1/ Difference in transcription and translation in Eukaryotes versus Prokaryotes:
Transcription
Prokaryotes
1/transcription rate is 50 bpairs/sec
2/1 transcription unit = many proteins
3/ 1type o RNA polymerase; similar to eukar. RNA polymerase II
4/ INITIATION
 Sigma factor (helps RNA polymerase to get on DNA)
 Doesn’t need energy to unwind double-stranded DNA helix
5/ELONGATION
 Elongation factors
 Supercoiling; corrected by DNA gyrase
6/ TERMINATION
 hair-pin formation
 use of EF1 and EF2
7/no RNA processing
Eukaryotes
1/transcription rate is 5bp/sec
2/1 transcription unit = 1protein
3/ 3 types of RNA polymerase:
 RNA poly.I (transcribes mRNA, tRNA, snRNA)
 RNA poly.II (transcribes proteins)
 RNA polyII ( transcribes mRNA,tRNA,snRNA)
4/INITIATION
■GTFs (general transcription factors)
* TFII A,B,C,D,E,F,G,H
* Activators
* Mediators
* Helicase acetylase
* Histone remodeling complexes
■ does need energy to unwind dsDNA
6/ ELONGATION
 elongation factors
 supercoiling (corrected by topoisomerase II – cuts both strands of dsDNA)
7/TERMINATION
 transcription of “cleavage information” gene

transcription of poly-A tail
o CstF + CPSF used
8/ mRNA processing
 5’CAP by
o Phosphatase
o Guanine transferase
o Methyl transferase
 Splicing of introns
 3’ poly-A tail
#2)
Packaging 2 meters of DNA into the nucleus of 6 micrometers:
The packaging of DNA occurs in five levels during the interphase of mitosis. The
DNA double helix is wound around histone cores 1.65 times with the help of histone
proteins, comprising the nucleosome. “Beads on a String” refers to the DNA packaged in
nucleosomes, made up of four histones (H2A, H2B, H3 and H4) that attract and bind to
the DNA. These nucleosomes connect by DNA strands roughly 200 bp apart. The DNA
is wrapped around the octameric core of the histone proteins. This level of packaging is
determined by DNA’s flexibility (short A-T rich regions) and other bound proteins. The
30 nm chromatin fiber provides three times the compaction. It creates loops to condense
the space it would take up if kept straight by packaging nucleosomes into fiber, with the
help of H1 histones linking the tail of the histone core to attach the nucleosomes. Then
these loops coil, compacting even more, with the aid of histone modifying enzymes and
remodeling complexes. The final compaction is higher order packaging of metaphase
chromosomes that are facilitated by condensins and methylations. The final compaction
ratio is 10,000 times.
# 3) Sketch a replication fork of bacterial DNA in which one strand is being
replicated discontinuously and the other is being replicated continuously. List 6
different enzyme activities associated w/ the replication process and Id the function of
each. Also Id the following: DNA template, RNA primer, Okazaki fragments, and
single stranded binding protein.

Enzyme activities associated w/ the replication process (represented by
numbers on illustration):
1. DNA polymerase: catalyzes elongation of new DNA by the addition of
nucleotides to the existing chain; on the lagging strand it replaces RNA
primers with new DNA
2. Primase: synthesizes RNA primers on lagging strand
3. Ligase: forms phosphodiester bonds; catalyzes bonding of 3’ end of a new
DNA fragment to the 5’ end of the expanding chain, on the lagging strand it
links Okazaki Fragments. Essentially it seals the nicks.
4. Helicase: unwinds the double helix of the parent DNA
5. Topoisomerase: prevents DNA tangling during replication by relieving super
helical tension.
6. Endonuclease: aids in the cutting of the phosphodiester backbone. Aids in the
removal of RNA primer
DNA template: a single strand of DNA whose nucleotide sequence acts as a guide for
the synthesis of a complementary strand
RNA primer: a short stretch of RNA synthesized on a DNA template, required by DNA
polymerase to initiate DNA synthesis
Okazaki fragments: short lengths of DNA produced on the lagging strand during
replication, which are joined by ligase to form a continuous strand.
Single stranded binding proteins: binds to prevent unwound parent strands from
recoiling at the fork during replication.