Iron is also the transition metal found in the periodic table. When iron has a 3 oxidation state, an octahedral complex can be formed. Fe3 tends to be stabilized which is relative to Fe2 by an anionic ligands since it have the greatest affinity for oxygen donor include phosphate, tartrate, citrate, oxalate and EDTA. The color of the complexes is normally pale in color due 6A1g ground state and the occurrence of spin-forbidden that is visible to be see. Fe3 in acidic solution consisted of an anions which have low ability of coordination.
Almost all ultraviolet spectrophotometers possess the photoelectric device which is used to measure the radiant energy. The 4 useful components of the spectrophotometers are a source of radiant energy, the spectrophotometer or monochromator, the absorption-cell assembly and the photometer or detecting device. The spectrophotometers components will permit the selection of radiant energy of the desired wavelength. A quartz prism or a ruled grating is normally employed as the dispersive element in order to separate a continuous spectrum into the constituent wavelengths.
The optical system of the spectrometer is designed to give different incidence angle. Hence, the radiant energy of a desired wavelength can be selected to emerge from the end of the exit slit of the spectrometer. The entrance slit is necessary to ensure that the light entering the spectrometers be parallel in order to limit its intensity; the exit slit limits the spectral width of the radiant energy emerging from the spectrophotometer to make this emergent beam as monochromatic. When there is an entrance-slit width is small relative to the end of the exit-slit widths, this will make the spectral range to be narrower but the intensity of the light emerging is weak. By increasing the width of the entrance slit relative to the exit slit will widens the spectral range. However, the relative intensity at the nominal wavelength is higher. In order to have sufficient intensity for photometric measurements with prism spectrometers it is necessary to vary the slit width when there is a change in wavelength, this requires a synchronous adjustment of the two slit widths.
The number of ligand that is attached to the metal can be calculate as follows:
y = ax
To calculate the molar absorptivity of the mixture is as follow: A= ?bc
0.1490 nm = ? (1 cm) (0.5 mol)
? = 0.298 L mol?1 cm?1
Discussion: Ultraviolet and Visible Spectroscopy
Ultraviolet and visible (UV/Vis) spectroscopy provides information about compounds with conjugated double bonds. It consist just enough right energy to cause an electronic transition which is the promotion of an electron from one orbital to another higher energy. When a molecule absorbs ultraviolet light, a UV spectrum is obtained. However, if the molecule absorbs lower-energy visible light, a visible spectrum is obtained.
The photographic methods of spectrophotometer are not very slow and expensive, but are also limited in accuracy in the measurement of absorption intensity. The accuracy will be in the range of ±2 to ±5%. The modern photoelectric spectrophotometer is known to be accurate within ±0.2%for the intensity measurement. The photoelectric instruments incorporate one or more photo-cell with certain sensitivity over the whole wavelength range.
Fe3 complex and salicylic acid
Ammonium Iron (III) sulfate is a double salt in the class of alums. It have the molecular formula of NH4Fe (SO4)2. Fe3 complexes is a tridentate compound which means that can attach to the central atom. However, salicylic acid is a bidentate compound which means that they are chelate agent which they have two groups that can attach to the central atom. The molecular formula of salicylic acid is C7H6 O3, which the OH group is ortho to the carboxyl group (COOH).
The empirical method shows that only single complex is formed between the reactants. This method also used to determine the complex stoichiometry of the molecular complexes, where hey have the ratio of 1:1. The more systematic method for the determination of complex stoichiometry is also known as Job’s method of continuous variation. This method is used for the photometric analysis of a mixture in the ratio of x: (1-x) volumes of equimolar solutions of concentration M of the two components A and B of the complex. It is assumed that there is no change in the volume when this 2 solution mixed. The equilibrium is expressed by the equation as the following:
where, K=instability constant of the complex C. At experiment condition specified that the equmolar solutions of A and B of concentration M mixed in proportion x: (1-x):
(1-x) M=[B] ? [C]=cB
where, quantities in the square brackets = actual concentrations
cA and cB=total concentrations of free plus complexes A and B
It is assumed that all the 3 species which are A, B and C obey the Beer’s law at the selected wavelength. The absorbance A of the solution in a 1 cm cell is as follow:
A= ?C[C] ?A[A] ?B[B]
and ? A=A- ?A[A]- ?B[B]= ?C[C]
is the difference in absorbance of an actual solution and a mixture when there is no complexing reaction occurs. ? A is proportional to[C]. The wavelength that is chosen is greatly different from ?A and ?B.
