 1975 [11]. The GA
is is a search heuristic that mimics the process of natural selection. GA is based on the operations of population reproduction and selection to acheive
optimal results. Through artificial evolution, successive generations search for fitter adaptations in order to solve a problem. Each generation consists of
a population of chromosomes, representing a series of candidate solutions (called individuals) to an optimization problem, generally evolves toward
better solutions by applying genetic operations of recombination and mutation to create a new offspring population from the current population. The
process evolution usually starts from a population of randomly generated individuals or, using domain background knowledge. The generation process
repeats for many generations with the aim of maximizing the objective Function (also called fitness) of the chromosomes that are evaluated each
generation. Usually, the GA termination cindition are set to the maximum number of generations. ii) Genetic Representation In a GA, a population of
chromosomes, representing a series of candidate solutions (called individuals) to an optimization problem, generally evolves toward better solutions.

Microscopy Has Long Been Proven Fundamental?
Abstract:
Microscopy has long been proven fundamental in structural biology, especially for the mechanistic understanding of virus cell architecture and
macromolecular functions. Cryo–electron microscopy (cryo–EM) is a variation of electron microscopy that allows imaging of viruses in cryogenic
solution (i.e. ethane solution cooled to near liquid nitrogen temperature) without having to grow crystals or embed samples in heavy metal salts (i.e.
negative staining), using electrons to focus specimens with a resolution power to near–atomic details. Cryo–EM employs thin vitrified layers of
unfixed, unstained and unsupported virus structures in cryogenic solutions (i.e. samples are preserved in or close to biological conditions) in easy
controlled settings, yielding resolution powers to a near atomic resolution, affording this technique an overwhelming popularity in structural biology.
Cryo–EM is now beginning to rival X–ray crystallography and NMR techniques to a near atomic details. This essay focuses on how cryo–EM have
been implicated in visualizing virus structures with particular emphases on bacteriophage MS2 virion.
Introduction:
For a mechanistic understanding of macromolecular and biochemical functions and processes of a wide variety of biological structures (i.e. cells,
proteins, bacteria and viruses) (Milne et al., 2013) optical devices (i.e. X–ray crystallography and NMR, among others) have long been implicated in
characterizing biomolecular structures into 3D

Protein Structure And Enzyme Action
Scientific Report–
Protein Structure and
Enzyme Action
Holly Tupper
Amino Acids
What is an amino acid and its chemical structure?
Amino acids are essential for the human body as they are referred to as the building blocks of proteins (Nutriology 2003). They are compounds that
contain a carboxylic acid group (–COOH) and an amino group (–NH2) also joined to them are various side groups which are bonded to the alpha
carbon (Thermo–fisher 2015).
Figure one showing the structure of an amino acid.
Date Accessed 12.3.16 https://www.google.co.uk/search?
q=amino+acids&biw=1280&bih=699&source=lnms&tbm=isch&sa=X&sqi=2&ved=0ahUKEwjrwLSj7nLAhVpDJoKHXvjDLsQ_AUIBigB#tbm=isch&
The ... Show more content on Helpwriting.net ...
When two or more amino acids and joined to one another with a peptide bond it is known then as a dipeptide bond. This is the formation of a
polypeptide or amino acid polymer.
The formation of polypeptides
The formation of polypeptides and protein chains involve a condensation reaction. Condensation reactions are the joining together of two molecules
and during the reaction water is released. The reverse of this is polymer disassembly into monomers involves a hydrolysis reaction whereby water is
used as a reactant and isn't released.
Figure three shows the condensation reaction clearly illustrating the formation and realising of the water molecule.
Date accessed 10.3.16
https://uk.images.search.yahoo.com/yhs/search;_ylt=A7x9Unu7eelWVCkAkjB3Bwx.;_ylu=X3oDMTBsYWhiN2NvBHNlYwNzYwRjb2xvA2lyMgR2d
_adv_prop=image&fr=yhs–iry–fullyhosted_003&va=condensation+reaction+polypeptides&hspart=iry&hsimp=yhs–fullyhosted_003 In order for a
protein to be formed 50–2000 amino acid residues must then be joined together. The reason it is now considered a residue is due to the condensation
reaction loosing water and thus the residue from the reaction is the polypeptide chain (BioFundementals 2012).
Properties of amino acid
Amino acids are solids and their properties include a very high melting point which is between 200–300°C. This is often considered surprising due to
how

Protein Structure
The six most abundant elements of life are carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur. Carbon is the most important element because
it is found in the atmosphere and all living matter. All living matter on Earth is made up of organic molecules. Organic molecules are formed of carbon
atoms, which bond to other carbon atoms , forming complex structures. The complex structure then bonds to other atoms found in essential elements.
Without carbon as a backbone, the molecule would break apart. All living things on Earth need carbon to live, grow, and reproduce. The carbon
compound CO2 is especially important because it is in all living matter. All life on earth is carbon based. There is more carbon found in living things
then ... Show more content on Helpwriting.net ...
The specific and unique order in the polypeptide chain is determined by the information from the cellular genetic code of the protein. Having one
amino acid in the structure causes the amino acid to not function properly or at all. There are four levels of protein structures, the primary structure,
secondary structure, tertiary structure, and quaternary structure. The primary structure explains the order of which the twenty amino acids in proteins
are held together to form a proper protein. The following amino acid structural characteristics are, carbons, hydrogen atoms, and carboxyl groups.
Alpha Carbon is a necessity to hydrogen atoms, carboxyl groups, and the amino groups in protein structures. The secondary structure causes the
structure to fold, curve, and make loops, that gives the protein its' dimentinal shape. The two types of secondary structures are alpha helix structures and
beta pleated sheet. The alpha helix structure looks like a coil and is bonded by multiple hydrogens. The beta pleated sheet is folded and held together by
hydrogen bonds in between polypeptide units. The third level, the tertiary structure is a broad dementinal structure that has several types of bonds and
forces to keep the protein in tact. The shaping of a protein is caused by the hydrophobic interactions. Amino acids and hydrophilic will make a great
amount of contact with their

