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Genetics
Exam 4
| Question | Answer |
|---|---|
| Transcription | the process by which the polymerization of ribonucleotides, guided by complementary base pairing, produces an RNA transcript of a gene |
| the template for RNA transcript | one strand of the portion of the DNA double helix that constitutes the gene |
| the enzyme that catalyzes transcription | RNA polymerase, binds to the double stranded DNA at the beginning of a gene |
| how does the polymerase know where to bind? | it finds the promoter, specialized DNA sequences near the transcription start site |
| promoters in E coli. | contain two characteristic 6-10 base pair sequences |
| RNA polymerase in bacteria | made up of a core enzyme and sigma subunit |
| purpose of the core enzyme in RNA polymerase | brings in ribonucleotides |
| purpose of the sigma subunit in RNA polymerase | involved only in initiation, increase the enzyme's affinity for a particular promoter |
| the whole RNA is called the holoenzyme | can hone in on a promoter, bind tightly to it, and form a closed promoter complex |
| after the RNA polymerase binds to the promoter | RNA polymerase unwinds some of the double helix----now called an open promoter complex |
| RNA polymerase finds the template strand (3' to 5') | it places two new ribonucleotides (complementary to the template strand) at the 5' end of the new RNA and joins them with a phosphodiester bond. |
| when does the sigma subunit release | soon after the first two ribonucleotides are added and bonded together |
| transcription bubble | region where DNA is unwound by RNA polymerase----the newly made RNA remains base paired to the template (a DNA-RNA hybrid) within this bubble |
| in already transcribed regions... | the DNA double helix reforms...the DNA strand kicks out the RNA strand--this hangs out of the bubble with a free 5' on the finished portion of RNA |
| multiple enzymes can transcribe the gene simultaneously | if the promoter is strong...typically in prokaryotes |
| Terminators | RNA sequences that signal the end of transcription , this releases both RNA polymerase and the completed RNA chain from the DNA |
| Intrinsic terminators | cause the RNA polymerase core enzyme to terminate transcription on its own |
| Extrinsic terminators | require additional proteins (the polypeptide Rho) to bring about termination |
| hairpin loops in termination | terminators often form hairpin loops in which nucleotides within the mRNA pair with complementary nucleotides in the same molecule (secondary RNA structure) --folds back on itself and takes RNA polymerase off the DNA |
| Promoters in eukaryotes | three different kinds of RNA polymerase exists that transcribe three different classes of genes |
| eukaryotic RNA polymerase II | transcribes genes that encode proteins |
| enhancers | sequences many base pairs away from the transcribed gene are needed for successful eukaryotic transcription |
| the result of transcription | a single stranded RNA molecule called the primary transcript |
| RNA processing for prokaryotes | there is none....the primary transcript is ready to enter protein synthesis |
| RNA processing for eukaryotes | primary transcripts must be processed in the nucleus before being transported to the cytoplasm for protein synthesis |
| 5' methylated cap | the nucleotide at the 5' end of eukaryotic mRNA is a G placed backwards and is connected to the first nucleotide in the primary transcript (the backwards G was not transcribed from the DNA, but added by a special capping enzyme) |
| methyltransferases | enzymes add methyl groups to the backwards G cap and to one ore more succeeding nucleotides in the RNA...makes a methylated cap |
| purpose of the 5' methylated cap | helps to stabilize the RNA and signal that it is ready for translation |
| 3' poly A tail | the 3' end of most eukaryotic mRNA has 100-200 As at the 3' end |
| addition of the 3' poly A tail | a ribonuclease cleaves the primary transcript to form a new 3' end (dependent on the AAUAA sequence found just a ways up from where the tail will be NEXT, enzyme poly-A polymerase adds As onto the 3' end |
| use for the methylated cap and the poly A tail | crucial for efficient translation, eukaryotic translation factors bind to the 5" cap and poly- A binding proteins associates with the tail-----shapes the mRNA into a circle |
| why in a circle? | helps to protect the mRNA from degradation---needed to circularize to initiate the translation of mRNA |
| sequences found both in the gene's DNA and the mature mRNA | exons---the parts that are kept |
