Cytoplasmic inheritance

Refers to transmission of genes on mitochondrial and chloroplast chromosomes, as opposed to nuclear chromosomes.

In many eukaryotic species, mitochondria and chloroplasts in fertilized eggs are

Uniparental

Organelle Chromosomes do not.....

Encode all the proteins needed for mitochondria function.

Carl Correns

Made reciprocal crosses between flowers on branches with differently colored leaves.

What were the results from Carl Correns tests?

Tests showed that progeny invariably exhibited the same phenotype as the female parent in the cross

Homoplasmic cells

Have organelles with the same genotype

Hereoplasmic cells

Contain a mixture of alleles

Mitochondrial Mutations can result in

Human genetic diseases

The phenotypes such as diseases are often highly pleitropic because.....

Because of the dependence of cells on mitochondrial function in oxidative phosphorylation

The double-membrane system in chloroplasts and mitchondria is derived

From a similar membrane system found in bacteria.

Are organelles and bacteria similar in size?

True

Organelle DNA is packaged similarly to that of _________, and differently than ____________ _______

Bacteria; Nuclear DNA

The transcriptional and translational machinery of the organelles closely resembels that of bacteria (T/F)

True

The closest living relatives of mitchondria are

Free living α-proteobacteria

Chloroplasts have also a single origin, descended from a

Single endosymbiotic event at leat 1.2 billion years ago

The closest relatives of chloroplasts are

Free-living cyanobacteria

Regulatory regions of a eukaryotic gene all contain which of the following sequences, which act only on one copy of the chromosome?

A) zinc fingers

B) cis-acting regulatory sequences

C) homeodomains

D) trans-acting regulatory sequences

E) leucine zippers

B) cis-acting regulatory sequences

You have identified a mutation in a gene which also seems to decrease transcription of another gene 2000 bp away from the mutation site. What regulatory sequence, which may be found within another gene, has likely been mutated in this instance?

A) core promoter

B) proximal elements

C) enhancer sequence

D) homeodomain motif

E) upstream activator sequence

C) enhancer sequence

In yeast, if you want to prevent the Gal4 regulatory protein from binding near each of the GAL genes, which sequence element would you target?

A) core promoter

B) proximal elements

C) enhancer sequence

D) homeodomain motif

E) upstream activator sequence

E) upstream activator sequence

In the presence of galactose, you unexpectedly find that transcription is still blocked. Assuming Gal80 is present and functional, which other protein may be mutated to prevent transcriptional activation?

A) Gal2

B) Gal3

C) Gal4

D) Mig1

E) Gal10

B) Gal3

Galactose is absent, but you find active transcription of the GAL genes. Which protein is likely mutated or absent to allow for constitutive transcription of the GAL genes?

A) Gal2

B) Mig1

C) Gal4

D) Gal10

E) Gal80

E) Gal80

Which protein binds to the silencer sequence and promotes transcriptional silencing in the presence of glucose?

A) Gal2

B) Mig1

C) Gal4

D) Gal10

E) Gal80

B) Mig1

If a mouse inherits a deletion in the SHH enhancer, what effect would you expect to see?

A) enhanced limb development

B) abnormal limb development

C) position effect variegation

D) increased β-globin production

E) abnormal β-globin production (thalassemia)

B) abnormal limb development

Which sequences would likely have both a nucleosome-depleted region (NDR) and a poly A/T tract to attract transcriptional activators to a transcription start sequence?

A) chromatin modifiers

B) enhancers

C) open promoters

D) closed promoters

E) insulators

C) open promoters

Molecular biologists can determine experimentally whether a region of DNA contains closed chromatin or open chromatin by assessing the sensitivity of the region to

A) nucleosomes.

B) histone deacetylase.

C) RNA polymerase II.

D) methyltransferase.

E) DNAse.

E) DNAse.

Chromatin remodeling involves both sliding and relocating of the nucleosomes. Which eukaryotic chromatin remodeling complex is likely involved?

A) ISWI complex

B) SWR1 complex

C) SWI/SNF complex

D) SHH complex

E) Mig1 complex

C) SWI/SNF complex

If you want to affect chromatin packaging, which amino acid could you mutate to affect both histone acetylation and methylation patterns?

A) arginine

B) methionine

C) histidine

D) lysine

E) asparagine

D) lysine

A region of chromatin has recently become DNAse I hypersensitive. Which enzyme has been activated to cause this change in chromatin structure?

A) histone methyltransferase

B) histone acetylase

C) histone deacetylase

D) phosphatase

E) kinase

B) histone acetylase

Prader-Willi syndrome is a genetic disorder involving a partial deletion of chromosome 15q on the paternal chromosome. When both copies of a gene (or chromosome) are functional but only one is expressed, this is an example of

A) position effect variegation.

B) X inactivation.

C) genomic imprinting.

D) histone acetylation.

E) chromatin modifications.

C) genomic imprinting.

When CpG islands are unmethylated,

A) chromatin in the promoter region is open, allowing access by transcription factors and RNA polymerase.