Dna Protein Protein Structure
DNA Polymerase
Proteins are arguably the most structurally and functionally complex structures known to man. Through evolution spanning billions of years, these
macromolecules have been perfected to perform many functions necessary for life. Proteins contain four distinct levels of structure and are composed
of simple organic compounds known as amino acids. (Alberts, Bruce et al 2000) Amino acids are joined together by peptide bonds made during protein
biosynthesis, and the linked amino acid chain is known as a polypeptide chain. DNA determines the amino acid sequence and the sequence is what
determines the primary level of protein structure. This level of structure determines the protein's shape, which affects the assembly and function of ...
This level is formed whenever multiple polypeptide chains come together to design a single protein. Some proteins are only composed of one single
polypeptide chain, and therefore, do not have a quaternary level of structure. The four various levels of protein structure give a small insight into how
structurally complicated proteins really are. Functionally, proteins are just as diverse, if not more, as they are structurally. They are responsible for
providing structural support of the cell, aiding biochemical reactions, assisting the plasma membrane, and a multitude of other functions. One important
aspect of proteins are enzymes, which is a type of protein that catalyzes biochemical reactions in the cell. A clear majority of enzymes are proteins, but
not all proteins are enzymes. It is safe to say, that without proteins, life would not be possible.
DNA polymerase is an extremely vital protein, located in all cells, that is capable of synthesizing DNA from nucleotides. (Bebenek, Katarzyna et al
2004) It is also classified as an enzyme, which means it acts as a catalyst to kick–start a biochemical reaction in the cell. While the function of this
protein may sound simple, it is anything but. This protein not only copies the DNA, but also proofreads and corrects any mistakes in the DNA
sequence. With the hefty responsibility of replicating DNA and passing genetic information from generation to generation, DNA polymerase is one of
the most significant enzymes

Structure Of Mcfabz Protein
concentration of inhibitors have been shown in Figure 8A–8F. Overall all the inhibitors binding leads to changes in tertiary structure of McFabZ protein
as evident from figure. Increase in the ligand concentration leads to changes in near–UV spectra arises of all three aromatic amino acids (Phe, Tyr and
Trp). BiochaninA and Genistein binding have produced similar kind of effect on near–UV spectra. Daidzein has affected more Phe (255nm –270 nm)
and Tyr regions (275 nm–282 nm). Catechin gallate has shown more effects in phe and trp (290 nm–305 nm) regions. Altogether we can say that
regular decrease in MRE at 280nm is observed upon inhibitors binding. Alternations in MRE towards more negative value corresponds to more
flexibility of ... Show more content on Helpwriting.net ...
λmax emission shifted to 343 nm, 349 nm and 348 nm as shown in Figure 9A. Biochanin A and Genistein showed similar kind of effect on McFabZ
fluorescence. In both cases fluorescence intensity decreased when compared to native spectra while red shift is observed in λmax emission (Figure 9B
& 9C). In case of juglone and daidzein blue shift is observed (Figure 9D &9E). Overall we can say that ligand binding to McFabZ protein leads to
decrease in fluorescence intensity. 3.6 Thermodynamic analysis of binding of inhibitors to McFabZ
The binding of McFabZ protein with different inhibitors was studied using Isothermal Titration Calorimetry (ITC). The compounds used for titration
against McFabZ were genistein, biochanin A, daidzein, juglone, myricetin and quercetin. ITC data obtained was solved using one site model analysis
program of Origin7. Thermodynamic parameters – Enthalpy change (ΔH), Entropy change (ΔS), Gibbs free energy (ΔG) and Equilibrium dissociation
constant (KD) have been calculated. Table 3 shows the thermodynamic parameters of binding. Α clear 1:1 stoichiometric binding was observed in all
cases except myricetin (N= 1.90 ± 0.293). Downward trend in the ITC profile (Figure 10) reveals an exothermic profile of reaction while upward trend
corresponds to the endothermic nature of reaction. ITC titration data describing the binding of biochanin A (A), daidzein

Solid Phase Peptide Synthesis And Solid-3 Synthesis Of A...
In this essay, solid phase peptide synthesis and solid phase synthesis of a primer will be compared and contrast. Solid phase peptide synthesis is the
production of peptides, whereas the solid phase synthesis of a primer involves the production of oligonucleotides. A brief summary of each will be
discussed in this essay. With understanding the processes involves, there are two similarities and differences that will also be discussed in this essay.
In the solid phase peptide synthesis, a protected amino acid with a tert–Butyloxycarbonyl protecting group is anchored to a chlorinated reactive resin.
Afterwards, the amino acid is deprotected with trifluoroacetic acid. After this is done, another protected amino activated with DCC is coupled to the last
amino acid at the N–terminal. Whenever all of the amino acids are done being added, the peptide is released from the resin using hydrofluoric acid.
In the solid phase synthesis of primers, a ß–cyanoethyl (ßCE) group is added to the 3'–phosphoryl oxygen atom, while a dimethoxytrityl (DMT)
protecting group is attached to the 5'–oxygen atom. Moreover, the 3' amine group of the activated monomer is coupled to the 5' hydroxyl group of a
nucleotide base attached to resin, creating a phosphite trimester intermediate. Next, the molecule is oxidized with I2, adding a carbonyl oxygen atom to
the phosphoryl group. Lastly, the molecule is deprotected with dichloroacetitc acid, which helps remove the DM, but leaves the ßCE intact.
To begin,

What Are The Four Levels Of Protein Structure
. Amino acids have attributes that make them hydrophilic or hydrophobic. Amino acids that contain electrically side chains are able to connect or attract
with water molecules. Amino acids that contain partial charges or polar side chains, forming hydrogen bonds, are hydrophilic or attract with water
molecules. Amino acids with nonpolar side chains are hydrophobic or do not attract with water molecules.
2.
2. 3. The four levels of protein structure are primary, secondary, tertiary, and quaternary. All of the levels are made from the primary structure of the
protein. Primary structure contains covalent bonds and is the foundation and basis for the other levels of a protein. Secondary structure is a repeated
continuation of a peptide chain.