| sequences found in the DNA but not the mature mRNA | introns...they separate the exon sequences that end up in the mature mRNA, they are removed |
| mature mRNAs | must contain all the codons that are translated into amino acids (also initiation and termination codons |
| 5' and 3' untranslated regions (UTRs) | located just after the methylated cap and just before the poly-A tail....they play an important role in determining efficiency of translation |
| RNA splicing | a primary transcript of all of a gene's introns and exons is made, then the introns are carefully removed by splicing----remove introns and join together successive exons |
| precision in RNA splicing | need remarkable precision--avoid losing or gaining bases that might shift the reading frame... |
| short sequences within the primary transcript that help ensure the specificity of splicing | splice donors, splice acceptors, and branch sites |
| mechanism of splicing | first cut is at splice donor site (5')...the 5' end attaches to an A a the branch site and forms a loop called a lariat, the second cut is at the splice acceptor site (3') and the intron is removed |
| what happens to the removed intron | it is degraded |
| intranuclear machine involved in splicing | splice some |
| rare primary transcripts that can splice themselves without the aid of a splice some or any additional factors | called ribozymes: RNA molecules that can act as enzymes and catalyze a specific biochemical reaction |
| alternative splicing | produces different mRNA molecules encode related proteins (similar a acids sequences and functions) It tailors the nucleotide sequence of a primary transcript to produce more than one type of polypeptide----puts the exons back together in different orders |
| translation | the process by which the sequence of nucleotides in a messenger RNA directs assembly of the sequence of amino acids in the corresponding peptide--occurs on ribosomes which coordinate movements tRNAs carrying specific amino acids |
| tRNA | transfer RNAs serve as adapter molecules that mediate the transfer of information from nucleic acid to protein (short, single stranded RNA molecules of 74-95 nucleotides long) |
| what is the difference between different tRNAs | each tRNA carriers one particular amino acid---at least one tRNA for each of the 20 amino acids---each tRNA has a specific anticodon region |
| the nucleotide sequence of tRNA | folds to form secondary and L shaped tertiary structures |
| the anticodon | found at the end of the L region--three nucleotides complementary to an mRNA codon specifying the amino acid carried by the tRNA---the anticodon never forms base pairs with any other part of the tRNA, stays available for pairing with mRNA codon |
| anticodon and codon are antiparallel | anticodon runs 3' to 5'. codon is 5' to 3' |
| amino acid attachment site | the other end of the L where the 5' and 3' end are found.....amino acid is attached to the 3' end |
| aminoacyl-tRNA synthases | connect the tRNA to the amino acid that corresponds to its anticodon; very specific enzymes---recognize features of the anticodon and the amino acid |
| the tRNA covalently coupled to its amino acid | called charged tRNA |
| a tRNA with no amino acid | called uncharged tRNA |
| some tRNAs can recognize more than one codon for the amino acid they carry | the anticodons of these tRNAs can interact with more than one codon for the same amino acid--the degenerate nature of the genetic code! |
| nucleotides in the tRNA can be chemically modified | the modified bases produced are enyzymatically altered nucleotides--at the 5' end make up the wobble position |
| the wobble position | the third nucleotide of the anticodon can often pair with more than one kind of nucleotide in the 3' position mRNA codon |
| a single tRNA charged with a particular amino acids can recognize several or even all of the codons for that amino acid | this flexibility in base pairing between he 3' codon and 5' anticodon positions is called wobble |
| the ribosome | facilitates polypeptide synthesis |
| how does ribosome interact in translation | recognize mRNA features for start of translation; stabilize the interactions between tRNA and mRNA; supply enzymatic activity to link amino acids; move 5' to 3' along the mRNA to ensure linear addition of amino acids into sequence |
| ribosomes in E. coli | three different ribosomal RNAs (rRNAs) and 52 ribosomal proteins form two subunits (one large-50S and one small-30S) |
| before translation....subunits are separate | they come together at the start of translation |
| the small subunit of E. coli ribosomes | the subunit that initially binds to the mRNA |
