Lecture 01 (September 23, 2011)

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

Lecture 02 (September 26, 2011)

o o o o o o o o o o Shape defines biology- structure determines function Why is the shape of molecules important? It defines the characteristic, and it determines how molecules recognize each other and interact with one another. Atomic number: number of protons; cations (donates positive) anions (receives positive). Vertical Columns on the period tables are similar due to the valence electron shell Electrons determine the reactivity of the atom. They are the first things that encounter another atom. Chemical reactions form from the exchange of electrons. Electronegativity refers to the ability of an atom in a molecule to attract shared electrons to itself- that is, to its nucleus. If two atoms have identical electronegativities must be of the same element. Isotopes are elements that have different numbers of neutrons; some are radioactive. H2 and O2 both share electrons which is why they are capable of bonding. When they bond it creates a strong bond. This is polar covalent bonding. + spends more time with the oxygen. This is the result of hydrogen bonding: weak bonds formed when a hydrogen atom covalently bonded to one electronegative atom (Oxygen or Nitrogen) is attracted to another electronegative atom because of the attraction of opposite

o o o

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

Acids increase [H]+ concentrations and have a pH up to 6.

Lecture 03 (September 28, 2011)

Organic molecules o The formal or proper names of organic compounds are based principally on 1. The length and shape of the carbon chain 2. The nature of C-C bonding: single, double and triple bonds 3. the chemical groups attached to the carbon chain or skeleton o Carbon chains with no double bonds are called alkanes. These hydrocarbons are said to be saturated with hydrogen o Alkaline homologous series: methane, ethane, propane, butane, pentane, hexane, heptane, octane, nonane, decane (anything that ends in ane does not have double or triple bonds) o Functional groups: organic functional groups are chemical groups that participate in chemical reactions in a characteristic way regardless of the carbon structure to which they attached. o STRUCTURAL ISOMERS - differ only in the arrangements of covalent bonds o Stereoisomers 1. Enantiomers: biochemical reactions in the cell distinguish between enantiomers. This is stereospecific.

Lecture 04 (September 30, 2011)

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

Lecture 05 (October 3, 2011)

Hemoglobin: is a quaternary structure. The Human Proteome Initiative. A proteome is the sum of all the proteins in the cell, and proteomics is the study of the proteome

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

Lecture 06: (October 5, 2011)

Lipids: fats are a certain type of lipids. Diverse and chemically unrelated in composure. They are hydrophobic or have very limited solubility in water o heart disease: there are bad fats such as trans fats and cholesterol. These types of lipids have been said to be high risk factors. o Fats are polymers. Glycerol is a 3 carbon chain. Fat is the storage of excess calories. o Fatty acids may be saturated (no double bonds) or unsaturated (multiple bond). Fatty acids with one double bond are said to be monounsaturated while fatty acids with two or more bonds are polyunsaturated. There are two groups of polyunsaturated family: omega 3 fatty acid (first double bond from methyl end while 6 fatty acids have the first bond six carbons from the methyl end. o Animal fats are principally composed of saturated fatty acids. They have higher boiling temperatures like butter and lard. They help insulate and also protect organs.

o o

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

Lecture 07: (October 7, 2011)

Atoms<molecules<macromolecules (like proteins, lipids, etc.)< cells< organism Genetic material 1. Carries information (carries a vast amount of information) 2. Is capable of being copied (reproduction genes are transferred from parents to children) 3. Is capable of undergoing change (leads to variation. Offspring is not identical to parents) Bacterial cell: they tend to divide to create a colony of bacteria. They are identical. Griffith (1928): a vaccine against pneumonia. He used Living S (smooth) cells and the mouse died. Living R cells led to a living mouse. If he heated the S cells the mouse was healthy there was dead bacteria which could not reproduce. Then he mixed heat killed S cells and living R cells to mouse died. Avery, MacLeod &McCarty (1944): Using the dead S cells. He separated the RNA, DNA, proteins, and polysaccharides. They added each to the rough cells. (side note: they believed proteins had to be the macromolecule to carry to code). They were checking if S cells would be created. They discovered DNA was the transforming principle. It was the only one that transformed R cells to S cells. Viruses are the only organisms(?) that have very little genetic material. Sulfur is not present it DNA. There is S32 and S35. S35 is radioactive and decays. S35 has 19 neutrons instead of 16. Hershey and Chase (1952): o BATCH 1: Took the T4 bacteriophages with 35S and infected protein. Only the particles inside the E.coli would remain. He took a centrifuge and separated the contents. If the pellet was not radioactive, the radioactive material never entered the bacterial cell at all. o BATCH 2: radioactive phosphorus 32P The DNA became radioactive. The pellet was radioactive which means the DNA is present inside the bacteria. For years the DNA structure was a mystery. James Watson discovered: o Nucleotide: nitrogenous base + sugar o There are two families of nitrogenous bases: Pyrimidines (cytosine, thymine)