What Can Studies Of Serine Proteases Tell Us About The...
What can studies of serine proteases tell us about the relationship between protein structure, function and evolution?
Serine proteases are a group of important proteases which can fracture the peptide bond in the macromolecules and proteins. The serine proteases take a
great part in mammal lives especially in digestion, coagulation and the complement system appears. The activation of serine proteases are all because
of the change of a set of amino acid residues which includes at least one serine and that's why the name became. Although there are about one third of
the known proteolytic enzymes are serine proteases, the principle of interactions are really same: a complicate combined interaction in the catalytic
triad––Ser–His–Asp. This essay will firstly talk about the mechanisms of the serine proteases and secondly mention the relationship of the protein
structure, function, and evolution during the serine proteases interact. In the first part, the chymotrypsin interaction will be analyzed as an example to
explain the mechanism of serine proteases interact.
Figure 1 the pymol figure of Trypsin
Figure 2 structure of the active center of chymotrypsin
Figure 3 the specific interaction of chymotrypsin
The Pymol figure shows a crystal structure of Trypsin, a typical kind of serine protease. In the middle of the Trypsin, there is a Ser–His–Asp. The
mechanisms of all serine proteases including Trypsin are: firstly the serine residues in the active center are activated by

Protein Structure And The Protein Structures
Stephanie Ahlemeyer
Dr. Hudson
Bio 2240
Protein Essay
18 September 2015
Alcohol Dehydrogenase
Proteins are the main building blocks that cells are assembled from and they make up most of the cell's dry mass. They contain important elements such
as oxygen, carbon, hydrogen, nitrogen and amino acids. Proteins also help provide the cell with shape and structure. There are some proteins, which are
embedded in the plasma membrane, and they form channels and pumps. These channels and pumps control the passage of nutrients and small
molecules in and out of the cell. In addition, some proteins send important messages to other cells or are signal indicators. The proteins that are
embedded in the plasma membrane act as motors ... Show more content on Helpwriting.net ...
The protein Alcohol Dehydrogenase can be found in our stomach and in our liver. In addition, it can assist in generation of aldehydes and ketones.
According to the article, How Alcohol is Metabolized in the Human Body,
Alcohol dehydrogenase is the workhorse of the alcohol enzymes. ––it breaks down the majority of the alcohol that enters the human body. Alcohol
dehydrogenase is actually the name for a family of enzymes which break down alcohol––each of which has a slightly different molecular structure.
Researchers have identified as many as 10 varieties of the alcohol dehydrogenase molecule.
All of them bring about the same chemical reaction––the difference is that some varieties of alcohol dehydrogenase work more efficiently than others.
As we shall see below, these variations in the alcohol dehydrogenase molecule can explain why some individuals react differently to alcohol than
others.
Based off this quote, alcohol dehydrogenase is an enzyme. An enzyme is a protein that catalyzes chemical reactions. In addition, alcohol dehydrogenase
often referred to as AdhD, can be found in all organisms. Adhd can be used in food, pharmaceutical, and fine chemical industries for the productions of
aldehydes, ketones, and chiral alcohols. (Machielsen et al., 2006). Alcohol dehydrogenase is made up of 3 main components, Zinc, Ethanol, and NAD.
According to the article, Alcohol Dehydrogenase,
Alcohol dehydrogenase uses

Essay On Protein Structure Assurance
In Roberto Tejero's lab, students were investigating Protein structure assurance by NMR techniques includes reconciliation of an extensive range of
programming apparatuses. The heterogeneous exhibit of programming instruments utilized as a part of the procedure of protein NMR structure
assurance presents authoritative difficulties in the structure assurance and approval forms, and makes an expectation to absorb information that
constrains the more extensive utilization of protein NMR in science. It also shows a coordinated arrangement of computational strategies for protein
NMR limitation investigation and structure quality evaluation, relabeling of prochiral iotas with remedy IUPAC names, and additionally numerous
techniques for ... Show more content on Helpwriting.net ...
Numerous PC projects and servers have been created that coordinate critical parts of the procedure, including information accumulation, information
preparing information examination and structure quality evaluation.
Specifically, the test and significance of protein NMR structure approval has been the subject of the ongoing project work and the research conducted
by the students. In any case, the heterogeneous programming condition of protein NMR spectroscopes keeps on bewildering and back off the endeavors
of amateurs and specialists alike, and challenges endeavors to institutionalize protein NMR structure assurance and evaluation. In this lab students have
mostly focused on definite description of the PDBStat programming, and feature a few of its significant computational capacities.
The common difficulties of working in the heterogenous programming condition that the students have found in the lab, which has advanced in the
protein NMR people group, is that the naming traditions and arrangements for nuclear directions are distinctive for different vital programming
apparatuses. The most widely recognized utilization of PDBStat by the students is for changing over between XPLOR/CNS, CYANA, and Rosetta
directions and restrictions. PDBStat can read nuclear arrangement and restriction records in any of these configurations and change over them to
standard PDB design organize documents, with redress prochiral hydrogen names, and a

Explain The Two-Step Aminoacylation Reaction Between Aars...
The two–step aminoacylation reaction that is required to attach an amino acid to the tRNA is displayed in Figure 6.
Figure 6: Word equation for the 2–step aminoacylation reaction within aaRS's. Please note that aa (amino acid), aaRS (aminoacyl tRNA synthetase),
and aaRS.aa–AMP (amino acyl adenalate) are the abbreviations within the word equation. Adapted from Ibba, M 2000:
Within the first step of the reaction, the binding of the ATP to the enzyme induces a conformational change, allowing the specific amino acid to bind to
the aaRS, thus forming the active amino acid AMP complex (aaRS.aa–AMP). The amino acid binds to the aaRS such that the carboxy terminus of the
amino acid is bound to the tRNA in step 2, and a O=C–O bond is formed between the OH group of the 3' end of the tRNA and the amino acid. The
DHU loop and the anticodon nucleotides are important structural features that determine the specificity between the amino acid and tRNA. A covalent
bond is formed ... Show more content on Helpwriting.net ...
To prevent incorrect amino acid joining to a tRNA, an editing domain is required. The 3.90.740.10 (connecting–peptide domain) is a post–transfer
editing and proofreading domain, which hydrolyses the misacylated tRNA, and is found in ValRS, IleRS and LeuRS. For example, isoleucine is larger
than valine by just one methyl group, therefore these aaRS's need to distinguish between the smaller amino acids to ensure the correct amino acid is
transferred to the tRNA. The 3.90.740.10 domain is inserted into the catalytic core and if valine enters the editing domain, it will be hydrolysed and
broken down, as is too small to accommodate the binding of isoleucine (Arnez. J, 2009). 1.10.730.10 (Orthogonal bundle) is another example of an
editing domain, and helps with the binding of the correct bases to the anticodon (Sugiura et al.

