Measuring A Computational Prediction Method For Fast And Determining The Protein Structural Class

Thiol groups are important to protein folding and forming disulphide bonds that are essential to protein structure. Determining the number of thiol groups in a protein is important in determining the tertiary structure of the protein. The ovalbumin is the experiment was purified from egg white using centrifugation and ammonium sulphate precipitation and then the thiol groups identified using DTNB and spectroscopy. The ovalbumin was found to have one thiol group; from this we were also to infer that DNTB alkylates thiolgroups; whereas SDS keeps proteins denatured.

3. Explain why the structure of a protein is important to how the protein functions. It’s important because it can make many complex shape and each shapes can have different functions.

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.

They are made up of amino acids (consists of amino group, carboxyl group, hydrogen atom, and R group). Polypeptide bonds form between amino acids to form polypeptide chains. Amino acid sequence is primary protein structure. The secondary structure is the bonding pattern of the amino acids (e.g. helix, sheet, etc.). The tertiary structure consists of the domain, where the sheets or helixes fold on each other and become stable. The quaternary structure consists of several polypeptide chains that form advanced proteins such as human leukocyte

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.

Proteins are made of amino acids, which are compounds built around a central carbon atom. Amino acids then join together through dehydration reactions. These are called peptide bonds. Many amino acids joined together are called polypeptides. A polypeptide becomes a protein when it folds into a three dimensional structure. This is the primary structure of a protein. The next structure in the hierarchy is the secondary structure. Secondary structures can either form alpha helixes, where an amino acid sequence forces the polypeptide to twist into a helical shape; or beta sheets, where an amino acid sequence forces the polypeptide into a zigzag shape. In the tertiary structure, the polypeptide folds several times on itself to form a more complex three dimensional shape. A quaternary structure is when two tertiary structures interact with each other. This is when a protein becomes a functional

The structure of an enzyme as protein has a primary, secondary, tertiary, and sometimes quaternary structure. The primary structure of an enzyme, like any protein, is the order of its amino acids. The secondary structure involves alpha helices and beta pleated sheets. Alpha helices are a coil that is formed by hydrogen bonding between every fourth amino acid. Beta pleated sheets are formed by hydrogen bonding between two or more parts of the polypeptide chain that are side by side. The tertiary structure contains disulfide bridges, ionic bonds, hydrophobic interactions, and hydrogen bonds. Disulfide bridges are the result of two sulfhydryl groups interacting because the the folding of the protein. Ionic bonds can form between polar groups on amino acids. Hydrophobic interactions are the cluster of amino acids with nonpolar side chains that is commonly seen in proteins. Hydrogen bonds can also form. The quaternary structure of an enzyme is when multiple proteins are bonded together in one complex made of proteins subunits.

Proteins are polymeric chains that are built from monomers called amino acids. All structural and functional properties of proteins derive from the chemical properties of the polypeptide chain. There are four levels of protein structural organization: primary, secondary, tertiary, and quaternary. Primary structure is defined as the linear sequence of amino acids in a polypeptide chain. The secondary structure refers to certain regular geometric figures of the chain. Tertiary structure results from long-range contacts within the chain. The quaternary structure is the organization of protein subunits, or two or more independent polypeptide chains.

. The 3-D tertiary structure of polypeptide proteins globular and is the result of interactions that occur between R groups. Tertiary structure is a result of the bonds between sidechains of amino acids, the R groups. The structure and bonds involve alpha helices, beta pleated sheets, and also regions unique to each protein. Tertiary proteins are held together by four different types of forces; hydrogen bonds, hydrophobic interactions (including Van der Waals interactions), ionic bonding (electrostatic interactions), and disulfide bridges (strong covalent bonds). Hydrogen bonds occur within and between polypeptide chains and the aqueous environment. Hydrogen bonding forms between a highly electronegative oxygen atom or a nitrogen atom and a hydrogen atom attached to another oxygen atom or a nitrogen atom. This links the amino acid

They are known to be the workhorses of the body cell that carries out diverse catalytic and structural roles into building the structures of all living organisms [15]. The basic structure of protein is a chain of amino acids that supplies energy to a body. There are 20 different naturally occurring amino acids that make all types of protein. Proteins come in various sizes and shapes. Some comes in a thread-like shape known as fibrous proteins and they tend to have structural or mechanical roles. Others come in spherical shapes, known as the globular proteins [16]. These spherical proteins function as enzymes, transport proteins, or antibodies. The key function of protein is based on its ability to recognize and bind specific ally to molecules, it also need to be in the right shape in other to function properly [15]. The primary structure of proteins is a linear sequence of amino acids encoded by DNA. This sequence controls how protein folds into three dimensional structure, the stability of its resulting structure [17], and functions. It is important to add that protein is an important building block of bones, skin, blood and

This assignment will outline the function of proteins in living organisms and the important roles of different types of protein. “Protein composes 10-30% of cell mass and is the basic structural material of the body” (Marieb E.N.M et al, 2004). Protein is a nutrient that living organisms need to exist and grow, as well as water being a key feature. “All protein contains carbon, oxygen, hydrogen and nitrogen” (Marieb E.N.M et al, 2004). Amino acids form links of 20, “The sequences at which they are bound together produces proteins that vary widely in both structure and function” (Marieb E.N.M et al, 2004).

Task 2b: A series of diagrams, with clear labels, of the different levels of protein structure (i.e. Primary, Secondary, Tertiary, Quaternary).

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

SNPs&GO (Single Nucleotide Polymorphism Database & Gene Ontology; http://snps.biofold.org/snps-and-go/snps-and-go.html) is an support vector machine (SVM) based method used to predict the disease related mutations from protein sequences with a scoring accuracy of 82% and Matthews correlation coefficient of 0.63. For SNPs&GO, FASTA sequence of whole protein is considered to be an input

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.