B) chromatin in the promoter region is closed, preventing transcription factors and RNA polymerase from binding.

C) chromatin in the enhancer region is closed, so they are unable to bind regulatory proteins to initiate transcription.

D) DNAse hypersensitivity in that region of the chromosome is lost.

E) genes downstream of the CpG islands cannot be expressed, because the promoter region is blocked by histones.

A) chromatin in the promoter region is open, allowing access by transcription factors and RNA polymerase.

The imprinting control region (ICR) involved in genomic imprinting on chromosome 15 is what type of sequence?

A) enhancer

B) insulator

C) silencer

D) promoter

E) intronic

B) insulator

During RNAi, what do miRNAs target for destruction?

A) heterochromatic regions of DNA

B) CpG islands

C) mRNAs

D) histones

E) ribosomes

C) mRNAs

Many types of cancer are known to overexpress the receptor protein tyrosine kinase. Which molecular technique can be used to reduce expression of an oncogene in vitro?

A) PCR

B) DNAse sensitivity assay

C) RNAi

D) Southern blotting

E) western blotting

C) RNAi

Inherited mutations in the Xist promoter lead to defects in which epigenetic process?

A) RNAi

B) X inactivation

C) genomic imprinting

D) position effect variegation

E) methylation of CpG islands

B) X inactivation

Which molecules bind regulatory sequences of DNA to encourage positive regulation of transcription?

Answer: activator proteins

Which protein complex directs DNA bending into loops that contact RNA polymerase and transcription factors bound at the core promoter or with protein complexes bound to proximal promoter elements?

Answer: enhanceosome

What are three proteins you would expect to find bound to the core promoter region in eukaryotes?

Answer: TBP, GTFs, and Pol II

Answer: TBP, GTFs, and Pol II

In gal+ yeast, what is the product of the galactose utilization pathway?

Answer: glucose-1-phosphate

In the GAL gene system, which protein acts as an activator protein through its transcription-initiating effect?

Answer: Gal4

In the GAL gene system, which protein binds to the activation domain of the activator protein, ultimately blocking transcription in the absence of galactose?

Answer: Gal80

Gal4 is mutated such that it still binds to the DNA but cannot interact with Gal80. What effect would you expect to see in the absence of galactose?

Answer: transcriptional activation

Gal80 is mutated such that it cannot interact with Gal3. What effect would you expect to see in the presence of galactose?

Answer: Transcription is blocked.

Eukaryotes use these highly specialized enhancer elements, which regulate the transcription of multiple genes packaged in complexes of closely related genes (e.g., β-globin).

Answer: locus control regions (LCRs)

What are the protein-binding sequences that direct enhancers to interact with the intended promoter and that block communication between enhancers and other promoter?

Answer: insulator sequences

For the following gene, which mutant likely has lost its enhancer?

Mutant # Deletion Region % Transcription

WT None 100%

1 1-200 150%

2 250-400 100%

3 500-800 50%

4 950-1100 0%

Answer: mutant 3 (region 500-800)

For the following gene, which type of regulatory sequence has likely been deleted in mutant 1?

Mutant # Deletion Region % Transcription

WT None 100%

1 1-200 150%

2 250-400 100%

3 500-800 50%

4 950-1100 0%

Answer: silencer

For the following gene, you notice the following results.

Mutant # Deletion Region % Transcription (lungs) % Transcription (kidneys)

WT None 100% 100%

1 1-200 150% 150%

2 250-400 100% 100%

3 500-800 50% 50%

4 950-1100 0% 100%

What type of sequence has been mutated in mutant 4?

Answer: tissue-specific (lung) promoter

What are the two mechanisms by which chromatin remodelers can move nucleosomes?

Answer: nucleosome sliding and repositioning

In yeast, which gene would you expect to be activated during phosphate starvation?

Answer: PHO5

In vertebrates and plants, what types of modifications to the N-terminal tails of histones lead to heterochromatin formation?

Answer: deacetylation and methylation

Which of the four nucleotides are typically methylated in "islands," resulting in closed chromatin structure?

Answer: cytosines

What effect does methylation of CpG islands have on human promoters?

Answer: reduced transcription

Which protein complex binds dsRNA fragments to generate ssRNAs for RNAi?

Answer: RNA-induced silencing complex (RISC)

Which enzyme cuts dsRNA into 21-25 bp fragments during RNAi?

Answer: Dicer

Gal4 binding leads to the formation of a multiprotein complex known as ________, which is an enhanceosome that forms after the activator protein binds.

Answer: mediator

In the GAL gene system, ________ are cis-acting regulatory elements, and ________ protein is a trans-acting regulatory protein.

Answer: UASG; Gal4

Demethylation and acetylation lead to open chromatin structure and are associated with ________ regions of genomes.

Answer: euchromatic

________ in Drosophila results from the movement of the transcriptionally active w+ allele into the centromeric region of the fruit-fly X chromosome.

Answer: Position effect variegation (PEV)

In animals, the ________ enzyme cuts pri-mRNA to produce mi-RNA.

Answer: Drosha