DNA Replication & Transcription
In principle: DNA replication is semi-conservative [HOMEWORK
#4]
H - bonds 'unzip', strands unwind,
complementary nucleotides added to existing strands
After
replication, each double-helix has one "old" &
one "new" strand
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 [iG1
10.10]
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
Formation of replication fork at Origin of Replication
[iG1 10.16, 19]
provides two single-stranded DNA template (ssDNA)
multiple replications forks (replicons) [HOMEWORK
#6]
Synthesis
of RNA
primer [iG1 10.15]
Addition of dNTPs by DNA
Polymerase (DNAPol III) at 3'
end only
continuous synthesis on leading strand [iG1 10.13]
discontinuous
synthesis on lagging strand [iG1 10.20]
Okazaki fragments
leading & lagging strand
synthesis simultaneously [iG1 10.21]
A single, dimeric DNAPol III replicates
both strands
Proof-reading by 3'
5' exonuclease activity [iG1
10.12]
Excision
of RNA primer by DNAPol I
ligation (connection)
of fragment ends at gaps by DNA
ligase [iG1 10.22]
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 on multiple chromosomes
Transcription: synthesis of messenger RNA (mRNA) (online
MGA2 animation)
What is a "Gene" [iGen3
05-03] [Structure
of a Eukaryotic Gene]
RNA transcribed from DNA by RNA Polymerase (RNAPol
I) [iG1 4.17]
(1) Recognition of transcriptional unit: ~ 'gene'
[iG1 4.18]
Promoters - short DNA sequences
that regulate transcription
typically 'upstream'
= 'leftward' from 5' end of sense strand [iG1
4.12]
(2) Initiation & Elongation [iG1 4.22, 23, 24]
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 [iG1 4.25], except
No primer is required
Transcription may occur from either strand
Most DNA is not
transcribed into RNA
(3) Termination
[iG1 4.27, 28, 29]
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
transcription
& translation are physically
separated
primary RNA
transcript is extensively processed
heterogeneous
nuclear RNA (hnRNA) mRNA
Post-transcriptional processing of eukaryotic RNA
is complex [iG1 4.9]
promoters [iG1 4.19] &
enhancers determine initiation &
control rate
'cap' (7-methyl guanosine, 7mG) added to 5'
end [iG1 4.26]
'tail' of poly-A
(5'-~~~AAAAAAAAAA-3') added to 3' end [iG1 4.33]
'splicing' of hnRNA : eukaryotic genes are "split"
intron DNA sequence
equivalents removed from hnRNA : "intervening"
exon DNA
sequence equivalents represented
in mRNA: "expressed" in protein
1 ~ 12's of exons /
'gene'
>90% of transcript may be 'spliced
out'
[An
important note on terminology] [or, to
put it another way]
Splicing mechanism uses donor and acceptor sites
[iG1 5.18, 19, 20]
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
Alternative splicing of the same transcript produces
different products [iG1 4.16]
Different exon regions
are combined as different mRNAs [iG1 5.01]
Alternative exon
combinations differ functionally [iG1
5.22]
Homework #7: Problem-solving with DNA & RNA
Ongoing Homework problem:
What is a 'gene'?
How do the discoveries of (1) introns and exons
and (2) alternative splicing in eukaryotic
genomes modify the concept?
