Ch. 12 Regulation Of Gene Expression In Eukaryotes

Front 1

Which of the following would be different between a heart muscle cell and a vascular smooth muscle cell?

General transcription factors

Regulatory transcription factors

Genome

RNA Polymerase

Back 1

Regulatory transcription factors. Everything else is the same in every cell.

Front 2

True or false: different types of cells in multicellular organisms contain the same DNA and make the same proteins.

Back 2

False. They make different proteins.

Front 3

What are eukaryotic genes controlled by?

Back 3

DNA sequences.

1. Promoter (TATA Box)

2. Regulatory Elements (enhancers and silencers)

3. Promoter-proximal elements (GC-rich box and CCAAT Box)

Front 4

What is a promoter-proximal element?

Back 4

The series of transcription factor binding sites located near the core promoter of a gene. It is a cis regulatory DNA sequence.

The GC-Rich Box and the CCAAT box. Located ~100bp upstream of the TATA Box promoter. They are necessary for efficient transcription.

Front 5

In gene regulation, what do general transcription factors do?

Back 5

Help RNA Pol II bind to the promoter region.

Front 6

What do one or more activator proteins do in eukaryotic gene regulation?

Back 6

They may stimulate the ability of RNA Pol II to initiate transcription.

Front 7

What do one or more repressor proteins do in eukaryotic gene regulation?

Back 7

They may inhibit the ability of RNA Pol II to initiate transcription.

Front 8

What are some ways that regulatory transcription factors are modulated?

Back 8

1. They can be bound by small effector molecules

2. They can have protein-protein binding interactions

3. They can have covalent modifications.

Front 9

What can regulatory proteins do to nucleosomes?

Back 9

Alter their compositions or arrangements in the vicinity of the promoter, thereby affecting transcription.

Front 10

What can DNA Methylation do to transcription?

Back 10

Inhibit it either by preventing the binding of an activator protein or by recruiting proteins that cause chromatin to become more compact.

Front 11

True or false: A cell cannot change the expression of its genes in response to external signals (like hormones).

Back 11

False. External signals can affect the function of the proteins involved in transcription and gene regulation.

Front 12

What happens when an activator binds to an enhancer?

Back 12

The gene is activated and transcription is increased.

Front 13

What happens when a silencer is bound by a repressor protein?

Back 13

The gene is repressed. No transcription takes place.

Front 14

What is TFIID?

Back 14

The first protein to bind to DNA during the formation of the pre-initiation transcription complex of RNA Pol II.

Front 15

How do activators interact with TFIID?

Back 15

Activator binds the enhancer sequence. A co-activator works with the activator to recruit TFIID to the core promoter. Transcription is activated.

Front 16

How do repressors interact with TFIID?

Back 16

Repressor binds to the silencer sequence, then inhibits the binding of TFIID to the core promoter. Transcription is repressed.

Front 17

What are Mediators?

Back 17

Proteins that can assist activators and repressors to activate or inhibit transcription

Front 18

What is another name for basal transcription factors?

Back 18

General transcription factors.

Front 19

What controls the rate of transcription of target genes?

Back 19

Regulatory transcription factors.

Front 20

What are regulatory/ response elements?

Back 20

Specific DNA sequences (like enhancers and silencers) that regulatory transcription factors bind to.

Front 21

What are the main differences between eukaryotic gene regulation and bacterial gene regulation?

Back 21

1. Eukaryotes have 3 RNA Polymerases. Bacteria only have 1.

2. Eukaryotic mRNA is processed. Bacterial mRNA is coupled/not processed.

3. Eukaryotic RNA Polymerases are larger and more complex

4. The default state of eukaryotic genes is off. The default state for bacterial genes is on.

5. Eukaryotes have nucleosomes and chromatin. Bacteria don't.

Front 22

What interacts in the major groove of DNA via hydrogen bonds, ionic bonds, and hydrophobic interactions?