To make the calculation easier, it can be assume that both ?A and ?B are 0. A plot of ? A against x is then curve with a maximum, which is corresponds to:
y = ?
Graph and Results
According to the graph plotted above, the curve with a highest peak can obtain ed. With the highest peak, the mole fraction of ligand and its absorbance can be calculated. The number of the ligand that attached to the metal can be mono-, bis-, or tris (5-fluorosalicylato) iron (III) complexes. In another hand, the complex can be formed together with the monohydroxo and dihydroxo side. Hence, the theoretical value for y may be 1,2 or 3. But for our case, the y value is 1. The y value of 1 indicated that for the mixture of salicylic acid and ammonium iron (III) sulphate have only 1 ligand that is attached to the iron (III) complex ion and they only have 2 bonds between the ligand and metal.. The ligand ratio may be due to different types of species distribution and electronic absorption band of the complexes in the spectrum. Besides that, by plotting the graph, the value ? can be calculated. The value of ? calculated is 0.298 L mol?1 cm?1. This indicate that the molar absorptivity of the mixture of ammonium (III) sulphate and salicylic acid is 0.298 L mol?1 cm?1.
Device used to determine the spectrum of the salicylic acid and ammonium iron (III) sulphate The device that can be used to determine the spectrum of the salicylic acid and ammonium iron (III) sulphate is infrared spectroscopy, NMR spectroscopy, mass spectroscopy, ultraviolet and visible spectroscopy.
The infrared spectroscopy can be used to identify the functional groups in the salicylic acid and ammonium iron (III) sulphate. The infrared spectrum can be obtained by passing a beam of infrared radiation through a sample of the complex. Then the detector will generate a plot of percent transmission of radiation versus the wavenumber or wavelength of the radiation that is transmitted.
NMR spectroscopy is used to determine the structure. It can also used to identify the functionality at a specific carbon, how the neighboring carbon appear and how the entire structure of a molecule. When a sample is subjected to a radiofrequency (rf) radiation, the nuclei in the ?-spin state can be promoted to the ?-spin sate (called ‘flipping’ the spin). When the nuclei return to their original state, they emit signals whose frequency depends on the difference in energy (?E) between the ?- and ?- spin states. The NMR spectrometer is used to detect the signals and display it as a plot of signal frequency versus intensity is known as an NMR spectrum.
The mass spectroscopy can give a structural information about the salicylic acid and ammonium iron (III) sulphate because the m/z values and relative abundances of the fragments depends on the strength of the molecular ion’s bonds and the stability of the fragments. In the mass spectrometry, a small amount of a compound is introduced into an instrument called the mass spectrometer where it is vaporized and then ionized (an electron is removed from each molecule). The common methods are a beam of high energy electrons is used to vaporize the molecule from bombarding them. The energy of the beam can be varied. When the electron beam hits a molecule, it knocks out an electron producing a molecular ion.
Ultraviolet and visible spectroscopy is used to determine the compounds with conjugated double bonds. When a molecule absorbs light of an appropriate wavelength, an electron can be promoted to a higher energy orbital. It is promoted from the highest occupied molecular (HOMO) to the lowest unoccupied molecular orbital (LUMO). This is called the electron transition and the molecule is said to be in the excited state. The electronic transition with the lowest energy is promotion of a nonbonding electron (n) into a ? antibonding molecular orbital. This is called the n ?8 transition. The higher energy electronic transition is promotion of an electron from a ? bonding molecular orbital into a ? antibonding molecular orbital, a ? ?8 transition. This means that only a compounds with electrons or nonbonding electrons can produce UV/Vis spectra.
Conclusion: The composition of the iron complex ions in solution can be observed by a spectrophotometer. With this, the complex ion can be determined by method of continuous variation or Job’s method. From this method, the number of ligand that attached to the metal can be determined. The determine value is y=1. This indicate that there are only 1 ligand is attached to the iron metal and they only have 2 bonds between the ligand and metal. The molar absorptivity (?) of the mixture of ammonium iron (III) sulphate and salicylic acid is 0.298 L mol?1 cm?1.
