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CH 19 Euks Genetics
Gene Expression Exam 4 content
| Question | Answer |
|---|---|
| What is chromatin and how does it affect transcription? | Chromatin structure often makes DNA unavailable to the transcription machinery. Regulation needs modifying histones to open regions for transcription |
| What is an enhancer? | DNA sequence--> a regulatory site keen to distance (up to tens of thousands of nucleotides away) from the promoter. |
| Where can enhancers be found? | may be located either 5' or 3' to the transcription start site |
| How many enhancers can a gene have? | A single gene can have one enhancer or several, and an enhancer may have multiple binding sites |
| What proteins bind enhancers? | Activators and repressors bind enhancer sequences to control transcription. |
| What is a transcription factor? | proteins that directly bind DNA at promoter or enhancer regions and influence transcription. |
| What is a basal factor? | assist the binding of RNA polymerase to the promoter. TBP binds the TATA box and recruits TAFs, forming the basal complex that produces basal transcription. |
| What is a Mediator? | mediates, forms a bridge between RNA polymerase at the promoter and activators or repressors at the enhancer |
| What is an activator? | bind enhancer DNA and increase transcription above basal levels and aides in opening chromatin |
| How do activators increase transcription? | Helping recruit basal factors and RNA polymerase. Recruiting coactivators that “open” chromatin by removing nucleosomes. |
| What is a helix-turn-helix motif? | One of the well-characterized DNA-binding structures used by transcription factors. |
| What is a zinc finger? | A common DNA-binding domain found mainly in eukaryotic proteins |
| What is a dimerization domain? | A domain that enables transcription factors to interact with other copies of themselves or different subunits to form multimeric proteins. |
| What is a leucine zipper? | A structural motif in many dimerization domains where helices contain leucines at regular intervals that allow two proteins to interlock. |
| What is a repressor and how does it work? | Repressors bind specific DNA sites (such as enhancers) and prevent the initiation of transcription, usually by recruiting corepressors |
| What is an indirect repressor? How do they inhibit activators? | prevent transcription initiation indirectly by interfering with activators. They work by: competing, quenching, or block the enhancers binding sites |
| How is chromatin modified? | acetylation or methylation (addition of groups to histone tails) |
| Can a gene have more than one enhancer? Can an enhancer have more than one binding site? | yes and yes |
| What are allosteric interactions? | effectors bind transcription factors and change their shape, altering DNA-binding affinity (example: steroid hormone receptors). |
| How do enhancers know which gene to control if they are far from the promoter? | Insulators organize chromatin into topologically associating domains (TADs), restricting which promoters an enhancer can contact |
| What is an insulator and how does it work? | DNA elements located between a promoter and an enhancer that block enhancer activity |
| What is alternative splicing and how is it controlled? | a way of bringing together different exons |
| How is alternative splicing controlled? | by spliceosomes (tons of proteins) and sequence-specific RNA-binding proteins |
| How does the length of the poly-A tail influence translation? | – by way of circularization of mRNAS. Circularization is dependent upon the tail. As are needed to make the circle. The longer the As, the longer the circle. |
| What is a decoy AUG (uORF) and how does it regulate translation? | Decoy AUG is a AUG sequence before the main one. If ribosome is able to recognize this, then it will start making a short peptide in stock and it will never make it to the main one |
| What happens if the decoy AUG is blocked? | the ribosome can make the protein it was designed to make. |
| What small RNAs are found in eukaryotic cells? | all small RNAs will associate with Argonaute protein family. There are microRNAs, small interfering RNAS, and piwi RNAS. |
| microRNAS (miRNAS) | Negatively regulate mRNAs complimentary to messenger RNAS, depending on what they’re complimentary to, they make their way to its target. perfect complementarity =will break it so mRNA can translate it. Designed to take mRNAS out of commission |
| Small interfering RNAs (siRNAs) | Derived from double-stranded RNA, guide Argonaute complexes to destroy complementary RNAs; help defend against viruses. |
| piwiRNAs (piRNAs) | block transcription & translation of mRNAs. Designed to keep transposons in place (Which normally pick up pieces of DNA and move them places on that DNA) |
| How do miRNAs work? | processed from pri-miRNAs by Drosha and Dicer → loaded into miRISCs with Argonaute → cause mRNA cleavage (perfect match) or translation inhibition (imperfect match). |
| How do siRNAs work? | Form complexes with Argonaute proteins and destroy complementary RNAs using mechanisms similar to miRNAs. |
| How do piRNAs work? | block both transcription and translation of transposable element mRNAs, preventing genome disruption. |
| What are Argonaute proteins? | Proteins that small RNAs associate with; they form ribonucleoprotein complexes that guide the small RNA to its complementary target sequence. |
| What post-translational modifications regulate protein activity? | add or remove functional groups via phosphorylation or glycosylation |
| Eukaryotic gene expression involves multiple regulated steps: | transcription initiation, transcript processing, export, mRNA stability, translation, and protein modification |
| Eukaryotes have: | Chromatin structure RNA processing Transcription in nucleus / translation in cytoplasm No polycistronic mRNAs |
| Enhancers | Eukaryotic |
| Eukaryotes do not have a unique | methionine |
| Introns | Euk --> regions of RNA transcription that need to be removed before the RNA can be transferred. |
| RNA polymerase | both euk and prok -->enzymes that read and make dna using dna as a template |
| nuclear membrane | euk |
| circularized mRNA | euk |
| tatobox binding protein | euk |
| promoters | both euk and prok bc it is a region where RNA polymerase binds and starts transcription. This is where tatobox would come into play as well but only for euks |
| 5'cap | euk |
| 3' polyA tail | euk |
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