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study guide for first half of midterm (condense notes from readings)

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PSYC 388
Ralph Mistlberger

Chapter 7 ` Molecular Clock: protein tick and RNA tock - Schrodinger = metaphorical cat can cat be both alive and dead at same time (cat in a box) ~ What is life considered 2 issues: 1. Ability to decrease entropy (characteristic feature of living systems) with consequent increase in order life = continual battle to maintain state of order in universe that runs towards disorders = living systems keep climbing entropy gradient by obtaining energy from sunlight and food (second law of thermodynamics - expression of the tendency that over time, differences in temperature, pressure, and chemical potential equilibrate in an isolated physical system) game goes to extra time and law gets everything at the end 2. Heredity suggested basis for heredity must e some kind of code where specific sequences of chemicals were written and interpreted and assumed code-script was contained in proteins in form of an aperiodic crystal (salt) ~ Once position of one pair of sodium and chlorine atom known = order and positions of all other atom are defined thought chromosome was aperiodic crystal = example of basic code arranged in order could contain vast of information (many different combinations) = lead to people working on these problems - Benzer aim to link classical gene maps with new molecular mechanisms (double helix) ~ rII phage mutants experiments = showed gene itself had structure, so gene could be dissected an cut into pieces (pieces = lengths of DNA) ~ showed correspondence between linearity of gene and section of DNA = help establish accepted view that buried within DNA of organism is its genetic blueprint (genotype) unique sets of instruction that provides basic code for building an individual - Genes direct production of specific proteins which interact with environment to determine how person will function and phenotype, but environment can influence expression of genotype and subtly alter how DNA blueprint is read = same genotype may have slightly different phenotype (differences in identical twins) - Genes dont make proteins directly RNA (ribonucleic acid/ single strand) = protein synthesis - Nucleotide building blocks of DNA and RNA consist of 3 smaller molecular components 1. Nitrogen base cytosine ( c), thymine (T), adenine (A), and guanine (G); RNA = (T) replaced by (U) uracil ~ 2 chain of nucleotides linked together by bases (C-G, T-U/A) - DNA is Schrodingers aperiodic crystal and list of bases in DNA strand is genetic code - Amino acids building blocks of proteins (20) various combinations = chains to produce different protein and activities - Codon - 3 bases in DNA strand ex. GGT code for particular amino acid - DNA unravel at cell division and single strand goes to each daughter cell to act as template to form complementary strand and re establish to double helix but most of time cell is not dividing or DNA is unravelling/splitting - Most of cells time spent in protein synthesis and degradation - Specific protein made in a cell only appropriate portion of DNA strand unzips by breaking links between bases = one side of DNA strand act as template to make complementary strand of RNA; free nucleotides in nucleus of cell line up along unzipped DNA strand to form RNA strand then single chain of RNA peels away from DNA strand strand of free RNA (mRNA) strand of mRNA leaves nucleus and enters cytoplasm of cell where it interacts with ribosomes (large protein) and information = translated when amino acids line up along mRNA strand to generate protein (protein synthesis) - Sequence of bases in mRNA strand mirrors sequences of DNA strand - Transcription - pprocess of creating a complementary RNA copy of a sequence of DNA - Double stranded DNA (dsDNA) unzip so single strand of DNA (ssDNA) can act as template for mRNA transcription begins with specific transcription factors usually proteins bind to promoter region of gene; complementary strand of RNA synthesised by RNA polymerase = leaves nucleus and enters cytoplasm of cell and mRNA interacts with ribosome with translate mRNA, codon by codon into protein (X) - Proteins act as regulators, communication signals, structural elements, enzymes while genes only code for proteins - Central dogma: dna makes rna; rna acts as template for A.A to be linked into a chain; chains fold into proteins - Benzer interested in how humans synchronised their activities by time - Konopka interested in genetic basis of Pittendrighs observations that clock regulated dawn emergence of Drosophila (circadian clock controls timing) (emergence rhythm = entrained by light and temperature