BIOL2010 Prokaryotic Transcription Review PDF

Prokaryotic Transcription What is the goal with the revision lectures? The goal is to show you how to approach this subject matter in such a way that it makes learning easier as the same learning method can be applied to all BIOL2010 topics (DNA replication & repair, transcription and tra...

Prokaryotic Transcription What is the goal with the revision lectures? The goal is to show you how to approach this subject matter in such a way that it makes learning easier as the same learning method can be applied to all BIOL2010 topics (DNA replication & repair, transcription and translation). This approach can be used across all modules. View it as part of the process of becoming an independent learner. We’ll start off by giving you an idea of the types of questions you will be asked in the exam, particularly MCQs and SAQs.  Example MCQs similar to those in the exam The exam is composed of the equally weighted parts: 1. MCQs 2. Short answer questions (SAQs) 3. One essay For the exam you will answer a total of 40 MCQs. All are compulsory. We will go through five examples using Vevox https://southampton.vevox.com/#/me eting/670191/polls SAQ Example Each SAQ is marked out of 5. Half marks are acceptable e.g., 3.5/5. Answer ANY 9 out of 12 SAQs. The 3 sections of MCQs, SAQs and Essay are weighted equally (1/3 of the total each). QUESTION - Describe how the RNAP recognises the promoter site. SAQ Example QUESTION - Describe how the RNAP recognises the promoter site. Where do you start? Giving a generic answer will get you the minimum marks e.g., The sigma factor recognises the promoter. The answer will be expected to contain sufficient information for at least 5 marks. NOTE this is not to say that there are only 5 points to hit. It’s about demonstrating to the marker that you understand and know the information. SAQ Example QUESTION - Describe how the RNAP recognises the promoter site. What promoter site are we asking about – prokaryotic or eukaryotic? What does a promoter site look like? What does the sigma factor look like and how does it bind? Is there only one sigma factor? Exam Doesisbinding 2 hrs in provide directionality? total hence on average each section should be given 40 minutes to answer. 40 minutes/9 SAQs  4.5 minutes per question. Essay question Each lecturer has provided a question that is based on their taught material. You select and answer only one of these questions. Timing is your limit, not word count or number of pages. The essay is given equal mark weights as the MCQs and SAQ but … … the essay tests your depth of knowledge. MCQs (breath of knowledge) – SAQs (breath and depth) – essay (depth). Prokaryotic transcription PROKARYOTIC EUKARYOTIC DNA Replication & Repair Matthew Bellamy Matthew Bellamy Transcription Me Ben Nicholas Prokaryotic transcription The goal of this review is to make you think. It is not a repeat of the lecture information. Ideally, you will go away with an APPROACH to learning. An approach that leads to you being an independent learner. Team based work skills, communication skills, evidence-based decision making, report What do employers writing, a wide range of presentation skills, want? interpersonal skills, adaptability, initiative, problem solving, time management, etc. What’s the story? All good stories have (1) a start, (2) a middle and (3) an end. This module focuses on the CENTRAL DOGMA which has three, excellent stories. START MIDDLE END Synthesis and Repair Initiation Elongation Termination Repair ? ? ? ? Synthesis Initiation Elongation Termination ? ? ? Synthesis Initiation Elongation ? Termination ? ? Where are you going to get caught out? The biggest mistake that students make over the years is distinguishing prokaryotic versions from the eukaryotic versions. The other big mistake involves confusion of DNA replication with RNA transcription or RNA transcription with protein translation. For example, the initiation of DNA replication involves an origin site whereas RNA transcription also involves specific sites called promoter sites. It is surprisingly easy to mix up transcription factors (TFs) with elongation factors (EFs) as both take part during elongation processes (TFs in transcription, EFs in How do you avoid making such mistakes 1. Read the exam question, very, very carefully. 2. Take a big breath and reread the question. Double checking that you are providing the correct answer. 3. Make sure that you can distinguish between prokaryotic and eukaryotic versions of the processes. 