| the large subunit of E. coli ribosomes | the subunit that contributes the enzyme (peptidyl transferase--activity of ribozymes) that catalyzes the formation of peptide bonds between amino acids |
| three tRNA binding sites on the ribosome | A- aminoacyl site P- peptidyl site E- exit site |
| three phases of translation | initiation, elongation, termination |
| initiation in translation | sets the stage for polypeptide synthesis |
| elongation in translation | the phase in which amino acids are added to a growing polypeptide chain |
| termination in translation | the phase that brings polypeptide synthesis to a halt and enables the ribosome to release a completed chain of amino acids |
| translation initiation in prokaryotes | the signal is the ribosome binding site (has two elements----shine dalgarno box and AUG codon) |
| shine dalgarno box | the first six-nucleotide sequence (AGGAGG) on a prokaryotic mRNA |
| the initiation codon | the sequence AUG that is recognized by tRNA anticodon CAU and adds an N-formylmethionine to the beginning of the polypeptide--its N end is blocked by a methyl group |
| translation initiation in eukaryotes | small subunit of ribosome recognizes the 5' methylated cap on the mature mRNA---many initiation factors and the small subunit arrive at the AUG initiation codon |
| first tRNA at eukaryotic initiation | carries an unmodified methionine--has a free N end |
| elongation factors | bring the appropriate charged tRNA into the ribosome's A site |
| the anticodon of the tRNA must recognize the next codon in the mRNA | allow the proper amino acid to come in next |
| process of the ribosome | holds the initiating tRNA at the P site and the next tRNA at the A site to bond the two peptide bond between the amino acids...the tRNA at the A site now carries two amino acids |
| the empty A site now receives another tRNA as determined by the next codon and the uncharged initiating tRNA leaves the E site and leaves the ribosome | the peptidyl transferase forms another bond adding a third amino acid to the C terminus at the A site |
| direction of growing polypeptide | adds to the C terminus so it is built N to C |
| movement of the ribosome | moves along the mRNA in the 5' to 3' direction so the polypeptide is grown in the N to C direction |
| many ribosomes can work on the same mRNA at one time | a complex of several ribosomes translating from the same mRNA called a polyribosome.....allows the simultaneous synthesis of many copies of a polypeptide from a single mRNA molecule |
| tRNAs do not carry anticodons complementary to any of the three stop codons | when a stop codon moves into the ribosome's A site, no tRNAs can bind to that codon |
| release factors | they recognize the stop codon and halt polypeptide synthesis by releasing the completes peptide from the tRNA for the C terminal amino acid |
| after translation reaches termination | the tRNA, mRNA, and the large and small subunits of the ribosome dissociate from each other |
| processes that may subsequently modify a polypeptide's structure | polypeptide modification |
| cleavage | can remove amino acids or generate several smaller polypeptides from one larger product of translation |
| zymogens | some proteins are synthesized in inactive forms that are activated by enzymatic cleavage to remove an N-terminal pro-segment |
| enzymatic addition of chemical constituents | phosphate groups, carbohydrates, fatty acids, other small peptides can be added to polypeptides after translation |
| posttranslational modifications | can alter the way a protein folds, the ability to interact with other proteins, its stability, its activity, or its location in the cell |
| translation and transcription in prokaryotes | takes place in the open intracellular space--no nuclear membrane |
| translation and transcription can happen simultaneously | transcription extends mRNAs in the same 5' to 3' direction as the ribosome moves along the mRNA....ribosomes can begin to translate a partial mRNA that the RNA polymerase is in the process of transcribing from the DNA |
| mRNA processing | introns only interrupt eukaryotic but not prokaryotic genes...splicing must happen for eukaryotic gene expression, also addition of methylated cap and poly A tail happen in Eukaryotes |
| Enhancers | sequences located far from the promoter that affect the stability of RNA polymerase's interaction with the promoter |
| chromatin | eukaryotic chromosomes are tightly wound around histone proteins in a DNA/protein complex |
| the promoter must be unwound from chromatin | in order for the promoter to be recognized, it must be unwound |
| polycistronic prokaryotic messages | many ribosomes can join to the mRNA at one time, the mRNA can contain the information of many genes which can be translated independently starting at different ribosome sites |