Structure And Function Of Proteins
Structure and function in proteins: the importance of shapes in biology
In biology, the structure of a molecule dictates its function. This essay describes the importance of the shapes of specific molecules and how proteins
acquire the structure they have and how changes in their shape can affect their functionality. According to Roberts et al. (2000), proteins are chemically
one of the most complex molecules known, as "they play a vital role in all organisms". Stated by Alberts et al. (2002), proteins come in a wide variety
of shapes, and are generally between 50 and 2000 amino acids long. The combination of any amino acid in any length and sequence leads almost to an
infinite number of conceivable structures and functions. Amino acids undergo condensation reactions to form polypeptides. These amino acid units are
linked by peptide bonds. The restricted rotation about the carbon–nitrogen bond in the peptide link has a large influence on the shape and structure of a
protein, which therefore determines its function.
The structure of a protein is determined by its primary, secondary and tertiary structure. The specific sequence of amino acids in a protein is known as
its primary structure. The atoms within a chain are held together by covalent bonds. The polypeptide chain forms a backbone in proteins. Its secondary
structure consists of several chains held in place by hydrogen bonds. The arrangement of a sequence of amino acids in polypeptides may be helical (α–
helix) for

Core Structure Of Proteins
Proteins themselves are made of long chains consisting of a possible 20 different amino acids that are linked together by peptide bonds made up by the
hundreds or thousands for each different protein. These different combinations of chains determine the specific protein's function and 3–D structure. A
large percentage of work that is put into every cell is the result of proteins, as well as many crucial factors of the body, such as functioning organs.
Proteins are not sectioned to perform any certain one function, but instead are responsible in varying areas all throughout the body. Enzymes,
antibodies, cell structure, along with a multitude of other tasks, are the product of the many types of proteins working in synergy. Proteins have 4 ...
The heavy chains consist of a globular head, with long ɑ–helical tails that twist around each other to form a dimer, and the light chains connect with the
neck region of each head that completes the myosin II protein, this is illustrated in figure A. Myosin II is the cause of the contractions that occur in the
muscular cells and the cytokinesis that transpires in every cell. Myosin I, in part with myosin V, are involved in the cytoskeleton–membrane functions.
Myosin I, like that of myosin II, has the same similar globular head, but unlike myosin II, is much smaller and lack the long ɑ–helical tails that form
dimers. Instead Myosin I, has a tail that can bind itself to other structure like that of membrane vesicles or organelles.
The entire structure of Myosin has been determined, all the way to the quaternary structure. With the first level of structure being the gene sequence and
the amino acid the protein is composed of. Myosin is an incredibly complex protein and in some organisms, contains a large gene sequence. In the
NCBI protein database, there are numerous links leading to the gene sequence of myosin in several species of animals, as well as certain parts of
myosin itself. The data base shows partial sequences, the heavy chain of myosin, and many different isoforms of this protein. That gene sequence just
makes up the primary structure in any protein, however the next three levels can be shown through a 3–D ribbon model, shown as

Essay On Protein Structure
In this article, it explains how DNA sequence data that researchers had collected from assorted environments has helped them create 3–D models of
more than 600 protein families for structures that were previously unknown. This led to predictions that before would not have been possible. Now, it is
possible to use computers to create better models of protein structures. Biologist can now build accurate models even if they have no template. Because
of the discovery that the sequence of amino acids determines the way a protein folds, scientist have been investigating different ways to figure a
protein's structure from its sequence. Every protein family has at least 1,000 different proteins in it. The models could cover about over a million of ...
The human genome contains millions of sequences. These sequences are described as "transposable elements, genetic units that "jump" around the
entire genome." These sequences used to be referred to as "junk DNA" until they were recognized that they were influencing the expression of genes.
Scientists have combined phylogenetics (the study of evolutionary relationships between different species) with genomics (the study of how the
genome of an organism conditions its biology). From comparing genomes of 203 vertebrates, they traced the first origin of KZFPs back to a common
ancestor of tetrapods (four–legged animals) and coelacanth (a fish that evolved over 400 million years ago). This helps learn more about its
fundamental importance. KZFPs can transform transposable elements into "fine–tuned regulatory platforms" that influence the expression of genes.
This takes place in stages of development and human tissues. I think that combining phylogenetics with genomics could help scientist learn and
discover more about evolution and how and why they've changed. This relates to what we learn about because it talks about proteins and stages of
development and human tissues. It also talks about DNA and how generic elements change.
3) Plant cells survive but stop dividing upon DNA damage https://www.sciencedaily.com/releases/2017/10/171006101817.htm Nara Institute of Science
and Technology (No author)
Science Daily
October 6, 2017
In this article, it talks about the cell

Protein Atherosclerosis
Proteins are very important to our lives because they carry out a multitude of tasks in our body. Proteins are linear chains of amino acids that adopt
unique three–dimensional structures and are packed into their particular native conformations. However, protein folding can also go wrong when the
inaccurate folding and clustering together of protein molecules, which are observed in numerous human diseases such as: diabetes, atherosclerosis,
cystic fibrosis, Creutzfeldt–Jakob, Huntington's, Parkinson's, Alzheimer's disease and many other neurodegenerative as well as non–neurological
diseases. Since the amyloidosis is the largest group of protein misfolding disease, Fabrozop Chiti and Christopher M. Dobson described clearly in the
article "Protein ... Show more content on Helpwriting.net ...
The misfolding proteins can lead to many different diseases for human bodies. So, it's important to prevent or disrupt the pathways to a misfolded
protein. To do so, we first need to understand the function of protein folding, amyloid fibril as well as alpha helix, beta sheets, Aβ , and α–
Synuclein...how they affected the structures of each protein in certain diseases. Then, it would be a good fundamental tool that may lead to the
development for treating diseases. However, the challenge in developing treatment to prevent the misfolding disorders is identifying the ideal stage at
which the protein misfolding and subsequent aggregation can be disrupted. For example, Alzheimer's Disease, treatment methods for AD, we need to
develop of protease inhibiters aimed at stopping the Amyloid beta release and prevent the aggregation of

