Classical Sociological Theory
Classical Sociological Theory SOCA 100
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This 17 page Class Notes was uploaded by Francesca Rath on Thursday October 22, 2015. The Class Notes belongs to SOCA 100 at University of California - San Diego taught by Staff in Fall. Since its upload, it has received 19 views. For similar materials see /class/226810/soca-100-university-of-california-san-diego in Sociology at University of California - San Diego.
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Date Created: 10/22/15
mikedavis45hotmailcom Week 2 Handout Section A04 Tuesday 5550 WLH 2207 SECONDARY STRUCTURE MOTIFS Seconda Structure Secondary structure refers to the folding of individual polypeptide chains to form relatively predictable structures such as the alpha 7 helix and Beta 7 sheet The bond that determines secondary structure is the hydrogen bond The Alpha Helix 7 In the binding pattern of the alpha helix a hydrogen bond is made between the carbonyl oxygen of a residue n and the amide hydrogen of a residue four places ahead of it in the polypeptide chain n4 7 With the exception of the rst and last all amide hydrogens and carbonyl oxygens are linked in intrastrand hydrogen bonding How does this make the alpha helix an ideal transmembrane structure 7 numbers given in class 36 the number of residues per turn of the helix 15 the distance between 2 consecutive residues 54 the pitch of the alpha helix 7 The alpha helix has a net dipole at the amino end and 7 at thearboxy end 7 Some amino acids favor alpha helix formation M A L E Some amino acids are rarely seen in alpha helices P Y G S proline is observed to cause breaks or bends in the alpha helix Why glycine is observed to cause oppy turns in the alpha helix Why 7 The location of an alpha helix within a protein can be predicted by looking at the amino acid side chain arrangement see g 24 Beta Sheets 7 Beta sheets are the other important secondary structure found in proteins Like the alpha helix beta sheets are stabilized by hydrogen bonding between NH and CO groups in the polypeptide bond 7 ln beta sheets the hydrogen bonding occurs between residues distant form each other for this reason the beta sheet is called an interstrand structure However the strands are part of the same polypeptide chain 7 The backbone of peptides in beta strands are extended giving phi psi angles of approximately l80 180 corresponding to the upper left quadrant of the Loops Motifs Motifs Ramachandran plot In this conformation the distance between consecutive residues is maximized 35 compare to alpha helix 7 Beta sheets contain strands which t different classifications Parallel strandshave successive beta strands running in the same biochemical direction with respect to amino and carboxy termini and form parallel sheets Antiparallel strandshave successive beta strands running in opposite directions amino to carboxy followed by carboxy to amino They form anitparallel sheets Mixed beta sheets contain both parallel and antiparallel strands 7Loops function to connect secondary structure elements 7Loops that connect adjacent antiparallel beta strands are called hairpin loops Type 1 hairpins turn to the left and type 11 hairpins turn to the right sometimes called supersecondary structures are simple combinations of secondary structure that occur in protein structures The wide variety of combination of alpha helices beta strands and loops give some motifs functional importance such as calcium binding or DNA binding You should know something about and be able to draw the following motifs 1 2 3 HelixLoopHelix g 212 213 7 HLH consists of 2 alpha helices joined by a loop region which may have ligand binding residues 7 The EFhand is and example of a HLH with ligand binding properties the 2 alpha helices E F are connected by a loop of 12 amino acid residues Five of the residues are calcium ligands Aspartic acid and Glutamic acid Residue number six must be glycine the rest of the amino acids should be hydrophobic ex T roponin C calmodulin parvalbumin BelaLoopBela g 214 7 7loop7 simply consists of a loop used to join two adjacent 7 strands and is present in most antiparallel beta stretches It can be isolated as a ribbon or form part of a more complex sheet 7 The beta hairpin is a specific type of betaloopbeta connecting antiparallel beta strands The loop is only 25 residues long The Greek Key