Cell Biology 201
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This 9 page Class Notes was uploaded by Christinee on Tuesday January 12, 2016. The Class Notes belongs to BIO 201 at University at Buffalo taught by LARA HUTSON in Spring 2016. Since its upload, it has received 140 views. For similar materials see Cell Biology in Biology at University at Buffalo.
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Date Created: 01/12/16
Lecture 2 – Cell Biology 02/07/2016 ▯ Bonds ▯ Forces that hold atoms together ▯ Important implications for biology ▯ ▯ Electron “shells” ▯ Shells = orbits ▯ The more electrons an atom has, the more shells they could potentially fill ▯ ▯ Octet rule ▯ Borrowing or sharing an electron through covalent bonds in order to satisfy octet rule ▯ ▯ EN ▯ Desire for electrons ▯ Closer it is to 8, greedy ▯ Closer you are to 1, the more you want to give up your electrons ▯ ▯ Hydrogen Bonds ▯ Not as strong as ionic bonds ▯ Forces between two dipoles ▯ ▯ Van Der Waals interactions ▯ Interactions between non polar molecules – no dipoles ▯ Individually weak; in combination very strong ▯ ▯ Strong Acids And Bases ▯ Acids – completely dissociates ▯ Bases – pulls H+ away completely ▯ ▯ Weak Acids & Bases ▯ Acids – some dissociates but not all ▯ Bases – takes some H+ from solution ▯ ▯ Functional Groups ▯ Combinations of covalent bonds that appear often ▯ May be acidic or basic ▯ ▯ Buffers ▯ Interferes with covalent bonds ▯ Weak acids & bases ▯ LeChatelier’s Principle ▯ ▯ Carbonate Buffer ▯ 3 step equilibrium ▯ multiple weak acids & bases ▯ ▯ Biological Macromolecules ▯ Carbon containing molecules ▯ Proteins – amino acids – carbon based ▯ ▯ RNA A – enzyme, which catalyze chemical reactions. End in Ase which breaks down molecules. ▯ ▯ ▯ Amino Acid Structure ▯ Central/Alpha carbon ▯ Simultaneously positive and negative charge because both acidic and basic functional group on it ▯ 3 dimensional geography ▯ 4 covalent bonds – tetrahedral – 109.5 degrees ▯ R1 is side chain ▯ ▯ Chirality ▯ If you have carbon bonded to 4 other atoms – possible of creating two different formula structures even though the chemical is exactly the same ▯ Isomers are two or more compounds that have the same chemical formula but different arrangement of atoms - butane ▯ If carbon is bound to 4 different atoms – can end up with 2 different isomers depending on the arrangements of the atoms ▯ It doesn’t work if two of the atoms are H+ - only works if all of the atoms are different ▯ Those two different isomers of carbon – are mirror images ▯ Dextro –Right. Levo- Left ▯ Amino acids are chiral ▯ ▯ Amino Acids ▯ All amino acids are Levo (left handed) in living organisms ▯ The arrangements around the central C give it left handed chirality ▯ Side chain for Alanine is CH3 – a methyl group ▯ Only find left handed amino acid, however, only exception is if the R group is Hydrogen – Glycine is the only one that’s not left handed ▯ If any of the two groups on C are the same, those can be mirror images of each other but they are super imposable – arrangements of those atoms are identical ▯ Glycine is the only AA that is not left handed. Same isomers. Aka not isomers same molecule therefore not chiral. ▯ ▯ AA are defined by their side chains (R groups) ▯ There are 20 different Amino Acids which are defined by their side chains ▯ There are different classes of R groups ▯ 1) Non Polar/Hydrophobic ▯ 2) Polar [uncharged or charged (+/- charged depending if acidic or basic)] ▯ 3) Special cases ▯ All Proteins are made up of 20 diff AA ▯ ▯ Non-polar (Hydrophobic) ▯ Contains all C’s and H’s – do not have to know the exceptions ▯ Exception is S and N ▯ Ala, Iso, Leu, Met, Phen, Tryp, Val ▯ ▯ Polar Uncharged Side Chains ▯ They are polar if any two atoms connected to each other that have differences in electronegativity – and therefore dipoles ▯ Contain –OH or both –NH2 and C=O ▯ Asp and Glut have an amino group NH2 which is not charged bc its connected to a C=O; the NH2 is not basic enough to steal a proton out of a solution ▯ ▯ Polar Charged (acidic or basic) ▯ NH2 or any other context will be protonated as NH3 ▯ Contain –NHx or –COOH ▯ Acidic have COOH (carboxylic acid) ending ▯ When there’s 2 its negatively charged. ▯ ▯ Special Cases ▯ Cys can form disulfide bonds – SH – very reactive; SH will combine with another SH to form a disulfide bond ▯ Gly – not left handed - non polar but can inhabit polar environments – not chiral – has H as side chain – in the middle can be happy anywhere ▯ Proline – extremely unusual AA - can form rings which restrict flexibility of backbone (“helix breaker”); side chain is not a side chain at all – it’s reactive and comes around and forms a covalent bond with the amino nitrogen on the backbone of the AA – rigid, not as flexible as the other amino acids ▯ ▯ Cys froms disulfide bonds in oxidizing environments (e.g. extracellular) ▯ Oxidation and reduction are two different