Monthly Archives: January 2012

4.1 Genes, Alleles, Chromosomes, Mutations

Sickle-cell anemia

Sickle-cell anemia is one of the most common genetic diseases in the world. This occurs because of a mutation of the gene that codes for hemoglobin (Hb). Most humans have the allele HbA. At some time in the past, a base substitution mutation coverts the sixth codon of the gene from GAG to GTG. This happened in the ovary or testic cell and my have occured in more than one person. The allele with the mutation is called HbS and when this alle is transcribed, the mRNA produced has GUG instead of GAG as its sixth codon which now produced the amino acid valine instead of glutamic acid. This change causes hemoglobin to stick together in conditions with low oxygen conditions. This distorts the red blood cells into sickle shapes and these cells damage tissues by getting trapped in blood capillaries blocking them and reducing their blood flow. When sickle cells return to high oxygen conditions in the lung the hemoglobin chains break up and cells return to their normal shape. These changes occur time after time. Both the hemoglobin and plasma membrane are damage so the life of a red blood cell is shortened and the body cannot replace the red blood fast enough so anemia develops.

Chromosomes, genes and genomes

Many scientists noticed a group of genes located on the X chromosome of Drosophila. By crossing experiments carefully, they were able to show that the genes were arranged in a linear sequence along the X chromosome. Groups of genes were then assigned to other chromosomes in Drosophila and were again arranged in this way. This pattern has been found in many species and is called the locus of a gene. Locus is the particular position on homologous chromosomes of a gene. If two chromosomes have the same sequence of the genes, they are homologous. xHomologous chromosomes are chromosomes that have the same genes as each other and arranged in the same sequence but do not necessarily have the same alleles of those genes. They are not usually identical to each other because for some of the genes on them, the alleles are different. Since Morgan, it has been discovered tahat all genes on a chromosome are part of one DNA sequence. Now,the sequence of bases along a chromosome can be discovered and this is called a genome. The genome is the whole of the genetic information of an organism.

Chromosome numbers

During mitosis and meiosis, chromosomes of eukaryotes can be seen using a microscope because they are quite large. This is because they are condensed so they have become shorter and fatter by coiling. Coiling involves histone proteins that are associated with DNA in eukaryotes and these proteins also help the process of controlling gene transcription.

Data-based question: differences in chromosome number 

1. No chromosomes have 13 because all chromosomes come in pairs homologous pairs. Therefore species end up with an even number of chromosomes and no odd numbers. If they end up with an odd number, they would probably die.

2. This hypothesis can be both supported and rejected in some ways. For example, one can see that the threadworm is not very complex and therefore has 4 chromosomes, whereas a dog, which is more complex has 78 chromosomes. However, this does not take into consideration plants, so the hypothesis is not always true.

3. Some chromosomes may be logner than others or can be fused together therefore the genome can’t be determined from the amount of chromosomes.

4.  Chimpanzees have one homologous pair more than humans. Two pair of chromosomes may have fused together and this caused to have 46 chromosomes instead of 48 chromosomes.

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8.2 Light Independent Reactions

Completing the light-dependent reactions 

The remaining parts of the light-dependent reactions is Photosystem I. The useful product of the reactions is NADPH which is needed in the light-independent reactions. NADPH has a similar role to NADH of cellular respiration as it carries pairs of electrons that can be used to carry out reduction reactions. Chlorophylls in Photosystem I absorb light energy and pass it to the special chlorophyll molecules in the reaction center and this raises an electron in one of the chlorophyll to a higher energy level. This is known as photoactivation. The excited electrons pass through the electron carries of Photosystem I and at the end of the carrier, it is passed to ferredoxin which is a protein in the fluid outside the thylakoid. Two molecules from the reduced ferredoxin are used to reduce NADP+ to NADPH +  H+. The electrons that Photosystem I gave to the chain of electron carriers is replaced by an electron carried by photocyanin. Now Photosystem I and II are now linked and the excited electrons in Photosystem II are passed alone the chain of carriers to plastocyanin and then given to Photosystem I. The electrons are excited again with light energy and are used to reduced NADP+ because the supply of NADP+ sometimes runs out. When this occurs the electrons go back to the electron transport chain that links Photosystem I and II rather than being vien to NADP+. As the electrons flow back to Photosystem I, they cause protons to pump and produces ATP. This process is the cyclic photophosphorylation.

