Write an essay on spectroscopy which includes : (15 marks)
Basic principles, nature of electromagnetic radiation, types of spectra-(absorbance, emission and fluorescene) types of spectroscopy – (principle, instrumentation and applications of atomic absortion spectroscopy, UV Visible Spectroscopy, Nuclear Magnetic Resonance Spectroscopy and Electron Spin Resonance Spectroscopy)
Spectroscopy is the study of the absorption and emission of light and other radiation by matter, as related to the dependence of these processes on the wavelength of the radiation. More recently, the definition has been expanded to include the study of the interactions between particles such as electrons, protons, and ions, as well as their interaction with other particles as a function of their collision energy. Spectroscopic analysis has been crucial in the development of the most fundamental theories in physics, including quantum mechanics, the special and general theories of relativity, and quantum electrodynamics. Spectroscopy, as applied to high-energy collisions, has been a key tool in developing scientific understanding not only of the electromagnetic force but also of the strong and weak nuclear forces.
The basic principle shared by all spectroscopic techniques is to shine a beam of electromagnetic radiation onto a sample, and observe how it responds to such a stimulus. The response is usually recorded as a function of radiation wavelength. A plot of the response as a function of wavelength is referred to as a spectrum.
Electromagnetic radiation consists of discrete packets of energy, which call photons. A photon consists of an oscillating electric field component, E, and an oscillating magnetic field component, M. The electric and magnetic fields are perpendicular to each other, and they are perpendicular to the direction of propogation of the photon. The electric and magnetic fields of a photon flip direction as the photon travels. The number of flips, or oscillations, that occur in one second the frequency, [pic]. Frequency has the units of oscillations per second, or simply s-1 (this unit is called Hertz). If the electric and magnetic fields of a photon could be recorded as the photon traveled some distance, it would leave the trail of E and M fields.
All photons (in a given, non-absorbing medium) travel at the same velocity, v. The physical distance in the direction of propogation over which the electric and magnetic fields of a photon make one complete oscillation is called the wavelength, [pic], of the electromagnetic radiation. The figure above shows the hypothetical history of a photon that has traveled the distance of one wavelength. The relationship between the light velocity, wavelength, and frequency is: v = [pic][pic] The electromagnetic nature of all photons is the same, but photons can have different frequencies. The names for different wavelength and frequency ranges are listed in the electromagnetic spectrum. The energy, E, of one photon depends on its frequency of oscillation: E = h[pic] = hv /[pic] , where h is Planck's constant (6.62618x10-34 J·s).
White light (what we call visible or optical light) can be split up into its colors easily and with a familiar result - the rainbow. All we have to do is use a slit to focus a narrow beam of the light at a prism. This set-up is actually a basic spectrometer.
The resultant rainbow is really a continous spectrum that shows us the different energies light (from red to blue) present in visible light. But the electromagnetic spectrum encompasses more than just optical light - it covers all energies of light extending from low-energy radio waves, to microwaves, to infrared, to optical light, to ultraviolet, to very high-energy X- and gamma-rays. Typically one can observe two distinctive classes of spectra: continous and discrete. For a continuous spectrum, the light is composed of a wide, continuous range of colors (energies). With discrete spectra, one sees only bright or dark lines at very distinct and sharply-defined colors (energies). The discrete spectra with bright lines are called emission spectra, those with dark lines are termed absorption spectra. Continuous spectra arise from dense gases or solid objects which radiate their heat away through the production of light. Such objects emit light over a broad range of wavelengths, thus the apparent spectrum seems smooth and continuous. Stars emit light in a predominantly (but not completely) continuous spectrum. Discrete spectra are the observable result of the physics of atoms. There are two types of discrete spectra, emission (bright line spectra) and absorption (dark line spectra).
