Chapter 18 - Regulation of Gene Expression

Question 1

What is the Operon Model ?

Answer 1

• Bacteria often respond to environmental change by regulating transcription
• Natural selection has favored bacteria that produce on the products needed by that cell
• A cell can regulate the production of enzymes by feedback inhibition or by gene regulation
• Gene expression in bacteria is controlled by the operon model.

Question 2

What is an operon?

Answer 2

• A cluster of functionally related genes that can be under coordinated control by a single “on-off switch”.
• The regulatory “switch” is a segment of DNA called an operator usually positioned within the promoter

An operon is the entire stretch of DNA that includes:

1. The operator - Segment of DNA that functions as the regulatory switch
2. The promoter - Usually where the operator is positioned
3. The genes that they control

Question 3

The operon can be switched off by a _ _ _ _ _ _ _ _ _ _ _ _ _ _ _. A _ _ _ _ _ _ _ _ _ _ _ is a molecule that cooperates with this protein to switch an operon off

How?

Answer 3

The operon can be switch off by a protein repressor. A corepressor is a molecule that cooperates with a repressor protein to switch an operon off.

• The repressor prevents gene transcription by binding to the operator and blocking RNA polymerase
• The repressor is the product of a separate regulatory gene
• The repressor can be in an active or inactive form, depending on the presence of other molecules

Question 4

What is a corepressor ?

Answer 4

corepressor

is a molecule that cooperates with a repressor protein to switch an operon off

For example, E.coli can synthesize the amino acid tryptophan

Question 5

Explain tryptophan(TRP) synthesis in relation to the TRP operon

Answer 5

• By default, the trp operon is “on” and the genes for tryptophan synthesis are transcribed.
• When tryptophan is present, it binds to the trp repressor protein, which turns the operon “off.
• The repressor is active (“on”) only in the presence of its corepressor tryptophan; thus the trp operon is turned off (repressed) if tryptophan levels are high.

Question 6

In negative regulation a repressor protein binds to an operator to prevent a gene from being expressed.

What are the two types of negative gene regulation?

Answer 6

1. Repressible operon

• is one that is usually ‘on’
• binding of a repressor to the operator shuts off transcription
• EX: the trp operon is a repressible operon

2. Inducible operon

• a molecule called an inducer inactivates the repressor and turns on the transcription
• Gene expression from drinking milk caused by inducible operon:

Question 7

How is gene expression from drinking milk caused by inducible operon?

Answer 7

• The lac operon (lac for ‘lactose’) is an inducible operon and contains genes that code for enzymes used in the hydrolysis and metabolism of lactose
• Lactose (milk sugar) is a disaccharide made up of the monosaccharides Glucose and Galactose
• Can be available to E. coli in human colon if host drinks milk
• The enzyme β-galactosidase splits lactose
• Few molecules of β-galactosidase are present if bacteria grown in absence of lactose
• Within 15 minutes of adding lactose to E. coli’s environment, the number of β-galactosidase molecules increases a thousandfold!

Question 8

What is the lac operon?

Answer 8

By itself, the lac repressor is active and switches the lac operon off

A molecule called an inducer inactivates the repressor to turn the lac operon “on”.

Allolactose is the inducer molecule. It is an isomer of Lactose formed in small amounts when lactose is present.

Question 9

• All organisms must regulate which genes are expressed at any given time*
• In multicellular organisms, regulation of gene expression is essential for cell specialization*
• Almost all the cells in an organism are genetically identical. A typical human cell might express 20% of its protein-coding genes at any given time.*

Differences between cell types does not result from different cells having different genes, but instead differences between cells result from what?

Answer 9

Differential gene expression

The expression of different genes by cells with the same genome.

Question 10

Eukaryotic gene expression is regulated at many different stages, what are these stages (6)?

Answer 10

1. Unpacking of Chromatin

2. Transcription

3. RNA processing

4. mRNA degradation

5. Translation

6. Protein processing and degradation

Question 11

In the first stage of gene expression , unpacking of chromatin , how does this affect gene expression?

Answer 11

1. Unpacking of Chromatin

Regulation of chromatin structure

• Genes within highly packed heterochromatin are usually not expressed
• Chemical modifications to histones and DNA of chromatin influence both chromatin structure and gene expression.

Histone modification (acetylation & methylation)

• In histone acetylation, acetyl groups are attached to positively charged lysines in histone tails.
• This loosens chromatin structure, thereby promoting the initiation of transcription.
• The addition of methyl groups (histone methylation) can condense chromatin; the addition of phosphate groups (phosphorylation) next to a methylated amino acid can loosen chromatin.

DNA Methylation

• DNA methylation, the addition of methyl groups to certain bases in DNA, is associated with reduced transcription in some species.
• DNA methylation can cause long-term inactivation of genes in cellular differentiation.
• This inactivation is essential during normal cell differentiation in the embryo.
• Deficient DNA Methylation can lead to abnormal embryonic development.
• Inactivation is usually permanent through successive divisions
• In genomic imprinting, methylation regulates expression of either the maternal or paternal alleles of certain genes at the start of development.