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)

Lecture 08: (October 10, 2011)

Metabolism: overall chemical reactions of a cell Kinetic energy potential energy (downhill process) o Energy must convert to other energies. No new energy is created. First law of thermodynamics. Potential energy: the capacity to do work because of its position Kinetic energy: capacity to do work because of its movement. Calorie: The energy needed to raise the temperature of 1 gram of water through 1 C. Second law: when energy is transformed from one object to another, some of the energy will be converted to heat. (tells us if it can, not will take place) Heat: a form of kinetic energy that cannot do useful work Entropy (energy that cannot perform useful work) is represented by the letter S o This is the degree of randomness. Free energy: Energy that can perform useful work, referred to as the letter G Enthalpy: a measure of the total amount of energy in the system (heat of combustion) ; the letter H G=H-TS where T is the temperature in degrees K. o Of the change in G= the change in H T times the change in S Cellular respiration is only 40 percent efficient Catabolism: degradative processes. Convert P.E. into K.E. (cellular respiration); take place with a decrease in free energy. They are exergonic or spontaneous (entropy goes up because you have energy that can be used). Anabolism: uphill reactions that increase free energy. (entropy goes down) Transforms K.E. into P.E. They are endergonic or non-spontaneous. (photosynthesis) The hydrolysis of ATP is a catabolic process. -7.3 Kcal/mole How do we start an endergonic reaction that does not want to take place we use ATP to forgo active transport. (coupling) Now this process is exergonic When nitrogen bonds to a double bond CO an amino acid is there. For every bond you subtract one water from total n.

Lecture 09: (October 12, 2011)

Bio-luminescent is more efficient than cellular respiration. (It was endergonic but it was coupled with ATP to make it exergonic) Energy profile of an exergonic reaction: AB+CD AC+CD Knows what it looks like for an endergonic reaction Catalysis reduces the activation energy. o Enzymes are a protein bind to the substrate at the active site. Its fit is induced fit because it is altered. o End in ase o The rate at which it goes is affected by temperature (too much heat would denature it) and pH affects it because it changes the ionization of the enzyme. o The enzyme level becomes limiting. It reaches its peak and stays there; it is called a threshold. o Enzymes are specific! This coordination is called metabolic regulation. o Allosteric regulation: is the principle way that metabolic control is achieved. This adds enzymes or get rid of-according to what the cell needs. They have multiple polypeptides They have a second site which is somewhere else which binds to a molecule that isnt the substrate and is not at the active site. It is called the allosteric effectors or allosteric regulators. It changes its shape. This helps decide how much is needed. These drag before reaching its maximum capacity. ATP makes the curve steep o Inhibitors deny the enzymes access. These can either bind on the active site or somewhere else. Look into this o Negative feedback inhibition: inhibits a previous enzyme which denies later enzymes the ability of work. This is the most common type of allosteric regulation. This could also be the product.

Lecture 10: (October 14, 2011)

Phospholipids have hydrophobic heads and hydrophilic tails (inner part) They are in liquid or crystalline state Cholesterol helps the fluidity. It is between the phospholipids membrane fluidity determines the types of interactions that take place between the lipid components of the membrane and the proteins occurring in and on the membrane glucose cant pass through the inner section because of its polarity. It must be broken down. Passive: moving down a concentration gradient. Facilitated Diffusion: transport using transport proteins. Passive.

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.

Lecture 11: (October 17, 2011)

Cell structure: ribosomes ; proteins do all the work in the cell o Genes determine the actions the cell will undergo. o Transcription is getting the code. There are messenger RNA leaves the nucleus, enters to cytosol and binds to the ribosome. The amino acids that will make the protein are transferred by transfer RNA. Then there is transcription. o Ribosomes are made of two subunits. o Nucleolus: ribosomes have millions of these. They are the DNA information millions of time ready for use. Three living domains: bacteria, archaea, eukaryotes. The Cell Cycle: o Interphase G1: first growth S: the synthesis phase is where the DNA replication takes place in preparation for cell division. G2: the second growth o Mitosis/ meiosis The endomembrane system: a continuous series of membranes beginning with the nuclear envelope and ending with the cell membrane. It isolates a continuous space within the cell. It never makes contact with the cytosol space. Ribosomes: o Free suspended in the cytosol: responsible for synthesis of proteins and maintenance. Many enzymes are synthesized by this o Bound to the membrane. On the nuclear envelope. They are directly bound to each other. This is an elaborate system that sends signals to the golgi apparatus. Endoplasmic reticulum: o Smooth and rough look these up o For the rough ER, the ribosome never leaves the ER. It is tethered. Golgi apparatus is the shipping and receiving center. o They modify ER o Manufacture certain macromolecules o Sorts and packages materials into transport vesicles

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.

