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Molecular Cell Bio Textbook 3.0 - 3.5 Summary

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Kim Dej

Bio 2B03Molecular Cell Biology Textbook30IntroductionProteinspolymers of aa3D structure dependent on 1 Variation in lengths and aa sequences 2 differences in number of disulphide bridgesor attachment of small molecules or ions to their aa side chains Conformation and aa side chains determine functionFunctions1 Structural proteinsdetermine shape of cells Acts as rails to direct movement of molecules2 Enzymescatalyze metabolic reactions3 Membrane transportpermit the flow of ionsmolecules across cellular membrane4 Regulatoryact as communication signals Sensors and switches 5 Signaling Proteinshormones and cellsurface receptors transmit extracellular signals to cell interior6 Motor ProteinsMoves other proteins organelles cell and whole organisms Proteins can have 2 functions at the same time Cellsignaling receptorsboth and enzyme and regulatory protein By catalyzing chemical reactions they transmit a signal Proteinsbind to other macromolecules DNA and small ionsmoleculesBinding produces conformational change which alters activityfunctionEnzyme Catalysisappropriate folding of a protein will permit the catalysis of covalent bonds Third activity involves folding into a channel through which ions can flow Proteins part listpossible through human genome sequencing Can determine aa sequence Compare protein sequence of unknown function to that of knownscientists can make deductions 31Hierarchical Structure of Proteins Protein folds into 3D shape that stabilizes with noncovalent interactions between linear sequence of aa FUNCTION DERIVED FROM SHAPE SHAPE DETERMINED BY NONCOVALENT BONDS BETWEEN LINEAR SEQUENCES OF AA INTERACTIONS SPECIFIED IN THE AA SEQUENCE Primary StructureSimply the aa sequence Individual aa linked by peptide bonds Occasional disulphide bonds covalently linking side chains together Peptide bondN from aminoCOO from carboxyl Release of HO 2Amino acids added at Cterminusfarthest to the right Peptide chainless than 2050 aa residues 200500 polypeptide Secondary StructureStable spatial arrangements of segments of a polypeptide chain held together by Hbonds between backbone amide and carbonyl group Adopted spontaneously Local interactions stabilize periodically ordered structures Will form regardless of aa side chains present Alpha helix B pleated sheet B turnHighly flexible portions of polypeptide that dont formhave any fixed 3Dstructure but still have a welldefined stable shapeare called random coils 60 of polypeptidealpha helices or beta sheets the remaindercoils and turnsAlpha HelixCarbonyl Oxygen Hbonded to amide H 4 aa residues towards the C terminus Helps maintain directionality cause all carbonyl groups have same downward orientation Varies in length but Bio 2B03Molecular Cell Biology Textbook width is always the same Complete turn at 36 residues Side chains point outwards Straight rodlike cylinder Hydrophobic or Hydrophilic quality of each helix within a protein is dependent on the sidechainsto elaborate in water soluble proteins hydrophilic tend to be on the outer surfaces while hydrophobic buried inside helices Beta pleated sheetlaterally packed short 58 residue Beta strands Hydrogen bonding occurs between backbone atoms carbonyl oxygen in one strand with H from amino group in another in separate but adjacent strands These strands can be bonded in an antiparallel or parallel direction all depends on orientation of the peptide bond These sheets form independent of sidechains Distinct B strands maybe within same polypeptide or with longshort loops between B strands segments or on different polypeptide chains Sidechains stick out above and below the planeBturnsComposed of 4 residuesOn surface of protein forms sharp bendsreverses direction of polypeptide backbone towards interior of protein Stabilized by H bonds at end residues Short Glycine and Proline at aa2sharp U bend B turns help large proteins fold into a highly compact structureTight B turnfew well defined conformationLonger loopsmany diff conforms Tertiary StructureOverall conformation of a single polypeptide chain 3D arrangement of all single aa residues in a single polypeptide chain Stabilized mainly by hydrophobic interactions and H bonds bw polar side chains and peptide bonds Stabilizing forces still weak so conform not rigidly fixed undergoes minute fluctuations Disulphide bonds between side chains of cysteine residues covalently link regions of proteinsincreasing stability Globular proteinswater insoluble core hydrophobic inside and water soluble surface hydrophilic Teritary structure proteinsfibrouscollagen globular water soluble myoglobin and integral membrane embedded in phospolipid bilayer Depicting conformconveys diff types of info C backbone trace Ribbons Ball and Stick Solventaccesible surface pg69 Structural Motifs Are Regular Combos of 2ndary and 3rdary Structures Combos of 2ndary or 3rdary structuresmotifs Appear in segments of diff proteinsGlobular Motifresponsible for entire structure of protein May perform one specific task One primary aa sequence may be similar to another Common sequence motif yields common 3D structural motif 1 COILED COILfibrous and DNA regulation proteins used transcription factors Two or more amphiphatic alpha helices from different polypeptide chains wrap around each other Heptad 7 with hydrophobic residue repeats at postion 1 and 4 Usually leucine helps bind the hydrophobic chain thats why its called leucine zipper motif2 Helixloophelixtwo short helices connected by a loop Binding of Ca2 to oxygen atoms in loop residues depends on Ca conc in the cell Once bound conformation changes Used to bind protein to DNA and for gene activity regulation3 ZincFingerone alpha helix connected to 2 beta ANTIPARALLEL strands Held together by Zn atom interacting after Cys or His residues have been positioned precisely4 Bbarrel motifnot mentioned in the textbook 410 antiparallel strands connected by hairpin Each strand added to previous until the last strand is Hbonded to the first Structural and Functional DomainsModules of Tertiary structureSecondary motifs combine to form domains either structural or functional
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