Carbon fixation and carbohydrates synthesis

Carbon dioxide is the source of carbon for all organisms carrying out photosynthesis. The carbon fixation reaction is very important because it is converted into another carbon compound. In plants and algae this occurs in the stroma of the chloroplasts. The product of this reaction is a three-carbon compound, glycerate-3-phosphate. For this, carbon dioxide does not react with a two-carbon compound to produce glycerate-3-phosphate but reactions with a five-carbon compound known as ribulose bisphosphate (RuBP) to produce two molecules of glyerate-3-phosphate. The enzyme used to catalyze this reaction is rubisco.

RuBP is a 5-carbon sugar derivative. When it is converted to glycerate-3-phosphate, it adds carbon and oxygen and the amount of hydrogen in relation to oxygen is reduced. In sugars and carbohydrates this ratio is 2:1. Hydrogen has to be added to glycerate-3-phoshphate by reduction to produce carbohydrate. This process involves ATP and NADH which are produced by light dependent reactions of photosynthesis. ATP provides the energy for this reaction to occur and NADPH+ H+ provides hydrogen atoms. The product is a three-carbon sugar derivative, triose phosphate.

Regeneration of RuBP

The first carbohydrrate produced in the light-dependent reactions is triose phosphate. Two triose phosphates can combine to form hexose phosphate and hexose phosphate can be combined by condensation to form starch. However, if all triose phosphates were converetd to either hexose of starch the supply of RuBP would be over quickly. So some triose phosphates therefore have to be used to regenerate RuBP. This process includes converting 3-carbon sugars into 5-carbon sugars and takes many steps. As RuBP is consumed and produced, these reactions form a cycle called the Calvin cycle. For this cycle to continue, as much RuBP needs to be produced and consumed. If three RuBP molecules are used, six triose phosphates are produced. Five of these are needed to regenerate three RuBP molecuels leaving one triose phosphate to be converted to hexose or starch. To produce one molecule of glucose, six turns of the Calvin cycle are needed and each contribute one fo the fixed carbon atoms in the glucose.

Chloroplast structure

Chloroplasts have a double membrane that form the outer chloroplast envelope. Inside the have an extensive system of internal membranes called thylakoids which are a green color. Inside the thylakoids are small fluid filled spaces. Outside of the thylakoids is the stroma that is a colorless liquid that contains many enzymes. In most chloroplasts, there are stacks of thylakoids called grana. If a chloroplast has been photosynthesizing fast, starch grains and lipid droplets are present in the stroma.

Structure-function relationships in chloroplasts

If chloroplasts are extracted from leaves carefully, the whole process of photosynthesis can be carried out. The structure of the chloroplasts are very efficient. There are large amounts of pigments spread out that absorb as much light as possible and are not soluble in water. There is a means for regenerating a steep enough proton gradient for ATP synthesis which as less photons of light as possible. Also, there is a site where enzymes of the Calvin cycle are concentrated and catalyze reactions using ATP and NADPH + H+ supplied by the light dependent reactions of photosynthesis.

Data-based question: the effect of light and dark on carbon dioxide fixation

1. The dark periods caused the concentration of ribulose bisphosphate to fall. On the other hand, the dark periods caused the concentration of glycerate-3-phosphate to rise.

2a. After 25 seconds it was dark therefore the RuBP was converted to glycerate-3-phosphate. Some of the energy of glycerate-3-phosphate is then converted into carbohydrates. Because this conversion is taking place, the concentration of glycerate-3-phosphate is increasing.

2b. After 25 seconds glycerate-3-phosphate can’t be converted back to RuBP so the concentration of RuBP decreases.

3. If the light is turned back on, the concentration of RuBP will rise and the concentration of glycerate-3-phosphate will decrease.

4a. The concentration of glycerate-3-phosphate would be lowered because carbon dioxide is essential in providing carbon for photosynthesis

4b. The concentration of ribulose bisphosphate would also be lowered for the same reason as glycerate-3-phosphate.