Structure and Function of Proteins
Whichever essay topic macromolecule you pick, you will need to outline the variety of structures in that family of macromolecules it may be useful to use diagrams for this, you will then need to explain how and where they are used in the cell and, where appropriate link macromolecule structure to function. You will also need to briefly outline where the molecules come from e.g. are they derived from the diet or synthesised within the cell. You should also include an explanation of how these molecules can contribute to health and/or disease.
Structure and Function of Proteins
INTRODUCTION Proteins are large macromolecules which consist of hydrogen, carbon and oxygen; proteins are polymeric chains that are built from monomers known as amino acids. Proteins have a major function in a living organism, for example, the replication of DNA, catalysing metabolic reactions (catalyst); stimulus response and also transporting molecules form one place to another. There are 20 different types of amino acids which synthesize proteins, however the function and different properties of each type of protein is due to the precise sequence and structure of the amino acids present. (Petsko and Ringe. 2004. Pp. 8)
Each amino acid consists of a central carbon atom (C), which is attached to a hydrogen atom (H), an amino group (also known as NH2 group), a carboxyl group (- COOH, this gives up a proton hence why this is known as an acid) and also a unique side chain or R group.
Amino acids are linked linearly via covalent peptide bonds, short chain amino acids are known as peptides whereas long chain formations of amino acids are called polypeptides, where the peptide bond is formed between the carboxyl group of one amino acid and the amino group on the neighbouring amino acid. This reaction occurs as a condensation reaction where there is a removal of a hydrogen atom from the amino group of one amino acid and the removal of a -OH group from the carboxyl acid from another amino acid forming a water molecule (Fig 1). (Andrew. 2001. Pp. 13)
The unique side chain or R group is what disguises one amino acid from another; the overall structure and properties of the proteins are therefore dependent on sequence of the R group of each amino acid (Campbell and Farrell. 2011. Pp. 61). Furthermore these variations of the R group and also the arrangements of the other amino acids would form a number of different polypeptides. Each protein consists of a different number of these polypeptide chains which are folded into complex three dimensional shapes therefore different proteins would have different shapes.
There are four levels of protein organization found in polypeptides; these structures are known as: primary structure, secondary structure, tertiary structure and also quaternary structure.
Primary structures is the basic structure of the levels of organization, the primary structure is the linear arrangements/sequence found of the amino acid in the protein, and also could be thought of as the covalent linkages found in the polypeptide chain or the protein, such as a disulphide bond (Vickie and Christian. 2008. Pp. 148).
The secondary structure is the areas of folding found within the protein, where there is an ordered arrangement of the amino acids in some localized regions of the polypeptide molecule; hydrogen bonds play a vital role in stabilizing the folding patterns which are found in the protein molecule (Lieberman and Marks. 2009. Pp. 92). Although the conformation of each protein molecule are considered unique, there are two main types of secondary structure, or folding patterns, that are often present; these are the alpha helix and the parallel and anti-parallel beta-pleated sheets, these two folding patterns are common due to the hydrogen bonding occurs between the N-H and C=O groups in the backbone of the polypeptide (Albert’s. Bray. Hopkins. Johnson. Lewis. Raff. Roberts. And Walter. 2010. Pp. 127). However there are a number of other secondary structures, but the alpha helix and the beta sheets are the most stable form of secondary structures found. Furthermore there may be a number of these two types of secondary structure found in a single polypeptide chain.
An alpha helix is spiral structure where this could be either a right handed or left handed spiral, in which the peptide bonds are found to be Trans conformational and planar, it would also be found that the amino group of each of the peptide bonds is generally in the upward position where as the carboxyl group points in the downwards position.
An alpha helix structure is generated when a single polypeptide chain has turned around itself to form a rigid cylinder where a hydrogen bond is formed between every fourth amino acid (fig 1.2), which links the C=O group of one peptide bond to the N-H group on another amino acid (fig 1.2).
There are two types of beta sheets; parallel and anti-parallel beta sheets. The Beta pleated sheets are extended polypeptide chains with another neighbouring polypeptide chain extending either parallel or anti-parallel to each other, this occurs due to the hydrogen bonds being formed between the segments of the polypeptide chain so are essentially place side by side. (Bradley and Calvert. 2006. Pp. 7). The parallel beta sheets is when the structure is shown to consist a polypeptide chain and neighbouring polypeptide chain that would run in the same direction (from the N-terminus to the C-terminus), is known as the parallel beta sheet (Fig 2.1), whereas when the polypeptide chain runs in the opposite direction of that of its neighbouring chain, it is known as an anti-parallel beta sheet (Fig 2.2).
