Protein-To Protein Essay

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.

Proteins are primarily considered to have one primary function to serve its role in an organism, however studies have observed to have multiple functioning proteins known as moonlighting proteins (Khan et al. 2014). Moonlighting proteins along with primary functions, have secondary functions that are not related to the primary function and does not correlate to the primary or other functions (Khan et al. 2014). The multifunctional proteins play essential roles in carrying out biochemical functions which aids in the cell growth but are not caused by gene fusion and multiple RNA splice variants (Amblee et al. 2015). The discovery of moonlighting proteins was first discovered by Piatigorsky and Wistow while observing crystallins (Khan et al. 2014). Crystallins, are structural proteins that are found in the eye lens that exhibit enzymatic activity to make the lens itself (Khan et al. 2014). Crystallin has a primary function to help form the lens of the eye by acting as a structural protein (Amblee et al. 2015). Besides enzymatic activity, crystallin was observed in other mammals to have secondary functions such as metabolic functions which are helpful in prokaryotic (Khan et al 2014). Most moonlighting proteins are characterized as cytosolic enzymes and chaperons, or in other words helping proteins (Amblee et al 2015). The multifunctional proteins or moonlighting proteins can also be identified as receptors, channel proteins and ribosomal proteins (Khan et al. 2014). Due to the

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 Functions of Proteins Introduction Protein accounts for about three-fourths of the dry matter in human tissues other than fat and bone. It is a major structural component of hair, skin, nails, connective tissues, and body organs. It is required for practically every essential function in the body. Proteins are made from the following elements; carbon, hydrogen, oxygen, nitrogen and often sulphur and phosphorus.

The lumen of the rough ER is the site of protein folding. Proteins are folded in sacs called cisternae by ER chaperone proteins. The rough ER will package properly folded proteins in vesicles and ship them to the Golgi apparatus. The rough ER is also involved in quality control of proteins; only properly folded proteins are transported to the Golgi.

Although approximately 42 dominant SCAs have been identified only 20 have been genetically identified. Most of the identified SCAs share a common mutation: SCA1 SCA2, SCA 3, SCA6, SCA7, SCA8, SCA12, SCA17 have all been linked to the same CAG trinucleotide repeat but in different varying chromosomes and loci. These are also known as polyglutamine (Poly-Q) diseases. Poly-Q proteins are extended proteins formed by an expansion of the mRNA that coded for the amino acid chain during translation. The Polyglutamine-expansion disease family encompasses at least nine heritable disorders, including Huntington disease (HD) and the spinocerebellar ataxias SCA1, SCA2, SCA3, SCA6, SCA7 and SCA17. 11 Normally the proteins formed

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.

The body makes many different types of proteins, each of which has a specific job. Oftentimes, the shape of the protein molecule is what allows it to do its unique job. A protein molecule is made up of a string of amino acids and each of these amino acids has a net positive, negative, or neutral charge. If two adjacent amino acids on the string both have a positive charge or both have a negative charge, then will repel each other and force each other to move apart. If one has a negative charge and the other a positive charge, they will move closer together. Thus all that pushing and pulling will determine the ultimate shape of the molecule. (Fowler, 2013)

Macromolecules rely on their environment for proper folding of their respective three- dimensional structure.10 This makes intuitive sense since the exterior, which is polar, is making contact to a polar solvent, like the cytoplasm that provide hydrogen bonds, electrostatic interactions, and conceal the nonpolar residues away from the polar solvent.10 The body has a stable pH and temperature that proteins take advantage to form amazing functional complexes. They can catalyze reactions as enzymes, transport compounds, and make complex units to reach a certain goal like ATP synthase10.They can be dangerous as well, such as binding to receptors on cells for virus entry4. Proteins lose their conformation when they are out of range in temperature

Chemists are seeking to learn about proteins and how they function not only together, but with other molecules. They are studying the fluctuation of these structures. They are questioning how proteins look when they merge with other proteins. The studies of how distinct proteins and other substances act together in the cell is called proteomics. This field of research is new, and

\textbf{A positive feedback mechanism to maintain the polarity patch on the plasma membrane.} \textbf{(a)} Cdc42 exists as GTP-Cdc42 (ON state) or GDP-Cdc42 (OFF state). The GTP-Cdc42 indirectly converts neighboring GDP-CDC42 into GTP-Cdc42, which sets off a positive feedback loop. GTP-Cdc42 exists predominantly in the plasma membrane and diffuses very slowly while GDP-Cdc42 diffuses fast in the cytosol. Since one of the components (the scaffold protein Bem1) that goes into causing the positive feedback gets depleted, the patch of GTP-Cdc42 stops growing. \textbf{(b) and (c)} Actin cables deliver patches to dilute the polarity patch to make it wander.}

Soluble state favors mere closer to protein in folding state which is like real functional environments.

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.

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.