| mutations in a gene's amino acid sequence | can generate a range of repercussions...the result is unpredictable |
| altered proteins can,... | function properly, less efficiently, more efficiently, not at all, or gain an entirely new function |
| silent mutations | a codon is changed to a mutant codon that specifies the exact same amino acid (most times happens at the third nucleotide of a codon--wobble position) |
| silent mutations do not alter the amino acid composition of the encoded polypeptide | mutations don't affect gene expression or phenotype |
| missense mutations | a codon is changed into a mutant codon that specifies a different amino acid |
| conservative substitutions | if the substituted amino acid has chemical properties similar to the one it replaces, this change may have little or no change effect on the protein function |
| nonconservative mutations | if the substituted amino acid has chemical properties very different than the one it replaces, it is likely that the protein will have noticeable differences |
| nonsense mutations | change an amino acid specifying codon to a premature stop codon- causes shortened truncated proteins lacking all amino acids after the mutant stop codon....polypeptide will be unable to function if it requires the missing amino acids for activity |
| frameshift mutations | result from the insertion or deletion of nucleotides within the coding sequence if not in a unit of 3, will disrupt the reading frame all downstream of the mutation----usually results in truncated dysfunctional proteins |
| changes in the sequence of a promoter | make it difficult or impossible for RNA polymerase to associate with the promoter---this diminishes or prevents transcription |
| mutations in promoters of enhancers | if prevented from being recognized by transcription factors, also diminishes the transcription of eukaryotic genes |
| mutation in termination signal | can diminish the amount of mRNA produced and thus the amount of gene product |
| prokaryotic gene expression main difference | there is no nuclear membrane |
| beginning the process of gene expression in prokaryotes | RNA polymerase transcribes a gene's DNA into RNA, requiring the sigma subunit to recognize and bind to specific DNA sequences at the promoter |
| RNA polymerase holoenzyme is needed in all three stages of transcription | begins at initiation to unwindDNA and add complementary bases to the DNA template...keeps going until reaches a termination signal in the RNA |
| switching from initiation to elongation | requires the release of the sigma factor when RNA polymerase moves away from the promoter |
| two types of termination signals for prokaryotes | rho dependent and rho independent |
| rho-independent termination | a sequence of bases in the RNA forms a secondary structure known as a hairpin loop that signals the release of RNA polymerase from the completed RNA and DNA template |
| rho-dependent termination | a protein factor called Rho, a helicase enzyme that unwinds the mRNA from the DNA template, helps dissociate RNA polymerase from the template |
| Transcription and translation in prokaryotes | translation of mRNA into a polypeptide can occur while transcription is still occurring |
| ribosomes bind to special initiation sites at the 5' end of the reading frame | this happens while transcription of downstream regions in the RNA is still in process |
| in prokaryotic translation- polycistronic mRNA | there are multiple spaces for ribosomes to initiate translation, therefore multiple open reading frames for multiple proteins to be made from one mRNA |
| the amount of a particular polypeptide made in a bacterial cell at one time | regulated by many aspects of control (either before, during, or after transcription) |
| DNA binding proteins | regulate gene expression by binding to DNA at or near promoters to control transcription-- the binding of DNA binding proteins either inhibits or enhances the effectiveness of RNA polymerase in initiating transcription |
| Catabolic pathways | involved in the breaking down of complicated molecules for use in the cell- need inducible regulation |
| inducible regulation | pathway should only be turned on when the complex molecules to be broken down are present (presence of substrate activates) |
| Anabolic pathways | involved in the formation of large complex usable biomolecules- need repressible regulation |
| repressible regulation | pathway should be turned on only well the cell does nor have enough of the needed end product (lack of product activates) |
