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Monday, February 4

  1. page Proteins and amino acids edited Proteins and Amino Acids {http://www.pnas.org/misc/proteins.jpg} http://www.pnas.org/misc/protein…
    Proteins and Amino Acids
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    The sequence of the different amino acids is called the primary structure of the peptide or protein. Counting of residues always starts at the N-terminal end (NH2-group), which is the end, where the amino group is not involved in a peptide bond. The primary structure of a protein is determined by the gene corresponding to the protein. A specific sequence of nucleotides in DNA is transcribed into mRNA, which is read by the ribosome in a process called translation. The sequence of a protein is unique to that protein, and defines the structure and function of the protein. The sequence of a protein can be determined by methods such as Edman degradation or tandem mass spectrometry. Often however, it is read directly from the sequence of the gene using the genetic code. Post-transcriptional modifications such as disulfide formation, phosphorylations and glycosylations are usually also considered a part of the primary structure, and cannot be read from the gene.
    By building models of peptides using known information about bond lengths and angles, the first elements of secondary structure, the alpha helix and the beta sheet, were suggested in 1951 by Linus Pauling and coworkers. Both the alpha helix and the beta-sheet represent a way of saturating all the hydrogen bond donors and acceptors in the peptide backbone. These secondary structure elements only depend on properties that all the residues have in common, explaining why they occur frequently in most proteins. Since then other elements of secondary structure have been discovered such as various loops and other forms of helices. The part of the backbone that is not in a regular secondary structure is said to be random coil. Each of these two secondary structure elements have a regular geometry, meaning they are constrained to specific values of the dihedral angles ψ and φ. Thus they can be found in a specific region of the Ramachandran plot.
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  2. page Photosynthesis-continued edited Photosynthesis-continued {http://www.hln-store.com/catalog/photos.gif} http://www.hln-store.com/c…
    Photosynthesis-continued
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    The thylakoids convert light energy into the chemical energy of ATP and NADPH. Light is a form of electromagnetic radiation. Like other forms of energy, light moves in rhythmic waves. The distance between crests of electromagnetic waves is the wavelength. Wavelengths of electromagnetic radiation range from less than a nanometer to more than a kilometer. The entire range of electromagnetic radiation is called the electromagnetic spectrum. The most important segment for life is a narrow band between 380 to 750nm, which is the band of visible life. While the light travels as a wave, some of the properties are those of a separate particle, which is the photon. Photons are not tangible objects but they have fixed quantities of energy. The amount of energy packed in a photon is inversely related to its wavelength. The shorter wavelengths of photons pack more energy. When a molecule absorbs a photon, one of those molecules electrons is elevated to an orbital with more potential energy. The electron moves from its ground state to an excited state. The only photons that a molecule can absorb are those energy matches exactly the energy difference between the ground state and excited state of this electron.
    There is an energy difference among atoms and molecules, and due to this a particular compound absorbs only photons corresponding to specific wavelengths. Thus, each pigment has a unique absorption spectrum. Excited electrons are unstable. When they drop back down, they release heat energy. Each light-harvesting complex consists of pigment molecules (which may include chlorophyll a, chlorophyll b, and carotenoid molecules) bound to particular proteins. Together, these light-harvesting complexes act like light-gathering œantenna complexes for the reaction center. When any antenna molecule absorbs a photon, it is transmitted from molecule to molecule until it reaches a particular chlorophyll a molecule, the reaction center. At the reaction center is a primary electron acceptor,which accepts an excited electron from the reaction center chlorophyll a. The solar-powered transfer of an electron from a special chlorophyll a molecule to the primary electron acceptor is the first step of the light reactions. Photosystem I (PS I) has a reaction center chlorophyll a that has an absorption peak at 700 nm. Photosystem II (PS II) has a reaction center chlorophyll a that has an absorption peak at 680 nm. The differences between these reaction centers (and their absorption spectra) lie not in the chlorophyll molecules, but in the proteins associated with each reaction center. Under certain conditions, photoexcited electrons from photosystem I, but not photosystem II, can take an alternative pathway, cyclic electron flow. As electrons flow along the electron transport chain, they generate ATP by cyclic photophosphorylation.
