week 2 390
U of L
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This 4 page Class Notes was uploaded by Mary-elizabeth Notetaker on Thursday September 1, 2016. The Class Notes belongs to Bio 329 at University of Louisville taught by Paul Himes in Fall 2016. Since its upload, it has received 4 views. For similar materials see Cellular Molecular Biology in Biology at University of Louisville.
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Date Created: 09/01/16
Week 2 Monday, August 29, 2016 12:03 AM Functional groups: Ester- alcohol on acid Ether- alcohol on carbon Amide- carboxyl w amine Sulfhydryl- SH groups together- forms disulfide bond Amino group behaves as weak base in organic mols Classes of bio mols in cell: Macromols:large stx and fx Short half life(bulk of cells dry weight) 4 major categories: carbs(CHO), proteins, nucleic acids, lipids All but lipids build polymers: Building blocks of macromols: Amino acids, nucleotides, sugars, fatty acids Cycle in and out of macromols Met intermediates- formed in met pathways Mols of misc fx- vitamins hormones, atp, etc CHOs: simple sugars + polysaccs(E storage mols) Formula: some multiple of CH2O n: triose, tetrose, pentose, hexose, heptose, etc Ketose: carbonly group on internal C Aldose: carbonyl on terminal C Sugars can be linear but usually rings C #1 at nearest C=O Linking sugars: Glycosidic bonds: -C-O-C- links btwn sugars Hydroxyl groups will dehydate(condensationrx) to form ether Dissacc: 2 sugars linked together Fast E source Oligosaccs: short chains(5-15) bound to cells, surface proteins, lipids Cell recog, moleculartargeting Polysacc: polymersof many sugars(many or diff) joined by glycosidic bonds Glycogen: animal product, branched glucose polymers Liver uses to regulate blood Gives 30 mins E in muscles Starch: plant product, glucose polymer Amylopectin-branched, polar Amylose-unbranched ..both made of glucose, alpha linkage Stx polysac: stable and not used for E Cellulose: unbranched, beta 1,4 linkage Most abundant organic compound(seenby Hooke) Chitin: invert exoskeletonof NAG Glycosaminoglycans(GAGs): repeats of 2 diff sugars In Ex cellular space Signaling, cushion, lubricate Proteins- polymersof AAs Stx(cytoskeleton),mechanical(dynein),enzymatic(bio catalysts) Composedof: amine(NH2), carboxyl(COOH),R group, H Peptide bonds(C=O to N) N terminus- free amino group C terminus- free carboxyl group Peptide bonds(C=O to N) N terminus- free amino group C terminus- free carboxyl group Sequences read from N-->C R group- attached to alpha C… affects inter/intramolintxs 3 groups: Polar charged- carboxyl on end(- charge) or amine group(+ charge) at physiological pH(3/4), acids lose H+ and bases gain Polar uncharged- alcohol on end, CONH2 attached on end, COCH3 attached on end Nonpolar-C groups on end, S w C's on ends, larger R groups w/C's Charged outer regions- good interactive surfaces Hydrophobic core: stability and shape Ionic bonds inside bc no water Salt bridges In transmembrane proteins- hydrophobic so NP AA's on outside w tails Post-translationalmods- change what AAs do Unique groups: gly, cys, pro Gly- H as R group..Flexy, fits in, non-chiral, phillic/phobic Cys- polar uncharged plus..makes C-S-S-C bonds Links parts of one protein & diff proteins Pro- NP, disrupts secondary stx R group rxs w amino group so it bends and changes protein shape Stx: Primary stx(1)- seq from N-->C of AA Critical to protein fx Secondary stx(2)- conformationof adj AAs Alpha helix (side chains H bond w each other) Beta sheets- zig zag line of proteins, H boning btwn lines "Local shape" Tertiary stx(3)- conformationof entire polypep chain Fibrous- stx Globular- enzymatic Often disordered regions Noncovalent bonds… has disulfide bonds- hold together strongly …disordered regions Outsides are np, insides charged/uncharged polar Seen by x-ray chromatographyor NMR Quarternary stx(4)- proteins w multiple subunits Homodimer/heterodimer How subunits intx Protein domains Domains: regions of 2 stx that intx w each other Often 2+ distinct stx regions Specific fx Bioinformatics-ID domain homologiesto figure out protein fx Synthetic bio- transfer domain to new protein w new fx Dynamic changes w proteins Conformationalchanges Non random motionstriggered by binding specific mol Role for disordered regions: get ordered when bind substrate Activation makes active site available Deactivationhides active site Protein folding Unfolding from denaturation Removalof denaturing agents may allow protein to reassemble and be fx again Tells: 1 stx has enough info for proper 3 stx Proteins tend to go to state of lowest free energy (2nd law of thermos) Molecular chaperones- prevent nonselectiveintx during protein folding Tells: 1 stx has enough info for proper 3 stx Proteins tend to go to state of lowest free energy (2nd law of thermos) Molecular chaperones- prevent nonselectiveintx during protein folding Only intx w self and desired peptides Aid movementof newly syth'd proteins across membranes (ex: into organelles) Linear req's smaller holes than globular HSP 70 family- bind emerging proteins Prevent inappropriate intxs Help heat denatured proteins slowly regain native shape Prevent heat denaturation of others Chaperonins- bigger GroEL essential for proper folding/assembly in E coli Self and phage proteins Similar proteins involvedin folding of large proteins in other orgs 2 rings of 7 subunits(hollow centers) Assoc w GroES(7 subunits too) Originally thought to be same gene, but smaller Attachment induces conformationalchange in GroEL protein Hydrophobic flip outside so core is hydrophillic and larger Changes how peptide being folded fits inside Two active sites per protein, used by 10% ecoli Certain residues imp for proper folding Specificity Chaperons don’t convey folding info, its in 1 seq Misfolding consequences: CJD from misfolded brain proteins PrP scrapie instead of PrP cellular.. Causes cellular correct version to unfold then misfold so it aggregates and kills cells Mad cow disease, Alzheimer's, downsyndrome APP(alzheimers)-membranebound protein brain beurons cleaved by secretase enzymes Ab42 peptide pproduced and misfolds then self assoc's into amyloid plaques More precurors--> more misfolds Protein-proteinintx Distinct proteins physically assoc --> multiproteincomplex Ezymes of same pathway are closer to each other Metabolic ints don’t get lost Noncovalentintxs Orgs adapt and evolve to thrive in envir Mutations may improve chance of survival of org in specific envir Genes can be mutated(not proteins) Membersof family from same commonancestor Homologs-membersof same family Paralog- 2 copies of same gene, one evolves to have dif fx Ortholog- same fxs in diff orgs 1 seq qill differ more than 2 and 3 Many ways to get to same endpoint Not all residues imp for shape/activity Isoforms-diff forms of same protein that are tissue/stagespecific Nucleic acids- polymersof nucleotides that store and transmit genetic info DNA- genetic info in orgs and some viruses 3 parts of nucleotide: phosphate group(5'), pentose(3'),nitrogenous base(purine or pyridine) Purines: A & G Pyridimines: T & C Stx: 1- Sequence read 5' to 3' 2- Dbl helix(major & minor grooves) Shape connected by base pairing (4bp) Stabilizes A-T: 2 H bonds A-T: 2 H bonds G-C: 3 H bonds 3- More kinds in rna 4- Nucleic acids and proteins together In chromosomesin dna, in ribosomesin rna rRNA- no info for translation Allows proteins to attach Catalytic activity Conserved among all life forms
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