In absorption spectra, the clouds of gas absorb certain wavelengths (colors) of light. A continuous spectrum that hits a cloud of cool gas will be partially absorbed. The transmitted spectrum is called an absorption line spectrum because certain lines are absorbed and is continuous except for the colors that were absorbed by the gas. In emission spectra, anything that absorbs also emits. A cloud of cool gas that absorbs certain colors from a blackbody will emit exactly those colors as the gas atom de-excite. The lines of emission have the same color as the absorption lines in the absorption line spectrum. If emission line spectrum is added with the absorption line spectrum then it will produce continuous spectrum. Fluorescence can be analyzed from a sample of material through a special form of electromagnetic spectroscopy. This fluorescence spectroscopy uses a beam of light that is tailored for the type of fluorescence detection needed in compounds. The usual option is an ultraviolet light that is used to excite electrons in the molecules. This causes them to produce a light emitting phenomenon of lower energy, which can be within the visible and non-visible light spectra. A complimentary technique that is often used with fluorescence spectroscopy is absorption spectroscopy. Absorption spectroscopy determines how much light is absorbed into the substance versus the amount of light that bounces back. Fluorescence can be observed in many different ways. The most notable type of fluorescence is ultraviolet radiation, which is visible when bounced off as emitted light. Normally, the ultraviolet light is invisible to a human’s naked eye. However, when it is applied in this manner, it is possible to see the visible emitted light. When ultraviolet light is exposed onto the fluorescent materials, it displays very bright, intense, neon-like colors.
Atomic Absorption Spectroscopy is a quantitative method of analysis that is applicable to many metal and a few of nonmetal. The principle makes use of absorption spectrometry to assess the concentration of an analyte in a sample. It requires standards with known analyte content to establish the relation between the measured absorbance and the analyte concentration. In short, the electrons of the atoms in the atomizer can be promoted to higher orbitals for a short period of time by absorbing a defined quantity of energy This amount of wavelength, is specific to a particular electron transition in a particular element. In general, each wavelength corresponds to only one element, and the width of an absorption line is only of the order of a few picometers (pm), which gives the technique its elemental selectivity. The radiation flux without a sample and with a sample in the atomizer is measured using a detector, and the ratio between the two values (the absorbance) is converted to analyte concentration or mass using the Beer-Lambert Law: A = ec l where A = absorbance [no units, because it is calculated as A = log10(I0/I), where I0 is the incident light’s intensity and I is the light intensity after it passes through the sample e = molar absorbance or absorption coefficient [in dm3 mol-1 cm-1units]; c = concentration (molarity) of the compound in the solution [in moldm-3 units]; l = path length of light in the sample [in cm units].
The instrumentation involve in this type of spectroscopy are as below.
The light source, called a hollow cathode tube, is a lamp that emits exactly the wavelength required for the analysis (without the use of a monochromator). The light is directed at the flame containing the sample giving a reasonably long path length for detecting small concentrations of atoms in the flame. The light beam then enters the monochromator, which is tuned to a wavelength that is absorbed by the sample.
The detector measures the light intensity, which after adjusting for the blank, is output to the readout, much like in a single beam molecular instrument. Also as with the molecular case, the absorption behavior follows Beer's Law and concentrations of unknowns are determined in the same way. All atomic species have an absorptivity, a, and the width of the flame is the pathlength, b. Thus, absorbances (A) of standards and samples are measured and concentrations determined as with previously presented procedures, with the use of Beer's Law
A = ec l where A = absorbance [no units, because it is calculated as A = log10(I0/I), where I0 is the incident light’s intensity and I is the light intensity after it passes through the sample]; e = molar absorbance or absorption coefficient [in dm3 mol-1 cm-1units]; c = concentration (molarity) of the compound in the solution [in moldm-3 units]; l = path length of light in the sample [in cm units].
The light is "chopped" with a rotating half-mirror so that the detector sees alternating light intensities. At one moment, only the light emitted by the flame is read since the light from the source is cut off, while at the next moment, the light from both the flame emission and the transmission of the source's light is measured since the source's light is allowed to pass. The electronics of the detector is such that the emission signal is subtracted from the total signal and this difference then, which is T, is what is measured. Absorbance, A, however, is usually what is displayed on the readout.