fig 215 16 7 The Greek key is a special motif by which four antiparallel betasheets can be joined DNA RNA PROTEIN franscripfion franslafion E on MATURE SIZE FUNCTION TYPE POL PROCESSED 118 Other ELIk Transcrigfion stfems 9486488 1 Pol I 2 Pol II gm m 4653mm 7 Nascenl DN mm RNA 5 hybrid regwon Polymerase I Txn39 39RNA produc r Upsmam Cur mam chum a 12 3939 pm mmmmmm P wan umwuluw Imon mm 39specific ups rream DNA m elemen rs 39 39 H4 f 0111 InrmHCFL TV A an amtr hum 39TF39s including TBP POI I I 1 39quotquot 39 uamani rin resis ran r Japan A W was mumquot mum Polymerase III Txn39 39RNA produc rs 39inTernal promo rer elemen rs 39specific TFIII39s including TBP Pol III 39 u amanifin sensiTive 55 aT high concentrations mm guns KCquot Poi Ill TFH TFIII TFIlIC iITJ U Uquot a c M Fig mi 125 Processin of rRNA and RNA 525529 1 nucleolus 2 prerRNA 285 185 585 3 TRNA mafur a rion 4 ribozymes Nucleolus subnuclear comparfmen rquot Pol III Txn rRNA processing and ribosome assembly Evlnmmm as as mmwi w minim 57 55 ms 5 mm rig 12734 Processing of pre rRNA info 3 separa re rRNAs rerRNA l SCr l P15 V snoRNPs cleavage Iz I rlluull ILuIIurlb Jackie Quach Thurs 1000 7 1050am Center 205 OH Tues 930 71030am PC Lobby Handout 2 Domain a polypeptide chain or a part of a polypeptide chain that can fold into a stable structure a unit of o Built from different combinations of secondary structure elements and motifs 0 Three main domain groups 1 or domains core made ofjust 0L helices 2 B domains core is antiparallel B sheets usually two B sheets packed against ea other 0L B domains made from combinations of BxB motifs that form a predominantly parallel B sheet surrounded by or helices Other groups 0 B usually one small antiparallel B sheet in one part of the domain packed against or helices those rich in disul de bonds or metal atoms E a Domain Structures Alpha helices are stabilized in solution by packing two helices together thru in a supercoil called a arrangement 0 Building blocks within a domain 0 residues per turn instead of the normal 36 for lefthanded supercoil of two right handed helices 9 pattern of sidechain interactions between the helices repeat every residues 9 repetitive sequences with a 7residue periodicity are called 0 d is usually Leu or Ile o a is o e and g are residues that provide ionic interactions that determine chain orientation In brinogen some RNA and DNA binding proteins GCN4 collectins spectrin dystrophin and myosin o Coiledcoil proteins pack according to the model Four helix bundle the simplest most frequent xhelical domain 0 side chains are buried between the helices and on the outer surface of the bundle o The at helices usually pack to the instances of packing by the knobs in holes model 0 Found in myohemerythrin cytochrome c cytochrome b562 ferritin human growth hormone and the Rop protein side chains are but there are side chain packing of 4helical bundle human growth hormone cytochrom e c The consists of 8 0L helices connected by short loops and arranged to form a pocket for the active site 0 0L helices wrap around the core in different directions with packing interactions between nonsequentially adjacent pairs Exception helices are antiparallel and interact o By looking at the globin fold in different proteins scientists can see the mechanism by which proteins adapt to mutations o Evolutionary divergence of globin structures has been constrained by a conservation of the of residues participating in helixhelix helixheme interactions 0 The relative positions of the or helices change to accommodate changes in the volume of the side chains involved in packing but the pocket is preserved o In hemoglobin and myoglobin the active site binds a group 0 Hemoglobin is a made up of two copies of or and Bglobin chains in adults 0 In sicklecell anemia residue of the is changed from to producing a hydrophobic patch on the surface 9 binds a hydrophobic pocket in deoxygenated form of another Hb molecule 9 Hb in cells polymerize to fibers that stiffen and deform the cells into a sickle shape 0 Sicklecell anemia gives resistance to aB Domain Structures N Consist of central parallel or mixed B sheet surrounded by or helices Most frequent of the domain structures Three main classes 1 TIM barrel core of twisted parallel B strands arranged close together with or helices connecting them on the of the barrel 2 Horseshoe fold the B strands form curved parallel B sheet with