Exam 1
Quiz yourself by thinking what should be in
each of the black spaces below before clicking
on it to display the answer.
Help!
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| ribozymes | RNA molecules that can act as enzymes
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| antisense RNAs | also known as microRNAs or small interfering RNAs that regulate gene activity
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| small nuclear RNAs | help process pre-mRNA into mRNA
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| what are the requirements for the molecule of inheritance | contain info that determines traits and funciton of organism, be stable but be able to change without causing harm to the organism and be carried on chromosome
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| what was once thought to be the molecule of inheritance | protein
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| what did Griffith's experiment teach us about molecule of inheritance | is responsible for transformation and so can transmit its characteristics to another
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| describe Griffith's experiement | virulent strain, nonvirulent strain, heat killed virulent strain, and mixture of nonvirulent strain with heat killed virulent strain were each individually inserted into mice
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| describe the results of Griffith's experiment | virulent strain-mice died and bacteria recovered, non-virulent strain-mice lived and bacteria not recovered, heat-killed virulent strain-mice lived and bacteria not recovered, mixture-mice died and virulent bacteria recovered
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| what did Avery, MacLeod, and McCarty's experiment prove | DNA was the transforming principle
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| describe Avery, MacLeod, and McCarty's experiment | treated individual heat killed virulent strains of bacteria with DNAse, RNAse, and proteases. and then each strain was mixed with a non-virulent strain of bacteria. then each mixture was injected each sample into mice
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| describe the results of the Avery MacLeod, and McCarty's experiment | the mice treated with the mixture of the virulent strain that were treated with RNAse and proteases died. only the mice with the mixture of virulent strain that was treated with DNAse survived
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| what did Hershey and Chase's experiment prove | that DNA not protein was the heritable substance
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| describe Hershey and Chase's experiment | bacteria radioactive P, bacteria radioactive S. T2 phage infect. T2 progeny infect normal bacteria. protein coat around bacteria. centrifuge, bacteria is pellet, protein coat is supernatant. radioactive P in pellet and radioactive S in supernatant
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| nucleoside | sugar + base
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| nucleotide | sugar + base + phosphate
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| difference between RNA and DNA | sugar. deoxyribose has one less oxygen atom and so only has Hydrogen instead of hydroxyl group such as ribose. DNA has thymine and RNA has uracil
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| how are nucleotides added | hooking the phosphate group on the 5' carbon of the nucleotide to the Oxygen on the 3'carbon to the previous nucleotide. so addition happens from 5' to 3'
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| pruines | adenine and guanine
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| pyrimidines | cytosines and thymines
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| what is the difference between AT pairs and CG pairs | CG pairs have 3 H bonds while AT pairs have 2 H bonds
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| what are the different DNA configurations | B-form: typical configuration in vivo, A-form: under high salt conditions and is more compact but is still right-handed. Z-form: left-handed helix seen in small pieces of DNA
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| RNA is single stranded and does not have any secondary structures. True or False | False. if RNA has complementary base pairings within itself then it can form secondary structures and a number of conformations such as stem and loops hairpins, loops, bulges, and right handed helices
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| DNA has polarity | one end of the strand has a free phosphate group attached ot the 5'carbon and the other end has a free hydroxyl group attached to the 3' carbon. so each strand has direction and the strands are antiparallel to each other
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| complementary base pairings allow | stability for the DNA but base pairings don't have to be in a particular sequence thus allowing variablity
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| how are nucleoside analogs used to battle cancer | nucleic acid derivatives have 5' ends look enough like real nucleotides that replicating cells incorporate them into newly synthesized DNA but they have no 3'O end so the DNA cannot be extended and when DNA can't be replicated then the cell dies
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| conservative replication | theory of replication where original DNA molecule stays intact and a completely new molecule is synthesized
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| dispersive replication | theory of replication where original DNA molecule gets fragmented and the fragments are used as templates for synthesis of new DNA and then the parts gets reassembled. the resultant DNA would have both old and new DNA scattered throughout it
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| semiconservative replicaiton | replication in which original DNA molecule unwinds and each strand is used a template for the synthesis of a new strand so the resultant DNA would have one old strand and one new strand
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| what did mesleson and stahl's experiment prove | that DNA replication was semiconservative
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| describe meselson and stahl's experiment | they grew bacteria in 15N medium so that all their DNA would have 15N. then took those bacteria and let them replicate in 14N medium. used equilibrium density gradient centrifugation to determine the weight of the DNA
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| results of meselson and stahl's experiment | original DNA is heavy. after one round of replication, the DNA was intermediate weight indicating either semiconservative or dispersive model. after another round of replication the DNA was intermediate and light indicating the semiconservative model
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| taylor's experiment | proved semiconservative model of replication. studied bean root tips. grew cells in radioactive tritium (labeled thymine) for one round of mitosis and then moved them to a medium without labeled thymine to observe radioactivity distribution in metaphase
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| taylor's experiment's result | 1round of mitosis both sister chromatids labelled so conservative model was out otherwise only 1 chromatid labeled. another round of mitosis only one chromatid was labeled indicated semiconservative because dispersive would have both chromatids labeled.