Structure And Structure Of Membrane Proteins Essay
Thickness: 6–8nm
Unit: Amphoteric phospholipid, claiming to be from a polymeric phosphate (hydrophilic), including the same unbranched chain fatty liver
(hydrophobic).
Distribution of 2 portions: hydrophilic heads would laid open of the outside nature 's domain alternately those cytoplasm. Those greasy liver chains
purpose inward, confronting one another because of hydrophobic impacts (staying out starting with water). membrane proteins need aid found On
Different positions inside the membrane, through particular associations with phospholipid particles These proteins comprise for 3 fundamental
groups:.. essential analytics proteins, outer–surface proteins Also inner–surface proteins They assume dissimilar parts clinched alongside cell division
exercises. .
Integral proteins: In the cytoplasmic membrane called UNIPORT3 solid basic tools to do the installation of the membrane, transporting material cross,
symporter more importantly antiporter
Outer–surface proteins: As a rule before, Gram–negative bacteria, vice–band unit, at about broad atom transfer periplasmic proteins.
Inner–surface proteins: To work together to win the building energy capacity is also important to reflect different cell division of different proteins.
How do bacteria store genetic information?
Both forms of genetic information in bacteria DNA sequence stored, i.e. bacterial chromosome and plasmids. The following are the properties of a
bacterial chromosome.
Location: Within nucleoid region

Mechanisms for the Regulation of Biological Processes
The regulation of essential biological processes such as metabolism, growth and reproduction is a hallmark of living systems. Cells, the fundamental
units of life, employ a variety of mechanisms to achieve this exquisite control, and regulation of the activity of proteins provides a means to fine–tune
cellular processes. One of the ways of controlling the activity of proteins is to alter the absolute levels of a protein in a cell. This is achieved either by
altering the levels of the mRNA coding for the protein or by altering the stability of the protein in the cellular environment. Transcriptional regulation,
along with the presence of microRNAs, is a common mechanism employed by cells to alter the levels of mRNA (1–5). The amount of a protein in the
cell is essentially determined by the balance of its rates of synthesis and degradation (6). The stability of a protein can be regulated by different
mechanisms including degradation (7, 8), molecular crowding (9), disulfide bond formation, and small molecule binding (10–12).
In addition to controlling the absolute level of a protein, the activity of a protein can also be regulated by covalent modification, interaction with other
proteins, or binding of small molecules. Covalent modification of a protein involves the attachment of a functional group resulting in phosphorylation
(13, 14), glycosylation (15), or acetylation (16). A protein can also be covalently modified by attachment of another protein resulting in

Pdb Enzyme Lab
The crystal structure of enzyme Plasmodium falciparum enzyme farnesyltransferase was not found available in Protein Data Bank (PDB) archive,
therefore the structure was built using homology modeling method. In order to predict the structure of enzyme (PfFT), the sequence of enzyme IDs
PF3D7_1242600 [alpha– subunit] and PF3D7_1147500 [beta subunit] were obtained from the web services (www.gene db.org), protein sequence data
bank in swiss prot or uniprock KB (Q8IHP6), NCBI (AAW78025). The only sequence of the active site (beta–subunit) was taken for homology
modeling. Phyre2 V 2.0 at server available online (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index). The X–ray crystallographic structure of
farnesyltransferase from aspergillus fumigatus protein ... Show more content on Helpwriting.net ...
Atomic charges were assigned to the receptor using AMBER7 FF99 force field. The protein complex was minimized using AMBER7 FF99 force field.
Finally the 3D structure of the prepared protein was saved as PDB file.
3.4.2. Protomol generation
The protomol is a representation of the enzyme's binding cavity in which putative ligands are aligned. The complexed ligand from the crystal structure
was used to construct the protomol, which was then stored as MOL2 file. Ligands were docked directly from molecular database or mol2 files.
3.5. Ligands Sources
Compounds used in and docking screening were downloaded as mol2 files from the web–based databases zinc docking org. (www. zinc.docking.org)
The ligand geometries were optimized with the Powel method using the Tripos force field and Gasteiger–Hückel charges for all atoms, until a gradient
0.01 kcal/mol/Å was

The Development And Progression Of Amyloid
As scientists, we are always trying to discover the answers to the how and why questions that comes up as science progresses. We all know that nothing
is ever straight forward and sometimes we end up with more questions than answers from our obtained results but this is not always a negative. A major
area of interest today is the development and progression of amyloid diseases such as Alzheimer's' disease, Huntington's disease, and transmissible
bovine spongiform encephalopathy. Despite extensive studies conducted on each one of these diseases, little is really known about their development
and progression because little is known about the mechanism behind amyloid fibril formation – the common link found in all of these diseases. Over
the ... Show more content on Helpwriting.net ...
Previous studies have shown that different proteins contain short identical sequences in their secondary structures that have completely different
functions and folding mechanisms. It has also been shown that these same sequences can be induced to form an α helix, β strand, or β sheet structure
depending on the context. These findings have suggested that chameleon sequences have a sense of structural plasticity which can pose a problem for
protein secondary structure prediction. While previous research has only focused on the notion of identical sequences within an α helix in one protein
whereas a different protein has the same identical sequence but instead of an α helix, the sequence is within a β strand; Guo et al. delve deeper into the
notion that there is also the possibility of these sequences being found within a β sheet or β hairpin conformation. To distinguish between the two, Guo
et al. introduced the terms chameleon–HS and chameleon–HE. Chameleon–HS refers to the sequences with helix and strand structures whereas
chameleon–HE refers to the sequences with helix and sheet/hairpin structures.
This study used two different data sets, Dataset No.1 and Dataset No.2. Dataset No. 1, used to search for chameleon sequences, consists of 6962 protein
chains generated from the Protein Data Bank (PDB). Dataset No.

