chapter 15

Question 1

The human body is estimated to have at least 300 different types of cells
with different functions. How are these cells different from each other

Answer 1

They have the same genes and alleles but express different genes.

Question 2

what enables cells to be different from eachother?

Answer 2

regulation of genes

Question 3

what is the importance of regulation of gene expression / what does it ensure

Answer 3

1. expression of genes in an accurate pattern during many developmental stages of life cycle
2. differences among distinct cell types in multicellular organisms
3. adaptive responses to changes in environmental stresses and nutrient availability

Question 4

what is the main way of regulating gene expression in eukaryotes and bacteria

Answer 4

regulation of transcription initiation

Question 5

regulation of transcription initiation in eukaryotes require what?

Answer 5

1. Regulatory sequences (in DNA, usually near the gene to be regulated)
   * Enhancers and silencers
   * These are bound by the transcription factors
2. transcription factors (proteins)
   * Activators and repressors
   * When they bind to enhancers and silencers, these influence the ability of
   RNA polymerase to transcribe a gene

Question 6

Characteristics of enhancers and silencers include…

Answer 6

• has nucleotide sequences
• positioned almost anywhere relative to start of a gene
• bind transcription factors that affect RNA poly. activity

Question 7

what is a domain

Answer 7

region of protein with specific function
- motif is a domain/portion of a domain which has similar structure in many diff. proteins

Question 8

helix turn helix

Answer 8

DNA binding domain

presence in a protein suggest that protein may be transcription factor bc it enables proteins to bind to DNA

Question 9

helix loop helix motif

Answer 9

dimerization + DNA binding domain

Question 10

zinc finger motif

Answer 10

DNA binding domain- found in glucocorticoid receptor

Question 11

leucine zipper motif

Answer 11

dimerization domain
- generally enable proteins to dimerize (form a two-protein complex).

Question 12

where does Glucocorticoid bind receptor in?

Answer 12

cytoplasm

Question 13

Glucocorticoid receptor releases from where

Answer 13

HSP90, exposing Nuclear
Localization Signal/Sequence (NLS) where the receptor then dimerizes and enters nucleus

Question 14

receptor dimer binds ______ and activates transcription of___

Answer 14

paired Glucocorticoid Response Element (GRE) sequence

activated transcription of adjacent gene

Question 15

How can transcription be regulated in eukaryotes? (6 ways)

Answer 15

1. Activator proteins increase transcription.
2. Repressor proteins inhibit transcription.
3. Activity of activators and repressors can be modulated by:
   * binding of small effector molecules
   * interactions with other proteins
   * covalent modification (such as phosphorylation)
4. Regulatory proteins can alter nucleosomes (proteins bound to
   DNA) around a promoter, altering transcription.
5. Methylation (chemical modification) of DNA around a gene can alter transcription.
6. Chromatin structure (the structure of chromosomes) can be
   altered.

Question 16

2 examples of transcriptional regulation in eukaryotes

Answer 16

glucocorticoid response and signaling through CREB protein

Question 17

what is glucocorticoids

Answer 17

a steroid hormone such as cortisol thats a stress hormone thats secreted by adrenal gland

it binds a receptor that goes to nucleus and the receptor + hormone binds to specific regulatory DNA sequences next to many genes and this results in changes in gene transcription

Question 18

where is glucocorticoids secreted into

Answer 18

into the blood stream and taken up by cells and it influences nutrient metabolism in most cells

Question 19

what does glucocorticoids promote

Answer 19

promotes glucose utilization, fat mobilization and protein breakdown

Question 20

Suppose the sequence of the Glucocorticoid Response Element
in front of one specific gene was changed at several nucleotides. The effect would probably be

Answer 20

Expression of the specific gene
would no longer be responsive to
glucocorticoids

Question 21

Suppose HSP 90 was mutated so that it bound more tightly to the
glucorticoid receptor and did not release it when glucocorticoid bound
the receptor. The effect would probably be

Answer 21

Expression of all glucocorticoid-
responsive genes would no longer
be induced by glucocorticoid

Question 22

what is the CREB protein

Answer 22

acronym for cAMP response element-binding: another regulatory transcriptional factor

Question 23

CREB protein becomes activated in response to what ? and it causes a ____ in cytoplasmic concentration of cAMP

Answer 23

activated in response to cell-signaling molecules that causes an increase in cytoplasmic concent. of cAMP

Question 24

what does cAMP stand for

Answer 24

cyclic Adenosine MonoPhosphate
- same cAMP that signals the presence or absence of glucose in E. coli—but CREB is in eukaryotic cells, not bacteria

Question 25

the CREB protein signaling pathway (7)

Answer 25

1. Signaling molecule binds receptor 2. Receptor activates G protein which activates adenylyl cyclase 3. Adenylyl cyclase synthesizes cAMP 4. cAMP activates protein kinase A 5. Protein kinase A enters nucleus and phosphorylates CREB 6. CREB binds CREB binding protein (CBP) + CRE (cAMP response element)\ 7. Transcription of target gene is activated

Question 26

In the CREB pathway, what would happen if adenylyl cyclase were inhibited?

Answer 26

transcription of CREB target genes would be inhibited

Question 27

In the glucocorticoid pathway, how is the activity of the transcription factor regulated?

Answer 27

1. by binding of a small effector molecule 2. by protein-protein interactions

Question 28

In the CREB pathway, what would happen if the CRE sequence in front of a target gene were changed?