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| theta replication | circular DNA in bacteria. double helix unwinds at single origin of replication creating replication bubble with a replication fork at each end (bidirectional replication). unwinding and replication happen simultaneously until 2 circular DNAs are produced.
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| rolling circle replication in viruses & plasmids which can happen many times | break in 1 strand happens so new nucleotides are added to 3'end with inner strand as template. 5'end of old strand is pushed off and 3'end grows around circle. old linear strand circulizes before/after serving as template for complementary strand
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| how many origins of replication do prokaryotes have? eukaryotes? | 1 for prokaryotes and many for eukaryotes
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| what are the requirements of replicaiton | template-unwinding of DNA to expose bases. raw materials: deoxyribose nucleoside triphosphate (nucleoside + 3 phosphates). breakage of 2 phosphates and enzymes provide energy and catalyst for phosphodiester bond formation
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| initiator proteins | prokaryotes. recognize origin of replication and unwind short section of DNA allowing other necessary proteins to access start site
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| DNA helicase | unwinds DNA by breaks hydrogen bonds between nitrogen bases and binds to lagging strand template at each fork and moves from 5' to 3'
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| single strand binding proteins | attach to single stranded DNA to prevent secondary structures from forming and to also prevent complementary strands from attaching again. they will bind to any nucleotide sequence
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| DNA gyrase | a topoisomerase in prokaryotes that creates a double stranded breaks outside of open region to control supercoiling of DNA to reduce torque
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| primase | synthesizes short stretches of RNA nucleotides-primers
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| primers | short RNA nucleotide sequences that provide 3'OH group for DNA polymerase. only one primer needed for leading strand and multiple primers are needed for lagging strand
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| DNA polymerase III | DNA polymerase in prokaryotes that uses complementary base pairings to add nucleotides to growing strand. it can also proofread and correct its mistakes
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| DNA polymerase I | DNA polymerase in prokaryotes that removes RNA primers and replaces them DNA nucleotides
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| DNA ligase | seals okazaki fragments together and the strands together of many replication bubbles by making a phosphodiester bond without adding nucleotides
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| differences between eukaryotic and prokaryotic replication | eukaryotes have a wider variety of proteins. the initiator is a multi-protein complex in eukaryotes not a single protein like prokaryotes. eukaryotes have more DNA polymerases than prokaryotes. in eukaryotes the primer has both RNA and DNA nucleotides
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| DNA polymerase alpha | lays down primer
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| DNA polymerase delta | replicates lagging strand
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| DNA polymerase epsilon | replicates leading strand
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| how do prokaryotes stop replication | Tus protein binds to ter sites & stops one of the replication forks by blocking helicase &allows other fork to come & meet it. topoisomerase II forms double stranded break allowing 2 circular DNAs to become untangled so they can migrate to 2 daughter cell
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| replication licensing factor (RLF) | contains proteins such as helicase&geminim. attaches to origin, unwinds little of helix releasing helicase. RLF is released but geminim stays bound to origin so replication cannot be initiated again at that site. geminim degraded in G1 of next cell cycle
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| what is the problem of the lagging strand at the end of replication causing the chromosome to get shorter and shorter every cell cycle? | DNA pol or DNA pol I removes primer at end of lagging strand, can't replace it with nucleotides because the 5' end is exposed not 3' end. leaving single-stranded overhang that gets chopped by enzymes along with some double-stranded DNA
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| telomeres (Human Telomeres TTAAGGG) | repeated sequences at the end of chromosomes that protect the actual genetic info from getting chopped off by enzymes because of the single-stranded overhang of the lagging strand. length determines if cell can undergo another cell cycle or apoptosis.