The most important and obvious point to be made is that these techniques are indeed atomic. This means that they cannot be applied to analytes that are molecular in nature. Atomic techniques are limited to ions of metals-those species, which can be atomized. Ions of nonmetals can be analyzed too, but only by an indirect method. An example would be the determination of chloride by measuring the silver ion before and after precipitation of the chloride. Silver can be measured directly; chloride cannot.
This instrument also can be used in environmental studies such as drinking water, ocean water, soil, in food industry, pharmaceutical industry, biomaterials such as blood, saliva, tissue, in forensics such as gunpowder residue, hit and run accidents and also in geology such as in identify rocks and fossils.
UV Visible spectroscopy measures the response of a sample to ultraviolet and visible range of electromagnetic radiations. Molecules and atoms have electronic transitions while most of the solids have interband transitions in the UV and Visible range. The most important kind of UV/Vis Spectroscopy is dispersion based spectroscopy. It involves a disperive medium like prism or grating to separate the different wavelengths. Ultraviolet spectroscopy is used for shorter wavelengths. The principle is the molecules containing π-electrons or non-bonding electrons (n-electrons) can absorb the energy in the form of ultraviolet or visible light to excite these electrons to higher anti-bonding molecular orbitals. The more easily excited the electrons, the longer the wavelength of light it can absorb.
For instrumentation, the spectroscopy work when a beam of light from a visible and/or UV light source (colored red) is separated into its component wavelengths by a prism or diffraction grating. Each monochromatic (single wavelength) beam in turn is split into two equal intensity beams by a half-mirrored device. One beam, the sample beam (colored magenta), passes through a small transparent container (cuvette) containing a solution of the compound being studied in a transparent solvent. The other beam, the reference (colored blue), passes through an identical cuvette containing only the solvent. The intensities of these light beams are then measured by electronic detectors and compared. The intensity of the reference beam, which should have suffered little or no light absorption. Over a short period of time, the spectrometer automatically scans all the component wavelengths in the manner described. As for the application, UV absorption spectroscopy is one of the best methods for determination of impurities in organic molecules. Additional peaks can be observed due to impurities in the sample and it can be compared with that of standard raw material. By also measuring the absorbance at specific wavelength, the impurities can be detected. Besides that, UV spectroscopy is useful in the structure elucidation of organic molecules, the presence or absence of unsaturation, the presence of hetero atoms. From the location of peaks and combination of peaks, it can be concluded that whether the compound is saturated or unsaturated, hetero atoms are present or not etc. UV absorption spectroscopy also can be used for the quantitative determination of compounds that absorb UV radiation. Lastly, UV absorption spectroscopy can characterize those types of compounds which absorbs UV radiation. Identification is done by comparing the absorption spectrum with the spectra of known compounds. UV absorption spectroscopy is generally used for characterizing aromatic compounds and aromatic olefins.
The Nuclear Magnetic Resonance phenomenon is based on the fact that nuclei of atoms have magnetic properties that can be utilized to yield chemical information. Quantum mechanically subatomic particles (protons, neutrons and electrons) have spin. In some atoms (eg 12C, 16O, 32S) these spins are paired and cancel each other out so that the nucleus of the atom has no overall spin. However, in many atoms (1H,13C, 31P, 15N, 19F etc) the nucleus does possess an overall spin. To determine the spin of a given nucleus one can use the following rules: If the number of neutrons and the number of protons are both even, the nucleus has no spin. If the number of neutrons plus the number of protons is odd, then the nucleus has a half-integer spin (i.e. 1/2, 3/2, 5/2). If the number of neutrons and the number of protons are both odd, then the nucleus has an integer spin (i.e. 1, 2, 3). In quantum mechanical terms, the nuclear magnetic moment of a nucleus will align with an externally applied magnetic field of strength Bo in only 2I+1 ways, either with or against the applied field Bo. For a single nucleus with I=1/2 and positive γ, only one transition is possible between the two energy levels. The energetically preferred orientation has the magnetic moment aligned parallel with the applied field (spin m=+1/2) and is often given the notation α, whereas the higher energy anti-parallel orientation (spin m=-1/2) is referred to as β. The rotational axis of the spinning nucleus cannot be orientated exactly parallel (or anti-parallel) with the direction of the applied field Bo (defined in our coordinate system as about the z axis) but must process (motion similar to a gyroscope) about this field at an angle, with an angular velocity given by the expression: ωo = γ Bo ; Where ωo is the precession rate which is also called the Larmor frequency. The γ magnetogyric ratio (γ) relates the magnetic moment μ and the spin number I for a specific nucleus: γ = 2πμ/hI Each nucleus has a characteristic value of γ, which is defined as a constant of proportionality between the nuclear angular momentum and magnetic moment. For a proton, γ = 2.674x104 gauss-1 sec-1.