Structure Of Protein Essay
The Structure of Proteins
Introduction
Campbell and Farrell define proteins as polymers of amino acids that have been covalently joined through peptide bonds to form amino acid chains
(61). A short amino acid chain comprising of thirty amino acids forms a peptide, and a longer chain of amino acids forms a polypeptide or a protein.
Each of the amino acids making up a protein, has a fundamental design that comprises of a central carbon or alpha carbon that is bonded to a hydrogen
element, an amino grouping, a carboxyl grouping, and a unique side chain or the R–group (Campbell and Farrell 61).
Proteins serve a myriad of functions whether within or outside of the cells. These functions include structural roles (cytoskeleton), transport of ... Show
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The primary protein structure can be likened to a human chain in which each person is assumed to be an amino acid and their hands viewed as the
carboxyl and amino groups. The person on one end of the chain, who has a free left hand, is assumed to be the free carboxyl group. The person on the
other end, who has a free right hand, is assumed to be the free amino group. Everyone in this chain has a left hand linked to somebody's right hand and
a right hand linked to somebody else's left hand forming peptide bonds. The heads and legs just like the side chains and hydrogens, do not take part in
the linking.
In most instances, protein molecules are usually embedded from hundreds to thousands of amino acids. A repertoire of twenty different amino acids,
joined in any possible sequence allows the existence of an inconceivably large number of proteins that is infinite in nature.
2. Secondary Structure of Proteins
Bettelheim, Brown, Campbell and Farrell assert that polypeptide chains do not extend in straight lines but rather they fold in various ways and give rise
to a large number of three–dimensional structures (594). This folding or conformation of amino acids in the localized regions of the polypeptide chains
defines the secondary structure of proteins. The main force responsible for the secondary structure is the non–covalent

Function, Structure, Synthesis And The Use Of The Protein...
The purpose of this paper is to discuss the function, structure, synthesis and the use of the protein elastin (ELN), which encodes for one of the two
elements of elastic fibers in the human body (NCBI 1). Addressing the fundamental aspects of the protein will allow us to explore the potential
applications and implications of the protein if it has been modified.
Introduction and Function
Elastin is the one of the key components in the elastic property of tissues found in human tissues such as arteries, lungs, and elastic cartilage to name a
few (Jacob, Sauvage, Osbourne 1). Elastin is mainly composed of amino acids glycine and proline, which are hydrophobic and are combined with
lysine residues in crosslinks (NCBI 1). It plays a fundamental role in the recoil of tissues after being stretched, which is critical in maintaining the cells
health (Weiss 1). Thirty percent of the dry weight of the extracellular matrix (ECM) in arteries is comprised of the protein elastin, hence, making it an
essential part of human tissue (Krettek, Sukhova, Libby 1). Elastin can be found abundantly in the dermis of the skin, the arterial walls, the pulmonary
tissues, which helps with the expansion of the lungs upon breathing and the recoil upon exhaling (Krettek, Sukhova, Libby 1). Elastin in the skin is
elastic tissue intertwined with other components in the dermis through fibers that are interconnected (Krettek, Sukhova, Libby 1). The skin is dense
with elastic tissue, which allows for the

The Structure And Function Of Proteins And Enzymes Essay
How does the structure and function of proteins and enzymes relate to each other?
A protein has multiple existing structures, these are the primary, secondary, tertiary and quaternary structures which occur progressively. A protein is
essentially a sequence of amino acids which are bonded adjacently, and interact with one another in various ways depending on the R group that the
amino acid contains. There are 20 different amino acids which are able to be arranged in any given order, thus giving rise to a potential 2.433x1018
(4.s.f) different combinations, and therefore interactions between the various amino acids.
Prior to the determination of the primary structure, the RNA strand undergoes splicing which alters the sequence. During splicing introns are removed
and exons are randomly re–arranged in a random order. There is 2 problems with this model of attempting to estimate the protein a sequence will form
from RNA. Firstly depending on the place of the body at which splicing is occurring, different introns will be removed and also secondly, we need to
know which random order the exons will shuffle themselves into.
The various interactions which can occur include the following:
1) Hydrogen Bonds – These arise between the R–CO–R and the R–NH–R, and increase the boiling point of the structure of the enzyme as more energy
is required to break the intermolecular bonds. This means that the enzyme can function at a higher than normal temperature.
2) Disulphide bridges – These

Protein Structure
Biochemistry Task 2 Donna Whittington 000337251 July 22 , 2016 A. (Wolfe 2000) B. (Borges 2014) (Wolfe 2000a) (Wolfe 2000c) (Wolfe 2000b)
C. (Hudon
Miller 2012) D. (Hudon
Miller 2012) E. Hydrophobic Interactions: Proteins are composed of amino acids that contain either hydrophilic or
hydrophobic R
groups. It is the nature of the interaction of the R
groups in the ... Show more content on Helpwriting.net ...
The normal prion protein structure is believed to consist of a number of flexible coils called alpha helices. In the abnormal form of the protein, some of
these helices are stretched out into flat structures called beta sheets. The normal protein is broken down by cellular enzymes called proteases but the
abnormal protein shape is resistant to protease and as a result, these prions replicate and are not broken down by proteases and accumulate in brain
tissue causing neurological defects. (DeHaven 2016) 2. Role of a Chaperone Protein in BSE Chaperone Proteins act as ushers that make sure that amino
acids continue to the next structure phase without folding incorrectly during the folding process. It is believed that BSE acts as a chaperone protein and
that is how the disease is spread. The misfolding of protein is hydrophobic inside the cell. In order for the misfolded protein to not be a minority in the
cell, it acts as a chaperone protein and converts normal protein into the misfolded protein. This is an irreversible act. The cell recognizes the decreased
amount of normal protein and creates more of it, but it is converted to misfolded protein. This happens over and over. Then all the abnormal protein
comes together to form a sticky accumulation of plaque called amyloid plaque.

