chapter 18: transcription regulation

Question 1

what are the steps gene expression can be regulated?

Answer 1

1. transcriptional control
2. processing control
3. translational control
4. mRNA degradation control
5. protein degradation control

Question 2

what factors contribute to the initiation of transcription by activators?

Answer 2

1. general transcription factors
   -TFIID: bind on TATA first
   -TFIIA: rely on D bind to CAT or GC
   -TFIIB: rely on D bind to CAT or GC
   -TFIIF: associated with RNA polymerase
   -TFIIH and TFIIE: break H bonds around TATA
2. enhancers: located upstream on the gene, bind to activator proteins, and help start initiation.
3. activator proteins: stimulate transcription of elongation, group of 3. interacts directly with DNA. can come in variations
4. mediator: not always needed, do not interact directly with DNA. interacts with GTF’s and activator proteins.

Question 3

describe regulation of translation initiation by repressors

Answer 3

-includes GTF’s
-silencer sequence: bind to repressor protein
-repressor protein: same as activator proteins, just a different combination. inhibit the use of a gene or slow it down
-mediator: interacts with repressor and GTF proteins, sometimes plays a role.

Question 4

what are the components of galactose utilization?

Answer 4

1. gal-4-P: activator protein
   2.gal-80: mediator binds between activator and GTF: inhibits.
2. genes that code for enzymes that digest galactose for ATP
3. GTF
4. galactose
5. enzymes that convert galactose to gal-3-P
6. gal-3-P: inducer, binds to gal-80 and moves it away

Question 5

describe the process that occurs when glucose makes it inside the cell for enzyme production:

Answer 5

1. galactose travels through secondary active transport with an NA-K pump across the membrane
2. the cell has enzymes present converts galactose to gal-3-P
3. gal-3-P: binds and moves gal-80
   4.gal-4-P contacts GTF and activates the transcription of enzymes.

Question 6

describe glucocorticoid receptor components

Answer 6

-glucocorticoid: steroid hormone
-Hsp 90: heat shock protein, binds to glucocorticoid receptor, makes it inactive.
-glucocorticoid receptor: known as a SHR (steroid hormone receptor), found in the cytoplasm of a liver cell, hormone diffuses through membrane and binds to it.

Question 7

describe glucocorticoid receptor pathway

Answer 7

-glucocorticoid passes through membrane using secondary active transport
- binds to glucocorticoid receptor and dislodges Hsp-90, activates the receptor
-the activated glucocorticoid receptor enters the nucleus, binds to DNA and activated or represses transcription of target genes

Question 8

glucocorticoid is a protein based horomone that is…

Answer 8

released and signal sequence binds to signal recognition particle-bind fused ribosome through ER-cis-Golgi-trans-released out and in the bloodstream

Question 9

what is signal transduction?

Answer 9

substance can influence the transcription of a gene without entry, can happen with hormones, polypeptide, steroids.
-it includes shape change of a protein that expands through a membrane

Question 10

what are the components of a signal transduction process? describe the pathway

Answer 10

-stimulus and binding of hormone to the receptor activates tyrosine kinase.
-tyrosine kinase: kinase can phosphorylate other proteins, quickly interacts with g-coupling protein
-g-coupling protein: once activated, it converts GTP to GDP, then activates adenyl cyclase.
-adenyl cyclase: enzyme, converts ATP to cyclic AMP (cAMP).
-cAMP: interacts with protein kinase A, dislodges it
-protein kinase A: becomes dislodged by cAMP, then enters nucleus, phosphorylates proteins- activator proteins to become active and begin transcription.

Question 11

what is the testis determining factor gene

Answer 11

-carried in the Y chromosome
-has its own promoter, enhancers, exons
-if present- transribed-remove introns-produces SRY protein
-SF-1 protein is made regardless.

Question 12

describe the components that are used in sex determination (signal transduction)

Answer 12

-SRY and SF-1 protein: activator proteins, bind to enhancer sequence. for the SOX protein
-SOX protein: activator: translated in cytoplasm, activator for the sex cord gene
-sex cord gene: has a signal sequence, is found on a ribosome
-gonad cell: accepts sex cord protein, causes gonad cell to undergo signal transduction pathway, activates and upregulates proteins that convert gonad to testis.
-testosterone: gene evolved from testis; hormone - released, upregulates through signal transduction. bone density increases, muscle mass, body hair, male traits. can activate or descrease estrogen production.

