Control of Gene Expression

Question 1

Blood cells

Answer 1

Erythroid cells
Lymphocyte
Monocyte
Platelets
Neutrophil
Basophil
Eosinophil

Question 2

Different cell types contain the same DNA

Question 3

Differentiated cells retain the ability to ”de-differentiate”

Question 4

a group of cells that can be grown indefinitely in a lab

Answer 4

Cell line

Question 5

Cell line examples

Answer 5

Embryonic stem cell
Liver cell
Muscle cell
Blood vessel cell
Blood cell precursor
Skin cell
Lung cell

Question 6

Cells become different because they synthesize and accumulate different sets of RNA and protein molecules.

Answer 6

Some RNAs and proteins are abundant in specialized cells in which they function and cannot be detected elsewhere

Question 7

GENE REGULATION

During development different cells express different sets of genes in a precisely regulated fashion

Question 8

a group of genes that are transcribed at the same time.

They usually control an important biochemical process.

Rare in eukaryotes

Answer 8

Operon

Question 9

_________________________
*Genes whose expression is turned off by the presence of some substance (co-repressor)
*__________ represses the trp genes

*__________ is typically the end product of the pathway

Answer 9

Repressible Genes -Operon Model

Tryptophan; Co-repressor

Question 10

Tryptophan Operon

*When E. coli is swimming in tryptophan (milk & poultry), it will absorb the amino acids from the media

*When tryptophan is not present in the media, then the cell must manufacture its own amino acids.

*E. coli uses several proteins encoded by a cluster of 5 genes to manufacture the amino acid tryptophan

Answer 10

a.) Tryptophan absent = repressor inactive = operon on

Question 11

_______________
*Genes whose expression is turned on by the presence of some substance

*___________ induces expression of the lac genes

*An antibiotic induces the expression of a resistance gene
*Catabolic pathways

Answer 11

Inducible Genes -Operon Model

Lactose

Question 12

This enzyme hydrolyses lactose into glucose and galactose

Answer 12

β-galactosidase

Question 13

*E. coli can use either glucose, which is a (monosaccharide, disaccharide), or lactose, which is a (monosaccharide, disaccharide)

*However, (glucose, lactose) needs to be hydrolyzed (digested) first

*So the bacterium prefers to use (glucose, lactose) when it can

Answer 13

Monosaccharide, disaccharide

lactose; glucose

Question 14

1. When lactose is absent

• A repressor protein is continuously synthesized. It sits on an Operator site

*The repressor protein blocks the Promoter site where the RNA polymerase settles before it starts transcribing

Question 15

2. When lactose is present

_________ binds to the lac repressor and makes it change shape so it can no longer bind DNA

Answer 15

Allolactose

Question 16

3. When both glucose and lactose are present

Answer 16

RNA polymerase can sit on the promoter site but it is unstable and it keeps falling off (low transcription)

Question 17

4. When glucose is absent and lactose is present

Answer 17

High transcription

Question 18

+ Glucose
+ Lactose

Answer 18

Operon OFF
Because CAP (Catabolite Activator Protein) is not bound

Question 19

+ Glucose
- Lactose

Answer 19

Operon OFF
Because Lac repressor bound and CAP (Catabolite Activator Protein) is not bound

Question 20

• Glucose
• Lactose

Answer 20

Operon OFF
Because Lac repressor is bound

Question 21

• Glucose
  + Lactose

Answer 21

Operon ON

Question 22

4 situations are possible

1. When glucose is present and lactose is absent the E. coli does not produce β-galactosidase.
2. When glucose is present and lactose is also present the E. coli does not produce β-galactosidase.
3. When glucose is absent and lactose is absent the E. coli does not produce β-galactosidase.
4. When glucose is absent and lactose is present the E. coli produce β-galactosidase.

Question 23

How does a cell determine which of its thousands of genes to transcribe?

