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CH18 ProKs Genetics
Gene Expression
| Question | Answer |
|---|---|
| what role the sigma factor plays in transcription initiation and elongation? | directs RNA polymerase to the right spot to bind the promoter. Once transcription is started it leaves. once sigma factor is released, elongation begins |
| Which way is RNA made? | 5' to 3' direction |
| What is Rho dependent termination? | involves rho protein. Rho binds behind RNA polymerase as it's transcribing, moves toward it, and helps kick it off |
| What is Rho-independent termination? | Doesn't involve rho protein. happens when the RNA folds into a *hairpin loop followed by a string of U residues. This secondary structure destabilizes RNA polymerase and causes it to release the RNA |
| Which termination mechanism uses a hairpin loop? | Rho-independent termination uses a hairpin loop to signal RNA polymerase to release the transcript. |
| Why are transcription and translation coupled in prokaryotes? | Bc prokaryotes lack a nuclear membrane, Even before RNA is fully transcribed, ribosomes latch onto the 5′ end and follow the Shine-Dalgarno and AUG start site. |
| What is polycistronic mRNA? | a single RNA molecule that contains multiple open reading frames, allowing several different proteins to be translated from the same transcript |
| catabolic pathways | use inducible regulation — they turn on only when the substrate (e.g., lactose) is present. |
| anabolic pathways | like tryptophan synthesis) use repressible regulation — they turn off when the end product is abundant. |
| How is the Lac operon regulated? | Inducible; turned on when lactose (allolactose) inactivates the repressor. |
| How is the Trp operon regulated? | Repressible; turned off when tryptophan activates the Trp repressor. |
| What is a helix-turn-helix (HTH) motif? | Found in secondary structure, binds major grooves, has two α-helices separated by a turn, and one helix fits into the major groove of DNA |
| What is a helix-turn-helix motif used for? | used in regulatory DNA-binding proteins. |
| Why can different helix-turn-helix proteins recognize different DNA sequences? | Because each HTH protein has unique amino acids on the recognition helix that interact with specific base pairs in the DNA major groove. |
| Which operon uses repressible regulation and why? | trp operon, (anabolic) → because the cell should stop making tryptophan when enough is present. |
| WHich operon uses inducible regulation and why? | lac operon, (catabolic) because the cell should only produce lactose-metabolizing enzymes when lactose is available. |
| What genes are found in the lac operon (sugar)? | The lac operon contains three structural genes: lacZ – β-galactosidase lacY – lactose permease lacA – transacetylase These genes are expressed only when lactose is present. |
| What is the operator in the lac operon? | The operator (O) is a cis-acting DNA sequence located near the promoter where the lac repressor binds to block transcription. |
| How do repressors work in the lac-operon? | Repressor present = genes off. |
| How do inducers work in the lac-operon? | Inducer binds repressor → turns operon on. |
| What is allolactose and what role does it play? | a molecule derived from lactose that acts as the natural inducer. Causes a conformational change and freezes up those genes so RNA polymerase can come bind and transcribe the genes. |
| What happens in the lac operon when no lactose is present? | repressor active → no gene expression or transcription occurs |
| What happens when lactose is present? | Lactose → allolactose → binds repressor Repressor falls off operator RNA polymerase binds promoter and transcribes all three genes Cell can import and break down lactose |
| How are the genes of the trp operon (amino acid) controlled in bacteria ? | can shut all 5 genes off at once by controlling the transcription |
| What role does tryptophan play in controlling the trp operon? | Genes & operon get turned off when trp is present. Now it is an anabolic enzyme. |
| When does the repressor bind to the operator? | only binds when tryptophan is attached to it. Usually repressors bind at or near the promoter and is physically blocked so it can’t transcribe the gene. |
| - No lactose repressors active= | no gene expression |
| - Trp works in opposite way: TRp turns off genes responsible for making | Trp |
| Tryptophan binds repressor = | Transcription of trp genes is turned OFF |
| - No trp = | repressor doesn’t bind, genes are turned on to make it. |
| What is meant by allostery? | conformational (shape) change in a protein when it binds an effector molecule. |
| What is an allosteric protein? | To bind to DNA or to not bind. A protein that can change shape when an effector binds, altering its ability to bind DNA or perform its function. |
| RNA Leader | prokaryotic --> The 5′ untranslated region (5′ UTR) of bacterial mRNA that can fold into structures affecting transcription or translation. |
| Terminator | prokaryotic --> A hairpin structure in the leader that causes premature transcription termination. |
| Antiterminator | prokaryotic--> An alternative RNA structure that prevents terminator formation, allowing transcription to continue. |
| attenuation | prokaryotic--> A regulatory mechanism in which translation of the leader peptide influences whether a terminator or antiterminator forms, fine-tuning gene expression (classic in the trp operon). |
| What are small RNAs (sRNAs)? | prokaryotic-->Short bacterial RNAsthat regulate gene expression by base pairing with mRNAs, blocking translation or promoting mRNA degradation. |
| N formylmethionine | prok |
| sigma factor | prok - helps RNA polymerase recognize a specific motor for specific genes. Released as soon as RNA polymerase transcribes a gene. |
| rho | prok - dependent kicks off translation |
| trancription/translation coupling | prok - bc no nucleus |
| RNA polymerase | found in both prok and euk |
| promoters | found in both prok and euk |
| Shine dalgarno box | prok - sequence right around AUG start site that tells ribosomes what AUG is the first one (when translation of mRNA starts) |
| nucelosome | prokaryotic - basic unit of chromatin structure |
| riboswitch | prokaryotic - control their translation |
| polycistrinic mRNA | prokaryotic - |
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