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| telomerase | found in single-celled organisms, germ cells, and rapidly replicating eukaryotic cells. protein-RNA complex that fills in telomeres
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| how does telomerase fill in telomeres | RNA portion binds to lagging DNA providing template for G-rich strand that has 3'end open. nucleotides are added. RNA template moves down. more nucleotides are added. telomerase is removed. synthesis of complementary lagging strand takes place
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| aging due to telomeres | as telomeres shorten, regulation of activity of genes in chromosome arm may be disrupted
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| cancer due to telomerase | telomerase is active in cells where it is not supposed to be active creating immortal cells
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| first step to transcription | chromatin reconfiguration by acetylation of the lysines in histone proteins to loosen their grip on DNA. lysines are positively charged, adding negatively charged acetyl groups will pull lysines in histones away from phosphates of DNA making it available
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| how many strands of DNA are used in transcription | one
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| transcription unit | stretch of DNA that encodes RNA that also has other sequences necessary for transcription
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| promoter | DNA sequence that transcription apparatus recognizes and binds to indicating which strand is template strand- lies next to RNA coding reigon and so is not transcribed itself
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| RNA polymerase I | makes rRNA
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| RNA polymerase II | makes pre-mRNA, snoRNA, miRNA, snRNA
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| RNA polymerase III | makes tRNA, small interfering RNA, some miRNA and snRNA
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| general transcription factors | with RNA polymerases form basal transcription apparatus
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| basal transcription apparatus | group of proteins that assemble near start site and start minimum levels of transcription. RNA polymerase, general transcription factors, and mediator
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| transcriptional activator proteins | bind to specific DNA sequences and stimulate assembly of basal transcription apparatus at start site
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| core promoters | located immediately upstream of RNA encoding area and is where basal transcription apparatus binds to. also includes one or more consensus sequences like TATA boxes
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| regulatory promoters | located upstream of core promoters and have different consensus sequences. transcriptional activators can bind and either directly or indirectly affect rate of transcription initiation. examples are enhancers
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| transcription initiation | regulatory proteins binds to DNA near promoter, modifying chromatin structure to recruit basal transcription apparatus to core promoter. TATA binding proteins bind to TATA to bend and unwind DNA to open complex
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| nontemplate strand is also known as | coding strand or sense strand
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| transcription elongation | RNA polymerase II makes pre-mRNA
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| transcription termination for RNA polymerase II after transcribing termination sequence that produces a string of uracil nucleotides | RNA pol II transcribes beyond end of pre-mRNA. pre-mRNA cleaved at site with Rat 1 endonuclease. pre-mRNA attached to RNA pol II gets degraded by Rat 1 starting at 5'end of trailing pre-mRNA. when Rat 1 reaches RNA pol II, transcription stops
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| transcription termination for RNA polymerase I | helicase protein binds to DNA beyond transcription termination site. when RNA pol I hits helicase, helicase unwinds the DNA/RNA hybrid and liberates pre-mRNA
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| transcription termination for RNA polymerase III | transcription goes past a string of adenines, then terminates
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| exons | coding regions
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| introns | noncoding regions
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| post transcriptional RNA splicing | introns and exons are initially transcribed but after transcription,introns are removed by splicing and exons are joined to yeild mature RNA
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| spliceosomes | complex of proteins and RNAs that splice introns out of pre-mRNA
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| what type of RNAs are in splicesomes | small nuclear RNAs, that when combined with proteins make small nuclear ribonucleoproteins SNRPs
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| how do spliceosomes know where to cut in pre-mRNA? | consensus sequences around intron/exon borders orient spliceosomes
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| methylated guanine 5'cap | 5'end of pre-mRNA usually has 3 phosphates. 1 phosphate is cleaved and 5' to 5' linkage is made and guanine is added on top of that. finally methyl groups are added to 5' end and to two position of the sugars preceding 5' to 5' linkage,
