13 - Prokaryotic Gene Regulation

Question 1

identify the main features of bacterial operons

Answer 1

• Operon – is a cluster of prokaryotic genes and the DNA sequences involved in their regulation. It can contain several to many genes. It is transcribed as a unit from the promoter into a single mRNA, as a result, the mRNA contains codes for several proteins (transcription unit).
• Operator – a regulatory DNA sequence in the operon. A short segment that is a binding sequence for a regulatory protein, which is encoded by a regulatory gene that is separate from the operon.
• Repressor – a regulatory protein that controls some operons. When bound to the DNA, reduce the likelihood that genes will be transcribed. These can control more than one operon.

Question 2

identify the function of repressor proteins

Answer 2

a regulatory protein that controls some operons. When bound to the DNA, reduce the likelihood that genes will be transcribed. These can control more than one operon.

Question 3

identify location of various components of the lac operon

Answer 3

Question 4

DNA signals in RNA-coding genes

Answer 4

• the promoter in the DNA does not get transcribed
• the SD box does get transcribed therefore it will be on the mRNA but does not get translated
• the start codon, transcription unit and stop codon are all transcribed and are present on the mRNA, the stop codon does not get translated
• the transcription terminator gets transcribed and is present on the mRNA but does not get translated

Question 5

DNA sequence of anticodon in tRNA gene, given the codon

Answer 5

example: Trp tRNA gene on DNA

• they only have a promoter and a transcription terminator, because they are not translated only transcribed
• the codon on the mRNA in translation of the Trp amino acid would be 5’ UGG 3’, therefore the anticodon on the tRNA would be 3’ ACC 5’
• that sequence on the DNA before transcribing the tRNA would be 5’ TGG 3’

Question 6

likely effect of base sequence substitutions in various DNA signals

Answer 6

• A mutation in the promoter means that the RNA polymerase wont be able to recognize the gene and will not transcribe it. Polymerase will just move on the the next promoter
• there could be mutations n the promoter that can increase the efficiency of the promoter
• in the SD box it depends. it can make it more ore less attractive, but it will have some effect on the efficiency of translation
• for the start codon, all you can do is brake it. It will destroy the start codon and probaly damages the gene
• in the codons it will depend because of redundancy, i.e
  
  • if it doesnt cause any damage it is called a silent mutation.
  • When a new codon is made that codes for a different amino acid it i callede missence.
  • when a mutation makes a stop codon, the peptide will be too short. this is called a nonsense mutation (more severier)
  • intel mutations, inserts a base, then reading frame is shifted all the way. A new set of amino acids would be made
  • remeber that there are three possible coding frame
• in a stop codon, the ribosomal machinery will not stop translating. This is why there is more than one top codon
• in the terminaton factor it will depend because it can strenghten the loop or disabalize the loop

Question 7

basic structure of lac operon

Answer 7

• The lac operon contains several genes.
• These are lac I, Z, and Y. Lac Y (permease) and Lac Z (galactosidease) are under control of the same operator, so they are transcribed together.
• Lac I codes for the repressor and it under control of a different operator.
• Repressor protein coded for by lac I is synthesized in an active form, but it can be inactivated in the presence of lactose by the binding of allolactose.
• When lactose is not present, the repressor is active and binds to the operator for lac Z and Y, thus stopping their transcription. This is negative control.

Question 8

mechanism of action of lac repressor

Answer 8

• The lac repressor is activated in the presence of allolactose. Allolactose binds to the repressor, changing its conformation and thereby stopping it from binding to, and inactivating, the operator which controls the transcription of Lac Z and Lac Y. the lac operon is also under positive control from the CAP site, where CAP/cAMP bind to the cap site when glucose levels are low, thereby increasing lac expression (making transcription of Lac Y+Z go faster).
• When glucose is present, cAMP levels decrease and as a result, so does lac expression. This is because cells prefer to use glucose for energy if it is available

Question 9

function of lac operon in the presence, and absence, of lactose

Answer 9

• In the presence of lactose, the lac repressor is deactivated and lac expression increases so that the lactose can enter the cell and be broken down.
• In the absence of lactose, the repressor is activated and binds to the operator for Lac Z + Y, stopping their transcription since they aren’t needed if there’s no lactose to metabolize.

Question 10

possible location of mutations in lac operon that give rise to a given phenotype

Answer 10

• Different mutations can give rise to a lot of different situations.
  
  • examples: a mutation in the CAP binding site that never allows CAP to bind. This results in the lac operon never being able to go full blast since CAP cannot exert its positive control.
  • a mutation in lac Y in which it is not transcribed properly. Permease would not be created so lactose would not be able to get into cells. This could result in a number of problems such as decreased energy availability (especially in the absence of glucose)

Question 11

phenotype that would arise from a given mutation in lac operon under given conditions

Answer 11

• Same as “possible location of mutations in lac operon that give rise to a given phenotype” but reversed