This precession process generates an electric fieldwith frequency ωo. If we irradiate the sample with radio waves (in the MHz frequency range) the proton will absorb the energy and be promoted to the less favorable higher energy state. This energy absorption is called resonance because the frequency of the applied radiation and the precession coincide or resonate. There are two general types of NMR instrument; continuous wave and Fourier transform. Early experiments were conducted with continuous wave (CW) instruments, and in 1970 the first Fourier transform (FT) instruments became available. This type now dominates the market, and currently we know of no commercial CW instruments bing manufactured at the present time. Continuous wave NMR spectrometers are similar in principle to optical-scan spectrometers. The sample is held in a strong magnetic field, and the frequency of the source is slowly scanned (in some instruments, the source frequency is held constant, and the magnet field is scanned). These systems are currently obsolete except for a few wide line experiments that are performed in specialty solid-state NMR applications. Fourier Transform (FT) NMR instruments, the magnitude of the energy changes involved in NMR spectroscopy are very small. This means that, sensitivity can be a limitation when looking at very low concentrations. One way to increase sensitivity would be to record many spectra, and then add them together. As noise is random, it adds as the square root of the number of spectra recorded. For example, if one hundred spectra of a compound were recorded and summed, then the noise would increase by a factor of ten, but the signal would increase in magnitude by a factor of one hundred - giving a large increase in sensitivity. However, if this is done using a continuous wave instrument, the time needed to collect the spectra is very large (one scan takes two to eight minutes).
In FT-NMR, all frequencies in a spectral width are irradiated simultaneously with a radio frequency pulse. A single oscillator (transmitter) is used to generate a pulse of electromagnetic radiation of frequency ωο but with the pulse truncated after only a limited number of cycles (corresponding to a pulse duration τ), this pulse has simultaneous rectangular and sinusoidal characteristics. It can be proven that the frequencies contained within this pulse are within the range +/- 1/τ of the main transmitter frequency ωο. For example a 5 μs pulse would generate a range of frequencies of ωο ± 1/0.000005 Hz (i.e. ωο ± 200,000 Hz). Following the pulse, the nuclei magnetic moments find themselves in a non-quilibium condition having precesed away from their alignment with they applied magnetic field. They begin a process called “relaxation”, by which they return to thermal equilibrium. A time domain emission signal (called a free induction decay (FID)) is recorded by the instrument as the nuclei magnetic moments relax back to equilibrium with the applied magnetic field. The versatility of nuclear magnetic resonance (NMR) spectroscopy has made it a widespread tool in chemistry for the study of chemical structure. In additional to the one-dimensional NMR spectroscopy used to study chemical bonds, two dimensional approaches have been developed for the determination of the structure of complex molecules like proteins. Time domain NMR spectroscopy is used to study molecular dynamics in solutions. NMR of solid samples can help determine molecular structures. There are NMR methods for measuring diffusion coefficients. NMR spectroscopy has contributed enormously to chemical knowledge. A wide range of techniques has been used with a range of magnetic fields including high-field superconducting magnets. NMR frequencies from 60 to 800 MHz have been used for hydrogens, compared to the range of about 15 to 80 MHz for medical magnetic resonance imaging (MRI). One of the major sources of chemical information is the measurement of chemical shifts in high-resolution NMR spectroscopy. The chemical shifts are a very sensitive probe of the chemical environment of the resonating nuclei. The principles of Electron Spin Resonance are quite analogous to those of NMR. Thus the electron has an intrinsic magnetic moment μe = -g_eS where g = 2.0023, _e = eh/4%mc = 9.2741 × 10-24J T-1 (Bohr magneton), and S = ½. The first order Zeeman Effect splits the two ms states of the unpaired electrons in a paramagnetic