How the Structure of Proteins Are Related to Their Function
How the structure of proteins are related to their functions
Rachel Morris
The basic building blocks of proteins are amino acids, the biuret reaction tests for protein. A solution of sodium hydroxide is added to a sample then a
few drops of copper sulphate solution, if positive – the solution will turn mauve. There are 20 different amino acids and they can be joined in any order.
Therefore there can be many different functions. A protein consists of one or more polypeptide chains (a polypeptide chain being multiple amino acids
joined together via condensation, producing a peptide bond). Different proteins have different shapes as the shapes are determined by the sequence of
amino acids.
The primary stage of a protein is a ... Show more content on Helpwriting.net ...
The structure of hair can induce courtship as certain species will be attracted to the opposite sex and the appearance of the way keratin is presented
(E.G. fur) will then establish that a species will be able to identify another. Tendons which consist of collagen, form connective ligaments within the
body and give extra support to the skin where needed.
Transport proteins such as Haemoglobin carry oxygen through the blood. Myoglobin performs a similar function in muscle tissue, taking oxygen from
the haemoglobin in the blood and storing it or carrying it around until needed by the muscle cells. The ability of haemoglobin to bind oxygen is
sensitive to several factors. They include pH, temperature, concentrations of O2 and CO2. The structure of the haemoglobin changes slightly in a way
that makes it better at binding to more oxygen, further enhancing its ability to carry more oxygen. Sickle cell anaemia points out another important
aspect of protein structure. The mutation of a base sequence leads to valine being produced instead of glutamic acid, this has a knock on effect on the
secondy, tertiary and quaternary structure. All in all the function of Hb is altered and results in the Hb having a "sickled shape" which does not easily
pass though capillaries or carry oxygen efficiently. Cytochromes operate in the electron transport chain as electron carrier proteins (fact from Google)

The Viological Structure Of G-Protein Coupled Receptorss
INTRODUCTION
G–protein coupled receptors (GPCRs) are highly specialised proteins responsible for the transmission of signals across the cell membrane. They sense
signaling molecules such as hormones and neurotransmitters, and thus play a very important physiological role in the human body (Venkatakrishnan et
al., 2017). GPCRs are also known as metabotropic receptors, which indicates that they are involved in intracellular signaling.
Scientific Background
The results from numerous research were combined to create a model for the structure of GPCRs and the heterotrimeric G protein, which aided our
understanding of the molecular nature of GPCRs and its functions. GPCRs are proteins that span the plasma membrane 7 times, hence the name "7 ...
De Lean and Lefkowitz carried out competitive binding experiments to investigate the interaction between extracellular ligands (both antagonist and
agonist), GPCRs and X – a membrane component.
Method
The antagonist [3H]DHA and the agonist [3H]HBI were incubated with freshly prepared plasma membranes and appropriate unlabeled ligand for 60
minutes at 25oC. The reaction was stopped by the addition of ice–cold buffer, and filtered on glass fibre filters. After additional washings with 5ml of
buffer, the concentration of radioactive ligands (antagonists / agonists) trapped on the filters was measured. Agonist binding is reversible, thus the
regular incubation period (60 minutes) was doubled to ensure that the conditions were compatible with true equilibrium. The binding of [3H]DHA and
[3H]HBI to the frog erythrocyte β–Adrenergic receptor were plotted in saturation and competition curves.
Results
It had been observed that the binding competition curve for antagonists are steep, and express low affinity, On the other hand, binding competition
curves for agonists are shallow, showing 2 distinct binding states: high and low affinity state. They discovered that the addition of guanine receptors
could convert the high affinity state to low. This observation was also described in numerous other GPCRs, such as

Macromolecules Using Sds
The testing of various proteins was performed by comparing the molecular weight of proteins using SDS PAGE. The molecular focus in the lab was the
testing of proteins, which are macromolecules consisting of amino acid monomers linked through chemical bonds. These proteins have a hierarchy of
structure that consists of folding that determines the direct function of each protein.. The molecular weight of these proteins were measured using SDS
PAGE. SDS PAGE stands for sodium dodecylsulfate polyacrylamide gel electrophoresis. SDS is an anion detergent that binds with the protein
structures and causes them to separate due to the change in bonding charge. SDS and heat are how the proteins are denatured. The process of denaturing
a protein is breaking

Protein Structure And Function Of A Protein
Proteins are biological macromolecules made from smaller building units called amino acids. There are 20 natural occurring amino acids which can
combine in various ways to form a polypeptide. There are four distinctive levels of protein structure: primary, secondary, tertiary and quaternary. The
primary structure of a protein is important in determining the final three dimensional structure and hence the role and function of a particular protein,
both in the human body and in life around us. The secondary structure of a protein can fall into two major categories; α–helices or β–sheets, other
variants also exist such as β–turns {{20 Brändén, Carl–Ivar, 1934– 1991}}. The precise folding or these secondary structures into a three dimensional
shape is known as the tertiary structure of a protein and multiple polypeptides bound together via covalent and non–covalent bonds forms the complex
quaternary structure of a protein.
The primary structure of a protein is a specific linear sequence of amino acids, it determines the final 3D structure. These amino acids form a covalent
bond via peptide bonds between the nitrogen on the α–amino group on one amino acid and the oxygen from the α–carboxyl group of another. This
joining of two or more amino acids to for a polypeptide chain is known as a condensation reaction in which a molecule of water is removed, Figure 1.
The ends of a polypeptide have specific names, the end with a free amino group is referred to as the N–terminal, whereas

Polyphen2.0 Synthesis
Polyphen2.0 (Polymorphism Phenotyping) a multi–sequence alignment server predicts the functional impact of an amino acid substitution. The
prediction is a straightforward empirical rule which is automatically applied to the structural, sequence, and phylogenetic information, and readily
characterizes the amino acid substitution (Ramensky et al. 2002). To determine the effect of variants on the protein secondary structure, inter chain
contents, functional sites, and binding sites, Polyphen2.0 utilizes PDB (Protein Data Bank), DSSP (Dictionary of secondary structures in protein), and
three–dimensional structure databases (Ramensky et al. 2002). We submitted the query in the form of the protein sequence with the mutational position
of two amino