| the lac operon | consists of three structural genes (lacZ, Y and A) , with a promoter region and operator site- is a catabolic operon |
| inducer | a molecule responsible for stimulating the production of a protein - causes induction |
| LacZ, LacY, and LacA | encode the enzymes that are responsible for splitting lactose into glucose and galactose |
| the repressor of the lac operon | binds to the operator and prevents transcription when there is no lactose present (a negative regulatory element) |
| when lactose is present | lactose is made into allolactose, the inducer for the lac operon repressor---binding of allolactose causes a conformational change to the repressor so it is no longer able to bind to the operator |
| once the repressor has left the lac operator | RNA polymerase joins access to the lac operon promoter and initiates transcription of the three lactose utilization genes- a single polycistronic mRNA is produced |
| clustering of genes with similar functions into an operon | simple and efficient way to coordinate gene expression |
| helix turn helix (HTH) motif | DNA binding proteins have the common helix turn helix motif--can fit into the major groove of the DNA |
| the alpha helices of each helix turn helix motif | carry unique amino acids that recognize a specific sequence of base pairs (many different kinds--transcription factors specific to sequence) |
| the trp operon | has five structural genes (trpE, D, C, B, A) and a promoter and operator sites is an anabolic operon |
| regulating the trp operator | responds to the presence of the pathway's end product by shutting down expression of the structural genes whose protein products manufacture the end product |
| tryptophan is the effector for the trp repressor, an allosteric protein----stop transcription in presence of high tryptophan | binding of tryptophan to trp repressor causes the repressor to change shape, enabling it to bind to the operator and inhibit transcription of the trp operon genes |
| Catabolic pathways (lac operon) | are typically in an off state (need to be turned on only when the starting substrate--lactose--is present |
| Anabolic pathways (trp operon) | are typically in an on state (need to be turned off when the end product of the pathway--tryptophan--is present |
| mechanisms that function after transcription is initiated | involve RNA sequences or RNA molecules that can terminate transcription or block translation |
| beginning of bacterial mRNA | has an untranslated region (UTR) or RNA leader sequence |
| RNA leaders form secondary structures | can be called hairpin loops (or stem loops)--can be modified due to a vast number of environmental cues |
| RNA leader hairpin loops | can terminate transcription prematurely or can prevent translation by blocking access of the mRNA to the ribosome binding site |
| attenuator | a portion of the RNA leader that determines if transcription terminates based on how the translation machinery interacts with the attenuator |
| attenuation | the control of gene expression by RNA leader-mediated premature termination of transcription that involves the unusual translation of part of the leader sequence |
| two stable conformations of the attenuator | (terminator or anti terminator) based on the complementary bases in the same molecule of RNA |
| terminator conformation | makes two hairpin loops (1:2 and 3:4)...when it forms in a transcript RNA polymerase contacts it and stops transcription..creates a shortened RNA |
| anti terminator conformation | makes one hairpin loop (2:3), the leader RNA cannot form the terminator and the transcription machinery continues to make a full length mRNA |
| early translation of a short portion of the RNA leader determines which conformation the RNA structure forms | while the rest of the RNA leader is still being transcribed |
| the key portion of the RNA leader that determines RNA conformation | a short open reading frame with 14 codons, two are Trp codons |
| when tryptophan is present...termination conformation is formed | the ribosome moves quickly past the Trp codons and proceed to the end of the leader's codons. allowing formation of the terminator |
| when tryptophan is not present...antitermination conformation is formed | the ribosome stalls at the two trp codons in the RNA leader because of the lack of charge tRNA trp in the cell, anti terminator is able to form, preventing the formation of the terminator--transcription proceeds! |
| why have Trp repressor and the attenuation mechanism | the trp repressor prevents transcription initiation in the presence of tryptophan, but the attenuation mechanism provides a way to fine tune this on/off switch even after transcription has started |
