DNA Replication & Transcription
In principle: DNA replication is semi-conservative
H - bonds 'unzip', strands unwind,
complementary nucleotides added to existing
strands [iGen3
03-02]
After
replication, each double-helix has one "old" & one
"new" strand
[note alternative conservative & dispersive models: Homework #4 ] [iGen3 03-01]
DNA is not the
"Genetic Code" for proteins
information in DNA must first be transcribed
into RNA
messenger
RNA
transcript is
base-complementary to template strand of DNA
& therefore co-linear with sense
strand of DNA
DNA & RNA syntheses occur only in
the 5' 
3' direction
DNA synthesis in prokaryotes:
Nucleotides are added simultaneously to both strands, but
DNA grows in the 5' 3' direction ONLY [iGen3 03-03]
Distinguish:
Replication:
duplication of a double-stranded DNA (dsDNA) molecule
an exact 'copy' of the existing molecule (cf. xerox copy)
Synthesis:
biochemical creation of a new single-stranded DNA (ssdNA) molecule
a base-complementary 'copy' of an existing strand (cf. silly putty copy)
occurs only
in the 5' 3' direction
DNA
Synthesis in
prokaryotes [iGen3 03-04, -05,
-06]
(1) Formation of replication fork
provides two single-stranded DNA template (ssDNA)
(2) Synthesis of RNA primer
(3) Addition of dNTPs by DNAPol III
at 3'
end only
continuous synthesis on leading strand
(4)
discontinuous
synthesis on lagging strand
Okazaki fragments
proof-reading by 3'5' exonuclease activity
(5) Excision of RNA
primer by DNAPol I
ligation (connection)
of fragment ends at gaps by DNA
ligase
A talkie animation of
DNA synthesis `[onlineMGA2
animation]
DNA synthesis occurs at multiple replications forks
(replicons) [iGen3 03-09]
DNA
synthesis occurs on leading & lagging strands simultaneously [iGen3 03-08]
A single, dimeric DNAPol
III replicates both strands
DNA synthesis in eukaryotes
Eukaryotic genomes are much larger [the "C-value Paradox"]
eukaryotic DNA synthesis
is more "efficient":
More DNAPol molecules,
slower rate of synthesis, more replicons,
E.
coli: 15 DNAPol add 100,000
bases/min over 3,500
replicons
4.2 x 106
bp genome replicated in 20
~ 40 min
Drosophila: 50,000 DNAPol add 500
~ 5,000 bases/min
over 25,000 replicons
330 x 106 bp diploid genome replicated in
< 3 min : net 600x faster
Transcription: synthesis of messenger RNA (mRNA) (online
MGA2 animation)
What is a "Gene" [iGen3
05-03]
RNA transcribed from DNA by RNA Polymerase (RNAPol I) [iGen3
05-01]
(1) Recognition of transcriptional unit: ~ 'gene'
Promoters - short DNA sequences
that regulate transcription
typically 'upstream'
= ' leftward' from 5' end of sense strand
(2) Initiation & Elongation [iGen3
05-04ab , -04cd]
mRNA synthesized 5'3' from DNA template strand
mRNA sequence therefore homologous to DNA sense strand
Colinear: mRNA and DNA
sense strand "line up"
(in
prokaryotes, but not eukaryotes:
see below)
Process similar to DNA replication, except
No primer is required
Transcription may occur from either strand
Some (most?) DNA is not
transcribed into RNA
(3) Termination
[iGen3
05-05]
Regulation of
transcription
In
prokaryotes, transcription &
translation may occur simultaneously
In eukaryotes,
transcription occurs in nucleus [ex.: Lampbrush chromosomes]
translation
occurs in cytoplasm (see next section):
RNA must cross nuclear
membrane
[iGen3
05-09]
transcription
& translation are physically separated
primary RNA
transcript is extensively processed
heterogeneous
nuclear RNA (hnRNA) mRNA
Post-transcriptional processing of eukaryotic RNA
is complex
promoters
& enhancers
determine initiation & control rate
'cap' (7-methyl guanosine, 7mG) added to 5'
end [iGen3 05-10]
'tail' of poly-A (5'-~~~AAAAAAAAAA-3')
added to 3' end [iGen3
05-11]
'splicing' of hnRNA : eukaryotic genes are "split" (MGA2
03-12,14,15,16) [iGen3 05-12]
intron DNA sequences
removed from hnRNA : "intervening"
[iGen3 05-14]
exon DNA
sequences represented in mRNA:
"expressed"
in
protein
1 ~ 12's of exons /
'gene'
>90% of transcript may be 'spliced
out'
[An
important note on terminology]
Eukaryotic genes & mRNA are not colinear!
DNA / RNA hybridization
produces heteroduplexes
DNA
introns 'loop out'
DNA exons pair with mRNA
Eukaryotic exons may be widely
separated
Summaries
of transcription [& translation] in prokaryotes
& eukaryotes
Homework #5:
Suggested problems from
Solved problems 1 & 2
problem ## 7, 8, 9, 11, 14, 15 , 18, 19, 21, 26, 27
for
extra
fun:
##
29
&
34
iGen3 (2010), Chapter 5, pp. 98-101
Problems ## 2, 4, 6, 7,
12, 13, 15, 16, 21
Ongoing Homework problem:
What is a 'gene'?
How does the discovery of introns
and exons in
eukaryotic genomes modify the concept?
