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MCB 250 notes 1 and 2

by: Ibrahim Notetaker

MCB 250 notes 1 and 2 33831

Ibrahim Notetaker
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About this Document

These notes cover day 1 and day 2 of lecture. *Disclaimer: the format of the notes has changed when uploading, so some figures may appear disjointed or appear to be missing parts
MCB 250
Kirchner, NShankland, SSlauch, J
Class Notes
CentralDogma, bonds, chirality, pH




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This 5 page Class Notes was uploaded by Ibrahim Notetaker on Wednesday August 24, 2016. The Class Notes belongs to 33831 at University of Illinois at Urbana-Champaign taught by Kirchner, NShankland, SSlauch, J in Fall 2016. Since its upload, it has received 19 views.

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Date Created: 08/24/16
Ibrahim Hilaly MCB 250 notes August 22, 2016 -Cells obey laws of chemistry. -In vitro (molecular). -In vivo (genetic). -MCB is a fusion of both. -Know 20 Amino-Acids and 5 Nucleotides. -Things will change in MCB. -Not everything is known. -MCB is an experimental science. -How do we know what we know? -Everything is recent. -All organisms have the same biology. -Models like Escherichia coli, etc. Prokaryotes (no nucleus) – bacteria and archaea Eukaryotes (nucleus) Universal Tree of Life – derived from ribosomal subunits Bacteria Archaea Eukaryotes The Central Dogma Replication(DNA) Transcription(RNA) Translation(Proteins) -Many proteins are enzymes -Metabolism: Ibrahim Hilaly Catabolism – breakdown Anabolism – building up Eukaryotic Molecular Biology has CHNOPS (main elements with some metals) Strong and Weak Bonds Covalent Bonds -sharing electrons -strong bond Example: Peptide bond Properties: Fixed angels: rotation, Resonance (*using organic conventions) Ethane Ethylene No rotation (flat) Cis Cl Cl Trans Cl Cl Aromatic Rings Benzene Example: Nucleic Acid bases “Conjugated” Bonds MCB 250 notes August 24, 2016 Absorbance of Light -Electrons are in “quantized” orbits -Absorption spectrum provides information about molecular structure -DNA and RNA absorb light at 260 nm. -Tryptophan at 280 nm (since it has aromatic rings) Stereoisomerism Chirality Ibrahim Hilaly -not superimposable -mirror images -19 out of 20 Amino-Acids exist in L or D stereoisomers. -Life only uses L-amino-acids. -All proteins are made from enzymes “Lock-and-key” High Energy Bonds -release energy when hydrolyzed Example: ATP hydrolysis Weak Bonds Hydrogen Bonds 2- -account for properties of water, Including lattice structure. 1+ 1+ Despite this structure, water flows because H-bonds break and reform rapidly. Biology happens in water -Water is polar -Protic solvent -H-donor and H-acceptor H-bonds are affected by orientation -covalently bound to Oxygen and Nitrogen -Delta G is 3-7 kcal/mole Ionic Bonds -Electrostatic interactions -5 kcal/mole -not directional Van der Waals Forces -All electron clouds attract each other extremely weakly. 6 -1/r Example: Two surfaces coming together. -Changes conformation slightly. Stacking Interaction of Aromatic Rings -Van der Waals -Overlapping pi-bonds Example: DNA “Hydrophobic Interactions” -misnomer -Phobic – hate -Philic – love, hydrophilic molecules have dipole moments Ibrahim Hilaly Example: Fatty Acids Amphipathic -part hydrophilic and hydrophobic Example: Phosphatidylcholine -Hydrophobic interactions drive formation of lipid bilayers -Stabilize folded structure of proteins. -Sum of all weak forces allow interaction of biological molecules. Biological Molecules Are Dynamic -If bonds were too strong, then enzyme complexes could not come apart. Many molecules are charged -5 amino acids have charged side chains. + pH – measure of proton (H ) concentration Keq =[H ][OH ] = 10 -14 + pH = log [H ] pH Scale 1 acidicbasic 14 -log scale pH 10 spinach pH 4 bottled water Weak Acids and Bases in Biology Carboxylic acid (COOH) – Weak Acid H + H + = - + H + Amino groups – Weak Base H H N+ H N + H + H H Henderson-Hasselback pH = pKa + log [A-]/[HA] [HA] = [A-], log 1 = 0 pKa = 50% protonated COOH = pKa of 4 Amino = pKa of 10 Ibrahim Hilaly


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