Lecture 7: Bacterial Genetics Flashcards
Describe the central dogma of bacterial genetics
1) From existing DNA to make new DNA (DNA replication)
2) From DNA to make new RNA (transcription)
3) From RNA to make new proteins (translation)
List and describe the 3 forms of DNA. Where are they typically found?
1) B form: the one typically seen
2) A form: a slightly tighter coil, found in dehydrated specimens
3) Z form: an even tighter coil, left-handed helix; unknown role in cells, but has been found in many animals (mammals, protozoans, plants) and may provide torsional strain relief (supercoiling)
What do complementary and antiparallel describe in terms of DNA?
1) Complementary: base pairing rules (A&T and C&G)
2) Antiparallel: backbones run in opposite directions
Describe DNA replication in microbes
1) Semiconservative replication
2) The two strands of the parental double helix unwind, and each specifies a new daughter strand by base-pairing rules.
3) “The daughter cells are born pregnant”; i.e. new DNA is already being formed in daughter cells as soon as they’re replicated.
Initiation of DNA synthesis predates what?
Any initiation of cell division
Name 3 features of DNA that are involved in replication in bacteria
1) OriC: origin of replication
2) Replisome: where proteins and nutrients go to aid in replication
3) Ter: site where replication ends
What direction is the replication of the E. Coli chromosome?
It’s bidirectional
Describe 3 ways a bacterial chromosome can be compacted
1) Can be circular
2) Negatively supercoiled
3) Negatively supercoiled and mediated by DNA binding proteins (histone-like proteins).
DNA binding proteins are what kind of proteins?
Histone-like proteins
Describe why DNA may be negatively supercoiled and mediated by DNA binding proteins (histone-like proteins).
The nucleoid is supercoiled and compacted, and the scaffolding from the DNA binding proteins keeps it compact, but also allows regions of the chromosome to be accessible.
More organization of the chromosome allows for what?
Faster gene expression
Describe the bacterial chromosome shape, replication speed, error rate, and okazaki fragment length
1) Chromosome: circular, some linear
2) Replication speed: 1,000bp/s
3) Error rate: 10^-8
4) Okazaki fragment length: 1,500nt
Describe bacterial transcription and translation
Transcription: Polycistronic & no post transcriptional modification
-Ribosomes can jump around and translate several proteins at once
Translation: 50S, 30S ribosomes / Protein splicing
Define polycistronic transcription
Ribosomes can jump around and translate several proteins at once
Describe the eukaryotic chromosome shape, replication speed, error rate, and okazaki fragment length
1) Chromosome: Linear
2) Replication speed: 100bp/s
3) Error rate: 10^-10
4) Okazaki fragment length: 100nt
Describe eukaryotic transcription and translation
1) Transcription: Monocistronic mRNA & post-transcriptional modification
2) Translation: 60S, 40S ribosomes / Protein splicing
Describe the reading frame of transcription and translation
1) There’s a coding strand (5’-3’) and template strand (3’-5’) used during transcription; mRNA strand ends up looking the same as the coding strand but with U instead of T.
2) Then translation occurs via ribosomes to produce a polypeptide from the mRNA
What are the 3 stop codons?
UAA, UAG, and UGA
Describe the importance of redundancy in genetic code
The redundancy of the genetic code allows for mistakes to be made, since a single nucleotide mutation may still be able to produce the same amino acid as the original
Define missense, nonsense, and frameshift mutations and describe what they result in
1) Missense mutation: The changing of an entire nucleotide (i.e. T&A) and you are now coding for a different amino acid
-The least detrimental to a cell
2) Nonsense mutation: Results in a premature stop codon
3) Frameshift mutation: A nucleotide is lost and affects all downstream amino acids; usually a very different protein
What is the least detrimental mutation to a cell?
A missense mutation
What are the 3 possible outcomes of genetic mutations?
1) No effect (no change in phenotype)
2) Change in phenotype
3) Fatality
What are the two types of point mutations?
1) Transition: purine > purine or pyrimidine > pyrimidine (staying the same type of nucleotide)
2) Transversion: purine <> pyrimidine (switching type of nucleotide)
What is the most common category of mutations?
Point mutations
What are the two main categories of mutations?
Point mutations and frameshift mutations
Define a transversion mutation and list its 3 possible outcomes
1) Transversion: purine <> pyrimidine (switching type of nucleotide)
2) a) None
b) Nonsense: truncated protein
c) Missense: different amino acid; altered protein
What are the two types of transversion mutations? What do each of these result in?
1) Nonsense: truncated protein
2) Missense: different amino acid; altered protein
List and define the 2 types of frameshift mutations
1) Deletion: deletion of 1 or more nucleotides
2) Insertion: the addition of 1 or more extra nucleotides
List 2 things that can cause mutations and give an example of each
1) Chemical mutation
-Ex: N-methyl-N-nitro-N-nitroguanidine can alter guanine into O^8 methylguanine
2) Environmental mutation
-Ex: The alteration of thymine with UV light into a thymine dimer
We must have ways to differentiate wild-type vs mutant; name and define what this process is called
Screening: detection system for a mutant phenotype
Name 4 types of mutations
1) Morphological mutations
2) Lethal mutations
3) Conditional mutations
4) Biochemical mutations
Give 2 examples of biochemical mutations and define them
1) Auxotroph: must obtain nutrient from the environment because it has lost the ability to synthesize it
2) Resistance mutant: resistance to a pathogen, chemical, antibiotic
Name 4 ways to screen for mutants
1) Replica plating
2) Mutant libraries
3) Phage-sensitivity
4) Plasmid selection
Describe the replica plating process for screening for mutants
Involves creating two replica plates (one with complete medium and one with an incomplete media) and looking for a species that grows on the complete media but not on the incomplete media
What does the Ames test do? Where has it previously been successful?
1) The Ames test is an inexpensive method using bacteria as test subjects to determine the potential carcinogenicity of a substance. (i.e. identifies mutagens)
2) Has been successful in identifying only half of animal carcinogens.
Describe the Ames test
1) A culture of auxotrophs is plated onto two petri dishes; one with a minimal media with a small amount of histidine, and another with minimal media with a test mutagen and small amount of histidine.
2) Then the first dish may lead to a few spontaneous revertants (some eventually learn how to survive without histidine), and the second dish can lead to many revertants induced by the mutagen (if the mutagen is a mutagen, this dish should have more revertants/ survivors).
Define genes, phenotype, and genotype
1) Genes: The basic unit of inheritance
2) Phenotype: features that are expressed (ex: blue eyes, metabolic trait, etc)
3) Genotype: the gene sequence that exists in an organism
Describe cis acting elements and name 3 of them
1) Elements that are intrinsic to the DNA itself
2) Promoter, operator, and terminator
Define promoter, operator, and terminator. Also, what do these 3 things have in common?
1) Promotor: areas where RNA polymerase binds and transcription starts
2) Operator: area where effectors bind to limit or allow transcription
3) Terminator: region of DNA that tells RNA polymerase to stop transcribing
4) They are all cis acting elements
What’s the differences between cis and trans acting elements?
Cis acting elements are a part of the genetic code, trans acting elements are not a part of the DNA