UNIT 2 EXAM REVIEW1) The Central Dogmaa) Eukaryotes vs Prokaryotesi) Chromosome highly packed into chromatinii) DNA is nucleus, protein synthesis machinery in cytosoliii) Eukaryotic genes have intronsb) RNA synthesized 5’-3’(DNA is read 3’-5’) by RNA polymerasec) RNA Transcriptiond) Pre mRNA processingi) RNA splicing: removes introns(1) Carried out by spliceosome(2) Made up of sNRNP’s + multiple proteins(3) Directed by sequences found at intron/extron boundariesii) 3’ end receives a poly-A taile) tRNAf) Translation Process2) Control of Gene Expressiona) `Common DNA-binding motifsi) Helix – turn – helix: two alpha helixes connected by a short unstructured stretch(1) Recognition helix: c-terminal end that makes sequence-specific contacts in the major groove of DNAii) Homeodomain: special case of helix-turn-helix; larger structure that includes other highly conserved structuresiii) Zinc fingers: one or more zinc ions is coordinated by amino acid side groups; often found in tandem cluster within a DNA-binding protein(1) 2 cysteines and 2 histidines to coordinate zinc between an alpha helix and a 2-strand antiparallel beta sheet(2) 2 zinc ions using 4 cysteines; one zinc ion stabilized a recognition helix and one stabilized a loop involved in dimerizationiv) Leucine zipper(1) Helix from one subunit binds to the corresponding helix in the second subunit in acoiled-coil structure(2) Serves both as the dimerization region and the DNA-binding regionv) Helix-loop-helix(1) Short alpha helix is connected to a longer alpha helix by a flexible loopb) Regulation of RNA transcriptioni) Promoter: region where RNA polymerase and the general transcription factors assembleii) Enhancer: independent region outside the promoter; cannot drive transcription on its own; can work with promoter from a different genec) Transcription Factors:i) Combinatorial control of multiple gene regulatory proteins control the rate of transcriptiond) Regulate gene expression viai) Unpacking chromatinii) Control recruitment of RNA pol and/or the general transcription factors to the promoteriii) Regulate the switch from intiation to elongationiv) Help recruit the histone-modifying enzymes to change the local chromatin structurev) Bend DNA to allow long-distance interactions between gene regulatory regionse) Post-trancriptional Regulationi) Alternative splicing: gene with just a few exons can produce many different mRNA’sii) Regulated nuclear export: allows RNA molecules containing some introns to be exported from the nucleus iii) Cystolic localization: place specific mRNA’s at specific locations in the cellsf) Non-coding RNA’si) RNA-induced silencing complex: after processing, a short double-stranded RNa is generated and associated with a set of proteins; one strand of RNA is degraded and the other makes base-pairing contracts with an mRNA targetii) siRNA’s: mediate process of RNA interferencesiii) dsRNA: base-pairing between complementary regions of separate RNA strandsg) Regulation of Protein Translationi) Information in the 5’ to 3’ untranslated regions can regulate translation efficiency as well as mRNA stabilityii) Riboswitch: uses binding of an ion or small molecule to switch between translation “on” and “off” statesiii) Repressors binding to 3’ UTR can prevent communication between 5’ and 3’ ends of mRNAiv) Phosphorylation of initiation factor eIF2 can inhibit global protein synthesisv) Context surrounding AUG can allow regulation by “upstream open reading frames”vi) Internal ribosome entry site: allows ribosome to skip the first AUG by binding to an internal site; allows two different protein sequences to be derived from a single mRNAh) Regulation of Protein Stabilityi) Ubiquitin/proteasome system allows for regulated destruction of proteinsii) “N-end rule” Identity of N-terminal amino acid defines intrinsic stabilityi) Epigentic Regulationi) Epigenetic inheritance: any heritable difference that does not rely on changes in the DNA nucleotide sequenceii) Mechanisms include(1) Stable expression of a regulatory protein via a positive-feedback loop(2) Covelent modification to histones, changing chromatin state(3) Methylation of DNA on cytosine residues(4) Stable changes in protein aggregation state3) Membrane Structure and Functionsa) Membrane Functionsi) Compartmentalizationii) Selectively Permeable Barrieriii) Scaffold for Biochemical Activitiesiv) Solute Transportv) Sending/Receiving Chemical Signalsvi) Energy Transductionb) Discovery of the Lipid Bilayeri) Langmuir Troughii) Freeze Fracture Electron Microscopyiii) Fluid Mosaic Modelc) Phosphoglyceridesi) Plasma membrane lipid distributions are asymmetrical; important for protein binding and cell signalingii) Typesiii) Sphingolipidsiv) Cholesterol(1) Highly abundant is eukaryotes, abset from prokaryotes(2) Provides rigidity(3) Modulates permeabilityd) Membrane Proteinsi) Integral Membrane Proteins: hydrophobic section of the protein is embedded in the hydrophobic core of the lipid bilayerii) Transmembrane protein: extend all the war through the lipid bilayeriii) Hydropathy plots: used to search for 20 amino acid stretches of hydrophobic amino acids in the primary sequence of a proteiniv) Serve as channels for ions/polar molecules are composed of beta sheets arranged into “barrels”v) Lipid anchored proteinsvi) Purifying1) Peripheral membrane proteins can be washed off the surface of the membrane – salt ions disrupt hydrogen bonding and electrostatic attractions2) Integral membrane proteins must be extracted from the membrane using detergents, amphipathic molecules surround the proteins and “lift” them out of themembrane4) Membrane Transport and the Electrical Properties of Membranesa) ∆G(x) = RT*ln ([Xside 2]/[Xside 1])b) Diffusion of CHARGED substances across cell membranesi) G(x) = RT*ln ([Xside 2]/[Xside 1]) + Z*F*∆Vc) Electrochemical differences are additived) Lipid bilayer allows free diffusion of select types of substances down their concentration gradientsi) Hydrophobic moleculesii) Small polar moleculese) Simple Diffusion vs Transporter-mediated diffusionf) Passive vs Active Transportg) Ion channels: allow net flux of specific ions across a membrane down their electrochemical gradients onlyi) What has to happen(1) Water shell surrounding the ion must be stripped away as the ion moves into the channel through the neck of the funnel(2) An attractive force strong enough to displace these water
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