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  3. page Photosynthesis edited Photosynthesis Chloroplast {http://www.biologycorner.com/resources/photosynthesis-overview.gif} …
    Photosynthesis
    Chloroplast{http://www.biologycorner.com/resources/photosynthesis-overview.gif} http://www.biologycorner.com/resources/photosynthesis-overview.gif
    Chloroplast
    is found
    ...
    in respiration.
    Photosynthesis is a redox reaction. It reverses the direction flow in respiratation. Water is split and elections are transferred with H+ from water to CO2, reducing it to sugar. Because the electrons increase in potential energy as they move from water to sugar, the process requires energy. Light provides the energy boost. Photosynthesis is two processes and each has multiple stages. The Light (photo) reactions convert solar energy to chemical energy. The Calvin Cycle (synthesis) uses energy from the light reactions to incorporate CO2 from the atmosphere into sugar. In the light reactions, light energy absorbed by chlorophyll in the thylakoids drives the transfer of electrons and hydrogen from water to NADP+, forming NADPH. The light reaction also generates ATP using chemiosmosis into a process called photophosphorylation. Therefore, The light energy is initially transformed to chemical energy in the form of two compounds, which are NADPH, and ATP. The Calvin Cycle is names for Melvin Calvin. With his colleagues, Calvin worked out many of its steps in the 1940s. The cycle begins with the incorporation of CO2 into organic molecules, a process known as carbon fixation. The fixed carbon is reduced with electron which are provided by NADPH.
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  4. page The Calvin Cycle edited The Calvin Cycle {http://www.daviddarling.info/images/Calvin_cycle.jpg} http://www.daviddarling.i…
    The Calvin Cycle
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    The Calvin cycle regenerates its starting material after molecules enter and leave the cycle. The Calvin cycle is anabolic, using energy to build sugar from smaller molecules. Carbon enters the cycle as CO2 and leaves as sugar. The cycle spends the energy of ATP and the reducing power of electrons carried by NADPH to make sugar. The actual sugar product of the Calvin cycle is not glucose, but a three-carbon sugar, glyceraldehyde-3-phosphate (G3P).To make one glucose molecule requires six cycles and the fixation of six CO2 molecules.
    The Calvin cycle has three phases. In the carbon fixation phase, each CO2 molecule is attached to a five-carbon sugar, ribulose bisphosphate (RuBP). This is catalyzed by RuBP carboxylase or rubisco. The six-carbon intermediate is unstable and splits in half to form two molecules of 3-phosphoglycerate for each CO2.During reduction, each 3-phosphoglycerate receives another phosphate group from ATP to form 1,3-bisphosphoglycerate.A pair of electrons from NADPH reduces each 1,3-bisphosphoglycerate to G3P. After fixation and reduction, we would have six molecules of G3P (18C).The other five G3P (15C) remain in the cycle to regenerate three RuBP. In a complex series of reactions, the carbon skeletons of five molecules of G3P are rearranged by the last steps of the Calvin cycle to regenerate three molecules of RuBP.
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  5. page Mutations(contd) edited Mutations continued {mutation.jpg} http://www.wingsofjoyaviary.com/images/GreyFactorMutations-lar…
    Mutations continued
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    During meiosis, the homologous maternal and paternal domains pair. Normally, these domains and homologous chromosomes are identical. This is different here. Due to the regular, balanced translocations, the chromosomes of Oenothera and a few other species form a ring when pairing: domain 2 of the maternal chromosome 1.2 pairs with domain 2 of the paternal chromosome 2.3. This again pairs with chromosome 3.4 and so on. The ring is closed by the pairing of chromosome 14.1 with chromosome 1.2. During anaphase I, the centromeres are distributed onto the daughter cells in a strictly alternating way. The result is that the chromosomes of the original maternal set stay together in one daughter cell and those of the paternal in the other. This explains the occurrence of just one coupling group.
    12
    ...
    genus Datura.