| riboswitches | allosteric RNA leaders that bind small molecule effector to control gene expression |
| leaders that act as riboswitches have a region called the aptamer | this binds to the particular effector directly---riboswitches regulate gene expression directly |
| the expression platform | a second structure on the riboswitch that controls gene expression by altering its hair pin loop structures in response to the aptamer configuration |
| the expression platform controls termination of transcription in some riboswitches | for the production of guanine, if the aptamer of the riboswitch is bound to guanine, the most stable conformation of the expression platform is a terminator (forms an anti terminator when no guanine is bound) |
| the expression platform in other riboswitches controls translation by blocking the ribosome binding site | the binding of the effector to the aptamer shifts the conformation of the leader in a way that blocks the ribosome binding site |
| small RNAs | bacterial genomes encode many small RNAs that base pair with the mRNA to prevent translation---the small RNAs made are complementary to several different mRNA targets |
| Some small RNAs activate translation | they disrupt formation of a hairpin loop structure in the leader of the mRNA that would otherwise block the ribosome binding site |
| small RNAs can also bind to the mRNA to promote degradation | the double stranded RNA resin causes the mRNA to be degraded by ribonuclease enzymes |
| Antisense RNAs | RNAs that are complementary in sequence to the mRNA because their transcription template is the opposite strand of DNA....may be complementary to the whole length of the of the mRNA transcribed from the opposite DNA strand or they may overlap only a part |
| Antisense RNAs can block the ribosome binding site | some antisense RNAs inhibit translation by blocking the ribosome binding site |
| other antisense RNAs---double stranded RNA formed by sense RNA and the mRNA | will be degraded by ribonuclease since it is double stranded RNA |
| the act of transcribing the antisense RNA itself can inhibit the expression of the sense gene | antisense transcription can interfere with initiation of transcription of the sense gene |
| regulation of transcription (prokaryotes and eukaryotes) | happens by the binding of DNA binding proteins to specific DNA sequences close to the transcriptional unit itself |
| complexion of specific eukaryotic regulation | chromatin makes DNA unavailable, RNA must be processed, there is a nuclear membrane, no polycistronic transcript exist, need to be specialized gene for many cell types |
| many steps in gene expression can be regulated | transcript processing, export from nucleus, translation, modifications of protein can all be monitored |
| eukaryotic promoter | usually contains a TATA box just upstream of the transcript initiation site---weakly attracts RNA polymerase weakly on its own (basal level transcription) |
| eukaryotic enhancer | a regulatory site that can be far away from the start site--binding of transcription factors to enhancer can augment or repress basal levels of transcription....can be either up or down stream of the promoter |
| a single gene can have one enhancer or several | and a single enhancer can have a binding site for multiple transcription factors |
| transcription factors | binding of proteins to a gene's promoter and enhancer controls the frequency of transcriptional initiation...once they bind they can recruit additional proteins that can also influence the gene'e transcript |
| basal factors | bind the promoter...assist RNA polymerase in finding promoter-has a TATA box binding protein (TBP) that interacts directly with the TATA box at the promoter |
| activators and repressors | bind the enhancers |
| the TATA box binding protein (TBP) | interacts with the TATA box at the promoter and recruits other proteins (TBP- associated factors TAF) to the promoter---forms the basal complex: can initiate a low level of transcription |
| Mediator | a multi subunit complex containing more than 20 proteins...doesn't bind the DNA directly, serves as bridge between RNA polymerase the promoter and activator or repressor at the enhancer |
| activators | bind to the enhancer...increase transcription above the basal level that occur by the action of the promoter alone...help recruit the basal factors and RNA polymerase to promoter sequences or recruits coactivators that open the chromatin structure |
| activator interacts with DNA at the basal complex | interacting directly or indirectly (through the mediator) made up of a DNA binding domain and an activation domain |
