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test 1 review

by: Mary-elizabeth Notetaker

test 1 review Bio 329

Mary-elizabeth Notetaker
U of L

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materials to review for test 1
Cellular Molecular Biology
Paul Himes
Study Guide
Bio, cellandmolecularbio, bio329
50 ?




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This 9 page Study Guide was uploaded by Mary-elizabeth Notetaker on Sunday September 11, 2016. The Study Guide belongs to Bio 329 at University of Louisville taught by Paul Himes in Fall 2016. Since its upload, it has received 58 views. For similar materials see Cellular Molecular Biology in Biology at University of Louisville.


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Date Created: 09/11/16
◦Positive control- what should work ◦Neg control- what should not wor Cell theory- schleiden & Schwann- ◦all organisms made of one or more cells ◦Cell is structural unit of life ◦Cells arise from pre existing cells by division  Cell props ◦Cells are Highly complex and organized ◦genetic program and means to produce ◦Capable of producing more of self ◦Acquire and use energy ◦Carry out multiple chemical rxs ◦Engage in mechanical activities ◦Robust- can handle change ◦Evolve  Prokaryotes- no organelles, bac & archae, unicellular, 2.7 byo fossils  Eukaryotes- protists, animals, plants, fungi, unicellular and multicellular • Commonalities:  Diffs: ◦similar plasma membrane ◦complexity: ◦Genetic code is universal  proks more simple ◦Similar mechs to turn genes into  Genetic material  proks: nucleotide region action transcription/translation  smallest euk genome ~= to biggest prok ◦Shared metabolic pathways genome glycolysis  Biggest euks(trees/amoeba) >1000+X  Euks: membrane bound nucleus  TCA cycle  Photosynth (similar) ◦Cytoplasm ‣ Similar ways to make energy(ATP)  euks- membrance bound organelles  Proks- none ◦Reproduction  euks: mitosis  Proks: binary fission... Exchange DNA w/out reproduction ◦Locomotion  euks: cytoplasmic movement, cilia, flagella  Proks: flagella(diff)... Slime extrusion, pulling with pilli  2 classes, 3 domains ◦monera- fewer shapes than species(sphere, rod, spiral)  3 distinct clusters ◦protists, fungi, plantar, animalia all close ◦2 groups of proks Domains  Archae -closer to euk than bac (extremeophiles)  mosaic genomes -horizontal gene transfer(HGT)   Euks Endosymbiosis theory- euks organelles used to be free-living proks  Unicellular- most euk cells, most complex cells • Multicellular ◦differentiation- need diff cells to do diff things  Stem cells- undiff'd cells... Self renew ◦HSC- replace abated bone marrow ◦Neuro stem cells- treat neurological disorders ◦Embryonic stem cells(ES)- greater potential for differentiation(pluripotent)  Cell replacement therapy- iPS(induced pluripotent stem cells) Synthetic bio- create living cell in lab ◦Make existing orgs into something diff, Give them traits to make new things ◦Species reassignment therapy- replaced genome of bac w genome from closely related species Viruses-intraellular obligate parasites ◦virion- virus particle outside host cell ◦Viral stx: Surface proteins bind specific host surface proteins(det's specificity) creates provirus by integrating own DNA into host DNA Bacteriophage- kill bacteria ◦Lytic infection- host makes copies of virus and host loses ◦Integration/lysogenic infection Adenovirus- used in genetic engineering of euks ◦Viriods- small pathogen, makes RNA mol.. No proteins ◦Prions  Chemistry of carbon Special valence e-; arrangement(can make 4 covalent bonds ) Functional groups: Methyl- ch3 Hydroxyl- oh Carboxyl- cooh Phosphate- po(oh)2 Carbonyl- co Ester- alcohol on acid: ROH Ether- ROR Amide- carboxyl w amine: RCONR2 Sulfhydryl- SH groups together- forms disulfide bond: RSH Amino group behaves as weak base in organic mols: RNH2 Bonds: Ester bond- btwn carboxylic acid and alcohol Amide bonds- btwn " " & amine Classes of bio mols in cell: Macromols: large stx and fx, 4 major categories: carbs(CHO), proteins, nucleic acids, lipids All but lipids build polymers: Building blocks of macromols: Amino acids, nucleotides, sugars, fatty acids Met intermediates- formed in met pathways CHOs: simple sugars + polysaccs(E storage mols) 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 sugarsoligosav Hydroxyl groups will dehydate(condensation rx) to form ether Dissacc: 2 sugars linked together Fast E source Oligosaccs: short chains(5-15) bound to cells, surface proteins, lipids Cell recog, molecular targeting Polysacc: polymers of 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(seen by Hooke) Chitin: invert exoskeleton of NAG Glycosaminoglycans(GAGs): repeats of 2 diff sugars In Ex cellular space Signaling, cushion, lubricate Proteins- polymers of AAs Stx(cytoskeleton), mechanical(dynein), enzymatic(bio catalysts) Composed of: amine(NH2), carboxyl(COOH), R group, H 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/intramol intxs 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-translational mods- 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)- conformation of adj AAs Alpha helix (side chains H bond w each other) Beta sheets- zig zag line of proteins, H boning btwn lines Tertiary stx(3)- conformation of 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 chromatography or NMR Quarternary stx(4)- proteins w multiple subunits..