Back 22

RTF amino acid residues and DNA nucleotides.

Front 23

What traits do RTFs possess one or more of?

Back 23

1. Domain that recognizes a DNA regulatory sequence (DNA binding domain).

2. Transactivation domain (allows interaction with other RTFs)

3. An activation domain (allows interaction with RNA Pol II and/or GTFs

4. A domain that can influence chromatin condensation directly or indirectly.

5. A domain that acts as a sensor of physiological conditions within the cell.

Front 24

What can RTFs be modulated by?

Back 24

1. An effector molecule (ex: hormones)

2. Protein-protein interaction (dimerization)

3. Covalent modifications (phosphorylation)

Front 25

What is a homodimer?

Back 25

When two of the same RTFs bind/interact via dimerization.

Front 26

What is a heterodimer? Why do they have an advantage over homodimers?

Back 26

When two different RTFs interact via dimerization. Have an advantage over homodimers because they increase the number of DNA sequences recognized by the RTFs.

Front 27

What is a nucleosome?

Back 27

A structural unit of a eukaryotic chromosome consisting of a length of DNA coiled around a core of histones.

The histone core is an octamer made of two H2A/H2B dimers and a tetramer of H3 and H4

Front 28

What is chromatin?

Back 28

The material of which the chromosomes of eukaryotes are formed. Consists of RNA, DNA, and protein. It packages long DNA molecules into a more compact, denser shape.

Front 29

What is GCR? What is it modulated by?

Back 29

Gluccocorticoid Receptor. It is an activator.

Modulated by:

1. The binding of a hormone

2. Dimerization

Front 30

What does NLS stand for?

Back 30

Nuclear Localization Sequence. Causes a receptor like glucocorticoid not to enter the nucleus until bound by its hormone.

Front 31

What is CREB? What is it modulated by?

Back 31

Cyclic AMP response element binding protein. It is an activator.

Modulated by:

1. Dimerization

2. Covalent modulation (phosphorylation)

Front 32

What is a reporter gene?

Back 32

A gene whose phenotypic expression is easy to monitor. Used to study tissue-specific promoter and enhancer activities in transgenes.

In reporter gene constructs, they are linked to the regulatory element.

Ex: lacZ or Green fluorescent protein

Front 33

What can be studied using reporter genes?

Back 33

DNA-binding and activation domains as well as the effects of enhancer locations and orientations.

Front 34

What is Euchromatin? Heterochromatin?

Back 34

1. Loosely packaged chromatin that is active and can be transcribed.

2. Tightly packaged chromatin that is inactive and cannot be transcribed.

Front 35

What are the two forms of heterochromatin?

Back 35

1. Constitutive (meaning it's always heterochromatin such as telomeres and the centromere)

2. Facultative, meaning it can go between being heterochromatin and euchromatin because it does contain genes.

Front 36

What are histones?

Back 36

Small, basic (positively charged) proteins composed of ~20-30% lysine (+) and arginine (+) residues that bind to the negatively charged DNA in the minor groove.

Include H1, H2, H2B, H3, and H4.

Front 37

What are the 4 major mechanisms that alter chromatin structure?

Back 37

1. Changing nucleosome position by chromatin remodeling complexes

2. Removing histones, known as histone eviction

3. Replacing common histones with histone variants

4. Adding/removing functional groups of histones, resulting in histone modification

Front 38

What can ATP-dependent remodeling complexes do?

Back 38

1. Change nucleosome position

2. Evict histones

3. Add histone variants

The SWI-SNF complex in yeast is an example of one.

Front 39

What is a histone tail?

Back 39

The end of a histone protein protruding from the core nucleosome and subjected to post-translational modification.

Front 40

What are three of the main histone modifications? How does each affect gene expression?