4. Use the naming conventions to help you remember e.g., eukaryotic mRNA transcription involves RNAP II, Roman numerals for two, NOT the number 2 and NOT just RNAP (prokaryotic version). The transcription factors associated with RNAP II are called Transcription Factors II (TFIIA, TFIIB, TFIID, TFIIE, TFIIF). You have to include the ‘II’ in the name as well as the specific subunit to show that you know this information. OK then there are two tables to complete Prokaryotic Eukaryotic  Prokaryotic Transcription Review Two main differences between DNA and RNA which applies to prokaryotic and eukaryotic systems: 1. Backbone sugar component 2. Thymine v uracil Lovely picture but not a lot of information. This is a 3rd to a 2:2 answer. Start off by thinking about the RNAP itself, what it is composed of and what activities does it require to carry out its function. Better but we’re still missing lots of information. Early 2:2 grade. Scientists love details as our research depends on the details. We expect you to know and demonstrate the details for your marks to be within the 2:1 to first What is a molecular machine? Molecular machines are a class of molecules typically described as an assembly of a discrete number of molecular components intended to produce mechanical movements in response to specific stimuli, mimicking macromolecular devices such as switches and motors. Naturally occurring or biological molecular machines are responsible for vital living processes such as DNA replication and ATP synthesis. Kinesins and ribosomes are examples of molecular machines, and they often take the form of multi-protein complexes. RNA polymerase (RNAP) is an enzyme that catalyses RNA synthesis from a DNA template via translocation on the DNA. RNA polymerases are therefore molecular machine, as are DNA polymerases and ribosomes. RNAP is a multi-protein complex – components and assembly 2a, b, b’  core enzyme 2a, b, b’ ,  holoenzyme RNAP has multiple functional activities ACTIVITIES 1. Helicase – transcription bubble formation 2. Polymerase – RNA formation 3. Proofreading  Structure of the RNAP Catalytic Centre A U G As part of an essay answer, this places you in a 1st class position. Independent learning.  SPECIFICITY For all biological machines, specificity is important. α What constitutes specificity for this RNAP machine? Core enzyme? Holoenzyme?  Do you think it is worthwhile knowing what the Sigma factors do? Surely the answer is yes if you want to understand how prokaryotes respond to their environment. Yes, if you want to control bacterial numbers. σ70 Yes, if you are ever σ38 required going to think about before going into using or even designing the stationary antibiotics. phase. We are training you to become scientists so What are the Sigma factors recognising? The promoter region, of course. Do Sigma factors turn on transcription of only one gene or a group of genes? If you know under what physiological circumstances Sigma factors are used, then you could have a good guess. What is the other name for sigma70? Does that help? What is the function of sigma38 – alternative name σS (S for stationary)? Many times, the name of proteins can help so understand how they are connected e.g., TFIID. Do you think that we as scientists (markers) would like you to give us examples and plenty of them? Why? What comes after specificity? Regulation From the perspective of transcription, why is regulation important? 1. Expressing all genes at once is a waste of resources. Biology prefers not to waste energy as organisms are always in competition. Those organisms that can save energy while still carrying out their essential functions have an advantage over other competing organisms. 2. Overproduction of some proteins are likely to be toxic. A simple example is ion channels or transporters. 3. Knowing how systems are regulated allows us the ability to manipulate the system. Protein over-expression systems are used extensively in the Biotech/Pharma industries. 4. Development and growth requires certain groups of proteins to be present at certain times. This can define how cells ultimately become tissue, how tissues become organs and how organisms are formed. 5. Responding to external stimuli can require changes in the proteome. For example, we all produce more melanin when exposed to UV light, apart How do prokaryotes regulate their gene expression? Some genes are constitutively expressed – on all the time e.g., lacI. Other genes are regulated in a positive and negative way e.g., see details of the lac operon. This brings up the question of what is an operon? What then follows is what is a regulon? Do eukaryotes regulate their genes in the same way? If not, then what are their positive and negative methods of gene regulation?  What stops a lecturer droning on? What stops transcription? Is it important to stop the process? Why? What is the signal or signals that tells the prokaryotic transcriptional system to stop making mRNA? Is this the same method in eukaryotes? Are we missing something? What’s our story? START MIDDLE END Initiation Elongation Termination Location – where is the mRNA located. Does it stay there forever? Does it breakdown and if so what by? If we don’t teach you this in this set of lectures, do you need to know? Are you becoming an independent learner? Has anyone noticed this in my area of the BIOL2010 Blackboard site? Have you looked at the Reading List? All online and available to you. As an independent learner, what are you doing to ensure that you All of biology is interconnected