material. The resonance condition is therefore h_ = g_B, but since the magnetic moment of an electron is 2-3 orders of magnitude greater than that of a magnetic nucleus an ESR spectrometer operates with smaller magnetic fields and higher frequencies than an NMR spectrometer. Compare a 300 MHz NMR spectrometer with a standard (“Xband”) ESR spectrometer NMR 3 × 108 Hz and B = 4.5 Tesla with ESR 9 × 109 Hz and B = 0.3 Tesla. Higher frequency (microwave) radiation requires different technology for ESR spectrometers. The instruments for the ESR are the klystron is the source of microwave radiation of “fixed” frequency. The cavity (corresponds to the NMR probe) is a hollow rectangular or cylindrical box, the dimensions of which are matched to the wavelength of the microwaves so that the sample (which is ins erted in a quartz nmr-like tube) is held in a region where the magnetic field component of the radiation is maximized and the electric field is minimized. The spectrometer is tuned so that the waveguides and cavity contain standing waves, and the detector records a constant intensity. When the magnetic field is swept to achieve the resonance condition, radiation is absorbed by the sample, and a small decrease in radiation intensity should be observed at the detector. Since it is much more efficient to detect an AC signal in the presence of a large DC background, the magnetic field is modulated (typically at 100 KHz) by means of coils embedded in the walls of the cavity. This generates a signal that looks like the first derivative of the absorption line. All application of ESR is based on three aspects, which are, study of free radicals, investigation of molecules in the triple state, and study of inorganic compounds. Study of free radicals refers to even in very low concentration of sample ESR can study via free radicals. It is also applied in determination of structure of organics and inorganics free radicals. The intensity of ESR signal is directly proportional to the no. of free radicals present. Hence using ESR we can measure relative concentration of free radicals. In investigation of molecules in the triple state, a triple state molecule has a total spin S=1 so that, its multiplicity can be given as 2S+1=3. While free radicals with S=½ has an odd no. of unpaired electrons. A triple state molecule has an even no. of electrons two of them unpaired. In triple state molecule the unpaired electrons must interact whereas in diradical, the unpaired electrons do not interact for they are a great distance apart. Lastly is in study of inorganic compounds. ESR is very successful in the study of inorganic compounds. The ESR studies may be used in knowing the exact structures of solvated metal ions. ESR is used in the study of catalysts. ESR is used in the determination of oxidation state of metal. eg. Copper is found to be divalent in copper protein complexes whereas it is found to be monovalent in some biologically active copper complexes. The information of unpaired electrons is very useful in various aspects in applications of ESR. Like, Spin labels, Structural determination, and Reaction velocities and reaction mechanisms.
Question 2
Name the organelle that provides an internal skeleton or structure for cells and explain its structure and functions. (20 marks)
The organelle that provides an internal skeleton is cytoskeleton, a three-dimensional network of fibers, composed of filamentous protein, which runs throughout the matrix of living cells by extending the network of fibers throughout the cytoplasm, providing a framework for organelles, anchoring the cell membrane, and providing a suitable surface for chemical reactions to take place. The cytoskeleton provides the cell with structure and shape, and by excluding macromolecules from some of the cytosol it adds to the level of macromolecular crowding in this compartment. Cytoskeletal elements interact extensively and intimately with cellular membranes. The cytoskeleton also provides the cell with motility which is the ability of the entire cell to move around and for material to be moved within the cell. Cytoskeleton is made up by three different fibers which made up of proteins. They are microfilaments, intermediate filaments and microtubules. They constantly change shape through cycles of polymerization or depolymerization and interactions with other proteins. Each type of fiber looks and functions differently.
