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Mark Siegal

Chapter 1 9/4/2013 6:37:00 AM Office hours: Monday, 3:00pm-4:00pm, 12 Waverly Place Room 306 The relationship between structure and function is crucial when understanding biology. Each cell type is specialized to do a particular job.  Red blood cells don’t have a nucleus.  Microvilli have a particular function for nutrient uptake All these different human cell types come from the coming together of two different kind of cells (egg and sperm) How do cells know where they are?  They listen to each other and their external environment (they send and respond to signals)  All cells are aware of where they are in the body There will be a protein that is responsible for receiving a signal from the outside and sending it to the cell via other proteins This signaling process is very coordinated between several proteins depending on the signal. There are layers of complexity This is called the signaling cascade (signaling transduction) Prokaryotes and eukaryotes (prokaryotes consist of anything that are not eukaryotes)  Organisms of our daily experience are only the surface of the organisms that are in biology o Enormous tree of life that has organisms we don’t even think about Prokaryotic cells  Consists of a nucleoid, inner membrane, outer membrane, and cell wall o Nucleoid is the genetic material (DNA) that is loosely organized in the middle of the cell o Double membrane system Eukaryotic cell  Consists of nucleus, golgi vesicles, lysosome, mitochondrion, and endoplasmic reticulum o Cytoplasm is far more complicated o Nucleus has the genetic material that is organized in the cell  Not uniform – it has structure Molecular and cell biology spans a huge size range  Nanometers to meters (10^-10 to 10^4)  A typical cell is around 10 microns o Protein molecules are much smaller (around ten nanometers)  270 million proteins inside of every cell  All diseases can be linked to the change in one genome for example sickle cell disease = base change in the DNA  a single change in an amino acid in a protein  different shape in a hemoglobin molecules  a very different shape in red blood cells  sickle cell diseases  The number of copies of DNA per cell (in our bodies that’s two. In some prokaryotes, that’s one) is a vast range of molecule numbers as well  Each of our cells have 6 feet of DNA. Multiply that by ten trillion cells.  Proteins are in extraordinarily high numbers two  Many copies of hemoglobin per red blood cell (we are basically a hemoglobin factory)  We need exquisitely sensitive methods for detecting particular proteins/molecules inside proteins  We need something super specific Biological molecules differ in size, shape, and function  The difference between a hemoglobin protein, insulin protein, enzymes, etc. has to do with the structure of their cells  Model organisms – organisms that are used for experiments all over the world o Biology has a certain kind of universality o Mice, fruit flies, viruses  There are commonalities between species  Example: a gene in flies that has to do with eye development (if you remove the gene, there is no eye). Remove this gene in humans, and we get amoridia (less of an eye in a human). Vast span of time – we’ve had a short flash of time compared to all the diversity in Earth The rise of non-model organisms  Now, people are directly studying organisms they are interested in  Increasing number of diverse species using sophisticated molecular- genetic, cell-biological, and genetic material  Chapter 2 9/4/2013 6:37:00 AM All activities in the cell happen simultaneously and must be coordinated.  Imagine that the cell is like a city.  Understand the government of the cell. The job of the cell is basically done by proteins – they are made in the cytoplasm (transportation issue)  Information is in the nucleus but the job is done by those made in the cytoplasm Central dogma here: DNA -> mRNA -> Protein  DNA makes messenger RNA, which makes Protein o All of your cells have the exact same DNA.  Cells are not different because they have different DNA – they are different in how they use the DNA they have. Difference between Molecular Biology and Biochemistry: both care about the chemistry of life. While biochemistry focuses on the reduction of science (focused on actual activities of molecules based on chemical properties). In MCB, we set this aside and focus on the information these molecules contain. We emphasize information. Proteins, nucleic acids, and polysaccharides – the most important macromolecules.  Phospholipids – make the outside of the cell  Monosaccharides Phospholipids and monosaccharides are excluded from the central dogma Chemical building blocks  Think about DNA and small molecule subunits. The macromolecules we care about (DNA, RNA, protein) are made of simple building blocks put together in long strings. The small molecule subunits of DNA are called nucleotides and the process of making DNA is the process of assembling these nucleotides one after one. DNA nucleotides – purine/pyramidine + five carbon sugar (deoxyribose) + phosphate  Deoxyribose has a Hydrogen in place of OH (ribose contains two OHs) Adenine + Guanine + Thymine + Cytosine in DNA. In RNA it is the same thing except you will have Uracil instead of Thymine. Purines – adenine and guanine (two rings) Pyramidines – Uracil, Thymine, Cytosine (one ring) Pyramidines pair up with purines The way DNA/RNA is made into a long polymer is when the phosphate end connects to the carbon of the previous phase (beginning the 5’ and 3’ ends) Always add new bases to the 3’ end of the molecule. You must specify which side the 5’ and 3’ end. Chemical Bond Energy  nucleotide triphosphates carry nuclear energy in them so they have high energy bonds. When you break these bonds, you get energy that powers polymerization of DNA/RNA in the cell. (ADP + Pi + Energy)  Adenosine Triphosphate is the most important energy currency in the cell. ATP means energy. o It is the energy currency but also the A that gets incorporated into DNA/RNA Nucleic acid polymerization is powered by NTPs.  Read from 5’  3’ when reading DNA  When you polymerize DNA from the template, directionality matters.  