Transcript in prokaryotes RNA polymerases require a sigma factor to bind DNA

DNA
Repair
Transcription
Differences Between RNA & DNA
1.) RNA has 2’ OH
2.) RNA has uracil instead of thymine
3.) RNA is single stranded (but can fold to self base-pair)
RNA Polymerases
--- catalyze the polymerization of RNA using a
DNA template
--- in prokaryotes RNA polymerases require a sigma
factor to bind DNA and initiate transcription
Sigma Factors
--- a protein that binds a specific nucleotide sequence,
called a promoter
--- a bacterium will generally have multiple sigma factors
(allows for better gene regulation)
--- one sigma factor usually controls most of the central
metabolic and biosynthesis genes ( d70 in E. coli)
Transcription
Regulation of Transcription
1.) Sigma factors
2.) Other DNA binding proteins
A.) Negative, block RNA polymerase’s access to DNA
--- lac repressor
B.) Positive, enhance recruitment of RNA polymerase
--- catabolite activation
--- sometimes both negative and positive systems compete
to operate on the same set of genes
--- genes in bacteria are often grouped into regulatory elements
called operons (groups of genes controlled by the same operator),
this saves time and energy for the cell
Lactose Operon in
E. coli
Tryptophan Operon
Positive Regulation: The Maltose Operon
Catabolite Activation, dual
regulation: (positive &
negative) in the lac operon
Two Component Systems
Translation
Requires:
1.) Ribosomes
2.) charged tRNAs
3.) mRNA
4.) accessory factors (initiation factor,
elongation factor, etc.)
5.) ATP & GTP
Based on Genetic Code
--- need at least 20 “words” so must have 3 nucleotide codons
--- code is degenerate, multiple codons specify the same
amino acid, effects:
A.) reduces likelyhood of mutational damage
B.) codon useage can vary between different
organisms
Translation
Other Tidbits:
RNA interference:
--- Use non-coding (ncRNA) to block translation or
trigger destruction of mRNA
Quorum Sensing:
--- Small rapidly diffusing molecules are used to measure
cell density
--- Often used by pathogens to time toxin release for
maximum effect
Mutation
--- a change in the genetic information (DNA sequence)
of an organism
--- cells spend considerable energy fixing mutations
--- preventing all mutation would actually be a bad idea, WHY?
Types of Mutation:
A.) Base Substitution: swap one base for another
1.) Transition: change from one purine or pyrimidine
base to another (AG or TC)
2.) Transversion: change from a purine to a pyrimidine
or a pyrimidine to a purine
--- only possibility of change to AA sequence of protein, WHY?
Types of Mutations (Continued):
B.) Insertion/ Deletion: add or remove one or more base pairs
--- these types of mutations can cause a frameshift, changing the
reading frame of the rest of the gene (often results in a premature
stop codon).
--- What is one case where there would be almost no effect
of a frameshift mutation?
Mutagens and Mutagenesis
Mutagen: something that causes DNA damage
1.) Chemicals, chemical modification of DNA bases can
easily result in mutation
2.) DNA intercalators, aromatic compounds that can
form p-stacking interactions with bases, are
often “read” as additional bases, creating
insertion mutations
3.) UV- induced thymine dimers
4.) Ionizing radiation, creates double stranded DNA
breaks, can be difficult to repair and may still
result in an insertion or deletion
--- mutagenesis is the process of purposely mutating an organism,
“wreck and check” strategy of protein study
The Ames Test:
--- measuring how mutagenic
a substance is