Question 13

describe pathway of a sex cord gene in sex determination

Answer 13

-testis determining factor gene is transcribed to a SRY protein
-SRY and SF-1 protein bind to enhancer sequence for SOX gene+ makes SOX protein
-SOX protein (activator) binds to enhancer sequence on sex cord gene= and makes a sex cord protein with a signal sequence
-sex cord protein is on a ribosome and binds to a signal recognition particle
-fuses with ER-cis-golgi (modified)-trans- outside of cell
-into bloodstream
-gonad cell accepts sex protein, undergoes signal transduction, activates and regulates proteins that convert gonad to testis
-testosterone is released from testis: upregulates through signal transduction

Question 14

the same activators or repressor proteins, in different combination, can influence the transcription of many genes

Answer 14

combinatorial regulation

Question 15

DNA packaging can influence

Answer 15

gene transcription

Question 16

genetics includes

Answer 16

the change in nucleotides

Question 17

epigenetics includes

Answer 17

modify base or histones by methylation of DNA or acetylation of histones

Question 18

describe what the DNAse I sensitivity essay and what it helps understand

Answer 18

how often a gene is regulated by its access/packaging
-DNAse I: it will chew up DNA when it is unpackaged, when DNA is tightly packaged it cant access it.
-uses southern blot
-result: liver cells are tightly packaged with melanin gene, shows up as a dark band meaning it is not destroyed. skin skills do not show melanin gene because the cell opened up the gene to use it, chewed up.

Question 19

if a mediator is phosphorylated with ATP

Answer 19

it makes the assembly more accessible and allows GTF to come in and bind to the promotor region.
-phosphorylates the promotor region

Question 20

acetylation allows

Answer 20

DNA to become more accessible

Question 21

what is HATS

Answer 21

histone acetylase, adds acetyl group to lysosine an amino acid in the histone complex.

Question 22

describe the acetylation process of histones

Answer 22

-acetyl groups are (-) charged, DNA is (-) charged, histones are (+) charged.
-if a (-) charge is added to a histone by an acetyl group, it competes with DNA for binding to the histone, therefore DNA will be less successful at binding to the histone

Question 23

Acetylation makes promotor more _______

Answer 23

accessible

Question 24

HDACS

Answer 24

remove actyl groups. they are attracted to methyl on C.-primarly attracted to CpG islands

Question 25

what are CpG islands:

Answer 25

long stretch of normal C’s and G’s

Question 26

what happens during fragile x mental retardation syndrome?

Answer 26

-lack of use of protein/gene causes syndrome
-region on a chromosome has CpG islands normally has 50 but increases to 200 repeats: attracts HDACS= causes the chromosome to stay packaged, fragile x mental retardation gene cant be used
-protein created from the gene is an activator for neuronal development genes

Question 27

what is imprinting

Answer 27

result from methylation of DNA strands, produces hemi methylated strands

Question 28

what is the process of imprinting and what is involved?

Answer 28

-EZH2: enzyme, stabilized by LNCR, binds hemi methylated DNA and will methylate it further.
-old strand: methylated DNA
-new strand: nonmethylated DNA
-in the next replication cycle, due to hemi methylated structure, any new DNA in a hemi methylated state leads EZH2 to bind and methylate, repeats across generations

Question 29

what is Prader Willi syndrome

Answer 29

example of imprinting
-lack of hypothalamus development causes feeling of constant hunger

Question 30

what happens to the paternal and maternal genes in the prader willi syndrome

Answer 30

maternal gene: ICE (control area for impriting) is methylated, chromosomes in egg get copied and continue to imprint due to methylation and EZH2 activity. it is heavily packaged, HDACS pull off acetyl, it is unable to get transcribed
-paternal gene: gene gets transcribed from father, makes LNCR

Question 31

what are the components and causes of prader willi syndrome

Answer 31

-ICE: serves as a promotor
-LNCR: helps stabilize activator
-activator: binds to enhancer region, sets up GTF for a gene needed in hypothalamus development
cause: ICE and part of LNCR get spliced- missing chromosome- cant get LNCR- no stabilization of activator- no binding between activator and enhancer- no hypo gene.

Question 32

what is dosage compensation

Answer 32

females will only unwrap and use one X per cell

Question 33

tortoise shell cats are always female because

Answer 33

-females inherit both X chromosomes, actively use one while packaging the other.

Question 34

what are the components in the mechanism behind X activation

Answer 34

XCE: X control element
XIST: X inactivation specific LNCR overlaps with TSIX
TSIX: reverse gene for XIST, share DNA
XIC: X inactivation center

Question 35

what happens in the mechanism of X activation

Answer 35

-includes unmethylated and methylated X chromosome
-unmethylated:
X unwinds
XIST and TSIX produce LNCR which link: useless
XIC: opens and acetylates: binds to histones. *triggering point
-methylated:
XCE promotor is methylated
X does not unwind
if XCE is methylated: no TSIX
XIST LNCR interacts with XIC
no HATS: condensed

Question 36

what happens during chromosome kissing

Answer 36

-supports if females inherit 3 X chromosomes, 2 will be methylated, 1 will not
-some genes on the same strand interact briefly.
-Solute carrier Family #2 protein; hemi methylates DNA
once methylated, EZH2 recognizes hemi-methylated area and methylates another strand.