Practical Gene regulation AI generated

Question 1

Describe the characteristics of pluripotent stem cells.

Answer 1

Pluripotent stem cells exhibit spherical, undifferentiated cell morphology with smooth membrane surfaces. They grow in tightly packed colonies with a high nucleus/cytoplasm ratio and prominent nuclei.

Question 2

Explain the difference between induced pluripotent stem cells (iPS) and embryonic stem cells (ES) in terms of immunological reactions.

Answer 2

iPS are derived from the patient’s own tissue, making them less likely to trigger immunological reactions compared to ES cells.

Question 3

Define chromatin and nucleosome in the context of DNA packaging in eukaryotes.

Answer 3

Chromatin is the complex of DNA and histone proteins, while a nucleosome is the basic unit of chromatin consisting of 8 histone proteins and approximately 146 base pairs of DNA.

Question 4

How does histone acetyltransferase (HAT) impact DNA accessibility for transcription?

Answer 4

HAT adds acetyl groups to histone tails, neutralizing their charge and loosening the tight packing of chromatin, making DNA accessible for transcription.

Question 5

Describe the structure of a nucleosome.

Answer 5

A nucleosome consists of 8 histone proteins (shown in green) and approximately 146 base pairs of DNA, with each histone protein having a tail of around 20 amino acids.

Question 6

Describe the role of histone modifications in gene regulation.

Answer 6

Histone modifications can affect the affinity of histones for DNA, leading to changes in chromatin structure and accessibility for transcription.

Question 7

How do activators and enhancers contribute to gene regulation?

Answer 7

Activators bind to enhancer sequences upstream of the promoter, facilitating the bending of DNA to bring regulatory elements closer to the transcription start site.

Question 8

Define transcription factors and their function in transcription.

Answer 8

Transcription factors are proteins that assist RNA polymerase in initiating transcription by binding to specific DNA sequences and forming the transcription initiation complex.

Question 9

What is the Central Dogma of molecular biology?

Answer 9

The Central Dogma describes the flow of genetic information from DNA to RNA to proteins.

Question 10

Do transcription factors play a role in determining cell-specific gene expression?

Answer 10

Yes, the specific set of transcription factors present in a cell determines which genes will be expressed in that particular cell type.

Question 11

Describe the role of enhancers and silencers in gene expression regulation.

Answer 11

Enhancers and silencers can influence gene expression by interacting with promotors located hundreds or thousands of nucleotides away, facilitated by DNA bending to bring them in close proximity.

Question 12

What is the genetic blueprint of retroviridae viruses?

Answer 12

Retroviridae viruses carry their genetic information in the form of an RNA genome.

Question 13

Define the term ‘transduction’ in the context of lentivirus use in the lab.

Answer 13

Transduction refers to the process of introducing exogenous genetic material into a cell using a lentivirus, a type of retrovirus.

Question 14

How does the expression of NANOG gene serve as a biomarker for stem cells?

Answer 14

NANOG gene is expressed exclusively in stem cells, making it a reliable biomarker to identify and characterize stem cells.

Question 15

Describe the process of cDNA synthesis starting from mRNA extraction.

Answer 15

To synthesize cDNA, a poly T oligonucleotide primer anneals to the 3’ poly A tail of mRNA, and a reverse transcriptase enzyme uses the mRNA template to create a DNA strand, forming an RNA-DNA hybrid molecule.

Question 16

Describe the purpose of a negative control in experiments.

Answer 16

Negative controls are used to check for nonspecific binding and false positive results by running samples without the material being observed, validating positive results.

Question 17

Define post-translational modification and its importance protein function.

Answer 17

Post-translational modification refers to changes made to a polypeptide after translation, such as proteolysis, glycosylation, and phosphorylation, to ensure the protein becomes functional.

Question 18

How does a signal sequence contribute to protein function?

Answer 18

A signal sequence on a polypeptide indicates where the protein belongs, guiding post-translational modifications and proper folding for functional protein formation.

Question 19

Do Western blots measure gene expression directly?

Answer 19

No, Western blots measure protein levels, which are the final proof of effective gene expression, as gene expression levels measured by RT-PCR may not always correlate with protein levels.

Question 20

Describe the process of glycosylation in protein modification.

Answer 20

Glycosylation involves adding sugars to proteins, forming glycoproteins, and typically occurs in the Golgi apparatus as a post-translational modification essential for protein function.

Question 21

Describe the role of post-transcriptional modifications in the between mRNA and protein levels.

Answer 21

Post-transcriptional modifications can explain the difference between mRNA and protein levels.

Question 22

Define the function of a plasma membrane in mammalian cells.

Answer 22

The plasma membrane acts as a barrier to the extracellular environment in mammalian cells.

Question 23

How does cell lysis impact the accessibility of proteins inside a cell?

Answer 23

Cell lysis breaks the plasma membrane barrier, allowing access to proteins inside the cell.

Question 24

Do Western blot results provide information about protein expression in different cell types?

Answer 24

Yes, Western blot results can show differences in protein expression among different cell types.

Question 25

Describe the significance of post-translational modifications in regulating protein activity in eukaryotic cells.

Answer 25

Post-translational modifications can affect the half-life of a protein, thereby regulating its activity in eukaryotic cells.