C and G forms three hydrogen bonds; A and U forms two hydrogen bonds  Pyrophosphatase converts two phosphate molecules linked together to two.  The phase where you release pyrophosphate is energetically favorable. Chemical equilibrium  forward and reverse rates balance at equilibrium.  Many reactions do run in both directions, but their rates are different. As products are formed, some of them will convert back to reactants. There will be a point where the number of products formed will equal the number of reactants that form from products. At this point, the rates are equal. o The reaction does not stop here. It keeps going, the rates are just equal. o A rate constant is not the same as a reaction rate. A rate constant describes the rate given the concentration of reactant (represent the speed at which the reaction will occur). The rate constant is high, the highest number of reactants will convert to products.  Reaction rates change. But a rate constant does not.  After the reactants are first mixed, the rate of the reverse reaction slowly increases while the rate of the forward reaction slowly decreases until chemical equilibrium is reached and the two rates are equal. o A useful way to summarize a reaction is through the equilibrium constant (Keq).  K(eq) = Kf/Kr (the forward constant/reverse constant).  If Kf is three times larger than Kr then you will have three times as much product than reactants in the reaction.  Cellular reactions are at a steady state, not equilibrium. o Test tube equilibrium concentrations o Intracellular steady-state concentrations. o There is a system/network of reactions that is happening. o Not every cell is in equilibrium – they could be at a steady state where concentrations don’t change.  DNA/RNA polymerization o Polymer + NTP > polymer + PPi 2Pi  This creates energy  By converting polymer + PPi into something else, you’re siphoning away the products of Polymer + NTP. In this case, the reverse reaction becomes much less likely. This adds an extra layer of security. The reaction will keep going forward instead of in reverse. Molecular complementarity  two different molecules fit together  Allows a complexity of function when you bring two or more things together like this  What makes it so that two proteins have an affinity for each other? o Shape – the shapes complement one another o Weak interactions that draw them together as opposed to repelling them  Covalent bonds, interactions, etc.  Ionic bonds – electrons are being exchanged  In proteins a part of the molecule will have a negative charge on it, and the other will have a positive charge. This causes them to be drawn together.  Hydrogen bond – weaker, longer than covalent bonds. But if you add them up together, you get a relatively strong bond.  Partial positive charge and partial negative charge  Hydrophobic effect – charged molecules dissolve easily in water. This is because water is a dipole (It has a little excess of negative and positive charge). In an aqueous environment, charge matters. o Methyl groups have no charge and don’t interact well with water so it separates from water o Protein does not separate from water, which is good. o Proteins form when hydrophobic residues go to the center of the protein (by bonding together)  van der Waals interaction – when you put two atoms really close together, the electrons start to perturb one another, which causes transient dipoles. One will become positively charged, the other will be negatively charged, and will eventually start to attract one another.  What happens if you have a mutation that changed the amino acid sequence of a protein? o The mutation can cause the stable complex to be less stable Hydrogen bonds create the double helix  GC pairs form three hydrogen bonds, AT pairs form 2.  Therefore the more GC pairs you have, the stronger the DNA will be (because there will be more triple bonds) o If you put a strong strand of DNA pairs in an aqueous solution, you would need a higher temperature to break these strands apart. o There are organisms that live in very hot environments (they tend to have more GC base pairs).  In order to keep these base pairs, you need to have more hydrogen bonds.  DNA strands are antiparallel  DNA is not evenly spaced – major groove and minor groove (the spaces between each helix is different) o DNA spins about once every 1.2 bases Recitation 9/10/13 9/4/2013 6:37:00 AM Study Question: The following sequence comprises one strand of a DNA double helix. What is the sequence of it’s paired strand?  AATGCTAGCTACGACTAC  Answer: Read in 5’3’ direction. So it has to be the opposite way. GTAGTCGTAGCTAGCATT How many turns of the helix will this DNA turn?  Around 2 Lecture prompt question  Nucleoside analogs serve what function in synthetic biology? o What is a nucleoside? o What is a nucleoside analog? o Functions?  A nucleoside is a nucleotide without the phosphates (a nucleoside is just the sugar and the base).  A nucleoside analog would be something that is similar to the nucleoside but not exactly the same (a nucleoside with a different base?) Nucleic Acids & Origin of Life (based on reading) What is life? Being able to reproduce and having cells How is a cell important to life? (Why is it the building block of life?)  A cell contains DNA and is the basic building block of life.  What is the paradox of cellular life? o It takes proteins and DNA to make more proteins. This paradox would disappear if molecules didn’t need proteins at all.  Earliest forms of life may have been able to get by without proteins, using their DNA (or close relative RNA) as catalysts to reproduce How were the first organic molecules synthesized?  Stanley Miller in his 1953 experiment, a laboratory simulation demonstrating that environmental conditions on the lifeless, primordial Earth  Spontaneous synthesis of some organic molecules with electrical discharges (simulated lightning as reactions in a primitive atmosphere of H2O, H2, NH3, and CH4 How did the first complex organic molecules form?  In a warm alkaline (basic) solution  Nucleobases can form spontaneously  Sugars are easy to assemble in those situations – the problem is finding the right sugar (ribose for RNA and deoxyribose for DNA).  Ribose can form from two simple
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