Epigenetic Inheritance

• Chromatin modifications just discussed (Histone modification & DNA Methylation) do not alter DNA sequence.
• But, they may be passed to future generations of cells.
• i.e the legacy of chromatin modifications is passed down to successive generations of cells in an organism during growth and development.
• Epigenetic Inheritance - The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence.

Question 12

During the first stage of gene expression, what is histone acetylation? (acetylation & methylation)

Answer 12

histone acetylation..

Acetyl groups are attached to positively charge lysines in histone tails

• This loosens chromatin structure, thereby promoting the initiation of transcription.
• The addition of methyl groups (histone methylation) can condense chromatin; the addition of phosphate groups (phosphorylation) next to a methylated amino acid can loosen chromatin.

Question 13

During the first stage of gene expression, what is DNA Methylation? (acetylation & methylation)

Answer 13

DNA Methylation

…is the addition of methyl groups to certain bases in DNA, assosciated with reduced transcription in some species

• DNA methylation can cause long-term inactivation of genes in cellular differentiation.
• This inactivation is essential during normal cell differentiation in the embryo.
• Deficient DNA Methylation can lead to abnormal embryonic development.
• Inactivation is usually permanent through successive divisions
• In genomic imprinting, methylation regulates expression of either the maternal or paternal alleles of certain genes at the start of development.

Question 14

What is Epigenetic Inheritance?

Answer 14

Epigentic Inheritance

The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence.

• Chromatin modifications just discussed (Histone modification & DNA Methylation) do not alter DNA sequence.
• But, they may be passed to future generations of cells.
• i.e the legacy of chromatin modifications is passed down to successive generations of cells in an organism during growth and development.

Question 15

In the first stage of gene expression , transcription, provide detail.

Answer 15

2. Transcription

Regulation of Transcription Initiation

• Chromatin-modifying enzymes provide initial control of gene expression by making a region of DNA either more or less able to bind the transcription machinery
• Once chromatin is optimally modified for expression, the initiation of transcription is the next major step at which gene expression is regulated.

Organization of a Typical Eukaryotic Gene

• Associated with most eukaryotic genes are multiple control elements
• Which are segments of noncoding DNA that serve as binding sites for transcription factors that help regulate transcription
• Control elements and the transcription factors they bind are critical to the precise regulation of gene expression in different cell types.

The Roles of Transcription Factors

• To initiate transcription, eukaryotic RNA polymerase requires the assistance of proteins called transcription factors
• General transcription factors are essential for the transcription of all protein-coding genes.
• In eukaryotes, high levels of transcription of particular genes depend on control elements interacting with specific transcription factors.

Question 16

Define:

Proximal control elements

Distal control elements

Answer 16

Proximal control elements

are located close to the promoter

Distal control elements

groupings which are called enhancers, may be far away from the gene or even located in an intron

Question 17

What is an activator protein?

Answer 17

Activator

An activator is a protein that binds to an enhancer and stimulates transcription of a gene

• Activators have two domains, one that binds DNA, and a second that activates transcription.

Question 18

A particular combination of control elements can activate transcription only when ……..

the appropriate activator proteins are present

Answer 18

A particular combination of control elements can activate transcription only when the appropriate activator proteins are present

Question 19

Unlike the genes of a prokaryotic operon, each of the co-expressed eukaryotic genes has a _ _ _ _ _ _ _ _ and _ _ _ _ _ _ _ _ _ _ _ _ _ _ _.

Answer 19

Unlike the genes of a prokaryotic operon, each of the co-expressed eukaryotic genes has a promoter and control elements.

• These genes can be scattered over different chromosomes, but each has the same combination of control elements.
• Copies of the activators recognize specific control elements and promote simultaneous transcription of genes.

Question 20

Some transcription factors function as repressor, inhibiting expression of a particular gene by three methods.

What are these methods?

Answer 20

1. Some bind directly to DNA to affect enhancers, block activators, or even stop transcription when activators are bound.
2. Some affect activator binding to DNA
3. Some affect chromatin structure
   * *Repressors act to silence transcription*

Question 21

In the third stage of gene expression regulation we have RNA processing , briefly summarize this.

Answer 21

3. RNA Processing

Mechanisms of Post-Transcriptional Regulation

• Transcription alone does not account for gene expression
• Regulatory mechanisms can operate at various stages after transcription
• Such mechanisms allow a cell to fine-tune gene expression rapidly in response to environmental changes.

RNA processing..

• In alternative RNA splicing, different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns.

Question 22

In the fouth stage of gene expression regulation we have mRNA Degradation , briefly summarize this.

