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Chapter 7 Cell Bio
Molecular Biology of the Cell Chapter 7
| Question | Answer |
|---|---|
| All cell types within a multicellular organism contain the same what? | Nucleotide sequence (i.e. genetic material) |
| The development of cells that are dramatically different in structure and function (neuron versus epithelial cells) must be at the level of what? | Gene expression |
| Give the steps in the frog experiment | 1. All genomic material was eliminated from an unfertilized frog oocyte. 2. The nucleus isolated from culture (diploid) frog epithelial cells was injected into the annucleated egg 3. Gave rise to a tadpole with its full range of differentiated cells. |
| Differentiated cells contained all the information necessary for the development of what? | Other cell types |
| Two different cell types from the same multicellular organism contain the same what? | Genetic material |
| Different cells end up differing at the level of structure and function due to differences in what? | The particular genes expressed |
| The path from DNA to protein has 6 distinct regulatory points. What are they? | 1. transcription frequency 2. Splicing and processing of mRNA 3. Which mRNA will be exported, cytosol localization 4. Which mRNA to be translated 5. Destabilizing mRNA 6. controlling protein activation, inactivation, degradation and localization |
| What are the three general Molecular players? | 1. General transcription factors (TFIID, TFIIB, TFIIE, etc) 2. RNA polymerase II 3. Promoter TATA box element |
| What are the players with a modulatory role? | 1. Specific DNA nucleotide sequences (promoter) 2. Gene regulatory proteins (transcription factors) |
| Specific DNA nucleotide sequences (promoter)- How long? What is it's function? | <20 nucleotides in length Act as recognition sites for regulatory proteins |
| Gene regulatory proteins (transcription factors)Where do they bind? What groove do they interact with? | Bind on the outside of double stranded DNA. Primarily major groove interaction |
| Give four common gene regulatory/transcription factor motifs | 1. Helix-turn-helix/Homeodomain 2. DNA-binding zinc fingers 3. Leucine zipper 4. Helix-loop-helix (HLH) |
| What protein motif is this? Two α-helices (red and blue) separated by an amino acid spacer (turn); C-terminal helix (red) binds within the major groove of DNA | Helix - Turn - Helix |
| Helix Turn Helix binds DNA as a what? | Homomeric dimer |
| (Helix Turn Helix)Amino acid side chains, which vary from protein to protein, defines what? | The specific DNA sequence recognized |
| (Helix Turn Helix) C-terminal helix is called what? | The recognition helix |
| All examples of helix turn helix motif are what kind of cell in origin? | Prokaryotic |
| What motif is related to the helix-turn-helix transcription factors from bacteria. It consists of three closely packed α-helices with helix-2 and -3 resembling the helix-turn-helix motif? | Homeodomain |
| What groove of DNA does Helix-3 make specific contact? What groove of DNA does Helix-1 make contact? | Helix-3: Major groove Helix-1: Minor groove |
| The conserved 60 amino acid motif that defines this family is called the what? | The homeodomain |
| Where are homeodomains found? | All eukaryotes from yeast to humans |
| Which motif contains several structurally distinct groups, but all require zinc atoms for DNA binding? | Zinc Fingers |
| What two amino acids are typically involved in coordinating the zinc atom? | Histidine (H) and cysteine (C) |
| The zinc finger typically forms a dimer; α-helix interacts with what groove of DNA? | Major groove |
| With Zinc Fingers, zinc binding presents the what helix to DNA for binding? | Alpha helix |
| What motif is this? DNA recognition motif is combined with a dimerization motif. Two helices are held together by hydrophobic amino acid side chains (e.g. leucine). It forms a Y-shaped structure that allows contact with the major groove of DNA. | Leucine Zipper |
| A long α-helix, followed by a loop and then a shorter α-helix HLH motif binds to DNA and to another HLH motif (dimerization) Can form homo- or heterodimers Truncated HLH proteins (green) can regulate DNA binding activity of the heterodimer | Helix-Loop-Helix |
| What two kinds of controls are there in gene regulation in procaryotes? | 1. Positive control: Transcriptional activators 2. Negative control: Transcriptional repressors |
| What aids RNA polymerase binding to the promoter and stabilizes the RNA polymerase transition state promoting the conversion from a DNA bound state to a transcriptional active form. It increases the rate of transcriptional initiation by 1,000X? | Transcriptional activators |
| What can compete for DNA binding with RNA polymerase? | Transcriptional repressors |
| Both activators and repressors bind to specific DNA sites that are located close to what? | The RNA polymerase binding site. |