Microfilaments also known as actin filaments are the thinnest, solid rods of protein that composed of linear polymers of actin subunits that enable cell to move or change shape when protein subunits generate force by elongation at one end of the filament coupled with shrinkage at the other, slide past one another and causing net movement of the intervening strand. They also act as tracks for the movement of myosin molecules that attach to the microfilament and "walk" along them.
Myosin (in enzymes) also has the ability to convert chemical energy into movement. The characteristic property of these so-called myosin molecular motors is their ability to bind actin in an adenosine triphosphate–sensitive fashion and to produce movement of actin filaments. Over fifteen different types of myosin motors have been identified. Some of them, such as those involved in cytokinesis and cell motility, are two headed, meaning they have two actin-binding motor domains, while others have only one head. Some of these myosin are involved in the movement of membrane-bound vesicles along actin tracks. The best characterized of these molecular motors, myosin II, slides actin filaments past each other either to power contraction of the contractile ring or to produce cell migration. A different version of this myosin motor forms the thick filaments that are responsible for the contraction of muscle.
In general, the functions of actin-associated proteins are to modify the properties of the microfilament network in cells. Some filament-associated proteins, for example the protein tropomyosin, bind along the length of the filament to stiffen it. There are also proteins such as villin or filamin that bind microfilaments together side by side to produce bundles of actin filaments. Other actin-binding proteins cross-link actin filaments to form meshlike structures such as those found in association with the cell membrane. Cells can also control the length of filaments through the action of proteins that can cut filaments to produce two shorter filaments. To keep the filaments a certain length, cells produce "capping" proteins that bind to the ends and prevent the addition of new actin subunits. By modulating the state of the microfilament network the cell can control the physical properties of the cytoplasm such as rigidity and viscosity. Next are intermediate filaments which averaging 10 nanometers in diameter. These filaments are more stable than microfilaments because of strongly bound and heterogeneous constituents of cytoskeleton. They also function in maintenance the cell shape by bearing tension as they act as cables. Besides that, intermediate filaments organize the internal tridimensional structure of cell, anchoring organelles and serving as structural components of the nuclear lamina and sarcomeres. They also participate in some cell-cell and cell-matrix junctions. They are many types of intermediate filaments. A different cell type, fibroblasts , have intermediate filaments that are formed from a single protein, vimentin. In heart tissue, the intermediate filaments can be formed from a different single protein, desmin. In nervous tissue the intermediate filaments are formed from yet another family of intermediate filament proteins called neurofilament proteins. There are even structures in the nucleus formed from intermediate filament protein family members called nuclear lamins.
Although intermediate filaments can also self-assemble from their constituent subunits, the filaments differ from microtubules and microfilaments in that they do not have an obvious polarity. Structurally, intermediate filaments are formed from a bundle of subunit proteins which themselves are extended in structure, as compared to the more globular-shaped protein subunits that form microfilaments and microtubules. Intermediate filaments are generally more stable structures than the other cytoskeletal systems, although recently it has been shown that subunits are capable of exchanging in and out of the filament all across their length. Like other filament systems, intermediate filaments have associated proteins, but interestingly no molecular motors that use intermediate filaments as their track have been identified.
Intermediate filaments are organized within cells so that they link the cell surface and the nucleus. Intermediate filaments are believed to play an important role in cells by stabilizing structural integrity. Of all the cytoskeletal systems, intermediate filaments are best suited to play this structural role since they have the highest tensile strength (resistance to stretch). At the cell surface, intermediate filaments attach to specific junctions called desmosomes and hemidesmosomes. These junctions attach cells to neighboring cells or the extracellular matrix.
