unit 16

explain the levels of gene regulation. Which apply to prokaryotes and which apply to eukaryotes (Fig 16.1) (5)

1. Genes can be regulated through the alteration of DNA or chromatin structure - modification to DNA or its packaging can help determine which sequences are available for transcription or the rate at which sequences are transcribed - happens in eukaryotes 2. transcription - limiting the production of a protein early in the process makes sense because otherwise, it would be waste of energy - happens in prokaryotes and eukaryotes 3. mRNA processing - all the modification of mRNA determine the movement of the mRNA into the cytoplasm and whether or not it can be translated or the rate at which it is translated - happens in eukaryotes 4. regulation of mRNA stability - the amount of protein produced depends not only on the amount of mRNA synthesized, but also on the rate at which the mRNA is degraded 5. translation - the number of enzymes present, the availability of amino acids all affect the rate at which proteins are produced - happens in eukaryotes and prokaryotes 6. post translational modification - the modification affect stability and whether the proteins become active

illustrate the trp operon when tryptophan is high (4)

1. RNA polymerase begins transcribing DNA producing region 1 of the 5' UTR 2. A ribosome binds to the 5' end of the 5' UTR and transates region 1 while region 2 is being transcribed 3. RNA polymerase transcribes region 3. the ribosome does not stall at the trp codons because tryptophan is abundant 4. the ribosome covers part of region 2 preventing it from pairing with region 3 so region 4 pairs with region 3 and attenuation occurs

illustrate the trp operon and rna polymerase when tryptophan is low (4)

1. RNA polymerase begins transcribing the DNA producing region 1 of the 5' UTR 2. a ribosome attatches to the 5' end of the 5' UTR and translates region 1 while region 2 is being transcribed 3. the ribosome stalls at the trp codon in region 1 because tryptophan is low which means that region two is not be translated while region 3 is being transcribed 4. when region 3 is transcribed, it pairs with region 2. when region 4 is transcirbed it cannot pair with region 3 because region 3 is already paired with region 2

illustrate attenuation in the trp operon (3)

1. The 5' UTR contains four regions: 1 is complementary to 2, 2 is complimentary to 3 and 3 is complimentary to 4 2. when tryptophan is high, region 3 pairs with region 4 which terminates transcription (attenuation) 3. when tryptophan is low, region 2 pairs with region 3 which does not terminate transcription

describe how antisense RNA can be used to regulate bacterial gene expression (Fig 16.17) (3)

1. antisense RNA - small RNA molecule that base pairs with a complimentary DNA or RNA sequence and affects its functioning 2. the book uses the example of the ompF gene in E. coli which encodes an outer-membrane protein that functions as a channel for the passive diffusion of small polar molecules such as water and ions across the membrane 3. there is a purple gene that makes purple protein under certain conditions. because its controlled by antisense RNA, that is what controls it (red gene). Red gene gets transcribed into an antisense RNA which can bind to the purple RNA and block it from being made

describe how the trp operon is also controlled by attentuation (2)

1. attenuation: transcription is initiated but terminates prematurely before structural genes are transcribed 2. depends on simultaneous transcription and translation

describe how the lac operon can also be under positive control using catabolite repression (2)

1. catabolite repression - the system of gene control in some bacterial operons in which glucose is used preferentialy and the metabolism of other sugars is repressed in the presence of glucose 2. the positive response comes in when there is low glucose, cyclic AMP increases and binds to CAP which binds to the promoter and makes it easier for RNA polymerase rto bind to the promoter

differentiate between environmental induction of gene expression and tissue specific gene expression (2)

1. environmental induction is when the environment changes, new genes are expressed, and proteins appropriate for the new environment are synthesized 2. tissue specific gene expression happens when a multicellular organism beings about the differentiation of cells that have a common set of genetic instruction

explain how a negative repressible operon functions in the presence and absense of a product

1. in the presence of a product, the repressor protein will bind to to the operon and turn off transcription. without the product the operon is always turned on and is constantly transcribing products

explain how a negative inducible operon functions in the presence and absence of an inducer

1. in the presence of an inducer, the regulator protein can not bind to the operator, thus the genes on the operon are transcirbed and the operon is considered "turned on"

differentiate between inducible and repressible operon (2)

1. inducible: transcription is off unless something turns it on 2. repressible: transcription is on unless something turns it off

list the two requirements for maximum transcription of the lac operon (2)

1. lactose present 2. low glucose levels

differentiate between positive and negative control with respect to operons (2)

1. negative: regulator protein is a repressor; repressor binds to DNA and turns transcription off 2. positive: regulator protein is an activator; activator binds to DNA and stimulates transcription

define operon. do prokaryotes have operon? eukaryotes? (2)

1. operon - a group of bacterial structural genes that are transcribed together, along with their promoter and additional sequences that control their transcription 2. prokaryotes have operons, eukaryotes do not

define regulator gene and regulator protein. how is this related to an operon? (Fig 16.3) (3)

1. regulator gene - gene associated with an operon in bacterial cells that encodes a protein or RNA molecule that functions in controlling the transcription of other genes - not considered part of the operon 2. regulatory protein - protein produced by a regulator gene that binds to another DNA sequence and controls the transcription of other genes 3. this is related to an operon because it can regulate the transcription of genes on the operon

define a negative repressible operon (Fig 16.5) (3)

1. regulator prortein is a repressor 2. because it is a repressible operon, it is able to be repressed meaning transcription is on and something would have to turn it off 3. since transcription is on, the repressor must be made in an inactive state so that it is. not repressing, it would have to be activated to repress the operon

define a negative inducible operon? (Fig 16.4) (3)

1. regulator protein is a repressor which means that when it is bonded to the operator, transcription is turned off 2. because it is an inducible operon, it is able to be induced, meaning transcription is off and something would have to turn it on 3. since transcription is off, the repressor must be made in an active state so that it can repress the operon

describe how the trp operon in E Coli is an example of negative repressible operon (2)

1. trp operon controls the biosynthesis of tryptophan 2. repressor is made in an inactive form because this is a repressible operon

why isn't repression enough?

because some transcription is initated even when the repressor is active

describe how riboswitches can be used to regulate bacterial gene expression (16.18) (3)

riboswitches - regulatory sequence in an RNA molecule. When an inducer molecule binds to the riboswitch, this changes the configuration of the RNA molecule and alters the expression of the RNA, usually be affecting the temptation of transcriptions or by affecting translation 2. Typically found in the 5' UTR of the mRNA and can fold into compact RNA secondary structures with a base stem and several branching hair pins 3. dictated by regulatory proteins

define gene regulation

the process used to control the timing, location, and amount in which genes are expressed