BIOL 4843 1st Edition Final Exam Study Guide Old MaterialThe central dogma - What is the central dogma? - theory of information flow with 3 main molecules: DNA, RNA, protein- Who first proposed it?- Crick- Have there been any modifications to the central dogma since it was first proposed?- RNA can produce DNA (reverse transcription)- Are the major processes that occur in the central dogma similar between the different domains of life?- bacteria utilize reverse transcriptaseProtein structure and function- What are the four categories of amino acids?- nonpolar aliphatic, polar uncharged, polar charged, nonpolar aromatic- Which of these categories would you expect to find in the portion of DNA-binding proteins that interact with DNA?- polar positively charged (basic) interact with the negative strands of DNA- What are the levels of protein structure? What are the main types of bonds/interactions important at each stage?- primary: peptide bonds- secondary: hydrogen bonds- tertiary: folded- quaternary: polypeptides interacting with each other- Are all proteins enzymes? Are all enzymes proteins?- all proteins are enzymes, but not all enzymes are proteins- How do proteins fold into their proper 3-D shape? Does it depend on the protein?- all info for final shape is in the primary structure- chaperones/chaperonins bind unfolded or improperly folded peptide chains- What is the one gene-one enzyme hypothesis? - one gene encodes one enzyme, so if gene is altered, the enzyme is changed- What were the modifications that were made to the hypothesis over time? Why were these modifications made?- one gene encodes one or more polypeptide- one enzyme is one or more polypeptide- an enzyme is not always a proteinDNA replication and chromosome structure- What happens during bacterial DNA replication (what are the stages, what happens in general terms during each one, what are the major types of proteins involved)?- genetic information is found on a single circular chromosome- replication begins at the origin- helicase unwinds strands, ssbps stabilize and prevent recoiling- DNA polymerase moves dNTP into position- What is the issue that occurs when replicating linear chromosomes? How are telomeres and telomerases related to this issue?- telomeres put a cap on the linear chromosome- telomerases extend the telomere repeats to solve the end replication problem- germ line cells have active telomerase since they are dividing- Describe the levels of chromosome compaction in bacteria and eukaryotes.- bacterial chromosomes are circular; eukaryotic chromosomes are linear- both are involved in supercoiling (euks have scaffolds that attach ends)- nucleosomes (DNA wrapped around histones) is the first level of compaction in euksDNA damage and repair- Will a mutation always have a negative effect in a cell? More specifically, how might a mutation affect transcription? What about translation?- a mutation can be silent, benevolent, or malevolent- Is there a difference between DNA damage and a mutation? Explain.- a mutation is DNA damage that is not repaired before replication- What is a transition mutation? What about a transversion? Which is more likely?- transition (purine to purine) is more likely than transversion (purine to pyrimidine)- Name the different pathways for DNA damage repair that we talked about in class. What type of damage does each one “fix”?- mismatch: replication error- direct repair- base excision: less bulky damage- nucleotide excision: bulky damage- recombination- translesion synthesisRecombination and mobile DNA- What are the general steps of double strand break repair? What are the major types of proteins involved in these steps?- DNA synthesis strands are ligated while still linked- Rec A and B are involved in migration, Rec C is resolution- What are the three general transposition pathways? Can you describe in general terms what happens in each pathway? In which of these pathways would a copy of the transposable element be left at the original location?- cut and paste, replicative, and retrotransposition are the 3 general pathways- cut and paste: one copy moves between DNA- replicative: one new and one old copy- retrotransposition: one new and one old copySynthesizing RNA- In transcription, what is meant by the phrases “coding strand” and “template strand”?- the coding strand is the newly synthesized DNA strand complementary to the template strand - How do they each relate to RNA?- RNA is complementary to the coding strand- In general, what does a bacterial promoter look like? What does a eukaryotic promoter look like?- the eukaryotic promoter is more complex and further upstream or downstream- How many RNAPs do bacteria have? What about eukaryotes?- eukaryotes have 3 RNAPs, bacteria have 1- What is the function of bacterial sigma factors? What is the consensus sequence?- sigma factors recognize the promoter and turn on gene expression- the consensus sequence is what the sigma factors bind to- Can you describe what happens during bacterial mRNA transcription (what are the stages, what happens during each one, what are the major types of proteins involved)?- initiation: abortive, no primer, - elongation: continuous, very processive until termination signal- proofreading: RNAP stalls and reverses- Rho independent/dependent- If you are given an image representing the process of transcription and asked whether it was occurring in bacteria or eukaryotes, what clues would you be looking for to help you determine the answer?- transcription and translation occur at the same time in bacteria- bacteria have open complex formationSynthesizing protein- What are the major proofreading steps during the process of translation? - aatRNA synthase proofreads amino acids by size instead of chemical properties- What are the wobble rules? - wobble is codon 3, anticodon 1: U, G, I- need two different tRNAs- Overall how does translation compare in bacteria and eukaryotes? Are there steps that aresimilar? Different? Explain.- bacteria initiation is started by the Shine-Dalgarno ribosome binding site- eukaryotes have many more initiation factors- How would you determine the proper start codon in bacterial mRNA? *What tRNAs recognize stop codons? Explain.- RF1 and 2 recognize 2 of 3 stop codons in bacteria- Shine-Dalgarno is upstream of start codon- fMet is the first amino acid- What situation(s) in a bacterial cell could cause a stalled ribosome? - tmRNA acts like tRNA and mRNA and