8.2 Light Dependent Reactions

The concept of limiting factors

Light intensity, temperature, and carbon dioxide concentration each limit the rate of photosynthesis if they are below the optimal level, therefore are called limiting factors. The factor that is the furthest from its optimum is the only limiting factor. If this factor is changed to get it closer to its optimum, the rate of photosynthesis will increase but the other factors will have no effect because they are not the limiting factors. However, if the factor is moved closer to its optimum while the other factors are constant, then this factor may no longer be a limiting factor if there is another factor that is father from its optimum. For example, at night light intensity is the limiting factor however when the sun is out, light intensity will increase (get closer to its optimum) so temperature will then become the limiting factor. This concept fits most experiments however there are times when increasing two factors can increase the rate of photosynthesis if both factors are equally close to their optimum.

Photoactivation and photolysis 

Chlorophyll and the accessory pigment are grouped in photosystems, or light-harvesting arrays. These photosystems are located in thylakoids of the chloroplast. There are two types of photosystems, photosystems I and photosystems II. Both these photosystems contain chlorophyll molecules that absorb light energy and pass it on to two special chlorophyll molecules located in the center of the photosystems. When these special chlorophyll molecules, like other chlorophyll, absorb energy from a photon of light, they excite an electron in the molecule. When this occurs, the chlorophyll is then photoactivated. Unlike other chlorophyll though, these special chlorophyll are able to donate excited electrons to an electron acceptor.

Light-dependent reactions start in Photosystem II, and the electron acceptor for this photosystem is plastoquinone. Plastoquinone collects two excited electrons from this photosystem and moves it to another location in the membrane. Since plastoquinone is hydrophobic, it may not stay in a fixed position but it remains in the membrane. Absorption of two photons of light produced one reduced plastoquinone. This causes one of the chlorophyll at the reaction center to loose two electrons. Photosystem II repeats this process so that the chlorophyll at the reaction center looses four electrons.It is then a powerful oxidizing agent and causes water molecules to split and give up electrons to replace the ones it lost before. The process is splitting water is known as photolysis and this is how oxygen, a waste product, is created in photosynthesis. plastoquinone is the useful product of Photosystem II and it can carry a pair of electron but also much of the energy absorbed from light. This energy drives the rest of the reactions of photosynthesis.

Photophosphorylation and chemiosmosis

Photophosphorylation is the production of ATP from energy derived from light. This is carried out by thylakoids, which are stacks of membranes that have small fluid-filled space and contain Photosystem II, ATP synthase, a chain of electron carriers, and Photosystem I. The main type of phosphorylation is non-cyclic. To carry out this process, reduced plastoquinone is needed, carrying the excited electrons from the reaction center of Photosystem II. Plastoquinone carries the electrons to the start of the chain of electron carriers and the electrons are then passed through the carriers in the chain. As the electrons pass energy is released and this is used to pump protons across the thylakoid membrane into the space in the thylakoids. This creates a concentration gradient of protons and is now a store of potential energy. Photolysis also contributes to the proton gradient. The protons can travel across the membrane and down the concentration gradient through the enzyme ATP synthase. The energy that is released by protons going down their concentration is used to make ATP from ADP and inorganic phosphate. This method of producing ATP is similar to the process that occurs in the mitochondria and has the same name, chemiosmosis. When the electrons reach the end of the chain they are passed to the plastocyanin which is a water -soluble electron acceptor in the fluid inside the thylakoids. For the next stage of photosynthesis, reduced plastocyanin is needed.

Data-based question: evidence for chemiosmosis

1a. As the pH of ADP solution increases, ATP production increases as well. Also, as the concentration of the pH increases, the gradient of the slope of ATP increases as well, until the pH of 8.0. After this, the rate is not as fast.

1b.The p of the ADP solution affects the ATP yield because concentration gradient is increased on the outside and inside.

2. The effect of changing the pH of the ADP solution on the ATP yield is that increasing the pH of ADP solution decreases ATP solution. This is because the lower the pH of an acid is, the higher the concentration of the protons is, so decreasing the pH of the ADP solution increases the ATP yield.

3. The movement of protons down the concentration gradient produces ATP, so there is only a short bust of ATP production because once this movement occurs the concentration difference decreases and therefore the production of ATP is lowered as well.

4. The experiment is preformed in darkness because light causes photolysis to occur which produces protons. These protons effect the concentration gradient so it is more efficient to preform this experiment at night when photolysis does not effect the concentration gradient.

3.8 Photosynthesis

Photosynthesis is the production of organic compounds such as carbohydrates, proteins and lipids, using lihgt energy and inorganic compounds such as carbon dioxide and water. Since light energy is converted to chemical energy, it is one type of energy conversion. Prokaryotes were the first organisms that performed photosynthesis 3500 million years again, and since then other algae and plants have followed.