Answer 23

Transcription regulators

Question 24

*Recognize specific sequences of DNA cis-regulatory sequences

Answer 24

Transcription regulators

Question 25

The region of the chromosome must be opened up in order for enzymes and transcription factors to access the gene

Answer 25

Chromatin remodeling

Question 26

The elements of transcriptional control: a model

Answer 26

1. Regulatory transcription factors recruit chromatin-remodeling complex and HATs. Chromatin decondenses. 2. When chromatin decondenses, a region of DNA is exposed, including the promoter. 3. Regulatory transcription factor recruits proteins of the basal transcription complex to the promoter. Note looping DNA. 4. RNA polymerase and the basal transcription complex join to form the initiation complex; transcription begins.

Question 27

*Contains 8 histone proteins *DNA is wrapped around each _________, like a string wrapped around a bead

Answer 27

nucleosome

Question 28

1. DNA packing as gene control * Tightly wrapped around histones (no transcription and genes turned off)

Question 29

* Darker DNA (H)=tightly packed * Highly condensed transcriptionally inactive region.

Answer 29

Heterochromatin

Question 30

* Lighter DNA (E) * Lesser coiled transcriptionally active region which can be easily accessed by RNA polymerase

Answer 30

Euchromatin

Question 31

2. DNA methylation * Blocks transcription factors (genes are turned off) * Attachment of methyl groups (-CH3) to cytosine

Question 32

*Addition of methyl groups can condense chromatin

Answer 32

Histone methylation

Question 33

are genomic regions that contain a high frequency of CG dinucleotides. particularly occur at or near the transcription start site of housekeeping genes.

Answer 33

CpG islands

Question 34

A gene involved in basic functions is required for the sustenance of the cell. _________ are constitutively expressed e.g. enzymes in metabolic cycle (e.g. glycolysis)

Answer 34

Housekeeping gene

Question 35

are those coding for specialized functions synthesized (usually) in large amounts in particular cell types. e.g. insulin (beta cells) & serum albumin gene (liver cells)

Answer 35

Luxury gene

Question 36

Histone acetylation unwinds DNA * Attachment of acetyl groups (-CoCH3) to histones

Question 37

Acetylation of histone tails promotes loose chromatin structure that permits transcription

Question 38

* DNA transcription control elements may be located many kilobases away from the promoter they regulate

Question 39

These proteins bind to selected sets of genes at sites known as silencers and thus slow transcription

Answer 39

Repressors

Question 40

These proteins bind to genes at sites known as enhancers and speed the rate of transcription

Answer 40

Activators

Question 41

These "adapter" molecules integrate signals from activators and perhaps repressors.

Answer 41

Coactivators

Question 41

________: mask the activation surface * binds to the activation domain of the activator protein thereby preventing it from carrying out its activation functions * binds tightly to the activator without having to be bound to DNA directly * Interacts with an early stage of the assembling complex of general transcription factors, blocking further assembly.

Answer 41

Repressor

Question 42

In response to injunctions from activators, these factors position RNA polymerase at the start of transcription and initiate the transcription process

Question 43

How repressor works

Answer 43

1. Masking the activation surface (binds tightly to activator) 2. Competitive DNA binding 3. Direct interaction with the general transcription factors 4. Recruitment of chromatin remodeling complexes 5. Recruitment of histone deacetylases 6. Recruitment of histone methyl transferase

Question 44

* Repressor that is expressed preferentially in the developing kidney *Children that produce no functional WT1 protein, invariably develop kidney tumors

Answer 44

Wilms’ tumor (WTI) gene

Question 45

Cytoplasmic Polyadenylation promotes translation in oocytes

Question 46

* Provides a point where the expression of a gene can be controlled * This allows a variety of different polypeptides to be assembled from the same gene

Answer 46

RNA Splicing

Question 47

* RNA-binding proteins that bind to exonic splicing enhancer sequences in exons * Critical in defining exons in the large pre-mRNAs of higher organisms.