all the or helices on the formed by amino acid sequences with 139ich motifs 3 twisted B sheet surrounded by or helices on both sidesias seen in Rossman fold Almost all the closed barrels so far have parallel B strands 0 Usually connect the parallel B strands and there is an or helix after the last strand 0 About amino acids are required N 160 form or helices and B strands and are structurally equivalent The rest vary because they are responsible for the catalytic chemistry in the various loops that connect at helices and B strands 0 Packing interactions between or helices and B strands are dominated by branched hydrophobic residues and 0 Every second residue of B sheet points outside to hydrophobic shell The rest point to the core which is solely made of B strand side chains 0 Lys Arg and Glu can participate in hydrophobic core formation because the ends are at the or of the barrel and contact the environment 0 Enzymatic function is associated with the barrel domain 0 Active site is at bottom of funnelshaped pocket created by 8 loops connecting the end of the B strands with the end of the or helices 0 Chemistry is important to preserve during evolution while specificity can be modified Leucinerich motifsrepeats form righthanded Bloop0L structures in the 1 B fold o B strands form a parallel B sheet curved like a horseshoe with one side of the B sheet facing 0L helices on the and the other side exposed to 0 Leu in leucinerich motif forms the hydrophobic core between the or helices and B sheets 3 1 B open twisted sheet structures have or helices on sides of the B sheet 0 A closed barrel can t be formed unless there are enough B strands to completely enclose the or helices on one side of the B sheet which has never been observed The binding site is in the at the edge of the B sheet Functional residues are at the loop regions there Each B strands contributes hydrophobic side chains to pack against or helices in two similar core regions B Structures This group is the most in function enzymes transport proteins antibodies etc Cores made of B strands mostly antiparallel 2 B sheets packed like a barrel with hydrophobic core and surface made from loops and B strands Most frequently occurring groups upanddown barrels Greek keys and jelly roll barrels Up and down B sheets barrels have antiparallel strands with connections 0 In RBP single polypeptide that transports lipid alcohol vitamin A aka retinol from liver to vitamin Adependent tissues 0 In a tetrameric protein on the outer lipid membrane of the RNA virus in uenza that facilitates release of progeny virions from infected cells by cleaving sialic acid Each subunit looks like a 6 blade propeller o Motif upanddown antiparallel B sheet of 4 strands 6 motifs in a subunit Greek key motif provides a ways to connect antiparallel B strands that are on opposite sides of barrel structure Connects strand n to 0 Found in the majority of antiparallel B structures 0 Gamma y crystallins have 2 Greek key motifs in each of its 2 domains Jelly roll motif is made of Greek keys wrapped around a barrel core 0 Basic structure B strands all adjacent B strands are antiparallel the strands form distorted and attened Usually divided into B sheets 0 In a protein on the in uenza virus envelope that l binds to sialic acid on host MB and 2 fuses with host MB at low pH to bring its RNA into host cytoplasm o Jelly roll domain forms receptor binding site Antibodies bind in hydrophobic channel 0 Structure changes with pH In low pH the changes are irreversible because the resulting structure is very stable Parallel B helix domains polypeptide chain coiled into wide helix formed by B strands separated by loopB strandloop regions 0 2 parallel planar B sheets 0 Basic structural unit amino acids 3 in each B strand 6 in each loop 0 Double repeat of residue consensus sequence DNA General characteristics doublestranded purinepyrimidine basepaired by helical linear molecule with diameter The sugarphosphate backbones are bulky and form ridges on the edges of each of the helix 0 Base pairs are asymmetrically attached to the sugar rings of the backbone 9 base pair edges form oor of and i Multithreading Models amp Coarsegrain multithreading Coarsegrain switch contexts typically several cycles on longlatency event MIT Alewife Finegrain switch contexts every cycle HEP Tera Sun Niagara Simultaneous Multithreading Compaq 21464 Intel Pentium 4 Power 5 6 g