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| Poly A Tail | a couple of nucleotides downstream consensus sequence AAUAAA in the 3' untranslated region, pre-mRNA is cleaved. polyadenylation takes place at 3' end creating Poly A Tail
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| describe mature mRNA | 5'cap, 5' untranslated region, protein coding region, 3' untranslated region, poly a tail 3'
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| Guide RNAs | bind to mRNA after post-transcriptional editing, causing nucleotided to be added/deleted/substituted so resultant mRNA and amino acid sequence will not match gene's coding sequence
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| translation initiation | ribosome initiation factors, initiation tRNA with amino acid (Met-tRNA) form an initiation complex that recognize and bind to 5'cap and protein bind to 3'poly A tail. interact with cap-binding proteins to enhance binding
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| kozak sequence | consensus sequence that surrounds start codon to help ribosome initiation factors and initiation tRNA locate start codon
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| translation elongation tRNA process | initiator tRNA binds to P site. charged tRNA+elongation factor Tu+charged tRNA form complex that enter A site. GTP->GDP and EfTu-GDP complex released. elongation factor Ts regenerates GDP->GTP
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| translation elongation peptide bond formation | peptide bond form between amino acids in A and P sites and tRNA in P site releases its amino acid. translocation of ribosomes releases tRNA into cytoplasm from E site
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| degenerative code | genetic code has more info than needed so one amino acid can have more than one codon definingit
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| tRNA charging | binding of tRNA to appropriate amino acid and there are 20 difference aminoacyl-tRNA synthetases, one for each amino acid and all its possible tRNAs
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| start codon is usually | AUG
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| shine dalgarno sequence | in prokaryotes this consensus sequence as bacterial ribosome attaching to it because it is upstream the start codon
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| missense mutation | one amino acid gets replaced by another. effects range from no effect to abolishing protein's activity
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| nonsense mutation | creates stop codon at site of mutation, protein is truncated and activity abolished
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| ribosomes have a reading frame | of codons, triples of nucleotides. change in amino acid by change in codon may or may not alter protein. deletion/insertion with not a multiple of 3 disrupts of reading frame, and a completely new amino acid sequence is created and protein wont function
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| translation termination | stop codon followed by 3'untranslated region. RF1 attaches to A site and RF3 forms complex with GTP and binds to ribosome. polypeptide is released from tRNA in P site. GTP->GDP and mRNA, tRNA, and releasing factors are released. ribosome disassembles
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| stop codon | no tRNA has complementary for stop codon so it signals to stop translating
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| releasing factors | proteins that bind to ribosome to terminate translation
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| nonsense mediated mRNA decay | rapid degradation of mRNA with premature stop codon. proteins are bound to exon-exon junctions in mRNA when pre-mRNA processed. ribosome removes them & premature STOP means ribsome doesnt remove all proteins. proteins remain and signal for degradation
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| unstoppable mRNAs | when transcription is incomplete and no STOP codon in mRNA. mutation changes STOP codon to amino acid codon. ribosome gets stuck on mRNA and can't be used elsewhere. need to be degraded
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| nonstop mRNA decay | when reading frame gets altered & ribosome gets to end of mRNA and has not encountered STOP then ribosome's A site will be hanging off the edge mRNA because there is nothing to fill which signals proteins that attach to mRNA to degrade from 3'end forward
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| post translational processing | folding into 3D shape, chemical side group adornments (glycosylation and phosphorylation and glycoproteins), joining with other proteins to make multimeric proteins
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| amino terminal amino acids | direct polypeptide to its final destination in cell and then they get cleaved off
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| constitutive genes | genes that are on all the time (housekeeping genes) because their proteins perform functions that are necessary for basic function, vitality, and maintenance of cell
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| regulatory genes | genes whose products, either RNA or protein, interact with other DNA sequences and affect transcription and translation and are often within the promoter region
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| pirbnow box | TATA sequence in promoter of a gene
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| sigma facors | allows RNA polymerase to bind to DNA by interacting with core enzyme forming holoenzyme that binds to promoter. localized unwinding and transcription happens and then sigma factor is released
