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University of Waterloo
BIOL 130
Heidi Engelhardt

Biology 130 Notes Me November 27, 2012 1 Lecture 1 Hooke ▯ddled with the the ▯rst microscope in the late 1600’s. He discov- ered that cork was formed from little compartments and from the latin word cellula (rooms) the term cell formed. Light microscopy began the ▯eld of cell biology. After an increase in optical strength from the microscopes it became possible to see many more objects. Leuwenhoek was a very passionate scientist devoted to using the microscope to look at anything he could get his hands on. As a result of this incessant hobby, he is famous for many discoveries. Later during the 1830s microscopes improved again. A knowledge of relative size is important. 30 nm ribosomes - 200 nm viruses - 6▯m Red Blood Cell - 200 ▯m minimum visbility by human. Cell Theory 1. All organisms consist of cells. 2. Cells are the basic unit of structure. 3. All cells arise from other cells. Di▯erent methods of microscopy: ▯ Light: Stains attract/grab certain obgjects within the cell: eg. nucleic acids. ▯ uoresence = cyto celetons 1 2 Lecture 3 - Intro to Basic Chemistry Atomic mass is calculated in the units of Daltons. Carbon13 and 14 are very important in spectral chemistry. The most important electrons of the valence electrons are the unpaired electrons. The valence of the element is determined by the number of un- paired electrons. Eg. C-12, valence 0; Ar, valence 0; Cl, valence 1. Reactivity changes: K more reactive than Na. Single elec pulled less towards the nucleus, so easier to take away. Reactivity is in uenced by the desire to ▯ll the shells, the other principle is to balance the +ve and -ve charges. Covalent bonds are strong bonds in biological systems. Non-covalent in order of strength: ionic bonds (very stable), hydrogen bonds (even though weak, in great numbers are very strong), hydrophobic interactions (interact with themselves and not water). There are two types of covalent bonds: non-polar (equal sharing -H2, O2) and polar (not equally shared between the elements). Pull on electrons are equivalent to the electronegativity. In ▯ H2O we write a ▯ beside the Oxygen to refer to the slightly negative polar charge around the molecule; ▯ around the Hydrogens. Bond lengths and types: the balance between attraction and repulsion is the stable position of the electron. Shorter the bond, the stronger the bond (as a rough principle): cov: 0.15; Ionic 25; Hydrogen 30; Vanderwaals 0.35nm. Ionic bonds: forms because of the desire to balance charges. Water. Solvent that can dissolve more things than any other solvent. Im- portant because of its polarity. Hydrogen bonding : electrical attraction between the electro negative atom and the partial positive oxygen. Weak individually, strong in large numbers. Importance because they are weak: they can continuously form and break. Hydrophilic - water loving (salts). Hydrophobic - water fearing(nonpolar molecules - oil; the hydrogens within the oil form hydrophobic bonds to ex- clude the water { oil droplets). All of water’s properities is a direct result of its ability to form H-bonds. Dissociation of Water: (see slides), understand strong and weak acids. Acidity: pH = - log[H ]. Carbon will not ionize in biological situations. 3 Lecture 4 - Intro to Chemistry Pt. 2 September 25, 2012 Oligosaccharides = polysaccharides (carbohydrates). 2 Building blocks are all di▯erent. The chemistry of coupling to make the macromolecule is the same: condensation. Taking two sugars lose water, water expelled. Hydrolysis - breaks the macromolecules. Proteins: These have the greatest diversity. Function is directly related to their struc- ture. Enzymes: function as catalists. Transport: cells enveloped in lipid protein. Proteins span the membrane to carry objects in and out. Support - cytoskeleton. Signalling: hormones, membrane proteins, intracellular mes- sengers. Movement - contractile proteins, agella. Defense - antibodies are proteins. Proteins made out of amino acids. 20 di▯erent amino acids. String the amino acids together create polypeptide. PP folds and coils to a speci▯c *conformation*. Primary sequence of amino acids dictates how the protein will conform. Structure that protein adopts dictates the function of the pro- tein. Amino Acid Structure: four di▯erent functional groups attached to the alpha carbon. Amino + Carboxyl group. Amino gains electron = positive. Car- boxyl loses = negative. Creates ionized molecule = zwitterions (hybrid ion, has both positive and negative formal charges). Electricall neutral. Optical isomers of aminos: L and D. Only L isomers is used in making polypeptides. The side chain group (R group) gives the ▯ngerprint or di▯erentiating fea- ture of the acids. We can classify the R groups as polar and nonpolar. Polar side chains: charged bonds - create formal ...