topic 19

Question 1

where does replication, transcription, and translation occur in bacteria? in eukaryotes?

Answer 1

in bacteria, DNA replication, transcription, and translation happen in the cytoplasm because bacteria lacks a defined nucleus.

in eukaryotes, DNA replication and transcription both occur in the nucleus while translation occurs in the cytoplasm. DNA that’s replicated is not transcribed at the same time, meaning both of the processes are spatially separate.

Question 2

what are the differences between transcription in bacteria and eukaryotes? (6) describe them

Answer 2

1. proteins used. bacteria uses 1 RNA polymerase while eukaryotes use 3 to 5 RNA polymerases. eukaryotes don’t require sigma factors, they use transcription factors instead. no rho is required for eukaryotes, but rho is sometimes required for prokaryotes.
2. no operons in eukaryotes. every gene in eukaryotes has its own promoter. unlike in prokaryotes where genes can be organized in to operons and share a single promoter.
3. compared to bacteria, eukaryotes have a highly complicated promoter structure. they don’t have -10 and -35 regions. in eukaryotes, promoter recognition is determined by a set of proteins, one of which (TATA-binding protein) recognizes the TATA box (20 bases before +1). there is also no sigma factor, they use transcription factors instead. initiation requires many different transcription factors.
4. in bacteria, the binding sites are adjacent to the gene. in eukaryotes, regulatory proteins often bind far away from the start site (+1) but on the same chromosome. they may be brought to a close proximity of the promoter with the process DNA looping, facilitated by the mediator protein.
5. eukaryotes use combinational control, where groups of proteins work together to determine the expression of a gene. many enhancers and silencers can work together to fine tune the expression of a gene. this helps a range of a thousand-fold be achieved.
6. in bacteria, DNA is almost always accessible for transcription. in eukarya, we run into problems caused by the organization of the DNA in the cell, the chromosome structure. to access the DNA, the DNA must be freed from the higher organization.

Question 3

in eukaryotes, which polymerases are used for each type of RNA?

Answer 3

polymerase 1 for rRNA

polymerase 2 for mRNA

polymerase 3 for tRNA and snRNA

Question 4

the promoter region may be covered by its binding to the nucleosomes. **nucleosomes are like beads on a string, they wind up the DNA and are composed of 8 histones subunit.

to expose the DNA, what mechanisms does the cell use? (2)

Answer 4

1. chromatin-remodeling complexes: mediate ATP-dependent conformational changes in nucleosome structure. the chromatin-remodeling complex is a very large complex that doesn’t dissociates nucleosomes from DNA, but instead repositions them.
2. histone-modifying enzymes: introduces covalent modification into the N-terminal tails of histone core. the goal is take DNA off the histones. to do this, the affinity between histones and DNA must be loosened. ***DNA is negatively charged and histones are positively charged. all modifications (acetylation, methylation, etc) change charge of the histone. the histone acetylase masks the charge of a residue, causing the residue and DNA to dissociate.

Question 5

how is transcription regulated? what are the mechanisms? (3) - they aren’t that specific

Answer 5

regulation of transcription often occurs through the action of one or more site-specific DNA binding proteins. the mechanisms by which they regulate transcription are similar.

1. the DNA binding proteins recognize internal or environmental signals, similar to allolactose for the lacI repressor in prokaryotes.
2. the regulatory proteins stimulate or repress the promoter binding or activity of RNA polymerase.
3. activation is through protein-protein interactions. similar to CAP interacting with RNA polymerase in prokaryotes. eukaryotes have many different gene-specific transcription factors.