| opening chromatin structures | allows gene expression, Promoter DNA covered with nucleosomes is inaccessible to basal factors and for a gene to be transcribed, the promoter DNA must be free of nucleosomes |
| common domains of transcription factors | zinc fingers and helix turn helices (zinc fingers are found mainly in eukaryotes, but helix turn helices are found in both) |
| a third domain on activators | some activators have a dimerization domain that enables them to interact with other copies of the same polypeptide or other transcription factor subunits to form multimeric proteins |
| dimerization domain | one common structural motif of the dimerization domain is a leucine zipper, a helix with leucines at regular intervals |
| repressors | eukaryotic transcription factors that bind specific DNA sites near a gene (enhancer) to prevent the initiation of transcription of the gene |
| corepressor proteins | repressors recruit corepressor proteins to the enhancers ...they cannot bind to DNA on their own, but can bind if the repressor is already bound to the DNA |
| two functions of corepressors | can interact directly with the RNA polymerase basal complex and prevent it from binding to the promoter, others are enzymes that modify histone tail amino acids resulting in closed chromatin |
| the domains of repressors | have DNA binding motifs, repression domains for interacting with the corepressors, and some have dimerization domains |
| the action of a repressor depends on the location of its binding | some transcription factors are activators if they bind at one site, and repressors if they bind at another |
| indirect repressors | regulatory proteins that prevent transcription initiation indirectly by interfering with the function of activators (competition, quenching, cytoplasmic sequestration,. and heterodimerization) |
| competition and quenching | can compete with activators for access to an enhancer because their bingding sites overlap......or they can do quenching...a protein can bind the activation domain of an activator bound to the enhancer and prevent the activator from functioning.... |
| cytoplasmic sequestration, heterodimerization | some bind to activators and hold them in the cytoplasm....some can form heterodimers with activators, if only homodimers can bind to the DNA, indirect repressors can titrate the activators so that few homodimers are able to form |
| histone modifications | gene transcription is related to the covalent modifications that can be made on specific amino acids of the N terminal tails in histone proteins |
| acetylation of particular lysine amino acids on histone tails | done by the enzymes called histone acetyltranferases (HATs) which favors gene expression by helping to clear promoters of nucleosomes (opens chromatin)...amny coactivators are acetyltransferases |
| methylation of certain lysines or arginines in histone tails | done by histone methyltranferases to activate or repress transcription depending on the particular proteins the methylated site recruits to the nucleosome |
| enhancer element | a sequence that controls a gene's expression in a particular cell type at a particular moment in time |
| eukaryotic transcription factor activity can be regulated through allosteric interactions with effectors | with steroid hormone receptor transcription factors, hormone binding causes a shape change in the receptor protein....increases affinity of its DNA binding domain for its target sequence |
| translation factors can be covalently modified by many chemical groups | can be phosphorylated by kinases...can either activate or deactivate the transcription factor |
| how phosphorylation affects transcription factors | can influence movement of factor into nucleus, can alter the factor's DNA binding properties, ability to multimerize, or ability to interact with coactivators or corepressors |
| insulators | DNA elements that organize chromatin so that enhancers have access only to particular proteins...this prevents an enhancer on a chromosome from influencing any promoter for any gene anywhere on that chromosome |
| insulators are located between a promoter and an enhancer | they block the enhancer from activating transcription at that promoter |
| connections between a protein bound to different insulators, along with the cohesion protein complex | facilitate the formation of DNA loops called topologically associating domains (TADs) |
| a promoter and an enhancer in separate TADs cannot interact with each other | when a promoter and an enhancer are on opposite sides of an insulator, they will be in separate TADs |