states of compounds ▯ Ox. Loses electrons ▯ Red. Gains electrons ▯ OIL RIG ▯ Oxidizing environments in a living organism refer to outside of the cell – extracellular proteins are in oxidizing environments ▯ Oxidation of SH & Cys leads to formation of these disulfide bridges ▯ Proteins outside of the cell if they have sulhydride groups – they will be oxidized ▯ Covalent bonds ▯ Cytoplasm is a reducing environment – put protein from outside to inside of cell it’ll be reduced ▯ ▯ Amino Acid Polymerization. ▯ All proteins are made up of some combination of all 20 amino acids strung into long streams of polypeptides ▯ AA polymerization due to condensation reaction. ▯ When C bonds to N to form a string – we lose O and 2 H to form water – referred to as a peptide bond ▯ Peptide: is a very short AA polymer ▯ Dipeptide: two AA ▯ Build an entire protein by adding on to the CARBON not the nitrogen – create a new – tripeptide bond ▯ ▯ Generalized polypeptide structure ▯ Always grow onto C-terminus, always to the right ▯ Polypeptides grow from N->C ▯ Where’s the peptide bond & in which direction should it be growing ▯ Nitro, C with side chain, C double bonded to the Oxygen. In this pic its going Right to left. ▯ Nitrogen bonded to the previous Carbon double bonded to Oxygen forms the peptide bond ▯ C double bonded to O is the last of the 3 atoms ▯ Amino Acid residue – what’s left of AA once incorporated into polypeptide ▯ ▯ Levels of protein Structure ▯ Once you have polypeptide chain – close to achieving protein ▯ Proteins defined by AA sequence ▯ In order to achieve functionality – always need to acquire 3D characteristics in either secondary structure, tertiary structure, or BOTH ▯ Some proteins made up of multiple polypeptide chains – quaternary ▯ ▯ Primary Structure ▯ Sequence of amino acids (N to C) ▯ Primary structure – chemical structure – abbreviated as AA ▯ ▯ X-Ray Crystallography ▯ Linus Pauling – Robert Corey – first attempt to discover 3D structure of proteins ▯ Concentration of purified protein – crystallize it & shine an Xray through it with a piece of photographic film on the other side ▯ ▯ Secondary – alpha helices and beta sheets ▯ Structure resulting from H bonding between functional groups on polypeptide backbone ▯ Most common feature of 3D structure – in particular a-helices ▯ Alpha Helices: intramolecular H-bonds (between functional groups in the same molecule) ▯ they’re spirals/coils that develop spontaneously in almost all proteins, so common that can almost be considered the default structure ▯ lowest thermodynamic state for proteins – very favorable, very stable ▯ Beta Sheet: intermolecular H-bonds between different polypeptides OR intramolecular H-bonds between different segments of the same polypeptide ▯ also very common, very stable ▯ These structures can be adopted NO MATTER what kinds of side chains the protein has ▯ ▯ A-helix Structure ▯ Groups of Backbone ▯ H – C ▯ O = C ** ▯ H – N ** ▯ Alpha helices form by forming a spiral ▯ Carbonyl oxygen (C=O) (electro negative) bonds to amide hydrogen (N-H) for amino acid residues beyond ▯ ▯ Beta sheet Structure ▯ Also groups in backbone & the same groups ▯ Alpha helices are just a single polypeptide ▯ Beta sheets form either between two different polypeptides or between two different strands of the same polypeptide ▯ So this involves folding or different interactions of other polypeptides ▯ Because of the 3D tetrahedral dimension of C, everywhere along the backbone and the N (planar), only every other O and H can bond ▯ Anti-parallel (opposite direction) vs. parallel (same direction) ▯ Anti-parallel beta sheets are more stable, since parallel beta sheets are at an angle ▯ Beta sheets – not as two polypeptides – but rows of polypeptides ▯ Silk ▯ ▯ Tertiary Structure ▯ Complete 3D structure of a polypeptide (usually also involves R-group interactions) ▯ Lowest energy of default structures of polypeptides ▯ Complex 3D structure that includes secondary structure + shape changes induced by side chain interactions ▯ 4 different types of interactions that we see: ▯ covalent bonds (disulfide) – sometimes in oxidizing environments – strongest interaction ▯ ionic bonds – acidic and basic groups will become charged & opp. charged groups will attract – both can break up a-helices or beta sheets in some cases and prevent from forming if they’re strong enough ▯ hydrogen bonds – most important – polar groups ▯ hydrophobic side chains – interior of protein or embedded in lipid membrane ▯ van der waals ▯ ▯ Conformation: 3D structure of protein ▯ ▯ Quaternary Structure ▯ Pattern of assembly for multi subunit proteins – proteins that are not functional until they are combined with other folded polypeptides ▯ Ex: hemoglobin - 4 subunits: 2 alpha and 2 Beta + heme which binds to Iron ▯ Heteromultimers – has alpha and beta chains ▯ Homomultimers – multiple identical chains. ▯
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