Finegrain multithreading g Simultaneous Multithreading Scalability Who are the arch enemies of MIT Alewife scalability Scalability Four Pronged v Approach v Programming Model v Coherent Shared Memory g LimitLESS Directory Unique features A Figure 4 A mmmm dmzclory entry In Alcwuc So why scalable 1 r 315quot Q y slur n W 3 1 Fight 1 The Atewn e architecture FunEmpty Bits g Latency Tolerance Store set full Load if full set empty Block Multithreading g Block CG Multithreading Aka coarsegrain multithreading What does it do well What doesn t it do well I mem con ict E long fp D short fp I long int I short int I load delays U control hazard I branch mispre I dcache miss I 1cacne miss dtlb miss I itlb miss I processor bus Simultaneous Multithreading Percent of toml issue cycles Hardware Multithreading W 60 tion u X U I I Conventional I g Multithreaded I g Issue Slots Processor D 2 Processor I 2 I I III III a 3 III III III III E 5 5 I I III III D E PC I Ea I III III III I a reg reg reg I EIEIEIEI D 5 PC I E I I I I D reg I EEEE CPU l CPU D I I D D I I El I El I 4 Time proc cycles v Superscalar Execution Superscalar Execution A Issue Slots A Issue Slots LE I I El El LE Hon39zontal waste gt gt O O O O 8 8 3 3 Q Q E E H H l Vertical waste l Vertical waste i Superscalar Execution 4 Time proc cycles Issue Slots Superscalar Execution with FineGrain Vi Multithreading E O 3 Thread 1 g E Thread 2 E Thread 3 Issue Slots Superscalar Execution with Fine Grain Multithreading Thread 1 Thread 2 Thread 3 lt Time proc cycles Issue Slots Horizontal waste g Simultaneous Multithreading lt Time proc cycles Issue Slots Thread 1 Thread 2 Thread 3 Thread 4 Thread 5 e 1 Hmmasm Throughput Instructions perCycl m Simultaneous Multjthreading The Potential for SMT FineGrain Multithreading Conventional Superscalar Goals We had three primary goals for this architecture 1 Minimize the architectural impact on conventional superscalar design 2 Minimize the performance impacton a single thread 3 Achieve significant throughput gains with many 0 threads 1 2 3 4 5 6 7 8 Numb er of Threads An SMT Architecture A Conventional Superscalar Architecture Instruction Cache Rena n integer instruction queu i39 teicn Unit oating point f i Data instruction queu um Cache Instruction Cache integer integer instruction queu 39 reg Renam i Perfqrmance of the Naive Design Unmodified Superscalar Throughput InslIuctions Per Cycle 0 I 1 l I I 2 4 6 8 Number of Threads Bottlenecks of the Baseline Architecture Instruction queue full conditions 1221 of cycles Lack of parallelism in the queue Fetch throughput 42 instructions per cycle when queue not full g Improving Fetch Throughput The fetch unit in an SMT architecture has two distinct advantages over a conventional architecture g Improving Fetch Throughput The fetch unit in an SMT architecture has two distinct advantages over a conventional architecture Can fetch from multiple threads at once Can choose which threads to fetch Improved Fetch Performance Improved Performance Fetching from 2 threadscycle achieved most of the performance from multiple 539 thread fetch Fetching from the threads which have the fewest unissued instructions in flight significantly increases parallelism 2 f and throughput ICOUNT fetch policy Unm di edsuperscalar 2 4 6 8 Number of Threads Improved Bakseline Instructions per cycle g This SMT Architecture then i Multithreading Models Borrows heavily from conventional Coarsegrain SWitCh contexts tYPicaIIY superscalar design several cycles on longlatency event MIT Al 39f Minimizes the impact on Singlethread M e Finegrain switch contexts every cycle DEWOman I I I HEP Tera Sun Niagara Achieves Significant throughput gains Simultaneous Mutithreading Over the superscalar 25X up to 54 Compaq 21464 Intel Pentium 4 Power 5 6 IPC Pros cons issues HEP Multithreading 11 Cool Tera Features Fullempty bits on memory Randomized memory why No bypassing Explicitdependence lookahead LIW No caches Highbandwidth network Which of these are related to multithreading Other SMT Research UCSD emphasis Compilation issues including instruction layout for icache performance Multiplepath execution Symbiotic job scheduling S nchronization and V arallelization Multithreading and power Helper threads speculative precomputation Multicoremultithreaded clustered multithreaded Multithreaded value prediction Eventdriven compilation
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