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o Charles Darwin (1809-1882) He did not understand the process in which species evolved but understood that species evolved and like humans and monkeys alike, from a far off ancestor. Watson and Crick- discovered DNA. Nucleotides are the building blocks of DNA. While the polypeptides are the backbone. "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." Human Genome Project (HGP): to sequence the entire human genome. They process in which all four nucleotides appeared. Also it was to identify the gene placement in the DNA molecule within the genome. For humans it is the particular part of the chromosomes. The technology that was created by this project that ended in 2003 has allowed us to examine the DNA of animals as well as human. We share 7600 genes with chimpanzees. However the genes in chimpanzees that are changing rapidly are the skull and muscle genes. Water of pure water is
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charges. It lasts a lot less than a second. They are continually being broken and made. Dissociation of water: occurs as a result of electrical polarity when a hydrogen ion or proton from one water molecule becomes attracted to a second water molecule, resulting in a positively charged The addition of a H proton with a OH electron is a one molecule in 554 million. pH= log10[H+] OR [H+][OH-]=10-14 -log[H+]=pH, whenever [H+]10-5 the pH is 5. When they give you the pH of [OH-] just subtract it from 14 to get the pH Lake: sulfur dioxide, water dissolves it, and it becomes acidic. If the lake has a pH of 3, hydroxide concentration is 11. Ionic bonding: because a molecule is so negative, it rips off a proton off of everything. Like NaCl= (cation) Na++ (anion) Cl How does this relate to molecular shape? Molecular shape is the result of covalent bonding. Electrons are in an orbit. They have distinctive shapes and orientations. S, p orbitals. Covalent bonds share electrons. There are polar bonds and nonpolar bonds. Shapes (tetrahedron, etc) CHON are the major organic components Group 1: CH: not electronegative Group 2: ON: strongly electronegative This only works with covalent bonds: polar covalent and nonpolar, only atoms in a polar bond to form a hydrogen bond.
Atoms in H bond must be 1 hydrogen + 1 atom from NO group\ Each atom in H bond must also be involved in a polar covalent bond
Sugar and polysaccharides Origin of life: What evidence in support of the interstellar space theory for the Origin of Life was compelling that NASA embarked on two space mission, STARDUST and DEEP IMPACT aimed at analyzing the chemical composition of comets? o a place in Australia named Murchison o a meterorite o enantiomers o a scientist named Max Bernstein Polymerization reactions build polymers; polymers are formed by dehydration (condensation) Four important macromolecules: 1. Carbohydrates (sugars) Energy source and energy storage. They are structure building blocks. Saccharides Glycosidic reactions produce disaccharides and polysaccharides by dehydration 2. Lipids (fats) 3. Nucleic acids(genetic molecules) 4. Proteins
Genome: 21,000 human protein-encoding genes; transcriptome; 100,000 human transcripts; proteomes: 1,000,000 human proteins o Why is this? Why are there more proteins than genes? What gives protein the ability to function as it is? Their structures. Proteins are polymers of amino acids. They have an amino and carboxyl groups; it has to be attached to the carbon group (the previous two groups). Every single amino acid has this in common. Nonpolar amino acids have no electronegative atoms There are polar amino acids as well. You dont need to know the structures or the names of these amino acids.
We must be able to recognize peptide bonds 1. The primary structure is the backbone of the protein or polypeptide chain. 2. Secondary structure is a (alpha helix) spiral shaped and also the beta plated sheet. 3. Tertiary structure is formed as the result from bonding between side chains and their functional groups within a single polypeptide chain. Hydrogen bonding is common in tertiary bonding. Hydrocarbon hates water. They all get together forming a hydrophobic group. This occurs in the middle of the proteins. We do not want them on the outside because that is where the water is. 4. Quaternary structure results from bonding between polypeptide chains. They contain multiple polypeptide chains
Sugars are right handed enantiomers. After the gene produces protein after synthesizing it returns to its correct structure. This occurs within a second. There are many diseases in which the protein is not put back together correctly or does not fold together correctly. To have the correct function you must have the correct structure. There are an infinite amount of possible structures. This process is spontaneous but not random; The Protein Folding Problem and Levinthals paradox: it would take an eternity for proteins to fold because of the huge number of possible conformations it had to explore before finding the correct structure for the correct function. Refer to: Blue gene production: sequence of IBM super computers simulating protein folding If there is a problem in the secondary structure, etc. it becomes a nonfunctional protein. o Sickle anemia is a disease caused by a nonfunctioning protein. Sickle cell is then a long fibrous rod like hemoglobin instead of the traditional round hemoglobin. The hemoglobin tends to stick together. The change in the structure does not allow oxygen to be distributed properly.
