Biol 211 Molecular Biology Test 2 Study Guide PDF

## Biol 211 - Molecular Biology ### Test 2 "Study Guide" a starting point ### DNA Replication - general concepts (from all three replication lectures) - Know what antiparallel means, and why it is important for DNA replication - It results in leading and lagging strands - why? - Know the differenc...

## Biol 211 - Molecular Biology ### Test 2 "Study Guide" a starting point ### DNA Replication - general concepts (from all three replication lectures) - Know what antiparallel means, and why it is important for DNA replication - It results in leading and lagging strands - why? - Know the difference between the leading and lagging strands - Know what complementarity is and why it is important. - Know how the different nucleotides pair together, and how. - Know the basic principles of DNA replication, and how each happens - the DNA has to unwind and the strands separate - the two strand then each act as a template (what does this mean?) - once replicated the strands, new and old, must reanneal and rewind - the new strands are identical to the parent strands - understand how DNA strands would behave in each of the three suggested models, with the greatest emphasis on semi-conservative replication - know what is meant by bidirectional replication, how it happens, and why this is important - know what a replication bubble and replication forks are, and how they form - know what each of the different enzymes do, when, where, and why they participate in DNA replication - helicase, single-stranded binding proteins, topoisomerases, primases, DNA polymerases, nucleases, ligase, sliding clamp, clamp loader - understand that primases are RNA polymerases. Why? Why do we need a primer? Where will primers be placed? - understand the cause and consequences of 5' to 3′ DNA polymerase activity - understand the difference between 5' to 3' and 3' to 5' exonuclease activity, and when each is used - understand the difference between endonuclease and exonuclease activity, and when each is used - know the difference between theta replication and linear replication - be familiar with the main features of rolling circle replication - that it is unidirectional and how that affects the other normal features of replication (strands, bubbles, forks, etc.) - know that DNA replication requires three main categories of reagents: - a template - nucleotides to be added to a new strand - many enzymes to recognize sequences, prepare the template, catalyze synthesis of DNA, - When does replication start and end? ### Bacterial Replication - All of the above concepts - What is required for initiation to happen? - Recognition sequence that contains specific elements (origin) - Why is AT-rich region relevant/important? - Initiator protein that recognizes and binds to origin - What happens when initiator protein binds? - Recruits other machinery - what? - Separates strands - why is this important? - How does initiator protein know not to bind a second time? - The direction that helicase moves in and the strand that it is bound to are connected - how? - Same for eukaryotic helicase - DNA polymerase III is the main bacterial replication polymerase - 5' → 3' polymerase activity and 3′ → 5′ exonuclease activity (what do these mean?) - DNA polymerase I is important for primer replacement - Also has 5' → 3' exonuclease activity (why is this important?) - Why do primers need to be replaced? - What does the holoenzyme consist of? The replisome? How do these complexes achieve efficient DNA replication? ### Eukaryotic Replication - All of the above concepts - Know the main differences, particularly with reference to genome size, when replication takes place, and the structure of the DNA molecules (i.e., the fact that they are linear) - Know how initiation works in eukaryotes - Sites have to be licensed to show that they are to be replicated (and have not yet been replicated) - why is this vital, and how is this done? - Involves the origin replication complex, loading proteins, and MCM2-7 which will ultimately become the helicase - How does MCM2-7 differ from helicase in bacteria? - DNA polymerase alpha synthesizes initiator DNA/primer - 5' → 3' RNA polymerase activity and 5′ → 3′ DNA polymerase activity - DNA polymerase delta and DNA polymerase epsilon are the main replication polymerases - 5' → 3' polymerase activity and 3' → 5′ exonuclease activity - Delta lagging strand, epsilon leading strand - What is one difference between what must happen on leading and lagging strands? - Different way to remove primers - Polymerase displaces primers, but does not remove them entirely - leaves a flap hanging off - FEN-1 removes displaced nucleotides - recognizes unannealed DNA - New histones must also be made as going from one molecule to two (so creation of new chromosomes) - Histones form tetramers or dimers and then assemble at random into nucleosomes - Linear chromosomes have ends - why is this problematic? - What are telomeres and what is their function? What happens if a cell has no telomeres? - What is telomerase? What type of enzyme is it? How does it work? - What happens when a cell has telomerase when it isn't supposed to? ### Overview of Gene Expression - What are the main steps in gene expression? - What is the purpose of each step? - What happens in each step? - How does gene expression differ between prokaryotes and eukaryotes? - Why are there differences? - How is transcription similar to DNA replication? How does it differ? - What is the product of transcription? - Directionality! - What direction is RNA synthesized in? - What direction is the template strand read by the RNA polymerase? - What direction do we read the sense strand in? ### Transcription - What are the key components of transcription? - What are the three main classes of RNA? - What is the difference between the template strand and the non-template strand? How do they compare to the RNA transcript? - What are the main differences between transcription in bacteria and eukaryotes? - What is a consensus sequence? What consensus sequences are important for initiation? - What happens at each of the three steps of transcription? - What is RNA polymerase? What does it do? - What are the different types of RNA polymerase? - What is a transcription unit? - What is a promoter? - Where are the promoters located? - What are the main consensus sequences for bacteria? and eukaryotes? - Describe initiation in bacterial transcription. - Describe initiation in eukaryotic transcription. - What is a transcription factor? Differentiate between general and specific transcription factors. - What is required for minimal transcription in prokaryotes? In eukaryotes - What extras can increase the rate of transcription in eukaryotes? - What happens during elongation? - How does transcription end in bacteria? - Rho-dependent termination - Rho-independent termination - How does transcription end in eukaryotes? - RNA pol I - RNA pol II - RNA pol III - What is a polycistronic transcript?