entire genetic complement of an organism; includes its genes and nucleotide sequences
usually ds, closed circular DNA
usually much smaller ds, closed circular DNA molecules; the genes carried on the plasmid are not essential for growth under all conditions
the genetic material of a bacteriophage which has incorporated into the genome of a bacterium and can form more phages if activated
DNA replication uses
a DNA-dependent DNA polymerase
What does semiconservative DNA replication mean?
new DNA molecules compose of one original strand and one daughter strand
Proteins required for DNA replication complex
helicase, ssDNA-binding protein (DBP), primase, DNA polymerase (a DNA-dependent polymerase)
removes helical stress that accumulates from unwinding of the two DNA strands during replication
target for quinoline antibiotics
All chain growth in DNA replication occurs in ___ direction
5' to 3'
Semidiscontinuous DNA synthesis
Leading strand synthesized continuously and lagging strand synthesized discontinuously
Why do two parental DNA strands need to be synthesized differently?
Because they are antiparallel
DNA polymerase III
DNA polymerase that E. coli use. One is needed for each parental strand
special type of RNA polymerase. Makes RNA primer chains to help initiate synthesis of both leading and lagging strand
*RNA primers are only temporary
chains of Okazaki fragments covelently attached to a RNA primase
DNA chains 100-1000 bases long that are covelently attached to a RNA primase. Beginning bases are RNA nucleotides
DNA polymerase I
a repair enzyme; replaces RNA nucleotides of Okazaki fragments with DNA nucleotides ("nick translation")
links together nucleotides to make a higher molecular weight DNA (seals sugar-posphate backbone)
Rate of error for:
after addictional error correcting mechanisms:
1 in 10000 nucleotides
1 in 10,000,000
1 in 109-1011
Bacterial DNA is methylated on which bases by what?
adenine bases (rarely on cytosines) by restriction modification systems
restriction modification system
a methylase and restriction endonuclease that recognize and modify the same nucleotide sequence
Restriction modification systems are important for
1. protection against viral infection and incoporation of foreign DNA into host chromosome
2. Knowing which strand is the parental strand during mismatch repair
Bidirectional beginning from _____ creates theta structures in bacterial DNA
origin for replication in E. coli
Can replication of a second DNA molecule begin before the first is completed?
helps RNA prolymerase find the promoter region for transcripiton initiation
Used to switch on or off large groups of genes by modifying RNA polymerase to detect different promoters
coding strand is ___ to the template strand
what has the same sequence as the RNA transcript? (Coding strand or template strand)
the coding strand (besides T in DNA and U in RNA)
Are promotor sequences transcribed?
A strong promoter will result in
many RNA molecules
Differences between RNA polymerase and DNA polymerase (5)
1. RNA pol does not require 3' OH primer to begin transcription
-although it does require one for elongation
2. RNA pol does not require helicase
3. RNA pol is slower than DNA pol
4. RNA pol lacks proofreading function
Why is a proofreading fuction not neccessary in RNA polymerase?
RNA is temporary in a cell
What % genes are expressed in bacteria? What are the other ones doing?
75% are expressed at all times. Others are dormant until cell needs them. This saves energy
clusters of coregulted genes that allow bacteria to respond to changes in thier environment. Code multiple proteins in the same mRNA (polycistronic)
has its own promotor and terminator. Results in an mRNA that encodes a single protein (monocistronic)
promotor binds to ____.
terminator ends ___.
transcription of the operon
Must be activated by inducer.
e.g. Lactose operon: allows E. coli to use lactose when no glucose is available
transcribed continually until deactivated by repressors
e.g. Tyrpotophan operon (repressed in the presence of Trp)
Prokaryotic ribosome subunits?
50S and 30S for a total of 70S (no that's not a typo)
30S subunit has important 16S rRNA
How many codons specify amino acids?
initiation codon? what does this code after chain has already been started?
AUG is the initiation codon. It also codes for Met within a polypeptide chain
the 3 STOP codons? what are these recognized by?
UAA, UAG, UGA
recognized by release proteins to terminate translation
Size of tRNA?
~75 nt or 4S
amino acyl-tRNA synthetase
consumes ATP to covalently attach an amino acid to the 3' end of a specific tRNA
-recognizes the amino acid and anticodon of the tRNA and pairs them up
Bacterial polycistronic mRNAs
transcribed from operons
located in mRNAs a few nts 5' to AUG codon. Function as ribosome binding sites. Complementary to a portion of the 16S rRNA of the 30S subunit
Eukaryotic mRNA is:
monocistronic (encodes a single polypeptide chain), spliced to remove introns from pre-mRNA (occurs in nucleus), and has modifed 5' and 3' ends b4 it leaves nucleus
What is the first amino acid that all bacterial proteins begin with?
all bacterial proteins begin with a formylated-Met at their amino terminus