(slides 9 and 10). pKa-R (slide 11) shows the properties of R groups as the pH changes. Nonpolar bonds - hyrdophobic. Polar - hydrophylic, easily dissolved. In general, the nonpolar amino acids are hydrophobic and similarly the other way too. Two amino acids are linked with condensation as well (slide 13). New bond that is formed is called an amide bond. The new functional group is calld an amide functional group. The start of the peptide is called N-terminus or amino-terminus. The end is called the C- terminus or carboxyl terminus. In biological situation, the growth of a polypeptide grows from the C- terminus. The ribosomes. Interesting fact: chemistry says it is easier to create proteins from the N-terminus! If we change the order of the primary sequence we will change the function completely (sickle cell ane- mia). Glutamate-6 changed to Valine...Glutamate hydrophyllic { valine, very hydrophobic. Conformation locally changed, and exaggerated by all hemoglobin molecules sticking together: Hemoglobin gives up oxygen changes it to carbon dioxide. Hemoglobin begins to stick together. Tissues starve of oxygen. 3 Protein structure: 1. primary: amino acid seq. 2. Secondary - folding into elements of structure. Alpha helises, Beta Sheets. 3. Tertiary. Final overall folded states. Interaction between the sec- ondary structure to form a ▯nal shape. The R groups encode if the structure is going to be alpha helix, or beta sheets. But they do not hold the structure together. H-bonds keep them strong. Helix can adopt faces by the arrangement of R groups pointing in (or out...check!). Things like coiled coil - the zipper. Decorate the outside of a helix with polar/hydrophylic R groups... Beta strand can have two di▯erent orientations, antiparallel and perfectly aligned or parallel sheet somewhat disaligned. R groups point away in Beta strands too. Thus once again, we can have di▯erent faces, polar and nonpo- lar sides. Tertiary strucutre: stabilized by non-covalent bonds - ionic, electrostatic interactions, H-bonds. Side chains can van der Waals interactions. The strongest driving force is the hydrophobic interactions. Apolar groups try to get away, and polar tries to get to lots of water. The protein will then collapse upon itself. Disulphide bond is special. Cys residues happen to be near - sulphide covalent bond can withstand more hostile environments. The ER is an oxidizing environment and you know... 4 Lecture 5 4.1 Remarks: pKa - pH = pKa, equal concentration; pKa < pH, speicies on the right (non- ionized; protonated form). Notes to myself: Study pKa values! Chirality is the optical properties of the molecule. Peptide bond is also called an amide bond. Peptide bond and sulphide bond are the only covalent bonds that mostly occur PkA measure of acidity of a compound, relationship between the pka and pH is an indicator of how much of each species there is. Peptide bonds, even though they are single bonds, they are not able to be rotated. 4 September 27, 2012 Q: How fast does the proteins fold? Must happen quickly! ..but why does it happen so fast? Levinthal Paradox. We take the simplest possible model. Peptide bonds, even though they are single bonds, they are not able to be rotated. There are only limited number of rotations. The main idea is that the rotation of the bonds is not enough to completely fold a protein. Therefore, protein folding is not a random process, it occurs in a directed fashion. Protein stability. The bonds to hold the conformation are weak. It is thus easy to denature the protein. Many changes can denature the protein: pH, salt concentration, temprature. Urea and guanidine are common denaturing agent. In many proteins, denaturation is a bidirectional process. Structure Function Paradigm: \One sequence = One structure = one function" Some consequences: we lose the function of the proteins; the proteins still folds properly, or it functions property, but it will lose stability and we will lose the functions eventually; protein misfolds, protein brings the cell down with it { Alzheimers (plaque in brain). Quaternary Structure The single protein does not function on its own. The single protein chain is called a monomer, many called polymer. Hemoglobin is a tetramer, alpha-2- beta-2 structure (tetramer). Actin is a structural molecule. Actin ▯lament is formed by hundreds of monomer and exhibits higher-order protein structure. Protein Domain - sometimes part of the structures are independant fold- ing regions. Even if we take them out of the larger structure, it will still fold and do the same function as in the original larger structure. Ex: Zinc ▯nger domain. 5 Lecture - Genetics Part 2 Triplet codons code for certain amino acids. Methionine and tryptophan are the only ones where there is only one triplet which encodes for them. Deletion of DNA sequence is known as a frame shift which completely alters the end-protein. Often we might get a premature stop codon. In order to translate, there should be a mechanism (an adaptor molecule) to H-bond with the codons and covalently bond. Such molecule is known as a tRNA. Three regions: anticodon and two others. 5 Loading tRNA. 1. ATP attaches to amino acids. 2. ATP goes to AMP and P goe2 away. 3. ...(see slide) How many tRNAs are there? 40 (but we need 64 codons!?!) Wobble Hypothesis (Francis Crick): Possibility of only two of the three base pairs bind successfully. The other one wobbles and just holds on. Components of Ribosomes (eukaryotic) Svedberg units measures how fast sedimentation of a particle. Ribosomal Structure and Mechanism of Translation Small ribosomal unit decoding process, large ribosome: synthesiz
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