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BIOC12Fall2012 Lecture Week 1 Notes

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University of Toronto Scarborough
Biological Sciences
Rongmin Zhao

BIOC12Fall2012 Lecture Week 1 Notes: Introduction (Chapter 1-3) Introduction to Biochemistry (Chapters 1 and 2) o 4 major groups of biomolecules, referred to as macromolecules  nucleic acids, proteins, carbohydrates and lipids o studies mechanism of functional molecules o metabolism and bioenergetics (the substance and energy flow) o the flow of genetic information o regulation of all cellular processes Proteins o building blocks: 20 amino acids o polypeptides = chains of condensed amino acids o will study structures, folding and enzymatic functions o analysis of proteins Lipids o group of molecules sharing the property of largely hydrophobic and only sparingly soluble in water o glycerolphospholipid, sphingolipids, steroids, and waxes o glycerolphospholipids are the major components of membranes Thermodynamics (Chapter 3) o first law of thermodynamics: Energy is conserved in an isolated system o enthalpy , H=E+PV = U+PV  E= energy, P= pressure and V=volume o spontaneous process cannot be determined by only evaluation of enthalpy change o the second law of thermodynamics : Systems tend toward disorder and randomness o entropy represents the degree of disorder and randomness in the system  amount of E in a system that is unavailable to do work o entropy tends to increase for an isolated system  entropy can decrease if there is exchange of energy between the system and the environment o if a reaction is reversible, then no change in entropy occurs  entropy of the system increases only if the reaction is irreversible o the life at the organismal level is a system o third law of thermodynamics: entropy of a substance is 0 if the temperature is at absolute temperature of 0 (-273.15 degrees C)  at this temperature there is no movement of molecules (so disorder cannot change) What can thermodynamic parameters tell s about biochemical events? Determination of spontaneous process o Gibb’s free energy  G = H – TS o H= enthalpy, T = temperature and S = entropy o For biological systems, the temperature is constant so: o o a spontaneous process can only occur when < 0 o this means that 1 o ATP is an important energy carrier molecule o ADP and ATP are formed by addition of phosphate groups via phosphoric anhydride linkages in a dehydration synthesis o Hydrolysis of ATP results in ADP  the pyrophosphate linkages are high in energy, so breaking them through hydrolysis will allow that energy to dissipate, therefore increasing entropy and making this whole reaction favourable o ATP + H2O  ADP + Pi 30.5kj/mol o The 3 phosphates are termed specifically as α β γ depending on how far they are from the ribose group (from the C-O)  the first attached phosphate would be the alpha phosphate o ATP is not an energy storage molecue  its cellular concentrations are very low 5mM  this makes sense because its hydrolysis into ADP occurs spontaneously, therefore a lot of the ATP probably gets converted into ADP o ATP/ADP pair serve as an intermediate energy-shuttle molecule as they can receive P from higher E biomolecules, and can also give energy to lower E biomolecules o In general, high-energy biomolecules have which means that their hydrolysis is favoured (exergonic) o Reactions and processes with unfavourable G can be made favourable by coupling with favourable processes such as the hydrolysis of ATP  hence why ATP acts as an intermediary of energy, rather than an Energy storage molecule Bond energies o In general single bonds have less energy than double bonds < triple bonds o o non- covalent bonds are usually called chemical forces between molecules Water: the medium of life (Chapter 2) o a water molecules is a large dipole 2 o the six outer orbial electrons of O atom are distributed in the 4 sp hybrid orbitals o the 2 hydrogen atoms are in the two corners of the orbital tetrahedron o the angle between the two O-H bonds is 104.3° instead of 109.5 in the perfect tetrahedron  because around the O there is an electron dense cloud, pushing the bonds down more than in a perfect tetrahedron o Properties of Water o one water molecule can form up to 4 hydrogen bonds o hydrogen bond strength = -20kj/mol o in ice, water molecules are using their maximum capacity to form H bonds (so there is a large space between molecules, which is why ice is less dense than liquid water) o the physical state of liquid water is very complicated  liquid water does not use its maximum H-bond capacity Comparison of water and ice o ice has 4 H bonds / water molecule o water has 2.3 H bonds / water molecule o H bond lifetime in ice is of 10 microseconds o H bond lifetime in water is about 10 picoseconds )10 o as temperature decreases, molecules have less kinetic energy which means that they move around less, and therefore can form more H-bonds than at higher temperature Interaction between water and solutes o Hydrophilic: salt and polar molecules are easily dissolved in water o When NaCl dissolves in water, water shells are formed around the ions  the water molecules form H-bonds with the ions of the substance dissolving o Dissolving of salt is a spontaneous process, so it releases energy Hydrophobic interactions/Hydrophobic effects o Hydrophobic interactions: non-polar substances tend to aggregate in water and makes a shape w
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