Structure Enzymes: Biological Protein Macromolecules
ENZYMES
STRUCTURE Enzymes are biological protein catalysts, that speed up chemical reactions by thousands of times by lowering an activation energy, and
do not get used up.
These protein macromolecules consist of a sequence of amino acids and are 3D because of the quaternary structure. Primary structure, like all proteins
or polypeptides, includes a sequence of particular amino acids, which is established by certain genes in DNA, linked together by peptide bonds in the
linear chain. The second structure is due to Hydrogen bonds between amino groups (NH2) and carboxyl (COOH) group. Consequently, the chain folds
upon itself and forms α–helix or β–sheet. Therefore, a protein can fold even further, getting itself a three–dimensional structure. ... Show more content
on Helpwriting.net ...
When the pH moves too far away from the enzyme's optimum pH, the enzyme will lose its shape and denature, therefore activity of enzyme will
decrease. For example, the optimum pH for the enzyme pepsin is around 2–3. If the pH increases to 5 or 6, the enzyme loses its ability to the
breakdown of proteins in the stomach, as is is a comfortable environment for pepsin to work in hydrochloric acid( HCl). Although most enzymes have
an optimum pH close to neutral (7) pH.
When heat is added to a solution it gives particles more activation kinetic energy and makes particles move faster and collide substrates and enzymes
more frequently, the rate of reaction increases. An optimum temperature for most enzymes is normally 40 ºC. However, if the temperature becomes too
high the bonds in enzyme start to vibrate and eventually break– denaturation of a protein(usually permanent). All effects caused by that are described
earlier in a passage.
Substrate concentration increase will cause an increase in the rate of reaction, but, because a number of enzymes are fixed, the rate will go up at first
and then become permanent, constant( horizontal), as more and more enzyme active sites will be filled

Zinc Binds To Protein
How does zinc binds to proteins?
Zinc coordinates proteins with four different surroundings with different roles: catalytic, co–catalytic, structural and interface. In many proteins Zn2+
ions also serve to correct polypeptide folding. Furthermore, zinc is a cofactor in all six enzyme classes.
Zinc ions in protein interface may influence the formation of stable quaternary structures, as in the case of hexameric insulin, which is formed from
three protein dimers and two Zn2+ ions. As has been said, zinc coordination in proteins varies widely, with a strong preference for histidine, cysteine,
aspartate and glutamate. Despite these different coordination surroundings, proteins have high affinity towards zinc ions. (6)
Zinc coordination spheres

Exploring Protein Structure With The Molecular...
Nariel Monteiro CHEM 456 Exploring Protein Structure with the Molecular Visualization FirstGlance in Jmol Introduction: The goal of this
experiment was to practice using the FirstGlance in Jmol molecular visualization to examine key structural features of proteins. This work is important
because protein structure can be related to function, multiple–sequence alignments and evolutionary preservation, and designing drug. FirstGlance in
Jmol makes it fairly easy to perceive structure–function relationships in the protein you chose. Using FirstGlance, it is easy to visualize and distinguish
chains, and disulfide bonds are obvious. Alpha helices and beta strands are evident due to the "cartoon" secondary structural schematic. Methods:
Firstly in this experiment, one had to get familiar with how to use many of the basic commands in FirstGlance in Jmol. To get familiar with the
program, one did a tutorial analysis of protein PDB ID: 1LGD at http://bioinformatics.org/firstglance/fgij//, following the specific step listed in the
handout.1 For the second part of the experiment, one had to use the knowledge learn from viewing protein molecules in FirstGlance in Jmol to analyze
the protein PDB ID: 4EEY. The analysis of this protein was done using the RSCB protein data bank (PDB) at
(http://www.rcsb.org/pdb/home/home.do).2 Results: Below are the answers to the given questions about the protein PDB ID: 4EEY. Find the primary
citation and download the journal article for reference.

Structure And Function Discovery Of Proteins
CHAPTER 1
INTRODUCTION
PROTEIN SEQUENCE
Proteins (Y.Vincent, et al.) are present in every cell of the organisms. They are involved virtually almost in all cellular activities. They are responsible
for the various metabolic activities, nutrition transportation, regulations and etc. They exist as single chain molecule, as a three dimensional structures
or even in the bundle or complex forms. The protein plays a vital role in cellular processes. The protein consists of twenty amino acids. They possess
different characteristics such as hydrophobic, hydrophilic, polar, non–polar and etc. It is the great challenge to the bioinformatics that to find which
combination of proteins are responsible for what kind of activities. The structure and function discovery of proteins in living organisms is vital role in
understanding the background of various cellular processes. It is helpful in treating various diseases, in detecting the drugs to peculiar diseases. The
IUPAC code for Protein from DNA code
The irregularity in the proteins can be found if their actual functionality and their protein complex are known. The biologist will interpret the
functionality of the protein complex based on their chemical properties.
Amino acid codes
1–letter 3–letter Description
AAla Alanine
R Arg Arginine
N Asn Asparagine
D Asp Aspartic acid
C Cys Cysteine
Q Gln Glutamine
E Glu Glutamic acid
G Gly Glycine
H His Histidine
I Ile Isoleucine
L Leu Leucine
K Lys Lysine
M Met Methionine
F Phe

Gallbladder Carcinoma Case Study
Materials and methods
Identifying SNPs involved in GBC
The SNPs for Gallbladder Carcinoma (GBC) were obtained from PolySearch 2.0 (http://polysearch.cs.ualberta.ca/) and were subjected to various in–
silico analysis and a pipeline was designed for selection of SNPs having structural and functional importance (Figure 1). SNPs involved in the GBC
were enlisted through PolySearch 2.0[14], with the query keyword "Gallbladder Cancer". A list of 45 SNPs was found to be related with GBC. Location
of these SNPs either in the coding region or non–coding region were found using Ensembl genome browser (http://www.ensembl.org)[15]. SNPs were
sorted based on their location in coding or non–coding region. The dbSNP database, being the most extensive database, ... Show more content on
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It provides five models based on the amino acid sequence and each model is assigned an individual C–score(confidence scores) calculated based on the
significance of threading template alignments and the convergence parameters of the structure assembly simulations[16]. A higher C–score indicates
greater confidence and vice–versa. It also provides a TM (template modelling) Score which measures the structural similarity between two structures. A
TM–score >0.5 indicates a model of correct topology whereas a TM–score <0.17 indicates a random similarity. It also predicts solvent accessibility and
ligand binding sites. Protein sequence was submitted to the webserver and the protein structure was obtained.
Verification of 3D model of protein
Verify 3D (http://services. mbi.ucla.edu/Verify_3D/) and RAMPAGE Ramachandran Plot Analysis were used for verification of 3D structures. Verify
3D provides an effective platform to determine the compatibility of the 3D model of protein obtained with its amino acid sequence by assigning a
structure class based on its location and environment.
Modelling nsSNPs on protein

Functions Of Protein Gamma Secretase Essay

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