| The bulk of transcription in bacteria requires only what two things? | RNA polymerase and sigma factor |
| For some promoters, the sigma factor and RNA polymerase are not sufficient, why? | 1. Some promoters are poorly recognized by RNA polymerase. 2. RNA polymerase is not able to open the double stranded DNA to initiate transcription |
| In cases where sigma factor and RNA polymerase are not sufficient, what is needed? | Regulatory factors/transcription factors |
| What kind of transcription regulation has a DNA bound repressor protein that blocks transcription? (Negative or Positive regulation?) | Negative regulation |
| What kind of transcription regulation has a DNA bound activator promotes transcription? (Negative or Positive regulation?) | Positive regulation |
| Transcription factors are either activators or a repressors depending on the location of their DNA binding site | The location of their DNA binding site |
| As a transcriptional activator the lambda repressor protein promotes a favorable interaction with what? | RNA polymerase |
| When the lambda repressor binding site is close to the ribosome binding site, lambda binding prevents what? | RNA polymerase association |
| Transcription factor binding can be at a distance from RNA polymerase binding but still effect what? | Transcription |
| An enhancer element binds several hundred base pairs from the transcriptional start site but through the process called what? | DNA looping |
| Bacteria express a number of different what each able to direct RNA polymerase activity at different promoters? | Sigma factors |
| Different sigma factors allow bacteria to activate an entire subset of genes involved in the same what? | Biological pathway |
| What are the similarities between prokaryotic and eukaryotic gene regulation? | 1. DNA looping occurs 2. They contain DNA regulatory proteins that can activate or repress gene activity |
| What are the differences between prokaryotic and eukaryotic gene regulation? | 1. More regulatory proteins and larger stretches of DNA 2. No operons; 3. The presence of chromatin 5. The presence of the accessory protein, Mediator, extends the contact area for transcription factor binding |
| Is mediator present in bacteria? | No |
| What is a 24 subunit protein complex that extends the contact possibilities between transcriptional regulators and RNA polymerase? | Mediator |
| Eukaryotic gene control region is called a what? | Promoter |
| The promoter region includes binding sites for what? | RNA polymerase, general transcription factors and additional regulatory proteins |
| What sites for regulatory proteins may be immediately upstream, far upstream, or downstream of the promoter and even within introns? | Binding |
| What allows DNA regulatory proteins at distant sites to influence RNA polymerase activity via the Mediator complex? | DNA looping |
| Not all regulatory proteins act through mediator, how else can they act? | 1. Directly interact with RNA polymerase 2.The general transcription factor machinery 3. Some regulatory proteins may have an indirect effect through their influence on chromatin structure |
| What are the possible roles for activator proteins in transcription? | 1. Bind general transcription factors and promote their assembly at an adjacent promoter site 2. Bring Mediator to a DNA region to promote RNA polymerase and general transcription factor assembly 3. Modify the surrounding chromatin structure |
| Transcriptional activators are what? (They have one domain that binds to a specific sequence of DNA and a second domain (activation domain) that accelerates the rate of transcription initiation) | Modular |
| By promoting a change in what, the enzymes recruited by gene activator proteins make the underlying DNA more accessible to the general transcription factor machinery, RNA polymerase and/or mediator? | Chromatin structure |
| Longevity of chromatin modifications varies how? | They can be rapidly reversible, or can last into the next cell division. |
| What remodeling provides an additional layer of transcriptional regulation forming short, medium or even long term memory of transcription patterns? | Chromatin |
| What makes histones more accessible to histone chaperones thereby promoting their removal? | Histone acetylation |
| Histone removal or remodeling promotes transcriptional initiation by increasing the accessibility of what? | DNA |
| Histone removal or remodeling facilitates the assembly of what at these sites? (3 answers) | Mediator, RNA polymerase and general transcription factors |
| Repressors work on a what by what basis? | Gene by gene |
| Repressor and activator proteins can compete for the same what? | DNA binding site |
| What can block the assembly of general transcription factors at the promoter. They may also block the release of general transcription factors from RNA polymerase II to prevent transcriptional elongation? | Transcriptional repressors |
