8 Regulation of gene expression

Question 1

how is genetic regulation and protein synthesis linked?

Answer 1

not all genes are transcribed at all times, only those that are needed are done at a per needed basis

constitutively transcribed genes are AKA housekeeping genes

Question 2

how is genes expression protein synthesis always linked in prokaryotes

Answer 2

translation of mRNA begins before transcription is complete

what is translated is controlled by what mRNA is made

Question 3

what is an operon?

Answer 3

set of polycistronic genes and their promotor that all encodes for different proteins that are used in a related pathway

Question 4

how is the positive and negative controls for transcription done in prokaryotes?

Answer 4

positive control makes it so a protein is needed for transcription to initiate

negative control is through requiring a protein to inhibit the transcription process

Question 5

what is the model operon that is used for most examples?

Answer 5

lac operon in which allows a bacteria to process lactose

Question 6

give an example of repression and inducers with a lac operon

Answer 6

Lac operon is constitutively repressed. allolactose is an inducer that binds away the repressor.

lac operon also needs coactivation to be transcripted which is a cAMP-CRP(cat rec protein) to begin transcription which is why when glucose and lactose is present, it will prefer glucose thus lowering cAMP

Question 7

what non specific factor will activate RNA polymerase in prokaryotes to bind to several promotors?

Answer 7

sigma factor

Question 8

explain the attenuation of transcription

Answer 8

hairpin structural arrangements will determine if transcription occurs by attenuation

ie. trp operon w/ 4 domains and trp coded sequence initially
trp low –> ribosome stalls at trp sequence –> 2+3 binds allowing transcription to occur

trp high –> trp sequence does not stall ribo –> 3+4 binds which creates termination signal

Question 9

what is a macrostructural feature of eukaryotes that can control transcription?

Answer 9

chromatin arrangement itself can regulate transcription

Question 10

what are the 4 main differences of transcription between euks and proks

Answer 10

euks have no operons

euks separate transcription and translation in two diff compartments

euks have genes for proteins of same pathway on different chromosomes

DNA in euks are in nucleosomes

Question 11

name the seven control steps in order for DNA regulation in euks

Answer 11

1. chromosome/gene rearrangement
2. transcription factors
3. RNA editing during transcript processing
4. RNA xport
5. ribo activation
6. mRNA stability
7. protein stability

Question 12

explain chromatin remodeling via histones

Answer 12

histones can be acetylated which will decrease the positive charges thus allowing unwinding of the negative DNA and allowing xcription.

reverse is true with histone deacetylation

Question 13

explain DNA methylation

Answer 13

cytosine can be methylated

G-C rich sequences ie. CpG isalnds are the ones that are most heavily methylated

methylation can activate or repress

usually on promotor sequences

Question 14

describe two related inherited disorders resulting from methylation

Answer 14

prader willi and angelmans syndromes originate from methylation of alternate sides but mutations lead to the side that covers for the methylated sequence is deleted. originates on chromosome 15

Question 15

describe the four ways genomes in cells can be regulated at the DNA/chromosome level

Answer 15

gene rearrangement
amplification/deletion
chrom translocation
triplet repeats

Question 16

explain and give an ie of gene rearrangement

Answer 16

segments of one DNA moving to another

ie. VDJ recombination then splicing similar to mRNA but then is retranscribed into mRNA, useful for b and t cell receptor genes

Question 17

explain gene amplification and its results

Answer 17

NOT normal

some sequences replicated at a high rate abnormally

forms excised double minutes that can insert in random places and cause amplification of the sequence in protein form

Question 18

explain gene deletions and translocations

Answer 18

deletions via errs of repl, division and damage
ie. loss of tumor suppressor -> cancer

translocations are when gene are abnormally relocated elsewhere thus affected by a diff promotor or gene

ie. 9:22 trans BCR+Abl 22- -> philadelphia chromosome -> CML
8: 14 trans -> burkitts lymphoma

Question 19

Give two demonstrations of triplet repeats expansion syndromes

Answer 19

fragile X where CGG triplet is expanded on the 5’ end of the FMR-1 gene
60-230 is carrier any more are affected

Huntingtons have a CAG expansion where any more than 35 triplets will cause disease

means that triplet expansions can be additive over generations

Question 20

Explain how external elements can affect transcription ie. steroid response

Answer 20

steroids like cortisol can bind with Hormone sensitive proteins found in cytosol which will then dimerize and xport to nucleus which will then bind with coactivator RNA polymerase complex and bind to NLS and activate transcription

Question 21

How does androgen insensitivity occur?

