Complex Macromolecules: A Protein Study

Proteins are the basis of the protoplasm (fluid living content of the cell that contains the cytoplasm and cell nucleus) and are found in all living organisms. Proteins make up the bulk of animals body’s non-skeletal structure. As enzymes, they catalyze biochemical reactions; as antibodies, they prevent the effects of invading organisms; and as hormones, they control metabolic processes (C. Bissonnette, 2011). The Biuret test was used to detect the presence of peptide bonds within proteins, and they were found present in test tube #9 (control for peptide bonds).

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 complex structures made up of chains of amino acids. Each protein has a different function such as enzymes to catalyze reactions or protein hormones to trigger certain functions of a cell. First let’s start with the most basic component of a protein: an amino acid. An amino acid is made up of a central carbon atom attached to a hydrogen atom, a carboxyl group, an amino group, and an R group which varies

Even today, after so much study, Alzheimer’s is not fully understood. However, researchers do agree that this degenerative disease is caused by the gradual buildup of fibrous protein compounds in the brain, which are known in the scientific world as amyloids. These amyloids in the brain area act like plaque and as a result of their presence, the normal brain functioning is disrupted.

their normal shape to an abnormal shape, however, the chemical composition of the protein remains

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

“Alzheimer’s Disease (AD) is a type of dementia, which is affecting the population that develops in the brain and can lead to problems with memory, thinking and behavior”. The Amyloid Hypothesis claims that the build up of the beta-amyloid in the brain is a cause in the development of Alzheimer disease in patients. This plaque of the beta-amyloid and its cascade of events can be linked to the deterioration and negative effects of cognitive function of the brain over time. The beta-amyloid is described to be a “sticky” protein located in the brain therefore plaques or build up of the amyloid is common. These plaques in turn can block the brain cells from communicating with each other. Which then activates an immune system, that leads to inflammation

There may also be sections where the secondary structure is neither helix nor sheet. Then the structure is called a random structure, indicating that it folds in random directions. The amino acids in an alpha helix are arranged in a right-handed helical structure resembling a spring. The alpha helix is the most common form of regular secondary structure in proteins. The beta-sheet is the second form of regular secondary structure in proteins consisting of beta strands connected laterally by three or more hydrogen bonds, forming a generally twisted, pleated sheet. The beta-sheet is sometimes called the beta pleated sheet since sequential neighboring atoms are alternately above and below the plane of the sheet giving a pleated appearance. Turns are the third of the three "classical" secondary structures that serve to reverse the direction of the polypeptide chain. They are located primarily on the protein surface and accordingly contain polar and charged residues. However, they are not very common in discussions of protein structure today.

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.

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

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

Collagen is characterized by the right-handed triple helical rod structure which is formed by three left handed helix polypeptide chain. Although the triple helical structure is the main characteristic of collagen, some globular proteins are indentified as collagen due to the repeating trilets and small triple helical rod (Prockop &

It is important to understand the properties of a peptide bond as it determines the later stages of a protein. A peptide bond formed between 2 amino acids has a rigid planar structure. This structure is due to interactions between electrons of the double bond of the carbonyl group and those of the C-N bond. This gives the bond, double bond characteristics which does not allow any rotation (see figure 3).

Processing involves the folding of the protein into its functional three-dimensional conformation. This folding is aided by molecular chaperones inside the rough ER. Additional modifications may take place, including attaching short sugar chains to the protein for the formation of glycoproteins (Karp & Patton,

Proteins play a part in every cellular activity and must fold into proper three dimensional configurations, or native state, to execute their intended functions. Proteomic stressors such as chemical exposure or elevated temperature can inhibit protein folding upsetting protein homeostasis and resulting in cell death and human disease (Broadley 2009). Excessive protein misfolding can lead to amyloid fibrillar aggregates which deposit around brain neurons contributing to the development or progression of neurodegenerative disorders: Alzheimer’s disease, Huntington’s disease and Parkinson’s disease are all fundamentally diseases of protein misfolding (Soto 2003, Hartl 2009).