The beta sheet are stable structures that produces a very rigid, pleated structure; this is due to the beta sheet being stabilized by hydrogen bond being formed between the amino group on one polypeptide chain and the carboxyl group on the adjacent chain.
Beta sheets have many different properties and functions, where this type of secondary structure is found in protein which their function would require strength, for example; this type of structure gives silk fibres their extraordinary tensile strength, beta sheets would also be found in the exoskeleton of insects which allows them not to freeze in cold conditions by providing the insect with an anti-freeze protein which forms a flat surface with a number of hydroxyl groups, the protein can therefore bind with the ice crystals which would prevent the growth of the crystals and therefore the insect does not freeze.
The tertiary structure of a protein is the full three dimensional structure of the arrangements of atoms found within the polypeptide chain, this structure is the final geometric shape that protein assume and would be the highest level structure that a protein can attain, the structures include the alpha helix, beta sheets, random coils and also other structures such as loops and folds, which are formed between the N-terminus and the C-terminus. (Stoker, H. S. 2012. Pp. 726)The tertiary structure is mainly stabilized by the formation of disulphide bonds, this is also known as a disulphide bridge because these bonds are formed by oxidation reaction of the side chains of cysteine, by oxidizing the two thiol groups (SH) which would form a disulphide bond (S-S) (fig 3).
The tertiary structure is the most important of all the structural levels of enzymes activity, where the tertiary structure of an enzyme would consist of all the peptide bonds, ionic bonds, hydrogen bonds and also the disulphide bonds therefore when all these types of bonds are combined, this would produce a three dimensional structure. The function of an enzyme require a three dimensional structure for the active site of the enzyme, the area of the enzyme that combines with a substrate, and cause a specific reaction to speed up.
However a mutation in the genetic code could lead to a human disease by disrupting the tertiary structure of the protein causing the protein or enzyme to be denatured (the enzyme would lose its catalytic power). If a protein loses its tertiary structure it could also lead to diseases such as cystic fibrosis, where there is a disruption in the CRTR protein.
The quaternary structure of a protein is the arrangements of many different types of coiled and folded polypeptides to form a unique functional protein and is stabilized by several non-covalent bonding, where some of these types of bonding are also found in tertiary structures, for example; hydrogen bonding, Van Der Waals interactions, hydrophobic interactions, ionic interactions and also disulphide bonding. This structure can only occur if there is more than one polypeptide chain present in a complex protein these are called multimers.
The Quaternary structures are usually found in biologically active proteins for example, in the pigment of haemoglobin, which is found in the red blood cells, contain two types of polypeptide chains but with a total of four tightly packed polypeptide chains which are alpha 1, 2 and beta 1, 2, where these are arranged in a globular fold. Each haemoglobin molecule contains four haem molecules where there is one attached in each subunit, so that oxygen would bind on the centre of each haem molecule (a total of 4 oxygen molecules) and when the oxygen binds to the haem group, the conformation of the haemoglobin protein changes (forming oxyhaemoglobin) where these changes in structure on one site of the protein may cause changes at a distant site, this type of protein which changes structure is referred as an allosteric protein. (Roberts. Reiss. Monger. (2000). Pp. 28-35)
However there is a genetic mutation that could affect the quaternary structure of a protein, an example is sickle cell anaemia where there is a single point mutation in the nitrogen base in a codon where the hydrophobic amino acid valine is coded in instead of the hydrophilic amino acid, glutamic, therefore this small change in the genetic code causes a normally round red blood cell to be a sickle shape.
CONCLUSION The structure of proteins plays a major and useful role in the functioning of the human body when it comes to the specific functions of the amino acids. There are a wide variety of functions that are accomplished by proteins, from enzyme activity to transportation and immune responses (such as antibodies). However the functions of proteins are affected in a major way if the conditions or structure of the amino acids are slightly changed for example, if conditions such as the temperature were to change slightly (increasing), an enzyme would lose its tertiary shape and would become denatured; therefore the catalysing reaction would slow down dramatically ie the decrease in the rate of reaction due the less than ideal condition surrounding the enzyme, this would therefore cause a reduction in specific reaction. Furthermore as long as the conditions and the structure of the polypeptide chains remain constant, the functioning’s of the protein molecules and, in turn the living organism, will not be affected.