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 homologies to figure out protein fx Synthetic bio- transfer domain to new protein w new fx Dynamic changes w proteins Conformational changes Non random motions triggered by binding specific mol Role for disordered regions: get ordered when bind substrate Activation makes active site available Deactivation hides active site Protein folding Unfolding from denaturation Removal of denaturing agents may allow protein to reassemble and be fx again, if so 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 nonselective intx during protein folding…Only intx w self and desired peptides Aid movement of 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 2 rings of 7 subunits(hollow centers) Assoc w GroES(7 subunits too) Originally thought to be same gene, but smaller Attachment induces conformational change 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 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)- membrane bound protein brain neurons cleaved by secretase enzymes Ab42 peptide produced and misfolds then self assoc's into amyloid plaques More precurors--> more misfolds Protein-protein intxs: Distinct proteins physically assoc --> multiprotein complex Ezymes of same pathway are closer to each other Noncovalent intxs 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) Homologs- members of 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 Isoforms- diff forms of same protein that are tissue/stage specific Nucleic acids- polymers of nucleotides that store and transmit genetic info 3 parts of DNA nucleotide: phosphate group(5'), pentose(3'), nitrogenous base(purine or pyridine) Purines: A & G Pyrimidines: T & C Stx: Sequence read 5' to 3' Dbl helix(major & minor grooves) Shape connected by base pairing (4bp) Stabilizes A-T: 2 H bonds G-C: 3 H bonds (stronger) Nucleic acids and proteins together In chromosomes in dna, in ribosomes in rna rRNA- no info for translation Allows proteins to attach Catalytic activity Conserved among all life forms amphipathic-has both polar and nonpolar end Amphoteric-act as buffer,can be acid or base -nucleic acid polymers ATP- Short term storage & E transfer (10s) Glycogen/starch- medium term storage Fats/triglycerides- long term storage High E bonds- like charges repel..phosphates(-) don’t like to be by each other E given off when stress relieved..ATP---> ADP + P ….releases E Bio membranes  Bio mols o Lipids- diverse group of NP mols  Triacylglycerol(triglycerides)  Glycerol-->ester bond-->3fatty acids(FAs)  FAs- unbranched hydrocarbons w carboxy, group… amphipathic  Saturated- all C have 2 H's, no dbl bonds, packed tight..Solid at room temp(Fats & waxes)  Unsat- one or more C=C, kink, not tight…Liquid at room temp(Oils)  Trans fats-made from adding H back to unsat fats and cis dbl bonds turn to trans dbl bonds  Membrane lipids:  Phosphoglycerides- phosphate group and something else(polar head group) on glycerol w FA  Diglyceride- 2 fatty acid on glycerol  Functional head group- choline, serine, ethanolamine, inositol  Sphingolipids- ceramines  Formed by attachment of sphingosine to FAs  Includes glycolipids- imp for neural connections  Cholesterol- smaller and less amphipathic-4 C rings  Precursor for steroid hormones (in animals)  Change fluidity of membrane- shape blocks flow of lipid tails  Small OH head out, rest of mol in membrane Stx/fx of membrane lipids  Plasma membrane- outer cell boundary o Various lipids: Macromol (not formed by polymerization), phospholipids, sph o Characteristic trilaminar appearance(3 layers).. Shared by all cell types  Stain binds polar head groups, Phobic tails unstained  Membrane fxs o Compartmentalization- sheets enclosing intracellular compartments o Scaffold for biochem activities- organizes enzymes for effective intx  Keep things together & Couple rxs o Selectively permeable barrier- allow regulated exchange o Transport solutes- move subs btwn compartments o Respond to external signals- signal transduction o Intracellular rx- mediate recog & intx btwn adj cells o E transduction: chem E->ATP  Nature of membrane o Like dissolves like: Membrane dissolving power like that of oil o Amphipathic o Lipid bilayer… 2:1 ration lipid to cell SA  Leaflet oriented heads out, tails in…lowest E state  Influences membrane protein actvity, phys state, solubility of certain mols  Formation of continuous sheet--> allows splitting Fluid mosaic model  Nonuniform- lipid rafts and other groupings  Lipids and proteins bound w non-covalent bonds- role for NP side chains  Membs have carbs  Protein/lipid ratios vary among membrane types-depends on fx  Membs of thermophyllic archae may be monoloayers/have ether linkages o Membrane lipid comp of specific membranes  Composition= fx  Allow membs to: fuse, make networks, separate charge  Lipid bilayers assemble in sol… liposome  Vehicle for transport of things to specific body parts  Antibody targets