Answer 21

defect steroid receptors in cells will cause failure of transcription and downstream effects thus cause ambiguous genitalia, but there may be high amounts of androgens present in the blood

Question 22

How are the effects of thyroid hormone produced by target cells in the body?

Answer 22

TH receptors are bound to a RXR complex which w/o T3 it will bind to a corepressor with HDAC so as to halt transcription

w/T3 TH rec and RXR will bind to coactivator with HAC and thus initiate transcription of the proteins that mediates the downstream effects of T3

Question 23

What are the four types of DNA binding domains?

Answer 23

zinc fingers, leucine zippers, helix turn helix, helix loop helix

all bind to the major groove of DNA via alpha helix

Question 24

Name a specific receptor that uses a zinc finger type binding domain

Answer 24

estrogen receptors has a Zn complexes with four cystein residues in a protein that will form an alpha helix that will bind over with a NRS that recognizes the specific major groove of the DNA

Question 25

What makes helix turn helix motifs different than all the other motifs?

Answer 25

HTH does not need to form dimers to function

Question 26

What is a regulatory cascade?

Answer 26

it is when one TF is coded for several DNA elements which can bring about different TF which further amplifies the effect as well as can create multiple different effects at the same time from only one TF

Question 27

Why can one promotor have several transcription factor binding sites?

Answer 27

allows for different responses to different mechanisms to affect the transcription of the same gene

Question 28

How does alternative splicing work?

Answer 28

in certain genes there are stop codons along with poly[a] sequences in both the intron and exons, normally the introns are spliced out as normal and only the exons are expressed. In other cases a binding protein will cover the intron splice site and prevent it’s excision.

when this occurs the stop codon in the intron will truncate the exon and the poly[a] tail will be added afterwards

Question 29

how does mRNA editing work and give an ie.

Answer 29

mRNA editing is when after transcription and can occur by indels or deamination to change a sequence

ie. ApoB in the liver is simply expressed into ApoB100 but in the intestines a CAA is deaminated to UAA a stop codon and is truncated to form a ApoB48.

ApoB100 = LDL

ApoB48 = Chylomicron

Question 30

Explain regulation of protein synthesis by eIF

Answer 30

eIF2 when phosphorylated by a kinase it is inactive and prevents translation. The kinase can be inactivated in the presence of a specific molecule such as heme

Question 31

why does reticulocytes require use of eIF to create heme?

Answer 31

Hbg protein can only be made in the presence of heme which will inactivate the kinase that inactivates eIF2alpha

this is because reticulocytes do not have a nucleus so this is the first level of regulation that is available to them

Question 32

Explain the dual roles of IRE-BP

Answer 32

IRE BP protects on two sites of the iron storing ferritin mRNA. on the 5’ end in the presence of iron it will unbind and allow translation of the ferritin protein.

at the 3’ end of a transferrin mRNA when there is too much iron the IRE-BP will unbind from the mRNA and expose it to degradation

Question 33

Explain how IFN work

Answer 33

IFN will activate JAAK-STAT which will bind to DNA and upregulate oligo2-5polyA which is a ribonuclease and IFN will also phosphorylate eIF2 and both of these will halt expression of proteins

used in leukemia

Question 34

define thalassemia and what the two different mutations it can be from

Answer 34

thalassemias are named by the globin that is lacking

this causes an excess of the unaffected globin and thus anemias leading to splenomegaly

alpha thalassemias cause excess beta globins which can bind into tetramers and ruin oxy dissc curve causing early death

beta thalassemias can be minor, intermedia or major depending on heterzogosity of the alleles affected (named beta+/beta+ for major)

beta Thalassemias result in alpha precip instead of tetramers in RBC causing them to die

mutations can result from stop codons formed in promotor leading to poor production of globins, the other is a stop codon in the globin gene itself leading to truncated globins which is worse