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34 Cards in this Set

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What is the mechanism of Actinomycin D and what organisms does it work against?

Actinomycin D prevents transcription.




Actinomycin D works against both bacteria and eukaryotes.

What is the mechanism of Puromycin and what organisms does it work against?

Puromycin disrupts translation.




Puromycin D works against bacteria and eukaryotes.

What is the mechanism of Tetracycline and what organisms does it work against?

Tetracycline prevents blocks the binding of aminoacyl-tRNA to the ribosome.




Tetracycline works on bacteria.

What is the mechanism of streptomycin and what organisms does it work against?

Streptomycin inhibits translation.




Streptomycin works on bacteria.

What is the mechanism of chloramphenicol and what organisms does it work against?

Chloramphenicol inhibits translation.




Chloramphenicol works on bacteria.

What is the mechanism of erythromycin and what organisms does it work against?

Erythromycin inhibits translation.




Erythromycin works on bacteria.

What is the mechanism of rifampicin and what organisms does it work against?

Rifampicin blocks the initiation of RNA polymerase, inhibiting RNA synthesis.




Rifampicin works on bacteria.

What is the mechanism of cycloheximide and what organisms does it work against?

Cycloheximide blocks the translocation reaction the ribosome, inhibiting translation.




Cycloheximide works on eukaryotes.

What is the mechanism of anisomycin and what organisms does it work against?

Anisomycin blocks the peptidyl transferase reaction on the ribosomes, inhibiting translation.




Anisomycin works on eukaryotes.

What is the mechanism of α-Amanitin and what organisms does it work against?

α-Amanitin block mRNA synthesis by binding to RNA Polymerase II and III




α-Amanitin works on eukaryotes.

Which properties are unique for RNA polymerase (compared to DNA polymerase)?

- Creates a cap on the 5' end


- Does not need a primer


- Has no nuclease activity


- Copies only certain genes, not the whole DNA

Which properties are similar between RNA polymerase and DNA polymerase?

Both:


- synthesize in the 5' -> 3' direction


- have similar mechanism of elongation


- have similar processivity


- work by hydrolysis of pyrophosphate

Name 3 proteins (not DNA polymerases) that can be found in the replication fork of E. coli.

Helicase, ligase and primase

Describe briefly the mechanism of the spliceosome.

The spliceosome is comprised of several snRNPs (small nuclear ribonucleic proteins).




One snRNP binds to the 3' end of the intron while another binds to the 5' end. Other snRNPs lead these two snRNPs together, making the intron into a loop. The snRNPs then cut out the loop and ligate the exons together.

Which transcription factor is the main regulator of TNF-α expression?

NF-kB is the main transcription factor of all pro-inflammatory cytokines, including TNF-α, IL-1 and IL-6.

Describe how the amino acid selenocysteine is be incorporated into proteins.

There is no codon for selenocysteine. Instead, special tRNA(Ser) will recognize some UGA codons (which is usually a stop codon) and insert the amino acid serine.




Serine is then selenylated by an enzyme to become selenocysteine.

Define the term "tumor suppressor".

A tumor suppressor gene encodes for a protein involved in either DNA repair, promotion of apoptosis or inhibiting cell proliferation.




When this gene is mutated, the protein product can no longer execute its normal function and can allow the cell to proliferate uncontrolled.

What is the role of Sirt1 in the regulation of FOXO transcription factor?

Sirt1 activates FOXO by removing an acetyl-group from it.

Define the term "proto-oncogene".

A proto-oncogene is a gene that encodes for a protein involved in cell proliferation or inhibiting cell death.




When this gene is mutated it can become an oncogene, which encodes for a protein that causes uncontrolled activation of cell division or uncontrolled inactivation of apoptosis.

Describe briefly processing of tRNA.

tRNA is transcribed by RNA polymerase III, and is then cut at the 5' and 3'-ends by RNases. The sequence CCA is then added to the 3'-end.




Many of the tRNA bases are then modified by posttranslational modification (methylation, deamination and reduction).

Which protein in the replication fork has no enzymatic activity?

Single-strand binding protein (SSB)

How does acetylation of histones regulate gene expression and why?

Acetylation of histones activates genes while deacetylation deactivates genes.




Acetylation relaxes the DNA around the histone, making it easier to transcribe.

How does methylation of DNA regulate gene expression?

Methylation of DNA deactivates genes.

What is the primer for reverse transcriptase?

tRNA is the primer for reverse transcriptase.




In HIV the primer is tRNA(Lys)

Name the enzymes involved in nucleotide excision repair.

ABC excinuclease, DNA helicase, DNA polymerase I and DNA ligase are involved in nucleotide excision repair.

Name the enzymes involved in base excision repair.

DNA glycosylase, AP endonuclease, DNA polymerase I and DNA ligase are involved in base excision repair.

Which enzymes are involved in direct repair?

AlkB


O6-methylguanine-DNA methyltransferase.


DNA photolyase

Which cofactors does AlkB need?

AlkB requires α-ketoglutarate and Fe2+ to work.

Which enzymes are involved in methyl-directed mismatch repair?

Mut-complex


Exonucleases


Helicase


DNA polymerase III and Dam methylase

What is the "secondary genetic code"?

The interaction between aminoacyl-tRNA synthetase and the tRNAs is sometimes called the "secondary genetic code".

What are the types of eukaryotic RNA polymerase?

RNA polymerase I


RNA polymerase II


RNA polymerase III

Which RNA polymerase transcribes tRNA?

RNA polymerase III

Which RNA polymerase transcribes mRNA?

RNA polymerase II

In what way can bacterial antibiotics be toxic to humans?

The mitochondria in eukaryotic cells are similar to prokaryotes, so bacterial antibiotics can affect mitochondrial DNA transcription and translation.