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| enhancer | sequence that lies at distance from gene's promoter and cause increase in transcription activity when transcription factor binds to it causing DNA between enhancer and promoter to loop and get cut out so interacts directly with RNA polymerase
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| cis-operating factors | transcription factors that affect activity on the same DNA molecule in which they reside. example: Promoter sequence
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| trans operating factors | molecules that bind to regulatory sequences and can affect activity of genes in other DNA molecules. examples: transcription proteins- activators and repressors
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| operon | contains structural genes that will encode proteins and promoter region where RNA pol can bind for transcription and an operator where repressor/activator can bind to prevent/activate transcription
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| inducible operon | transcription is usually silenced and needs to get turned on by an inducer
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| repressible operon | transcription is usually ongoing and needs to get turned off by repressor binding to operator
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| negative control | regulator gene that makes a repressor
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| positive control | regulator gene that makes an activator
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| negative inducible operon | transcription is off usually. regulator gene makes repressor that is made an active form. inducer induceds transcription by inactivating the repressor and preventing it from binding to the operator
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| positive inducible operon | transcription is usually turned off. activator is made in inactive form. inducer induces transcription by activating activator
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| negative repressible operon | transcription is usually on. repressor is made in inactive form. corepressor activates repressor enabling it to bind to operator
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| positive control operon | transcription is usually on. activator is made in active form. represoor represses transcription by inactivating activator
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| lac operon contains | lacZ: beta-galactosidase, lacY: permease, lacA: transacetylase, and opterator and promoter
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| lacI gene | encodes lac repressor which binds the operator and prevents transcription. gene lies at a distance from operon so repressor is trans-acting
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| lac operon is what type of operon | negative inducible operon
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| describe activity of lac operon | lac operator is off. lacI produces repressor in active form that keeps transcription off. with lactose->allolactose. allolactose is an inducer that binds to repressor preventing it from binding to operator and that induces transcription
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| trp operon is what type of operon | negative repressible operon
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| describe activity of trp operon | trp operon is on usually. repressor is made in inactive form. when there is enough tryptophan in the environment, tryptophan can act as a corpressor that binds to repressor, activates it, and repressor binds to operator and transcription is stopped
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| how did jacob and monod discover the mechanisms for gene regulation in the lac operon | by using bacteria strains with mutations. they used partial diploid cells that had taken up a plasmid that contained its own copy of the lac operon
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| are lacZ and lacY independent or dependent | independent on each other. bacteria with lacZ+ lacY- / lacZ- lacY+ produced one working copy of each gene and produce beta-galactosidase and permease
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| even thought Z, Y, and A genes are independent of each other in the lac operon, how could a mutation in one affect the other? | all three genes are part of the same operon and so are transcribed together. a nonsense mutation in the Z gene (that is first after the promoter, Z, Y, then A) would then prevent translation of Y and A
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| how did jacob and monod find out that the repressor from the lacI gene was a trans acting factor | a mutation in lacI gene causing the repressor protein to remain inactive. lacI+ lacZ-/lacI- lacZ+ did not produce any beta-galactosidase in the absence of lactose but did produce it when lactose was present. lacI+ was dominant over lacI-
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| supressor mutation lacIs | prevents inducer from binding to repressor so that repressor is always active and the inducer is unable to induce transcription. lacIs lacZ+/ lacI+ lacZ+ does not produces beta-galactosidase even when lactose is present. trans-acting factor is dominant
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| constitutive motuation in lac operator | lacOc prevented the repressor from binding and so transcription was always on. lacOc lacZ+/ lacO+ lacZ+ always produced beta-galactosidase even in the absence of lactose
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| is lacOc cis acting or trans | cis acting. can only cause beta-galactosidase production when genes lie together.