| an enhancer can not travel outside of the limits set by the insulators surrounding it | it can only work on the promoters within the insulators in the region it is in |
| post transcriptional regulation | can include regulation of RNA splicing, mRNA translation, use of small RNAs, and post translational modifications to proteins |
| eukaryotic cells can make more than one type of protein from a single mRNA | alternative splicing.....splicing primary transcripts into mRNA |
| splicesomes that assemble at the splice junction sites of primary transcripts | can contain more than 100 proteins |
| spliceosome proteins recognize specific base sequences in the primary transcript | either facilitates or prevents the use of a particular splice junction sequences |
| exons are spliced together based on the interactions of splicesosomes with additional sequence specific RNA binding proteins | these splicesomes are present in some cells and not others |
| translation begins in eukaryotes | when small subunit of the ribosome recognizes a protein complex bound to both the 5' cap of the mRNA and the polyATail (circularizing the mRNA) the ribosome finds the first AUG which is the initation codon for Methionine at the N terminus |
| eukaryotic mRNAs cannot be polycistronic | they only have one one location for the start of translation |
| eukaryotic cells are able to respond to extracellular stimuli because of elF4E binding protein 1 (4E-BP1) | this protein can bind to the translation initiation factor elF4E and this blocks assembly of the remainder of the initiation complex on the 5' cap....kinases phosphorylate 4E-BP1 so it can no longer bind to elF-4E, initiation complex can continue at 5' |
| association of initiation factors at the 5' cap and poly-A binding protein (PABP) | causes circulation of mRNA....this is the physical mechanism for regulation of translation indirectly through control of poly A tail length |
| longer tails attract PABP more efficiently than shorter tails do | the longer the tail, the more translation |
| sequence specific RNA binding proteins bind to sites on the mRNA... | recruit enzymes to either add or remove As to the tail |
| upstream open reading frames (uORFs) | certain mRNAs have one or more uORFs that begin with decoy AUGs and encode small peptides that have no function |
| if the ribosomes translate the uORF, the translation of the major ORF in the mRNA is inhibited | choice between the two open reading frames is a potential point at which gene expression can be regulated...the choice is influences by proteins that bind specific sequences in the mRNA near the decoy start codon |
| small RNAs --specialized RNAs that prevent the expression of specific genes through complementary base pairing | there are three classes: micro-RNAs (miRNAs) small interfering RNAs (siRNAs) and Piwi-interacting (piRNAs).....each class are made differently (each are 21-30 nucleotides long) |
| each small RNA class | forms ribonucleoprotein complexes with distinct members of the Argonaute protein family...each small RNA serves to guide the complex to particular targets |
| miRNAs | one of the most abundant...negatively regulate target mRNAs to prevent translation-transcribed into long primary transcripts (pri-miRNas) with miRNA double stranded hairpin loops...undergo processing by ribonucleases for short, single stranded miRNAs |
| miRNA-induced silencing complexes (miRISC) | each miRISC contains a protein of the argonaute family ....miRNA gets incorporated into miRISCs and guides the protein to mRNA that has complementary sequence to miRNA...causes cleavage if perfect match |
| argonaute family | the proteins that cut RNA |
| miRNAs where there is less complementation to the mRNA | the mechanism is usually inhibition of translation (not complete degradation of the mRNA) |
| siRNAs | result from the processing of double stranded RNAs--produce single stranded RNAs that form complexes with argonaute proteins |
| ribonucleoprotein complexes with siRNAs | use single stranded RNAs as a guide, can interfere with gene expression of complementary mRNA (degrade RNA or inhibit translation) |
| piRNAs | block both transcription of TEs in the genome and translation of the TE mRNAs that do get transcribed |
| Transposable elements (TEs) | propogate themselves by mobilization and transposition....the movement of TEs must be limit to prevent genome damage by constant shuffling |
| post translational changes | can alter or destroy protein structure in order to rapidly change protein activity---example is protein phosphorylation (can change a protein's activity of intracellular localization) helps with transportation or activation or degradation |
Created by:
Gracie Cook