Back 40

1. Acetylation of lysine (loosens chromatin, allowing transcription. Deacetylation tightens it).

2. Methylation of lysine and arginine (can activate or repress gene expression, but typically represses it).

3. Phosphorylation of serine (loosens chromatin if kinases add phosphate groups (adding negative charge). Tightens if phosphatases remove phosphate groups).

Front 41

What does acetylation of a histone tail do?

Back 41

Addition of acetyl groups neutralizes positive charge of lysine residues, reducing histone tail interaction with negatively charged DNA backbone.

Front 42

What does histone tail methylation do?

Back 42

Histone Methyltransferase (HMTase) adds 1, 2, or 3 methyl groups to a specific amino acid residue of the H3 histone tail. Doesn't affect charge, but does create binding sites for other proteins to activate or repress gene expression depending on residues modified.

Typically, unmethylated genes are active, and methylated genes are inactive.

Front 43

What is the histone code?

Back 43

The pattern of histone modifications. Different patterns result in different levels of chromatin compaction to hide or expose genes for expression.

Front 44

What is HAT enzyme? What is HDAC enzyme?

Back 44

Histone Acetyltransferase. Adds acetyl groups to loosen chromatin and increase gene expression.

Histone Deacetyltransferase. Removes acetyl groups to tighten chromatin and reduce gene expression.

Front 45

What are NFRs?

Back 45

Nucleosome free regions. They flank many genes.

Front 46

What is epigenetic inheritance? What are some examples?

Back 46

A modification of a gene or chromosome or DNA segment that alters gene expression during gametogenesis or early embryo genesis.

Affects the phenotype but not the genotype of an individual.

Ex: Genomic imprinting and dosage compensation

Front 47

How are nucleosomes passed from parent DNA to daughter molecules?

Back 47

1. Histones in parental cells are disassembled

2. Parent histones are distributed randomly in daughter molecules.

3. Parent histones are used as templates to build/modify new histones.

Front 48

What are CpG islands?

Back 48

A type of DNA methylation that can be inherited epigenetically.

They are groups of unmethylated CG dinucleotides found in clusters near gene promoters. They're methylated by DNA methyltransferase. Associated with inactive regions of the genome.

Front 49

How does CpG methylation inhibit transcription?

Back 49

1. Preventing activators from binding

2. Causing methyl- Cfc pG-binding proteins (MECPs) to bind, which recruit HDACs, resulting in DNA compaction.

Front 50

What are insulators?

Back 50

DNA segments that function as a boundary between two genes. They protect a gene from the regulatory effects of a neighboring gene.

Front 51

What are barrier insulators?

Back 51

They are DNA elements that prevent the spread of heterochromatin by serving as binding sites for proteins that maintain euchromatic modifications such as histone acetylation.

Front 52

What are enhacer-blocking insulators?

Back 52

Regulatory DNA elements positioned between a promoter and an enhancer so the promoter can't be activated. Prevent neighboring enhancers from activating nearby genes.

Front 53

_______ bind in the minor groove of DNA, whereas _______ bind in the major groove.

Back 53

Histones in minor

Regulatory transcription factors in major.

Front 54

What is functional genomics?

Back 54

The study of the function, expression, and interaction of gene products.

Front 55

What is the transcriptome?

Back 55

The sequence and expression patterns of all RNA transcripts.

Front 56

What is the proteome?

Back 56

The sequence and expression patterns of all proteins.

Front 57

What is the interactome?

Back 57

The complete set of physical interactions between proteins and DNA segments, between proteins and RNA segments, and between proteins.

Front 58

What are DNA microarrays for? What is the procedure?

Back 58

Used to study the transcriptome, so to see what genes are active in a particular cell under certain conditions based on the mRNA you find.

1. Extract mRNA

2. Make cDNA and label them with fluorescent dyes

3. Hybridize to microarray

4. Laser excitation at dye-specific Hertz

5. Detect laser emission

6. Computer calculates relative levels of hybridized probes

7. Red = gene expression increased, green = gene expression decreased, black = gene always expressed at same level.

Front 59

What is the yeast two-hybrid system used to study?