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| lacI+ lacO+ lacZ-/ lacI+ lacOc lacZ+ | produces beta-galactosidase all the time even in the absence of lactose
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| lacI+ lacO+ lacZ- / lacI+ lacOc lacZ- | produces beta-galactosidase but only in the presence of lactose
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| promoter mutations | prevent RNA polymerase from binding to promoters demonstrating that promoter is a cis-facting factor
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| lacI+ lacaP+ lacZ+ / lacI+ lacP- lacZ+ | beta-galactosidase production is normal and only when lactose is present
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| lac operon also exhibits positive control in catabolite repression | glucose present then lac operon off. activator binding site upstream lac operon. CRP is activator but needs to bind to cAMP to be active. glucose low, cAMP increases. CRP-cAMP complex binds to activator binding site and transcription starts
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| trpL | gene in trp operon between operator & structural genes. region 1: leader sequence with 2 tryptophan codons, region 3 can form stem-loop structures by binding with region 2 ( allows transcription) or region 4 (inhibits transcription)
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| describe attentuation of trp operon when tryptophan levels are high | ribosome reads through two tryptophan codons in trpL and translates to STOP codon which means it sits on trp codons and blocks formation of stem loop of region 2 and 3 so region 3 binds with region 4 halting transcription
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| describe attentuation of trp operon when tryptophan levels are low | ribsome stalls as it tries to translate the leader peptide in trpL because it can't find the tryptophan it needs. allows stem loop to form between region 2 and 3 which allows transcription all the way through the structural genes coding for tryptophan.
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| interfering RNAs regualte translation by | having sequences that are complementary to certain genes' mRNAs, they can bind to these mRNAS and either increase or decrease translation by changing the secondary structure of mRNA and either allowing or blocking ribosome from attaching to it
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| riboswitches | region on mRNA where proteins can bind & control whether translation is on or off. regulatory protein, mRNA configuartion that masks ribosome binding site. with regulatory protein absent mRNA has configuation that makes ribosome binding site available
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| ribozymes | mRNAs that can cleave themselves when other molecules bind to it. high concentration of product molecule results in binding to ribozyme and mRNA cleaves itself
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| insulators | prevent gene activation by transcription factors. boundary elements of DNA sequences that block or insulate effect of enhancers in position dependent manner
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| response element | sequence within promoter region of several genes that coordinate gene regulation of those proteins. so a number of signals can affect on response element or a one signal can affect many response elements. heat/stress
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| chromatin reconfiguration to regulate gene activity is done by | epigenetic factors, methylation and acetylation of histones depending on the specific amino acids that get methylated or acetylated.
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| methylation of histones regulates flowering | FLC gene makes a protein that causes histones to be methylated inhibiting genes that enable the plant to flower. FLD genes encodes a histone deacetlyase so FLD expression enables flowering
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| chromatin-remodeling complex | complexes of transcription factors and other proteins that can move nucleosomes down linker DNA or change the conformation of DNA and/or nucleosomes, to expose DNA for transcription without chemically modifying histones
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| how do chromatin remodeling complexes know which DNA to bind to | transcription activators or repressors attach to complex and then bind to promoter region of DNA
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| DNA methylation | methyaltion of cytosine bases in promoter region can silence transcription because it prevents transcription afctors from binding.
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| CpG islands | found near transcription start sites and they are for long term gene repression. methylation of Cs followed by Gs represses transcription
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| X-chromosome inactivation | X that gets inactivated makes RNA X-inactivation specific transcript, XIST that coats chromosome and supercondenses it and fosters methylation of promoter region.