    The DNA sequence of a gene can be altered in a number of ways. Gene mutations have varying effects on health, depending on where they occur and whether they alter the function of essential proteins. The types of mutations include:
    ...
    mutation (illustration)
    This type of mutation is a change in one DNA base pair that results in the substitution of one amino acid for another in the protein made by a gene.
    ...
    mutation (illustration)
    A nonsense mutation is also a change in one DNA base pair. Instead of substituting one amino acid for another, however, the altered DNA sequence prematurely signals the cell to stop building a protein. This type of mutation results in a shortened protein that may function improperly or not at all.
    Insertion (illustration)
    An insertion changes the number of DNA bases in a gene by adding a piece of DNA. As a result, the protein made by the gene may not function properly.
    Deletion (illustration)
    A deletion changes the number of DNA bases by removing a piece of DNA. Small deletions may remove one or a few base pairs within a gene, while larger deletions can remove an entire gene or several neighboring genes. The deleted DNA may alter the function of the resulting protein(s).
    Duplication (illustration)
    A duplication consists of a piece of DNA that is abnormally copied one or more times. This type of mutation may alter the function of the resulting protein.
    ...
    mutation (illustration)
    This type of mutation occurs when the addition or loss of DNA bases changes a gene’s reading frame. A reading frame consists of groups of 3 bases that each code for one amino acid. A frameshift mutation shifts the grouping of these bases and changes the code for amino acids. The resulting protein is usually nonfunctional. Insertions, deletions, and duplications can all be frameshift mutations.
    ...
    expansion (illustration)
    Nucleotide repeats are short DNA sequences that are repeated a number of times in a row. For example, a trinucleotide repeat is made up of 3-base-pair sequences, and a tetranucleotide repeat is made up of 4-base-pair sequences. A repeat expansion is a mutation that increases the number of times that the short DNA sequence is repeated. This type of mutation can cause the resulting protein to function improperly.
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  7. page Mutations- Gene and Point edited Mutations {chromosome.jpg} http://penningtonresearch.org/images/chromosome.gif Chromosomes and …
    Mutations
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    Chromosomes and genes can alter as a result of structural changes. These changes are called mutations. The original state can usually not be re-established. The loss of hereditary information is irreversible. A change caused by a mutation is kept throughout all following generations, if it does not cause lethality. A number of different mutations were identified with the help of polytene chromosomes. They occur also in normal chromosomes.
    021. A deficiency is the loss of a chromosomal end fragment. Since it occurs normally only in one of two homologous partners, the result is a pairing of a defect and an intact chromosome. Deficiencies can be recognized by this. The intact partner chromosome shows how large the missing fragment of the defect chromosome is.
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  9. page Human Genome Project and its Result edited Human Genome Project and its Result {hgp2.gif} http://cse.stanford.edu/class/sophomore-college/pr…
    Human Genome Project and its Result
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    To start the Human Genome Project, the scientists needed to know all about genes. We all know that genes contain vital information for everyday life functions. To be more specific many genes hold data needed for the creation of proteins. In order for the proteins to be made the genetic code is used to translate the genetic sequence into protein sequence. They also needed to know about gene splicing, otherwise known as recombinant DNA and genetic engineering. Gene splicing involves cutting out a piece of DNA and replacing it with a new one. To be more precise, a specific restriction enzyme will split apart a certain strand of DNA leaving behind a gap in the genetic code. When a new strand of DNA is added, it takes the place of the binds to the ends of the DNA strands that were originally cut. Another enzyme called ligase is used in the repair process. Once the new DNA is in place, the function of the gene changes. In cases where a defective gene is repaired, the new gene will begin functioning correctly, producing the appropriate enzymes for its type.
    The Genome project was used to map the entire human genome. They needed first to know how to map chromosomes. Gene and chromosomal mapping involves identifying which gene belongs to which chromosome. For example, the red-green color blindness gene is carried on one of the x chromosomes. Also, they couldn't immediately start with humans, they first had to use other organisms. The organisms they used were: Saccharomyces Cerevisia (yeast), Caenorhabditis Elegans (roundworm), Drosophila Melanogaster (fruitfly), and Arabidopsis Thaliana (small plant). From there, they were able to start using human cell lines to map the human genome.
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