Answer 22

4. mRNA Degradation

• The life span of mRNA molecules in the cytoplasm is a key to determining protein synthesis.
• Prokaryotic mRNA typically exists only a few minutes whereas
• Eukaryotic mRNA can exist for hours, days, even weeks.
• Nucleotide sequences that influence the lifespan of mRNA in eukaryotes reside in the untranslated region (UTR) at the 3’ end of the mRNA molecule.

Question 23

In the fifth stage of gene expression regulation we have Initation of Translation , briefly summarize this.

Answer 23

5. Initiation of Translation

• The initiation of translation of selected mRNAs can be blocked by regulatory proteins that bind to sequences or structures of the mRNA.
• Alternatively, translation of all mRNAs in a cell may be regulated simultaneously
• For example, translation initiation factors are simultaneously activated in an egg following fertilization.

Question 24

The final stage of gene of expression is protein processing and degradation. What happens?

Answer 24

6. Protein Processing and Degradation

• After translation, various types of protein processing, including cleavage and the addition of chemical groups, are subject to control.
• Proteasomes are giant protein complexes that bind protein molecules and degrades them.

Question 25

Transformation from zygote (sexuall cell from 2 gametes) to adult results from what 3 interrelated processes?

Answer 25

1.Cell division

2. Cell differentiation

The process by which cells become specialized in structure and function.

3. Morphogenesis

the physical processes that give an organism its shape.

• Differential gene expression results from genes regulated differently in each cell type*
• Materials in the egg can set up gene regulation that carries out as cells divide.*

Question 26

What are cytoplasmic determinants?

Answer 26

Cytoplasmic Determinants

are maternal substances in the egg that influence early development

• An egg’s cytoplasm contains RNA, proteins and other substances that are distributed unevenly in the unfertilized egg
• As the zygote divides by mitosis, cells contain different cytoplasmic determinants, which lead to different gene expression

Question 27

The other important source of developmental information is the environment around the cell, especially signals from nearby embryonic cells.

In the process called _ _ _ _ _ _ _ _ _, signal molecules from embryonic cells cause transcriptional changes in nearby target cells

Answer 27

In the process called induction, signal molecules from embryonic cells cause transcriptional changes in nearby target cells

Thus, interactions between cells induce differential of specialized cell types.

Question 28

Define:

Pattern formation is the development of…….

Positional information are the molecular cues that…..

Answer 28

Pattern formation

is the development of a spatial organization of tissues and organs.

In animals, pattern formation begins with the establishment of the major axes

Positional information

the molecular cues that control pattern formation, tells a cell its location relative to the body axes and to neighboring cells.

Question 29

Explain the origins of the model system for the body plan formation in fruit flies.

Answer 29

• 1940’s Edward B. Lewis proposed that genes were responsible for embryonic development
• 30 years later, German scientists Christiane Nüsslein-volhard and Eric Wieschaus worked to identify the genes responsible for body plan formation
• They examined flies with mutations to see what impact the mutation of a particular gene might have on embryonic development.
• Pattern formation has been extensively studied in the fruit fly Drosophila melanogaster.

Combining anatomical, genetic and biochemical approaches, researchers have discovered developmental principles common to many other species, including humans.

Question 30

Explain the life cycle of Drosophila (fruit flies)

Answer 30

In Drosophila, cytoplasmic determinants in the unfertilized egg determine the axes before fertilization.

After fertilization, the embryo develops into a segmented larva with three larva stages.

Question 31

Edward B. Lewis discovered the homeotic genes, which……

Answer 31

Edward B. Lewis discovered the homeotic genes, which……control pattern formation in late embryo, larva, and adult stages.

Question 32

Maternal effect genes encode for cytoplasmic determinants that initially establish the axes of the body of Drosophila.

These maternal effect genes are also called egg-polarity genes because they control orientation of the egg and consequently the fly

One maternal effect gene, the _ _ _ _ _ _ gene, affects the front half of the body

Answer 32

One maternal effect gene, the bicoid gene, affects the front half of the body

An embryo whose mother has no functional bicoid gene lacks the front posterior (i.e, tail) structures at both ends.

Question 33

Bicoid research is important for what three reasons?

Answer 33

1. It identified a specific protein required for some early steps in pattern formation2.
2. It increased understanding of the mother’s role in embryo development
3. It demonstrated a key developmental principle that a gradient of molecules can determine polarity and position in the embryo

Question 34

Give an overhead view of Chapter 18- Regulation of Gene expression

Answer 34

1. Operons: The Basic Concept

• What are they?
• How are they regulated?

2. Eukaryotic gene expression: How is gene expression regulated during transcription & translation

• Unpacking of Chromatin
• Transcription
• RNA processing
• mRNA degradation
• Translation
• Protein processing and degradation

3. Embryonic Development & Gene expression

4. How do cells become specialized? Embryonic Development & Gene expression

• How does the “body plan” become established?