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| what happens if methylation patterns are not established properly | child will either have two or zero working copies of its imprinted genes
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| DNA methylation is coupled with what | Histone Deacetylation. methylated DNA binding proteins have domain that binds methylated DNA and domain that has histone deacetlylase activity
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| paramutation | heritable changes in gene expression due to epigenetic effects
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| specialized DNA methyltrasnferase | DNA full methyalted b4 replication. new DNA strands are made without methyl groups. after replication each DNA molecule hemimethylated meaning- only methylated on 1 strand. methyltransferase adds methyl groups to unmethylated strand
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| different isoforms of proteins come from | different splicing of a pre-mRNA when protein's genes are distributed across exons. different sets of exons can be spliced out resulting in different proteins
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| sex determination in flies | 2 X-chromosomes=female-specific promoter activated transcribing Sxl gene=Sxl protein regulates splicing pre-mRNA of tra gene=tra protein + tra 2 splice pre-mRNA of Dsx protein=female fly
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| poly-A binding proteins | bind to poly-A tail and stabilize mRNA but if poly-A tail shrinks too much then poly-A-binding proteins can't bind anymore and mRNA degrades by RNAse
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| small interfering RNAs or microRNAs and RISCs | dicer cleaves double-stranded RNA to siRNAs or miRNAS that pair with proteins to form RNA-inducing silencing complex RISCs that use complementary base pairings to bind to mRNA or gene to inhibit translation
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| difference between miRNA and siRNAs | siRNAs are exogenous double-stranded taken into cell. miRNAs are single stranded and endogenous-transcribed from cell's genome. .
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| RNA cleavage | RISC complex with siRNA includes endonuclease that cleaves double-stranded RNA and then degrades
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| inhibition of translation by miRNA | miRNA uses complementary base pairing at 5' end of mRNA to prevent ribosome from attaching to ribosome
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| interfering RNAs regulating gene expression by direct interaction with gene | miRNAs attach to complementary sequences in DNA and attract methylating enzymes which methylates DNA or histones inhibiting transcription
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| long noncoding RNAs | inhibit transcription by repressing action of transcription factors
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| ubiquitin tags | ubiquitin brings proteins to preteasomes to be degraded. proteins attach ubiquitin to specific target proteins can be increased or decreased across lifespan of cell
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| forward vs reverse mutation | wildtype to variant vs variant back to wildtype
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| point mutation | single nucleotide mutation
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| somatic mutations | arise in somatic tissuesthat do not produce gametes leading to clones. earlier in development, larger the clone population. gets passed down to 1/4 of cells
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| germ line mutation | arise in cells that produce gametes, passed to future generations in gametes and somatic cells
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| silent mutation | do not change amino acid sequence
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| frameshift mutation | cause ribosomes to read wrong codons and incorporate the wrong amino acids into polypeptide caused by insertion or deletion that are not multiples of 3
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| neutral mutation | changes in amino acid content of the protein has no functional consequence
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| surpressor mutation | mutation that silences other mutation so it restores the wildtype phenotype. double mutant with normal phenotype
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| intragenic supressor mutation | mutations within same gene's coding sequence
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| intergenic supressor mutaiton | mutations in second gene's coding sequence
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| conditional mutations | some mutations only cause consequences under certain conditions
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| transition | purine replaced by another purine or same with pyrimidines
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| transversion | purine replaced by pyrimidine or vice versa
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| loss of function mutations | cause complete or partial absence of normal protein function. recessive. protein can't function properly
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| gain of function mutations | causes cell to produce protein or gene produce whose function is not normally present. dominant
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| lethal mutations | premature death
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| mutations in chromosomes | deletions and duplications or inversions and translocations. or entire chromosomes can be added or deleted
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| positively charged amino acids | arginine, histidine, and lysine
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| negatively charged amino acids | glutamic acid and aspartic acid
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| synonymous mutations may change the splicing of mRNA | creating new splice sites and either add intronic nucleotides or delete exonic nucleotides, either way it will incorporate wrong amino acids
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| mutations in coding sequence can change activity of molecule or protein whereas mutations in regulatory sequences | affect rate at which gene makes proteins and therefore number of proteins in body
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| trinucleotide repeats | can happen in both coding regions and/or regulatory sequences where 3 bases get repeated and the larger the repeated string the more it disrupts function