Answer 28

transcription of just that CREB target gene would be inhibited (Only the gene whose CRE was mutated would be affected, because CREB could no longer bind in front of that gene to activate its expression in response to a signal. Other genes with non-mutated CREs would be regulated normally)

Question 29

in order for glucocortoid receptor to be activate it must...

Answer 29

bind to glucocorticoid and must not be bound to HSP90

Question 30

In the CREB pathway, how is the activity of the transcription factor regulated?

Answer 30

1. by protein-protein interactions 2. by covalent modification

Question 31

for CREB pathway to be active CREB must be...

Answer 31

phosphorylated (a covalent chemical modification) and must bind to CBP

Question 32

how are the activity of transcription factors regulated?

Answer 32

by signaling pathways (glucorticoids, CREB) through : binding. of small effector molecule, changes in protein-protein interactions, covalent modifications

Question 33

You identify a new protein that has both a leucine zipper motif and a helix-turn-helix motif. What does the presence of these motifs in the protein suggest about its function?

Answer 33

The protein binds DNA and The protein acts as a dimer

Question 34

what is the difference in subunit composition between fetal hemoglobin and adult hemoglobin?

Answer 34

Fetal hemoglobin has 2 alpha (α) and 2 gamma (γ) subunits, whereas adult hemoglobin has 2 alpha (α) and 2 beta (β) subunits.

Question 35

Gamma (γ) globin in fetal hemoglobin is replaced by___ in adult hemoglobin.

Answer 35

beta (β) globin

Question 36

How do the alpha (α), beta (β), and gamma (γ) globin genes change in their expression during fetal development and after birth?

Answer 36

1. Expression of α globin increases early in development and stays high 2. Expression of γ globin increases early and then decreases between 3 months before birth and 3 months after birth 3. Expression of β globin increases during late fetal development and stays high by 3 months after birth.

Question 37

In the CREB pathway, what would happen if CREB were mutated so it could no longer be phosphorylated?

Answer 37

transcription of all CREB target genes would no longer be turned on by the extracellular signaling

Question 38

why is Phosphorylation of CREB required

Answer 38

for it to bind to CRE and activate the target genes

Question 39

what is the Dimerization of CREB required for

Answer 39

to bind to CRE and activate the target genes.

Question 40

what might cause the change in γ globin gene expression before birth?

Answer 40

change in methylation of the DNA for the gamma globin gene or in acetylation of the histone proteins around the gene

Question 40

Infants with sickle cell disease (SCD) generally do not show symptoms of their disease until they are a few months old, why?

Answer 40

SCD is due to mutations in the gene for β globin. This gene is not strongly expressed until about 3 months of age, so mutations affecting this gene would not show effects until then. Before that, the γ globin gene is expressed instead. This gene does not have sickle cell mutations.

Question 41

What do you predict would be the effect of deleting the erythroid-specific enhancers of BCL11A expression on expression of BCL11A?

Answer 41

BCL11A expression in erythroid cells (red blood cells and their precursors) would be reduced

Question 42

What do you predict would be the effect of deleting the erythroid-specific enhancers of BCL11A expression on gamma globin gene expression?

Answer 42

Gamma globin gene expression would increase

Question 43

When BCL11A is no longer expressed in erythroid cells....

Answer 43

the expression of γ globin in these cells would no longer be inhibited, so γ globin would be expressed.

Question 44

What do you predict would be the effect of deleting the erythroid-specific enhancers of BCL11A expression on someone with sickle cell anemia?

Answer 44

Deleting the erythroid-specific enhancers of BCL11A should have the same effect: deletion of BCL11A enhancers → no BCL11A expression in erythroid cells → γ globin now expressed in erythroid cells → γ globin expression compensates for defective beta globin expression

Question 45

What technique could be used to delete erythroid-specific enhancers in the BCL11A gene?

Answer 45

CRISPR-Cas mediated gene editing could be used to delete precisely the erythroid–specific enhancers in the BCL11A gene.

Question 46

what is BCL11A protein?

Answer 46

transcription factor that represses expression of the γ globin gene in erythroid cells (red blood cells and their precursors) in adults by binding to a silencer element at about -115 in the γ globin promoter.

Question 47

what is DNA methylation

Answer 47

DNA can be chemically modified by addition of a methyl (-CH3) to cytosine (usually when C is next to G, called “CpG”) Methylation can block proteins’ ability to bind to DNA, and thereby can affect gene expression.

Question 47

what are chromatins

Answer 47

Eukaryotic DNA in chromosomes is bound to proteins to form a complex

Question 48

what are histones

Answer 48

Most proteins in chromatin, which are very conserved and positively charged

Question 49

what are nucleosomes

Answer 49

DNA (which is negatively charged) wraps tightly around 8 histones to form these and these are not very accessible to proteins for transcription

Question 50

when can DNA become more accessible to transcription factors and RNA polymerase when:

Answer 50

- nucleosomes are moved - histones are chemically modified

Question 51

what is activation

Answer 51

Addition of acetyl (-COCH3) groups to histones blocks the histones’ positive charge and causes histones to bind less tightly to DNA making DNA more accessible for transcription

Question 52

both ______ can establish stable patterns of gene expression by affecting chromatin

Answer 52

methylation of DNA and modification of histones

Question 53

Which changes around a gene would you predict would increase that gene’s expression?

Answer 53

decrease methylation and increase histone acetylation since Both of these changes make the DNA more accessible to transcription factors and thus would tend to increase gene expression.