Central Dogma
RNA = Ribonucleic acid
In RNA the base thymine is replaced with uracil
DNA is usually double stranded whereas RNA is usually single stranded
ds = double stranded
ss = single stranded
Process of transcription
Non-template strand= Coding strand = sense strand
mRNA (messenger RNA):
a) carries information for just one or a few genes
b) identical in sequence to the coding strand (except U for T to the non-template or coding strand of DNA)
The promoter is not transcribed (-35 to -1 region)
The start site of transcription is +1
Everything to the left of the structural gene is UPSTREAM
Everything to the right of the structural gene is DOWNSTREAM
Sequences of the promoter regions:
-35: TTGACA
-10: TATAAT
The sigma component of RNA polymerase recognizes and binds to these promoter sequences. The core enzyme together with the sigma factor compose RNA polymerase. Sigma finds the -35 and -10 regions and then falls off. The core enzyme then transcribes the gene.
How the RNA sequence is transcribed
a) inverted repeat
b) run of AAAAAA (in template strand)
The hair-pin loop followed by the string of U's (in mRNA) compose the terminator. These inverted repeats make a stem-loop structure. These are also called hair-pin loops.
Palindrome: reads the same forwards and backwards:
ABLE WAS I ERE I SAW ELBA
Inverted Repeats: in nucleic acid sequences, are not true palindromes, the repeat is on the other strand
Which genes are turned on? and when?
A) Housekeeping genes:
- on all of the time (e.g. DNA polymerase, RNA polymerase, genes for essential components which are always needed)
- promoters often similar to consensus promoter sequence
- "constitutive"
B) Regulated genes
- turned on only when needed
- promoter often unable to bind sigma unless help is provided
Gene activator proteins helps RNA polymerase (sigma) bind
- recognize DNA sequence in upstream region
- help RNA polymerase to bind
Positive regulation:
An inducer binds to the inactive activator forming an activator which binds to the DNA.
Example of positive regulation: the MalT protein detects maltose. Maltose induces genes for using maltose in E.coli.
Negative regulation: repressor proteins turn genes off due to transcription being blocked.
Example of negative regulation: the lactose repressor.
The regulator protein is an allosteric protein which changes shape when it binds to an another molecule.
Most DNA binding proteins have subunits. When they are separate, they are in the non-binding form. The subunits change shape when they bind head to head. This form binds to the DNA at an inverted repeat.
Global regulation:
- control lots of related genes
Crp protein:
- choice of sugars in bacteria like Escherichia coli
- global regulator
cyclic AMP (cAMP)
- signal molecule for Crp
- a regulatory nucleotide
Crp = cyclic AMP receptor protein
When favorite carbon source runs out then: cyclic AMP levels rise. Crp is active when cAMP binds. Active Crp needed for genes for less favored nutrients.
Lac genes have dual regulation:
- specific
- global
To switch on we need:
a) inducer
b) absence of glucose i.e. high cAMP
When is the Lac operon on or off?
Operon:
- one or more genes transcribed together to give a single mRNA
- only in prokaryotes are more than one gene on the same mRNA
- historically the first operons were controlled by repressors binding to operators
Structure of the Lac operon
Quorum sensing: bacterial "democracy"
Genes are expressed in response to population density
Auto-inducer: signal molecule which freely enters and leaves cells. (i.e. it carries signal between cells)
Bioluminescence: light emission by bacteria
LuxI makes auto-inducer
LuxR = regulator NOT repressor, it is an activator
Regulation by antisense RNA:
Fur: Ferric uptake regulator
-global regulator
-detects and binds Fe
Fe bound to Fur functions as a repressor that binds DNA and turns off:
a) lots of genes needed in iron scarcity
b) anti-bfr (turns off bfr) - therefore bfr is turned ON overall
Bacterioferritin (bfr) and its role in gene regulation
Questions and comments about MICR 302 to: bender@micro.siu.edu
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SIUC / College of Science / Microbiology / courses / MICR302
URL: http://www.micro.siu.edu/micro302/transcription.html
Last updated: 07-Mar-99 / laa