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| trinucleotide repeat expansion | newly synthesized DNA forms hairpin loop which causes DNA polymerase to replicate that portion of the template strand again and then both the template and new DNA have expanded repeats
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| common fragile sites | all over genome, in everyone's chromosomes which are not associated with disease
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| rare fragile sites | sites where chromosome looks like it is about to break because it is stretched and these sites are related to disease
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| anticipation | the larger a trinucleotiode repeat gets the more severly it disrupts function and subsequent generations affected earlier and more severely
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| transposable elements | sequences that can move about in genome and cause mutations
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| short flanking direct repeats | present on both sides of the transposable element. does not move with element but instead is filled in when element is inserted into DNA
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| terminal inverted repeats | inverted complementary sequences at the end of transposable elements that are recognized by transposase so transposition can occur
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| transposase | enzyme coded for by transposable element, makes staggered breaks in DNA and integrates transposable element into new DNA site
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| DNA transposons | transposable elements that are DNA sequences. uses replicative transposition
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| retrotransoposons | RNA is transcribed from DNA and reverse transcriptase then transcribes it into DNA. uses nonreplicative transposition
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| replicative transposition | copy and paste. new copy incorporated into new DNA site while old copy remains where it was so number of transposable elements increases
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| nonreplicative transpositoin | transposable element is excised from old site and is incorporated into new site
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| control of transposition is done by | methylation of DNA or interfering RNAs to interrupt transposase production
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| transposable elements can cause chromosome rearrangmene | deletion, inversion, or duplication
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| spontaneous mutation | error in DNA replication or base changes after DNA replication
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| induced mutation | environemental agents causing mutations
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| depurination | lose of purine base causing an apurinic site
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| deamination | loss of amino group from base that can cause a transition mutation can be caused by nitrous acid
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| incorporated errors | mismatched base has been incorporated into newly synthesized nucleotide chain which leads to replicated error
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|
||||
| replicated error | an original incorporated error creates a permanent mutation because all base pairings are correct but sequence is wrong
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|
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| base analogs | chemicals with structures similar to that of one of 4 nucleotides and so is incorporated into new DNA molecule because DNA polymerase cannot distinguish. example: is 5'bromouracil
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|
||||
| alkylation agents | chemicals that donate alkyl groups to nucleotide bases that make them have mismatched base pairs producing incorporated and replicated errors
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|
||||
| hydroxylamine | mutagen that adds hydroxyl to cytosine that causes it to pair with adenine creating incorporated and replicated error
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|
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| oxidative mutation | reactive oxygen causes transversion mutation that causes icnorporated errors and replicated errors
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| intercalating agents | sandwich themselves between adjacent bases in DNA-distroting 3D structure cuasing single nucleotide insertion or deletions which causes a frameshift mutation
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|
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| pyrimidine dimers | UV brings two neighboring nucleotides closer together leaving bases unable to bond with complementary bases preventing DNA replication and so cell goes into apoptosis
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||||
| base mismatch repair | excise section of wrong new DNA and fill in gap using old DNA as template
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|
||||
| how does mismatch repair complex distinguish between old and new DNA strand when repairing a base mismatch repair | old strand has methyl groups on adenine on special sequence GATC and it nicks unmethylated strand at GATC site
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| direct repair | does not replace altered nucleotide but changes them back into original structures
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|
||||
| base excision repair | DNA glycosylase cleaves nucleotide by cleaving bond between base and sugar creating apurinic/apyrimidic site. AP (apurinic/apyrimidic) endonuclease cuts out phosphodiester bond. DNA polymerase adds nucleotides to exposed 3'OH group. DNA ligase seals
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|
||||
| nucleotide excision repair | enzymes scan for leisions. enzymes separate strands while single-stranded bindinging proteins stabilize. both sides of sugar phosphate backbone cleaved. damaged strand peels away by helicase. DNA polymerase fills and DNA ligase seals
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|
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| double-stranded break | both strands of helix are broken
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|
||||
| homologous recombination for double-stranded breaks | uses sister chromatid as template. double stranded break. removes nucleotides at broken ends. a free 3' end invades and displaces unbroken strand so that it can be used as a template for DNA polymerase to replicate. creates 2 holiday junctions
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|
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