UNIT 2 EXAM REVIEW 1 The Central Dogma a Eukaryotes vs Prokaryotes i Chromosome highly packed into chromatin ii DNA is nucleus protein synthesis machinery in cytosol iii Eukaryotic genes have introns b RNA synthesized 5 3 DNA is read 3 5 by RNA polymerase c RNA Transcription d Pre mRNA processing i 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 boundaries ii 3 end receives a poly A tail e tRNA f Translation Process 2 Control of Gene Expression a Common DNA binding motifs i 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 DNA ii Homeodomain special case of helix turn helix larger structure that includes other highly conserved structures iii 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 dimerization iv Leucine zipper coiled coil structure 1 Helix from one subunit binds to the corresponding helix in the second subunit in a 2 Serves both as the dimerization region and the DNA binding region v Helix loop helix 1 Short alpha helix is connected to a longer alpha helix by a flexible loop b Regulation of RNA transcription i Promoter region where RNA polymerase and the general transcription factors assemble c Transcription Factors transcription ii Enhancer independent region outside the promoter cannot drive transcription on its own can work with promoter from a different gene i Combinatorial control of multiple gene regulatory proteins control the rate of d Regulate gene expression via i Unpacking chromatin ii Control recruitment of RNA pol and or the general transcription factors to the promoter iii Regulate the switch from intiation to elongation iv Help recruit the histone modifying enzymes to change the local chromatin structure v Bend DNA to allow long distance interactions between gene regulatory regions e Post trancriptional Regulation i Alternative splicing gene with just a few exons can produce many different mRNA s ii Regulated nuclear export allows RNA molecules containing some introns to be exported from the nucleus f Non coding RNA s iii Cystolic localization place specific mRNA s at specific locations in the cells i 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 target ii siRNA s mediate process of RNA interferences iii dsRNA base pairing between complementary regions of separate RNA strands g Regulation of Protein Translation i Information in the 5 to 3 untranslated regions can regulate translation efficiency as ii Riboswitch uses binding of an ion or small molecule to switch between translation iii Repressors binding to 3 UTR can prevent communication between 5 and 3 ends of well as mRNA stability on and off states mRNA iv Phosphorylation of initiation factor eIF2 can inhibit global protein synthesis v 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 mRNA h Regulation of Protein Stability i Ubiquitin proteasome system allows for regulated destruction of proteins ii N end rule Identity of N terminal amino acid defines intrinsic stability i Epigenetic inheritance any heritable difference that does not rely on changes in the i Epigentic Regulation DNA nucleotide sequence ii 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 state 3 Membrane Structure and Functions a Membrane Functions i Compartmentalization ii Selectively Permeable Barrier iii Scaffold for Biochemical Activities iv Solute Transport v Sending Receiving Chemical Signals vi Energy Transduction b Discovery of the Lipid Bilayer i Langmuir Trough ii Freeze Fracture Electron Microscopy iii Fluid Mosaic Model c Phosphoglycerides i Plasma membrane lipid distributions are asymmetrical important for protein binding and cell signaling ii Types iii Sphingolipids iv Cholesterol 1 Highly abundant is eukaryotes abset from prokaryotes 2 Provides rigidity 3 Modulates permeability d Membrane Proteins i Integral Membrane Proteins hydrophobic section of the protein is embedded in the hydrophobic core of the lipid bilayer ii Transmembrane protein extend all the war through the lipid bilayer iii Hydropathy plots used to search for 20 amino acid stretches of hydrophobic amino acids in the primary sequence of a protein iv Serve as channels for ions polar molecules are composed of beta sheets arranged into barrels v Lipid anchored proteins vi Purifying 1 Peripheral membrane proteins can be washed off the surface of the membrane 2 salt ions disrupt hydrogen bonding and electrostatic attractions Integral membrane proteins must be extracted from the membrane using detergents amphipathic molecules surround the proteins and lift them out of the membrane 4 Membrane Transport and the Electrical Properties of Membranes a G x RT ln Xside 2 Xside 1 b Diffusion of CHARGED substances across cell membranes i G x RT ln Xside 2 Xside 1 Z F V c Electrochemical differences are additive d Lipid bilayer allows free diffusion of select types of substances down their concentration gradients i Hydrophobic molecules ii Small polar molecules e Simple Diffusion vs Transporter mediated diffusion f Passive vs Active Transport g Ion channels allow net flux of specific ions across a membrane down their electrochemical gradients only i 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 molecules is provided by carbonyl oxygen atoms protruding throughout the channel from the polypeptide backbone of nearby selectivity loops 3 Orientation of the oxygen atoms
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