Back 59

Protein-protein interaction. Such interaction will result in the expression of a reporter gene.

Answers question: do proteins A and B interact.

Front 60

What is the ChIP assay, and what is it used for?

Back 60

Chromatin immunoprecipitation assay. Used to study protein-DNA interactome.

Answers question: what DNA sequence does a certain RTF bind to.

Front 61

What is genomic imprinting?

Back 61

When a DNA segment is marked, and that mark is retained throughout the individual's lifetime. Results in monoallelic expression where either mom's allele is silenced or dad's allele is silenced. Only one is active.

Front 62

What is an example of genomic imprinting?

Back 62

1. Igf2 (insulin-like growth factor-2) expression in mice. Only paternal allele is expressed. Mother has a silenced copy.

copy.

Front 63

What is Angelman syndrome? Prader-Willi syndrome?

Back 63

Disease influenced by genomic imprinting.

1. Mothers have active AS gene but silent PWS gene.

2. Fathers have active PWS gene but silent AS gene.

3. The two genes are right next to each other on chromosome 15. Must have 1 functional copy of both to be normal.

4. Angelman syndrome develops when a deletion in chromosome 15 from Mom is inherited. (AS not expressed)

5. Prader-Willi syndrome occurs when a deletion in chromosome 15 from dad is inherited. (PWS not expressed).

Front 64

What is the imprinting control region (ICR)?

Back 64

It acts as an enhancer-blocking insulator when bound by CTC - binding factor (CTCF). Prevents the transcription of Igf2 in female mice.

In male mice, ICR is methylated, allowing Igf2 to be expressed.

Front 65

What are the steps required for genomic imprinting?

Back 65

1. Imprints from parental genes erased from primordial germ cells.

2. Imprints initiated in primordial germ cells.

3. Egg and sperm unite to propagate imprints. Followed by fertilization and development.

Front 66

What is dosage compensation?

Back 66

Relates to the fact that expression of the genes on the X chromosome must be similar in both sexes. Since females have two X's, they have twice as many copies of genes on X chromosome than males.

Front 67

What is a Barr body?

Back 67

In female mammals, it is the inactivated X chromosome that can be seen in the nucleus as a highly condensed structure.

Front 68

Why do black and white heterozygous female mice have patchwork fur? Same question for tortoiseshell cats (orange and black patchwork fur)?

Back 68

In every cell, one X chromosome is randomly silenced as a Barr body. This means each cell will express either the paternal color or maternal color, leaving a patchwork pattern.

Front 69

Why aren't there normally any male tortoiseshell cats?

Back 69

Male cats only have one X and can't be heterozygous. The cat would either be black or orange, but not both

Front 70

What is the Lyon Hypothesis? How does it work? Where are the genes found?

Back 70

The mechanism of X inactivation.

1. When the Xist gene is expressed, the Xist RNA coats the X chromosome = inactivation.

2. When the opppsitely oriented Tsix gene is expressed, Tsix RNA inhibits transcription of Xist gene = prevents inactivation.

Xist (X inactive specific transcript) is expressed in inactive X chromosomes (Barr bodies).

Tsix is expressed in active X chromosomes.

Genes are found in the Xic region of the X chromosome.

Front 71

What are the three phases of X inactivation?

Back 71

1. Initiation: Occurs during embryonic development. # of Xics is counted. If two, one X deactivated.

2. Spreading: Occurs during embryonic development. Begins at Xic and progresses toward both ends till chromosome is inactivated (Coated by Xist RNA = Barr body).

3. Maintenance: Occurs from embryonic development through adult life. Inactivated X maintained during mitosis.

Front 72

What determines viability in IVF?

Back 72

The DNA quality. To be a viable, fertilized egg, it must have both a female pronucleus and a male pronucleus. One gene set from each parent. XX and YY are not viable.