| Repressors may recruit what to the nucleosomes, returning the chromatin to its compact pre-initiation state? | Chromatin remodeling complexes |
| Repressors can also attract what? By removing the acetyl group from histone the repressor can prevent transcriptional initiation | Histone deacetylases |
| A repressor can attract what to the chromatin? This results in methylation of specific amino acids in histone. This modification promotes the association of proteins that maintain the chromatin in a transcriptional silent form | Histone methyl transferase |
| Gene regulatory proteins (i.e. enhancers) can work at a distance taking advantage of what? | DNA looping |
| Mechanisms in place to prevent the inappropriate activation of an adjacent gene include what? | Insulator elements and barrier sequences |
| Barrier sequences prevent the spreading of what (highly condensed form of DNA) into genes that need to be expressed? | Heterochromatin |
| Is gene expression is 'off' or 'on' in areas of heterochromatin? | off |
| What prevents the spreading of heterochromatin formation? | The barrier sequence |
| What prevents enhancer elements from activating the transcription of inappropriate genes? | Insulator elements |
| Insulator elements only work when they are positioned where? | Between the enhancer element and the promoter |
| Name some methods at the level of gene regulation | 1. Attenuation 2. Capping 3. Splicing 4. 3'-end cleavage 5. Possible RNA editing 6. Nuclear export 7. Localization in the cytoplasm 8. mRNA degradation 9. translational regulation |
| In bacteria, some genes are transcriptional regulated by "sensing" the availability of small metabolites through their use of what? | Riboswitches |
| What are the steps of purine synthesis in the absence of guanine? | The 5' end of an RNA adopts a folded conformation that permits continued RNA polymerase transcription promoting the expression of genes in this operon |
| What are the steps of purine synthesis in the presence of guanine? | When guanine levels in the cell increase the 5' end of the same RNA molecule associates with guanine adopting a different conformation This new RNA structure forces RNA polymerase to terminate transcription, shutting down expression |
| What removes intron sequences from precursor RNA? | RNA splicing |
| Splicing occurs differently in different cell types generating many different polypeptide chains from the same DNA sequence. This process is called what? | Alternative splicing |
| In some cases alternative splicing occurs because the choice of a splice site is unclear and the final selection is made simply by chance However, in most cases the choice is a what? | Regulated one |
| Cells contain regulatory molecules that influence splice selection by what? (2 answers) | Promoting the recognition of a particular splice site or preventing its recognition by binding to and blocking the splice site |
| In eukaryotes, termination of transcription is mediated by an RNA cleavage event which results in one of the RNA transcripts lacking what? | A 5' cap |
| RNA molecules lacking a 5' cap are quickly degraded. This stimulates RNA polymerase dissociation promoting what? | Transcriptional termination |
| The selection site for what is another regulatory step in gene expression? | RNA cleavage |
| RNA cleavage is modulated through levels of what protein present within the cell? | CstF |
| CstF binds to what regions found in RNA cleavage and polyA sites and promotes RNA cleavage | G/U regions |
| Under conditions of low CstF activity, only what sites are chosen as cleavage sites? | optimal sites |
| Only what kind of mRNA transcripts are exported out of the nucleus? | Fully processed |
| What test does a mRNA transcript undergo after leaving the nucleus? | Nonsense mediated decay test |
| The process of regulation by moving the mRNA to different areas of the cytosol commonly occurs early in development to establish what? | Asymmetry or cell polarity |
| How are mRNAs localized in the cytosol? | Random diffusion and trapping Trapping coupled with generalized degradation Directed transport on cytoskeletal elements (actin, microtubules) |
| In eukaryotes, mRNA transcripts contain what two things? | A 5' cap and a 3' polyA tail |
| Removal of either the 5' cap and 3' polyA tail results in mRNA degradation by what? | Cellular exonucleases |
| Removal of the 5' cap leads to what? | 5' to 3' degradation |
| Internal mRNA cleavage by a specific nuclease generates two mRNA transcripts; What are they? | One lacking a 3' polyA tail with the other half lacking a 5' cap |
| Proteins that block nuclease recognition inhibit mRNA cleavage protecting the transcript from what? | Degradation |
| What acts as a sensor for iron availability in the cell | Cytosolic aconitase |
Created by:
sngoebel
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