liposome to specific cell type  Then memb fuses w cell memb & delivers:  Aqueous drug needed inside cell  Lipid sol drugs  Small mols  Other things you want targeted not destroyed/metabolized  Asymm of membrane lipids  Inner/outer memb-> diff compositions  Diff intxs & diff physio-chem props  Memb lipids move easy in leaflet but rarely flip flop bc act as indep monolayers  PC(outside): helps in reception of signals  PE(outside): imp for curvature  PS(inside): intx w protein…. Flips to Outside to mark old cells  Membrane carbs: 2-10% membrane mass… 90% glycoproteins…rest glycolipids o All on excellular surface- away from cytoplasm or outside cell o Glycoporteins- short branched oligosaccs(10-15 sugars..same or diff)  Intxs w other cells and stxs outside cell o Glycolipids- monosaccs to short clusters, Cell to cell recog sites  Ex) Blood-group antigens  Membrane proteins- attach asymm to bilayer….. Give membrane sidedness-lipid variation o 3 classes  Integral membrane proteins  25-30% proteins  Roles: receptors, channels, energetic  Amphipathic  Phobic domains anchor them to bilayer… need 20 NP AA to cross membrane  Phillic regions form fx domains outside- van der waals intx w FA tails  Peripheral " "- noncovalently attached  Soluble, Both leaflets  More known about internal ones..inner membrane skeleton  GPI-anchored proteins- covalently attached to membrane, Lipid anchored  Distinguished by: lipid anchor type & orientation  Glycophosphatidylinositol- outer leaflet… include receptors PrP^c  No sugars on lipids on inside of cell  Condensation rx can happen btwn charged FA and mol  Inner leaftlet proteins- anchored to memb lipids by long hydroC chains  Prenylation  RBC: Hemolysis- membrane ghosts(pop in low salt sol) Memb proteins purified, characterized--> SDS-PAGE electrophoresis  o Denature and separate by size, smallest=furthest o Proteins show as bands, intensity matters o Peripheral proteins(P's) separate from memb easiest  2 most abundant Ps: both glycoproteins o Band 3- 2 homodimers  Exchange Cl- & HCO3- across memb  Transport CO2 from body  Buffers blood  More than 12 transmembrane domains o Glycophorin A- dimer..16 oligo chains  Neg charge-->prevent RBC clustering  Docking point for malaria paarasite(plasmodium)  Peripheral Ps- under membrane o Spectrin- huge (100Nm)  Attached to membrane by ankyrin w noncovalent bonds  Memb lipids & fluididty o States:  Liquid crystal- most common, Keep orientation but FA tails rotate  Frozen gel- little/no movement o Depends on: Temp, lipid composition & saturation, and cholesterol presence(prevents close packing, makes memb less permeable)  Unsat fat= lower transition temp… pack looser o Fluidity- from P's in memb, growth & assembly  Most orgs T changes w external T…need to keep fluid o Remodeling lipid bilayer  Denature single bonds in acyl chains- desaturases  Shuffling FA btwn phospholipid mols- phospholipidases or acytransferases  Changing phospholipids made  Lipid rafts- “float” thru memb o Cholesterol/sphingolipids--> pack close--> highly ordered microdomains o Favorable envir for cell surface receptors & GPI anchored Ps o Proteins that work together concentrate here o Integral ps organize inner leaflet  Diffusion of memb ps after cell fusion o Ps/lipids diffuse freely w/in memb  2 sec to cycle around bac cell for lipids, Days to flip memb  Cell fusion: virus/polyethylene glycol  P tracked/labeled by FRAP or SPT o P usually random movement but can be directed or immobile o Limited intxs w ps, cytosol, extracellular mats o Dragged ps w/in memb- some have barriers to lateral diffusion  Remove intracellular/extracellular domain to ID restriction  Ex) intra- travel- memb skeleton- peripheral ps Ex) Extra- rate of travel  Mobility restrictions: Ps & lipids o Limited to 1 leaflet o Confined for brief periods to certain areas- moved to another and stuck Integral memb ps attached to membs act as fences   Disrupt attachment & lipids diffuse freely  Cells of organized tissues--> unequal P distribution o Epithelia- p of apical memb distinct from lateral & basal  Larger than lipid rafts  Substance movement across memb o Selectively permeable o Net flux: diff btwn influx and efflux o Passive or active transport  Energetics of movement of solutes o Diff spontaneous movement of materials from high concentration to low o Uncharged mols- move down gradient and give off E  Higher gradient=more E change= more use  Powered by inc in entropy--> equilibrium  More outside than in, goes in (& reverse) o Electrolyte movement- electrochemical gradient  Reason for antiporters o Lipid permeability  Partition coeff- sol in H2O of NP solvent? Moves easier  Size  Polar: big polar(slow), charged(don’t move), gas(straight thru)  Diffusion of water thru memb- osmosis  Water moves to eq, not solute  Hypotonic- more ions out of cell than in, water comes in, cell swells  Hypertonic- " " in cell than out, water leaves, cell shrivels  Isotonic-same  …intestines often change osmotic conds o Animals are isotonic o Plants have turgor… in hypo  If hyper, plasmolysis- cell shrivels & memb pulls from cell wall


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