Lecture 12: (October 19, 2011)

Catalytic RNA molecules are called ribozymes o They are involved in the process of translation o Thomas Chec discovered this o Proteocells are the very first cells. o RNA World Walter Gilbert said RNA was the first genetic material. o Mitochondria and chloroplasts have a double membrane o Chloroplasts actually have 3 membranes. o Endosymbiotic relationship between a proteocell and primitive bacterial cells were one capable of cellular respiration and photosynthesis. o Chloroplast genome contains 128 functions genes including rRNA and tRNA genes. So does mitochondria.

Lecture 13: (October 24, 2011)

Endosymbiosis: cellular respiration requires oxygen. Anaerobic does not have oxygen. Catabolism: Cellular Respiration o Oxidation: a loss of electrons (in pairs) o Reduction: a gain of electrons (in pairs) Conversion of glucose and 6 Oxygen and makes 6 Carbon dioxide, 6 waters, and energy 1. Glycolysis: glucose is broken down to G3P (3 carbon compound) which is converted to pyruvate. It splits sugar. It is oxidized (loses its electrons). This is an exergonic process. ATP provides two phosphates. The phosphates are added before splitting up the glucose o Fermentation: pyruvate is reduced to something else during glycolysis without oxygen. o Lactic acid fermentation: 2. Krebs Cycle: the pyruvate is transported into the mitochondrion and de-carboxylated to acetyl-coA in the mitochondrial matrix. 3. Electron Transport Chain (ETC) Oxidative Phosphorylation. Anabolism: photosynthesis 6 Carbon dioxides, 6 waters and energy make glucose and 6 Oxygen. o NAD+ manages the electrons during redox reactions. They will gain electrons and grab a hydrogen ion.

Lecture 16: (October 31, 2011)

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

Lecture 17: (November 2, 2011)

Errors DNA replication can be repaired: o Lesion o Excision o Repair o Ligation Properties of genetic material: o Carries information o Is capable of being copied o Is capable of undergoing change Fertilization: o combining of sex cells or gametes to

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

Lecture 18: (November 4, 2011)

Cell Cycle o Tubulinso Subunits o Kinetochore o Actin is used in the band. It starts accumulating as it integrates o Microtubules can have two classes of motor proteins- dynine which goes in one direction

o o o

READ ABOUT THIS!!!! Check points Clock

o o

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.

Lecture 19: (November 7, 2011)

Mendelian Genetics o Knew the basics, but not the chromosomes. He worked with the Sweet Pea. Mitosis Meiosis document Mendels Laws o Laws of Segregation: allele pairs separate during meiosis o Law of independent assortment: Each allele pair separates independently of the pairs during meiosis o Law of dominance: some alleles are always fully expressed, even if the allele pair is heterozygous Probability o The probability that two independent events will occur together is the product of their individual probability. Example: Coin toss heads, once. Coin toss, tails second. times = Incomplete Dominance o One allele is not completely dominant over another allele so the heterozygote is an intermediate of the two traits CACB Co-Dominance o Both alleles are equally expressed. IAIB= AB blood Multiple Alleles o A trait has more than two alleles Pleiotrophic o A single gene has multiple effects Epistasis o One set of alleles effects the expression of the a separate set of alleles DNA replication models: Meselson and Stahl o Conservative: Parent strands serve as template then they recombine, new strands combine 1. Two bands, one at the top, and one at the bottom 2. Never did it since it was eliminated o Semiconservative: parents serve as template then each new double helix had one new strand and one parent strand

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)

Lecture 20: (November 9, 2011)

(fill in notes)

Lecture 21: (November 14, 2011)

(fill in notes)

Lecture 22: (November 16, 2011)

Fill in notes

Lecture 23: (November 21, 2011)

tRNA occurs in the nucleus need a minimum of 20 tRNAs synthetases. RNA is more important than proteins Translation: o Small ribosomal unit binds to RNA

o o o o o o o o

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

Lecture 24: (November 23, 2011)

Mutations, etc. o Base substitutions total bases stay the same A single base pair is altered o Insertions or deletions Total number of bases. Sickle cell carriers survive they carry crystalline structures.

Lecture 25: (November 28, 2011).

18.1&18.2 nothing else. Bacterial gene expression: Operon (from promoter to the genes transcribed). Inactive repressor- cannot bind to DNA sequence and genes are turned on. Compressor denies genes to be expressed. Expression of gene is regulated: o Spatially o Temporarily o In response to cues Before the start(promoter genes) there are short sequences called enhancers. Another name of them is cis-elements. o Short stretches of DNA sequence (6-15 bp) o Enhancers are usually present upstream of coding o (look at slides) o Transcription factors are specific to gene representation

Lecture 26 (November 30, 2011)

Heating- cooling- replication cycle. Target and amplify gene to replicate it. You heat it to 94 degrees Celsius to break it. This denatures it, like helicase, etc.

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