Download The Central Dogma of Molecular Biology

The Central Dogma of Molecular
Biology
by
E. Börje Lindström
This learning object has been funded by the European Commissions FP6 BioMinE project
The flow of information
DNA molecule
• General structure:
- double stranded
- complementary
- helical
- antiparallel
• Strands:
- backbone of alternating phosphate and
deoxyribos units
- four different bases; adenine (A), guanine (G),
cytosine ( C ), and thymine (T).
• Double helix:
• Major and Minor groove
- due to base pairing: A=T and GC
DNA molecule, cont.
• Size:
- units: kilobase (kb) or kilobase pairs (kb pairs)
- E. coli chromosome  4 700 kb pairs
• Form:
- closed chromosome molecule (in bacteria)
-  1 mm long  packing problem in bacteria
- solved by supercoiling
• DNA binding proteins:
Un-specific:
- histones
Specific:
-Repressors
- RNA polymerase
- restriction enzymes
- modification enzymes
DNA molecule, cont.
DNA molecule, cont.
DNA replication
General
• Semi conservative:
-new DNA molecules contain:
1 old strand and
1 new strand
• use a ’template’:
- one of the strand is used
• ’primers’:
-usually a piece of RNA
- DNA-polymerase unable
to start replication
Initiation of replication
• Start point:
-only one (1) on the chromosome (300 bp)
- origin (ori)
ori
• bidirectional:
- both directions
Synthesis of DNA (replication)
• several enzymes involved (~ 20 pc)
- DNA helicase
Unwinding the molecule
- DNA gyrase
(topoisemerase II)
Open up (cut)
the strands
- DNA-binding enzymes
Protect ss-DNA from nucleases
- Primase
Synthesises the RNA primer
- DNA-plymerase III
Synthesis in direction 5’3’
There are 3 enz. in E. coli; pol I, II and III
- DNA-plymerase I
Removes the primer
Repair any missing bp in DNA
- DNA ligase
Makes a phospho-di-ester bond
(glueing)
Synthesis of DNA, cont.
• ’leading’ and ’lagging’ strands:
- leading: continous synthesis
- lagging: dis-continous synthesis
• proof-reading:
- checking if any mitakes has been made
- pol. III removes the wrong nucleotides (3’ 5’)
Figures, DNA replication
RNA transcription
Three types of RNA:
• mRNA (genetical)
• tRNA (aa-carrier)
• rRNA (structural)
Structure:
-ss-stranded (internal ds secundary structures)
- ribose
- four different bases; adenine (A), guanine
(G), cytosine ( C ), and uracile (U).
Synthesis of RNA
• ds DNA is the template:
- only one of the strands
• RNA polymerase:
- consists of four different subunits
- a2bb’s
- a2bb’ = core enzyme
- s recognises the start site
• Direction of synthesis:
- 3’5’
Start and stop of RNA synthesis
• Where is the start ?
- Note! No primers necessary!
- The polymerase binds to the promoter
- s recognises and attaches to the promoter region
- ds-DNA opens up and the synthesis starts
- s is detached and the core enzyme continues
• Where does the synthesis stop?
-termination at special DNA-sequenses, terminators
- inverted repeates in DNA  ’stem-loop’-structures in
RNA
Promoters
A sequence in DNA upstreams a structural gene:
P
-35bp
• -10 sequence
SG
-10bp
Pribnow box
• Strong promoters bind s effective
mRNA
• Short half-time
• Polycistronic (in bacteria)
- information from several structural genes
• Definitions:
- operator (O): a gene that can be effected by a repressor protein
- operon: structural genes with the same repressor
P
O
SG1
SG2
SG3
Translation
Necessary substances:
• mRNA
• ribosomes
• tRNA + aa  tRNAaa (attached aa)
• different factors
• enzymes
• energy
tRNA
• DNA-genes:
- Linear tRNA form (primary) 
- cloverleaf structure (secundary)
• Two peoperties:
- binds aa (enzymatic)
- binds to mRNA (codon) with its anti-codon
tRNA, cont.
Synthesis of proteins
A four (4) step process:
• Initiation
• Elongation
• Termination-release
• Peptide folding
• Initiation:
-a complex of
- 30S subunit,
- f-meth-tRNA, (start codon AUG in mRNA)
- mRNA and
- initiation factors are formed
• Shine-Delgarno sequence
-3-9 bases in mRNA
- complementary to 16S rRNA
- addition of 50S subunit
Synthesis of proteins, cont.
• Elongation:
-several elongation factors are needed
- Next aa-tRNA is added to the A-site (ribosome)
- a peptide bond is created
- the peptide is moved to the A-site
- translocation to the P-site during
- movement of the ribosome forward
- a free A-site is created …
-Etc.
• polysomes:
- mRNA with several ribosomes
Synthesis of proteins, cont.
• Termination:
-stop codes in mRNA
- UAA, UAG and UGA; nonsence codes
- no tRNA for these codes exist
- release factors RF1-3 release the protein
- the ribosomes disintegrate
• The genetic code:
- in mRNA
• 3 bases
- 1 aa
• 43 = combinations
-but only 24 aa
- degenerated code
- the aa has several codes
Reading frame
• Open reading frame (ORF):
S D-G
AUG
• Codon usage:
- a gene
UAG
-The code (tripletts) does not mean the
same in all organisms
- The mRNA or ORF give different
products
The wobble concept