Last type of fiber protein is microtubules which is the largest filaments. Microtubules are hollow cylinders about 23 nm in diameter (lumen = approximately 15 nm in diameter), most commonly comprising 13 protofilaments which, in turn, are polymers of alpha and beta tubulin. They have a very dynamic behaviour, binding GTP for polymerization. They are commonly organized by the centrosome. In nine triplet sets (star-shaped), they form the centrioles, and in nine doublets oriented about two additional microtubules (wheel-shaped) they form cilia and flagella. The latter formation is commonly referred to as a "9+2" arrangement, where in each doublet is connected to another by the protein dynein. As both flagella and cilia are structural components of the cell, and are maintained by microtubules, they can be considered part of the cytoskeleton. Microtubules resist compression and act as cellular support beams. Microtubules have many roles in cells. They functions in intracellular transport by transporting organelles such as mitochondria and vesicles for exocytosis. In intracellular transport, the microtubules are associated with dyneins and kinesins. Besides that, microtubules also function as axoneme of cilia and flagella, synthesis the cell wall in plants and acts as mitotic spindle. The dynamics of microtubules are also important for mitosis. Each time the cell goes through division the microtubule network is completely disassembled and the tubulin subunits are reassembled into a new structure called the spindle. The spindle is responsible for the segregation of chromosomes into each daughter cell and also plays an important role in specifying the position of the cleavage plane that will separate the two daughter cells (during cytokinesis). The functions of microtubules in vesicle transport and chromosome segregation are dependent on molecular motors that bind to and move along microtubule tracks. These motors are divided into two families, kinesin and cytoplasmic dynein. Kinesin was the first microtubule motor to be identified. It is responsible for moving vesicles (the cargo of the motor) toward the plus ends of microtubules, that is, from the center of the cell toward the plasma membrane. Since discovery of the first kinesin, the family has been shown to consist of many members, some of which are important for spindle function during mitosis. Some of these kinesins move toward the minus ends of microtubules. In contrast, the other type of microtubule motor, cytoplasmic dynein, appears to move cargo exclusively toward the minus ends of microtubules, that is, from the cell periphery back towards the center. The ability of these motors to move organelles around inside of cells is critical for processes such as hormone secretion, transmission of nerve impulses and recycling of membrane.
|Type |Diameters |Structures |Subunit example |
|Microfilaments |6 |Double helix |Actin |
| | | |vimentin (mesenchyme) |
| | | |glial fibrillary acidic protein (glial cells) |
|Intermediate filaments |10 |Two anti-parallel helices / dimers, |neurofilament proteins (neuronal processes) |
| | |forming tetramers |keratins (epithelial cells) |
| | | |nuclear lamins |
|Microtubules |23 |Protofilaments, in turn consisting of |Alpha and beta tubulin |
| | |tubulin subunits | |
Question 3
Explain first law of thermodynamics. (10 marks)
The first law of thermodynamics is often called the Law of Conservation of Energy. This law suggests that energy can be transferred from one system to another in many forms. Also, it can not be created or destroyed. Thus, the total amount of energy available in the Universe is constant. Einstein's famous equation (written below) describes the relationship between energy and matter: E = mc2 In the equation, energy (E) is equal to matter (m) times the square of a constant (c). Einstein suggested that energy and matter are interchangeable. His equation also suggests that the quantity of energy and matter in the Universe is fixed.
|First Law of Thermodynamics: | |[pic]Euniv = [pic]Esys + [pic]Esurr =|
| | |0 |
A more useful form of the first law describes how energy is conserved. It says that the change in the internal energy of a system is equal to the sum of the heat gained or lost by the system and the work done by or on the system.
|First Law of Thermodynamics: | |[pic]Esys = q + w |
The sign convention for the relationship between the internal energy of a system and the heat gained or lost by the system can be understood by thinking about a concrete example, such as a beaker of water on a hot plate. When the hot plate is turned on, the system gains heat from its surroundings. As a result, both the temperature and the internal energy of the system increase, and [pic]E is positive. When the hot plate is turned off, the water loses heat to its surroundings as it cools to room temperature, and [pic]E is negative.