Pigments and light absorption

Absorbing sunlight is the first stage. Sunlight is a mixture of different wavelengths of light that is visible and we see this as colors including blue, green, and red. Light absorption involves chemical substances known as pigments. Pigments are substances that absorb light and so the color is shown, Black is the result of pigments that absorb all colors because no light is emitted. Pigments that absorb all colors except for blue look blue to us because that is the only color of the sunlight that is not absorbed and is instead reflected. Photosynthesis uses a variety of pigments but the main one is chlorophyll.

Photosynthesis-the effect of light intensity

The intensity of light can affect photosynthesis. At low light intensities, the rate of photosynthesis increases when the light intensity is increases. At high intensities, further increases in light intensity have no effect on photosynthesis. Several steps in photosynthesis are achieved using the light energy that is absorbed by chlorophyll. These steps are that firstly, ATP is produced, from ADP and phosphate. Also, water molecules are split to release hydrogen which is the process of photolysis. Hydrogen is needed later in photosynthesis to make carbohydrate .Splitting water also releases oxygen, a waste produce that is allowed to diffuse out into the surrounding water or air.

Photosynthesis- the effect of carbon dioxide concentration

Though carbon dioxide concentrations in the atmosphere have been increasing over the years, it is still low enough to effect the rate of photosynthesis. At low carbon dioxide concentrations, increases in the concentration cause the rate of photosynthesis to rise. However at high concentrations, further increases will once again have no effect on the rate. Carbon dioxide is important for photosynthesis because it is the source of the carbon needed to make organic compounds. The conversion of carbon dioxide to solid or liquid carbon compounds is known as carbon fixation. ATP is needed to give energy and hydrogen from photolysis of water is needed as well. In darkness carbon fixation stops and in low intensities it slows down due to low supplies of ATP and hydrogen.

Photosynthesis- the effect of temperature

Temperature also effects the rate of photosynthesis. At low temperatures the rate of photosynthesis is low or zero. As temperature increases, the rate of photosynthesis increases as well until it reaches a maximum, which is the optimum for photosynthesis. Above this temperature, the rate eventually stops. This is similar to the effect temperature has on enzymes. The fixation of carbon dioxide is catalyzed by enzymes and the enzymes work faster as the temperature increases. For plants, the optimum temperature is between 25 and 35 degrees Celsius.

Action spectra and absorption spectra

An action spectra is a graph that shows the rate of photosynthesis at each wavelength of light. An absorption spectra is a graph that shows the percentage of light absorbed at each wavelength by a pigment or group of pigments. They are very similar because photosynthesis can only occur in wavelengths of light that chlorophyll or other pigments are able to absorb.

Absorption of light by chlorophyll is explained in terms of units of light energy, each of which is called a quantum of light or photon. The energy photons carry depends on the wavelength. The shorter the wavelength is, the greater the energy. An electron in a pigment molecule can absorb the photon f the energy that is carried by it allows the electron to riseup from one energy level to a higher one. If the photon carries too little or too much energy, it can’t be absorbed.The electron raised to a higher level is called an excited electron. There are different types of chlorophyll with different light-absorbing properties but all of them absorbed red and blue parets of the spectrum. The other pigments present, or the accessory pigments, absorb other wavelengths and transfer the light energy to chlorophyll.

Data-based question: measuring the effect of temperature by data logging 

1. pH is measured to see the uptake of carbon dioxide in the pondweed. As the pH increases, the carbon dioxide concentration decreases and as the pH decreases, the carbon dioxide concentration increases.

2. The independent variable is temperature and the dependent variable is pH.

3. The x axis should be temperature as it is the independent variable and the y axis should be pH as it is the dependent variable.

4. The optimum temperature could be between 22.5 and 27.5 degrees Celsius. However, this is a hard judgement to make because the differences in the pH are not very large so temperature does not seem to have a very big effect on pH. This could be due to an uncertainty in the pH sensor itself.

5. Different algae have different optimum temperatures depending on their surroundings. For example, if they are kept in cooler places, they optimum may be lower than those kept in warmer places.

6. The range of temperature was not very high and the changes in pH are not very large. The range of temperatures should expanded so that one can see the changes more clearly between cooler and warmer temperatures. Also, there could also be more time intervals so that there is more data to work with.