compensated) ~ exposed flies to chemicals that cause random mutations in DNA (sperm) clock mutants (slow/fast/arrhythmic clocks) = RESULTS: crossing mutants with wild-type flies reveal mutation linked to behavioural change in flies clock was due to single gene = mutations in this gene (period(per) gene) altered period of flys circadian rhythm ~ He and Benzer tied behaviour to a gene and identified first clock gene to be found in any species - time-sensitive emergence of adult Drosophila = behavioural curly wings - initially, PER thought to function at junctions between cells, for cell cell communication later PER might be involved in clock function - Siwicki and Hall detected and localized PER within individual cells of flys body showed PER present in very many different tissues of body, small group of cells in fly brain (lateral neurones) and eyes showed 24 hour rhythms of abundance in PER protein - Normal flies (perN), protein levels peaked early at night (8pm) then drop In middle of day; rhythms in PER peaked early in per short (perS) mutants and late in perL mutants and no PER protein could be detected in arrhythmic per0 flies (per mRNA peaks 4-6 hours earlier before peak in PER protein) perS mutants peaks in per mRNa advanced ~5 hours, perL mutants had mRNA rhythms delayed ~ 5 hrs compared to normal flies; per 0 flies = no rhythms in per mRNA + no detectable PER protein - PER rhythmic in eyes and lateral neurones, patterns of protein abundance mirrored circadian behaviour rhythms of per mRNA drove rhythmic production of PER protein (flies collected at different times in day and night then frozen by liquid nitrogen = place din mesh sieve and shaken to separate heads from bodies = per mRNA measured = per m RNA showed 24 hour cycle) - Hardin & Hall proposed PER protein was involved in negative feedback loop where it inhibit its own production for rhythmic expression of PER (made sense because PER synthesised in cytoplasm and high levels of PER protein concentrated in nucleus) = proposed per mRNA transcribed form per gene = allow production of PER protein so as PER levels build in cytoplasm = protein enters nucleus and inhibits production of further per mRNA by binding with promoter = reduced levels of per mRNA transcription resulting in reduced levels of PER protein production so all PER translation stops = PER protein broken down then releases per gene from inhibition, per mRNa can now transcribed and cycle restart proposal dont answer how this generates stable rhythm (negative feedback = keep system in stable equilibrium but oscillation is different; oscillation system in regular manner moves away form equilibrium before returning) - Simple per alone model first model for circadian clock in Drosophila based on transcriptional/translational feedback loop of PER protein and per mRNA = PER protein inhibit further transcription and hence translation of PER= half-life of protein and mRNA would determine 24 hour dynamics of system ~ Major problem = dPER playing role of transcriptional regulator because dont have features expected of a protein that would bind promoter region of a gene = need a partner - To oscillate on 24hr cycle, inhibitory effects of PER on per transcription need to be turned off, per mRNA production needs to be turned back on again, has to be delay of many hours in feedback process - Tension between positive element of loop = promote transcription and translation of PER and negative element inhibit this transcription = rhythm - Sehgal & Price identify new Drosophila circadian mutant timeless (tim) analysis of tim gene suggested tim and per = act similar = flies lacking tim gene (tim0) are arrhythmic, mutations in tim can alter period length of circadian behaviour, TIM protein accumulates in same cell nuclei as PER protein, tim and per mRNA oscillate with same circadian phase, both peaking 4-6 hours before protein levels, PER protein never decreased in cell nuclei of tim0, TIM never detected in cell nuclei of per0 flies - PER rapidly degraded in absence of TIM protein = PER and TIM proteins bind to each other using PAS domains PER/TIM model for circadian clock in Drosophila ~ PER/TIM interaction required for nuclear localisation of both proteins = enter nucleus PER/TIM complex able to suppress per and tim gene transcription= stability of PER/TIM protein complex will determine duration of transcriptional suppression of per and tim genes = rate of entry of PER/TIM complex into nucleus and how long PER/TIM complex can persist before its degraded in nucleus, will determine extent of negative feedback on per and tim transcription and hence period of circadian oscillation ~ cycles in per and tim mRNA transcription are regulated by cycles of nuclear
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