Enantiomer
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Plant fats are principally composed of unsaturated fats and are liquid at room temperature like oils Steroids: lipid molecules containing the complex four ring structure known as the phrenathrene nucleus. Usually end in sterol Cholesterol: principle sterol found in animals. Plants have sterols but not cholesterol. What are the bad fats? Saturated fats and cholesterol trans fat. Can lead to atherosclerosis. This is the hardening of the arteries: fatty materials in the artery accumulates on the outside of the wall. It accumulates, minimizing the size of the vessel and it may end up completely full. This is called plaque. The flexibility of the artery is minimal as it becomes hard. A blood clot will form on the plaque and the blood clot continues and may lead to a heart attack. The lipid hypothesis: there is a direct relationship between the amount of saturated and cholesterol. Framingham- study of 5,000 people. There were two studies groups: one consumed little and the other a lot. It does not support the lipid hypothesis. They hydrogenate vegetable oil where a significant portion of the double bonds in the plant oils are removed to increase the melting point. Trans fats arise from this hydrogenation which contain trans geometric isomers of fatty acids Trans Cis Saturated
o They are usually crooked. These are serious factors in heart disease o . LDL: low density lipoproteins. Transports cholesterol from the liver to the periphery where it could land on the artery walls. o HDL: high density lipoproteins transport cholesterol from the liver to dispose of. o Trans fats increase the bad cholesterol which decreases good cholesterol which leads to atherosclerosis.
Hans Bang and Jorn Dyerberg publish The Lancet which observed that eskimos living in Greenland suffered that the Danes in Denmark were eating diets high in cholesterol, etc. Eskimos ate a lot of blubber and other fats but their risk was lower. The Eskimos had very high levels of Omega 3 fatty acid in their lipids while the Danes did not. So Omega 3 is the number one way to help prevent or decrease the chances of cardiovascular disease. Plant seed oils also have Omega 3. Canola oil is rich in Omega 3
Purines (adenine, guanine) Chargaff (1947) the discovery that there were a same amount of A and T; G and C nitrogenous bases. Watson took a peek at Rosalind Franklins diffraction photo of a DNA crystal and he knew it was two strands and helical. You could not have two purines for it was too wide; you could not have two pyrimidines because it was too short. Then he realized that the pyrimidines and purines were paired and thats why there was an equal amount of A & T; G & C. There were also 3 hydrogen bonds. Watson and Crick figured out the phosphates were on the outside because they were hydrophobic. There is also a reverse of 5 to 3 and the parent 3 to 5. (look into it)
Osmosis: the movement of water to change concentration gradient if the membrane is impermeable. Active transport goes against the gradient. It requires energy. The ions create a voltage. Proteins work as pumps. Two forces: o Electrochemical gradient, and chemical gradient.
Lysosomes: membranous sac of hydrolytic enzymes. It breaks down proteins and recycle organelles. Must know the order of how things are called for. GDP and GTP: look at past notes and lecture slides how does this work? o GDP is guanine based energy that works from GEF, GTP, GDP, Gphase Anabolic has a positive delta G. Review Ribozyme: a catalytic RNA molecule
Basic and acidic chains are only found on the side chain. Basic groups have an amino side chain. An elements chemical properties come from its electrons. Hydrophobic binding would contribute less to the tertiary structure of a protein Enzymes have multiple subunits or quaternary structure. Free energy change is the first part of the data
Cis is facing the same way, trans face out in out. DNA, ATP, and ribosomes are present. Mitochondria and Chloroplasts contain their own DNA. Double bonds form a kink in the tail forcing lipids to be further apart. Hexane is nonpolar, so is CO2 so it can pass through and contain a lot of carbon. Size, polarity, similarity to others, and charge matter to get a target cell Membrane potential is called the voltage Structural and storage polysaccharides are shaped differently because of alpha and beta helixes.
Chargaff (1947) the discovery that there were a same amount of A and T; G and C nitrogenous bases. James Watson used cardboard to make their model. Hundreds of thousands of base pairs. DNA 1. Specific experiments with genetic material and DNA: Griffiths; Avery; Hershey & Chase; Meselson and Stahl; concept behind these experiments; various uses of radioactive and non-radioactive isotopes in experiments. 2. Structure; what bonds stabilizes the structure; clues that led Watson & Crick to solve the structure (Rosalind Franklins X-ray diffraction and Chargaffs). 3. 3. Base-pairing (you should be able to write out complimentary strands, predict stability etc). http://www.youtube.com/watch?v=_EK3g6px7lk
The strand on the left is a template for the strand on the right Parent molecule is together, then separates, then a daughter DNA molecule has one of the separated strands with a new pair. o This is a semi-conservative model where the DNA is use again to make a new replicated model o Meselson and Stahl sought out an experiment to prove Watson and Cricks idea of a semi conservative model of DNA (Biology 312). They cultured E.Coli with 15N (a heavy isotope) and successfully transformed the bacteria; then they used 14N (lighter isotope) and transformed it again (Biology 312). Two DNA samples were taken from this flask, one at 20 minutes [where they put it in the gradient] and one at 40 minutes [where the bands- heavy, light, or medium- moved], after the first and second replications respectively [which were needed so that the DNA strands would gather either 14N or 15 N] (Biology 312).The isotopes rose or fell depending on their density (lighter rose, heavy fell) in the medium that allowed manipulations to it. They wanted to make sure that Watson and Crick were correct, but to do so they had to test all three models: conservative, semi-conservative, and dispersive. If DNA replicated with the conservative model where the strands would once again combine, the old strands containing 15N would bind once again after being a template, and the new DNA strands with 14N would bind together; this was not so because after the second replication there would be three 14N strands and one 15N strand and there were not two strands completely at
different regions, but rather lumped in the center. They also conducted the dispersive model, where fragments of the old and new nitrogen combine on a single strand after the first replication. Then after the second, the same product should occur, and there would be medium-heavy bands in the middle of the medium. This did not occur. What did occur was the semi-conservative model: the idea that the old 15N strand and a new 14 N strand would combine every time. After the first replication, there would be medium heavy bands; after the second replication there would be two medium heavy bands and two light bands. All in all, the dispersive and conservative model did not concur with the results, so the only model it could be was the semi conservative model. Look at slide and image 007 GIF
The template strand is the base 3 to 5and it is the strand that is replicated Helicase binds to the strand and opens the double strand using ATP. Single strand binding proteins put the strand back together. o DNA replication look at previous notes on the topic Leading and lagging strands Okazaki fragment
Four carbon reaction is probably in the kreb cycle Acetyl coA is a co-enzyme
produce a zygote. If a cell is not called a gamete it is called somatic. A zygote is a diploid. A Gamete is a haploid.