The relationship between internal energy and work can be understood by considering another concrete example: the tungsten filament inside a light bulb. When work is done on this system by driving an electric current through the tungsten wire, the system becomes hotter and [pic]E is therefore positive. (Eventually, the wire becomes hot enough to glow.) Conversely, [pic]E is negative when the system does work on its surroundings. The sign conventions for heat, work, and internal energy are summarized in the figure below. The internal energy and temperature of a system decrease ([pic]E < 0) when the system either loses heat or does work on its surroundings. Conversely, the internal energy and temperature increase ([pic]E > 0) when the system gains heat from its surroundings or when the surroundings do work on the system.
Question 4
Give the definition of enzyme. How do enzymes lower the activation energy of a reaction? (10 marks)
An enzyme is a protein (or protein-based molecule) that speeds up a chemical reaction in a living organism. An enzyme acts as catalyst for specific chemical reactions, converting a specific set of reactants (called substrates) into specific products. Enzymes are very specific. Each enzyme is designed to initiate a specific response with a specific result. There are many enzymes in the human body. In cystic fibrosis, the term enzyme generally refers to the enzymes created by the pancreas that are intended to initate a reaction that digests food. Enzymes lower the activation energy of a reaction by weakening the bond. Activation energy is amount of energy needed to push the reactant over an energy barrier. At the summit, the molecules are at unstable point, the transition state (changing state). The different between free energy of the product and free energy of the reactant is the delta G.
There are two types of model of enzymes that lowering the activation energy. Firstly is lock and key model. In this model, the shape of substrate and the active site must be complementary each other. Only substrate that bind to the site that fits its own shape will produce reactions. The binding of the substrate into the site will cause the formation of enzymes-substrate complex. Enzymes-substrate complex is highly unstable and the complex decomposed to produces product and let the enzymes free. This process resulted in the production of energy.
Second model is induced-fit model. In this model, the active site does not necessarily have a fixed and rigid shape, but can change its shape to allow for a better fit between substrate and enzyme. Before the reaction occurs, the binding site of the enzyme is different before the substrate is bound. But to allow the reaction occurs, the enzyme and substrate must become enzyme-substrate complex by change the conformational of the binding site. The binding in the active site involves hydrogen bonding, hydrophobic interactions and temporary covalent bonds. The active site will then stabilize the transition state intermediate to decrease the activation energy. But the intermediate is most likely unstable, allowing the enzyme to release the substrate and return to the unbound state.
Enzymes are flexible, not rigid and induced by substrate. Based on this model, enzymes have greater range of substrate specificity. This proved that a single enzyme can catalyze more than 1 substrate as at the end the enzyme will change shape to the original shape.
Question 5
Explain how the following factors may affect the enzyme activity. Suitable graphs should be included in the explanation. (15 marks)
a) Enzyme concentration
From the graph, we can see the relationship between enzyme concentration and rate of reaction is directly proportional. This means the higher the enzyme concentration the higher the rate of reaction. This condition can occur when the pH and the temperature are constant.
b) Substrate concentration
From the graph, the rate of reaction increases with the substrate increases. But until the point of saturation, any further increase in substrate produced is no significant. At this time, the active sites of the enzymes are virtually saturated with substrate and any extra substrate has to wait for the enzyme to release the product. To increase the productivity at this point, more enzyme reactant must be added.
c) Temperature
As the temperature increases, the rate of reaction also increases until the optimum temperature. The rate of reaction is maximum during the optimum temperature where all the enzymes are in active state. But this is depends to the enzyme as each enzyme has their own optimum temperature. Most of the enzymes in human body have an optimum temperature at 37 degree Celcius. Then the rate of reaction decreases as the temperature increases after the optimum temperature. The rate of reaction drop sharply. The loss of catalytic activity of the enzyme is because of the denaturation of the enzyme. Higher temperature increases the kinetic energy of the enzyme atoms so much that they break bonds, change shape of the active site.
