L5- Gene Expression

Question 1

Cells in the brain and cells in the liver contain the same DNA. How is it that these cells are different cell types?

Answer 1

Each cell type has a distinct pattern of gene expression.

Question 2

What is a housekeeping protein and in which cell type is it found?

Answer 2

These are proteins associated with basic metabolism, translation, transcription, replication, and cell structure of a cell. They are generally present in all cell types.

Question 3

What is heterochromatin?

Answer 3

Heterochromatin is condensed chromatin. It tends to be transcriptionally inactive, and it is less sensitive to DNAse I digestion than euchromatin.

Question 4

What is euchromatin?

Answer 4

Euchromatin is relaxed (i.e. non-condensed) chromatin, and is usually associated with transcriptionally active genes.

Question 5

What are hypersensitive sites and where are they located with respect to genes?

Answer 5

Hypersensitive sites are short regions of chromatin that are exceptionally sensitive (i.e. very accessible) to nucleases such as DNase I. They are often found in the upstream control regions of active genes.

Question 6

What are locus control regions (LRCs) and how do they work?

Answer 6

LCRs are chromosomal elements that act over long distances to control the expression of multigene families. They regulate gene expression indirectly by regulating chromatin organization over certain chromosomal domains. Sections of DNA containing LRCs may form loops over desired genes to enhance their expression.

Question 7

Name a protein complex that can alter chromatin structure via nucleosome remodeling.

Answer 7

SWI-SNF.

Question 8

What is the function of histone acetyltransferases?

Answer 8

These enzymes catalyze the acetylation of histones, which leads to the unfolding of chromatin. This increases the accessibility of transcription factors to DNA.

Question 9

What is the function of DNA methyltransferases?

Answer 9

These enzymes methylate cytosine residues at carbon 5 after DNA replication has occurred. Methylation of DNA represses gene transcription.

Question 10

Which amino acid residue in histones is typically most susceptible to acetylation?

Answer 10

Lysine.

Question 11

Where are CpG islands found?

Answer 11

They are found in promoter regions of genes that are actively transcribed in all cell types (i.e. housekeeping genes). CpG islands almost always lack methylation.

Question 12

The assembly of basal transcription factors requires the presence of what other class of transcription factors?

Answer 12

Activators.

Question 13

Activators bind to what regulatory regions of DNA?

Answer 13

Enhancers.

Question 14

What is the function of coactivators?

Answer 14

They allow communication between activators and basal transcription factors.

Question 15

The complex of coactivators binds to which protein?

Answer 15

TATA Binding Protein (TBP).

Question 16

What is the function of repressors? To which sequence of DNA do they bind?

Answer 16

They block the initiation of transcription by interfering with the function of activators. The sequences that repressors bind to are called silencers.

Question 17

What is the result of activator-coactivator interactions?

Answer 17

Activator-coactivator interactions allow basal transcription factors to position RNA polymerase II at the beginning of the protein-coding region of a gene and set the polymerase in motion.

Question 18

True or False. Genes are generally alike with regards to the combination of promoter and enhancer (or silencer) elements they carry.

Answer 18

False. This is how cells are able to control the transcription of every gene individually.

Question 19

Under conditions of elevated temperature, cells from all organisms suspend transcription and translation except for which set of genes?

Answer 19

Genes encoding proteins that help with survival of cells at high temperature (i.e. genes encoding heat shock proteins).

Question 20

What causes heat shock factor protein (HSF) to become active?

Answer 20

Heat shock (elevated temperatures). Other stresses (such as toxins) may also activate a heat shock response.

Question 21

What is the function of heat shock factor (HSF) proteins?

Answer 21

After heat shock-induced activation, HSF proteins bind to specific DNA sites upstream of certain genes and increase transcription of those genes.

Question 22

Binding of heat shock factor (HSF) proteins to DNA is not sufficient to increase transcription of heat shock genes. What else must occur after binding (hint: what modification must occur to the HSF proteins because they can become active)?

Answer 22

Phosphorylation of HSF proteins.

Question 23

Estrogen, testosterone, and progesterone all belong what class of hormones?

Answer 23

Steroid hormones.

Question 24

Steroid hormones are all derivatives of which metabolite?

Answer 24

Cholesterol.

Question 25

What is the mechanism by which steroid hormones affect the transcription of genes?

Answer 25

Steroid hormones are fat soluble and can therefore diffuse across membranes. They form complexes with their receptors. These complexes translocate to the nucleus where they displace nucleosomes from promoter regions. This facilitates binding of other transcription factors.

Question 26

What are the DNA binding sites for steroid hormone/receptor complexes called?

Answer 26

Hormone response elements.

Question 27

What information can be extracted from DNA microarrays?

Answer 27

Levels and patterns of gene expression.

Question 28

How are DNA fragments able to attach to the underlying slide of glass in a DNA microarray?

Answer 28

The DNA stick to the slide because the slides are coated with poly-L-lysine, which is positively charged (recall that DNA is negatively charged because of the phosphates in the backbone).

Question 29

DNA microarrays are useful in determining what kind of information?

Answer 29

The relative expression levels of genes. The sample applied to the microarray is fluorescence-labeled cDNA.

Question 30

How does antisense therapy affect mRNA translation?

Answer 30

In antisense therapy, a fragment of nucleic acid that is complimentary to an mRNA of interest is introduced into a cell. If the nucleic acid binds to a complementary fragment of mRNA, it blocks ribosomes from translating the mRNA.

Question 31

In antisense therapy, a nucleic acid fragment is introduced into a cell. How is the antisense nucleic acid fragment protected from intracellular degradation?

Answer 31

The oxygen atoms that make up the phosphate links between nucleotides of the DNA backbone are replaced by sulfur atoms, rendering the nucleic acid immune to immediate degradation.

Question 32

What are some problems with antisense therapy that remain to be overcome before clinical use?

Answer 32

Evaluation of the toxicity of introduced nucleic acids, keeping nucleic acids inside the cells once they are introduced, identifying the genes that are causative of the diseases we intend to treat, etc.

Question 33

What is RNA interference?

Answer 33

RNAi is a technique in which double-stranded RNAs homologous to a gene of interest are introduced inside a cell with the goal of silencing that gene.

Question 34

What is the function of the enzyme Dicer?

Answer 34

It cleaves double-stranded RNAs into smaller double-stranded RNA fragments called siRNAs.

Question 35

How do siRNAs silence gene expression?

Answer 35

siRNAs are separated into single strands. The single strands then bind to the RISC complex, facilitating degradation of complementary mRNAs before they can be translated by ribosomes.

Question 36

What is the RISC complex?

Answer 36

It is a protein complex that binds to single strands of siRNAs. The siRNAs serve as a template that recognize complementary mRNAs. Once recognized, the RNase subunit of the RISC complex cleaves the complementary mRNAs so that they cannot be translated.