Answer 47

SR Proteins

Question 48

* Result from mutations in a region of the genome containing two closely related genes, SMN1 and SMN2 SMN2 encodes a protein identical with SMN1, but it is expressed at much lower level because a silent mutation in one exon interferes with the binding of an SR protein, leading to exon skipping in most of the SMN2 mRNAs. SMN2 mRNAs that are correctly spliced is sufficient to maintain cell viability during fetal development, but insufficient of spinal cord motor neurons in childhood, resulting in their death and associated disease

Answer 48

Spinal muscle atrophy

Question 49

* Mechanism of silencing gene after transcription by causing degradation of some specific mRNA molecules

Answer 49

RNA interference (RNAi)

Question 50

specific mRNA molecules for RNA interference (RNAi)

Answer 50

* Small interfering RNAs (siRNAs) -dsRNA of 20-25 bps *Micro RNAs (miRNA) -Small non-coding RNAs of 21-22 nucleotide long, that hybridize to the 3’ untranslated regions of specific target mRNAs

Question 51

is an RNAse III nucleases that converts either long dsRNAs or hairpin RNAs into siRNAs

Answer 51

Dicer

Question 52

RNA-induced silencing complex (RISC) contains ________ which is an endonuclease capable of degrading mRNA whose sequence is complementary to that of the siRNA guide strand

Answer 52

argonaute

Question 53

RNAi Pathway 1. Long double-stranded RNA (dsRNA) is processed in the nucleus by _______ (RNAse enzyme). The resulting shorter dsRNA is exported to the cytoplasm, binds to dicer (RNAse enzyme), and is cleaved into small fragments, called small interfering RNAs (siRNAs) or microRNAs (miRNAs), 21-25 base pair RNA strands. 2. The siRNA or miRNA is recruited by the RISC complex, unwinds, and incorporates into a protein-RNA complex 3. RISC + siRNA or miRNA bind to a complementary, targeted messenger RNA (mRNA). 4. mRNA is cleaved in a specific site and then degraded in the cell, thereby disrupting protein synthesis of the target gene.

Answer 53

Drosha (add* DGCR8 recognizes this double-stranded miRNA) (add* transported to the cytoplasm by the protein Exportin 5) (add* it is recognized in the cytoplasm by dicer which cleaved the stem loop leaving a short ds miRNA molecule) (add* AGO2 binds to the miRNA and 1 strand is released and the guide strand left forms the RISC complex) (add* 2 types of RNAi at work 1. Cut off mRNA 2. inhibition of translation)

Question 54

* Steroid hormones that regulates the metabolism of glucose * Stimulate breakdown of fat * Is released during time of starvation and intense physical activity, stimulating liver cells to increase the production of glucose form amino acids and other small molecules

Answer 54

Glucocorticoid hormone

Question 55

a DNA sequence that activates a transcriptional enhancer when bound by a glucocorticoid receptor (GR). GREs are involved in the regulation of genes that are responsive to glucocorticoids. required for maximal initiation of transcription

Answer 55

Glucocorticoid response element (GRE) *enhancer

Question 56

When the GRE is absent, the GRE receptor dissociations

Question 57

* Iron storage protein that stores surplus iron and release it when the body needs it.

Answer 57

Ferritin

Question 58

Where do erythropoiesis take place

Answer 58

In the bone marrow

Question 59

Protein synthesized in the liver that serves as the main transporter of iron in the body

Answer 59

Transferrin

Question 60

Control mediated by Iron *An increase in iron concentration in the cytosol lead to the increase synthesis of ferritin that bind to extra iron *Also, this decreases the synthesis of transferrin receptor in order to import less iron across plasma membrane *Mediated by _________ an iron-responsive regulatory protein which can recognize stem loop structure

Answer 60

aconitase

Question 61

The binding of aconitase of the ferritin mRNA blocks translation initiation.

Answer 61

During iron starvation - Cytosolic aconitase bound to mRNA - no ferritin made, transferrin receptor made During excess iron - Cytosolic aconitase not bound to mRNA - ferritin made, no transferrin receptor made

Question 62

Roles of miRNA

Answer 62

Metabolism Stem cell division Development Apoptosis Cell proliferation Cell cycle control

Question 63

Protein that allows import of lactose from outside the cells inside

Answer 63

Permease