2n=46; 2n=diploid
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Kinesis add a phosphate group 1. Post-translational phosphorylation Cyclins and kinases control the cycle. Cyclin levels increase, cyclin binds to kinasesforming MPF- and triggers cell to from from G2 to M. 1. Only works in the M phase Mutagens- radiations, etc.
1. A band in the center 2. Middle (one old, and one new) and top (new strands) o Dispersive: each new strand had pieces of parent and new. 1. Center 2. One band in the center They used heavy nitrogen (N15) and harvested bacteria They put the heavy nitrogen with the light nitrogen for one replication(20 minutes). They centrifuge it, and it separates by density. Then there was a single band in the middle They put it again in N14 Then there was a band at the top, and another at the middle o DNA is semi-conservative method is correct Sister chromatids are completely identical (there is no variation) Homologous chromosomes have the same trait at the same spot but could be different alleles. Meiosis 1: homologous chromosomes split (two chromatids) Meiosis 2: sister chromatids splits (one chromatid)
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Met binds to it; called initiation The large unit binds to the small subunit and EPA sites. Stop codons that terminate translation When it is moving, it moves in steps of threes, energy is always required. Attacking the ribosome is the best thing to do to fight bacteria. The side groups are different. C-terminus end, N-terminus end. Dosage compensation: inactivate one of the x chromosomes by condensing to heterochromatin thus cannot be transcribed. Inactivated x known as Barr body. Calico cats the fur color is based on the x chromosome. Can be inactivated or activated. Mutations Chromosomal mutations- why pregnant people have miscarriages Deletion: ABCDABD Inversion: ABCDACBD Duplication: ABCDABBCD Translocation o Reciprocal: ABCD WXYZABYZ WXCD o Non-reciprocal: ABCD WXYZAB WXYZCD Non disjunction:
(and during meiosis I) 50% will be affected If it occurs in meiosis II, only 25% will be affected Down Syndrome is the most common (extra x). DNA mutations Deletion: AATGCGCAAGCGC Substitution: AATGCGCATGCGC
Frame shift: with adding or deleting; ruining the rest of DNA; must not be in threes Silent: not noticed Nonsense: premature stop codon Missense: mutation from one amino acid to another
Then is annealing. You have to lower the temperature of the solution You get a primer for whatever you are targeting. DNA polymerase works to reattach the separated strand. Negative DNA phosphate will begin moving towards the positive gel. The larger pieces will move slower, the smaller pieces will move faster. Bypass DNA replication in a test tube. Can do it to fragment of interest (gene). Run it on a gel and separate it by size. DNA cloning is an alternative. You can generate recombinant bacteria. You need restriction enzymes to cut DNA Original plasmid called a cloning vector.
Extra studying
Transcription: enzyme zips along DNA to form RNA, guanine nucleotide is added to the beginning; (RNA processing) introns are removed; adenine nucleotides are added to the 3 end, the completed product is mRNA and it now leaves the nucleus Three steps of translation: Initiation: small subunit binds to the 5 RNA end; the anticodon binds to the start codon (MET). The initiator tRNA sits on the p site. tRNA brings each amino acid. Elongation: Peptide bonds connect them. A goes to P site. P goes to E site. The tRNA leaves with the as the mRNA leaves the exit site (E) Termination: stopped by a stop codon
Protein Procession after mRNA arrives Guanine 5---- Poly A tail 3 The ribosome docks on the rough ER, transfers on a vesicle to the golgi apparatus. Operons: o Repressible Regulatory gene (gene before the promoter, codes for a repressor protein) RNA polymerase unzips DNA. The end product does not allow DNA to be unzipped o Inducible Repressor protein is already on. The product binds to remove the repressor protein. RT-PCR binds to mRNA to form cDNA. The poly-A tail is the promoter for the RT-PCR. o You amplify these genes with: In situ hybridization uses fluorescent dyes attached to probes to identify the location of specific mRNAs in place in the intact organism