Microbiology Ch.8
What is promoter region made up of?
-35 sequence, 16-18bp region, -10 sequence
Where is the promoter located?
At the start of a gene
What are four ways that bacteria acquire new genes?
Conjugation Transduction Transformation Lysogenic Conversion
RNA Polymerase
Copies RNA from a DNA template
What are the components of bacterial RNA polymerase holoenzyme?
Core enzyme and sigma factor
Endonucleases
Cut DNA backbone in a strand of DNA; facilitate repair and insertions
Exonucleases
Cut DNA from an exposed end of DNA; facilitate repair
___________ ________ contain the information for formation of sex pilus
F factors
What is a nonsense codon?
Stop codon
Lysogenic Conversion
Temperate phages inject their DNA into bacterial cell. Bacterial cell exhibits new properties, directed by the viral gene
Missense mutation
a single base substitution that changes codon for one amino acid into codon for another amino acid. e.g. sickle cell anemia
How long are RNA Primers?
about 10 nucleotides
Does the sigma factor in bacteria RNA polymerase have catalytic activity? What is its purpose?
no catalytic activity but it helps the core enzyme recognize the start of genes
Mutant
organism causing the mutation
Attenuation
termination of transcription within the leader region (leader peptide
What is the antiterminator loop in mRNA for the Trp operon?
2:3 loop; allows translation (small speed bump)
What is the complementary template strand for the start codon?
3'-TAC-5'
What is the terminator loop in mRNA for the Trp operon?
3:4 loop; no translation occurs (large speed bump)
Sense codons
A codon that codes for an amino acid.
Nonsense codons
A codon that does not encode any amino acid
Intron
A region in a eukaryotic gene that does not code for a protein or mRNA.
Exon
A region of a eukaryotic chromosome that encodes a protein.
Gene
A segment of DNA (a sequence of nucleotides in DNA) encoding a functional product.
Codons
A sequence of three nucleotides in mRNA that specifies the insertion of an amino acid into a polypeptide
Methylase
Adds methyl group to selected bases in newly made DNA
Primase
An RNA polymerase that makes RNA primers from DNA template synthesizes short complementary strands of RNA (10 nucleotides) to serve as primers needed by DNA polymerase
In arabinose what is the protein that has transcriptional control (both negatively and positvely)?
AraC
Which organisms have coupled transcription and translation?
Bacteria and Archaea Have polyribosome characteristic
_____ and _____ coding information in genes is normally continuous
Bacterial and Archael
Which organism did we look at that DID have some overlapping genes and why did it?
Bacteriophage; some regions that coded for proteins overlapped in order to increase coding efficiency of phages genome.
What are three categories of mutations?
Beneficial Harmful (some lethal mutations) Silent Mutations
What does DNA polymerase do?
Catalyzes DNA synthesis proofreading for fidelity
Transposase
Cuts DNA backbone, leaving single-stranded "sticky ends"
Which organism did we look at that did not have overlapping genes?
E.coli
DNA Polymerase
Enzyme that synthesizes DNA by copying a DNA template.
Conjugative plasmids such as__________ can transfer copies of themselves to other bacteria during conjugation.
F plasmids
In what direction does the sex pilus attach?
F+ to F-
A leader sequence is transcribed into mRNA and it is translated (T/F)
FALSE; transcribed but NOT translated
How many chains do most bacterial RNA polymerases have in the core enzyme?
FIVE
How many polymerases does E.coli have and which one plays the largest role?
Five; Polymerase III
Who created the Central Dogma theory?
Francis Crick discovered that cells are governed by a cellular chain of command
What is the advantage of semiconservative replication?
Helps copied DNA to remain faithful to original template. Each offspring cell gets one strand of DNA from the parent cell, which survived to reproduce
Why is one strand "upside down" relative to the other strand? Why can't both strands "face" the same way?
If both strands were parallel to each other the nitrogen base pairs would not line up correctly
What is in F factors that assist in plasmid integration?
Insertion sequences (IS)
DNA Ligase
Makes covalent bonds to join DNA strands; Okazaki fragements, and new segments in excision repair
What amino acid is encoded by the start codon in prokaryotes?
N-formylmethionine (fMET)
Is polycystronic DNA only present in bacteria?
No; both bacteria and archaea
Genome
One complete copy of the genetic information in a cell.
Ribozyme
RNA enzyme that removes introns and splices exons together
What occurs during termination stage of transcription?
RNA polymerase dissociates from template DNA DNA sequences mark the end of gene in the trailer and the terminator some terminators require the aid of rho factors
snRNP
RNA-protein complex that removes introns and splices exons together
Degeneracy
Redundancy of the genetic code; that is, most amino acids are encoded by several codons
DNA Gyrase
Relaxes supercoiling ahead of the replication fork topoisomerase also introduces negative supercoiling to help compact bacterial chromosome
short tandem repeats (STRs)
Repeating sequences of 2-to-5- nucleotides.
What type of replication does DNA have?
Semiconservative
What defines an operon?
Set of promoter and operator sites and the structural genes they control.
What sequence is important in initiation of translation?
Shine-Dalgarno sequence
small nuclear ribonucleoproteins (snRNPs)
Short RNA transcript plus protein that combines with pre-mRNA to remove introns and join exons together
What does a coding region end with?
Stop codon immediately followed by trailer sequence which contains a terminator sequence used to stop transcription
In most microbes most proteins are either ___________ or _________.
Structural, enzymatic
DNA Polymerases
Synthesize DNA; proofreads and repairs DNA
Which strand is mRNA made from?
Template strand
Phenotype
The external manifestations of an organism's genotype, or genetic makeup. "actual expressed properties, such as organism's ability to perform a particular chemical reaction"
Genotype
The genetic makeup of an organism. "potential properties but NOT properties themselves."
Genetic code
The mRNA codons and the amino acids they encode.
Semiconservative replication
The process of DNA replication in which each double-stranded DNA molecule contains one original strand and one new strand
Transcription
The process of synthesizing RNA from a DNA template.
Genetics
The science of heredity and gene function.
Terminator
The site on a DNA strand at which transcription ends.
Origin of replication
The specific location on a DNa strand where replication begins.. Prokaryotes typically have a single origin of replication, while eukaryotes have several per chromosome.
Promoter
The starting site on a DNA strand for transcription of RNA by RNA polymerase.
Chromosome
The structure that carries hereditary information, chromosomes contain genes.
Genomics
The study of genes and their function.
Anticodon
The three nucleotides by which a tRNA recognizes an mRNA codon.
Transfer RNA (tRNA)
The type of RNA molecule that brings amino acids to the ribosomal site where they are incorporated into proteins
Messenger RNA (mRNA)
The type of RNA molecule that directs the incorporation of amino acids into proteins; carries the coded information for making specific proteins from DNA to ribosomes, where proteins are synthesized
Ribosomal RNA (rRNA)
The type of RNA molecule that forms ribosomes.
Translation
The use of mRNA as a template in the synthesis of protein
In addition to transcription initiation control,what else is controlled in trp operon?
Transcription continuation
Which two types of gene transferral involve bacteriophages?
Transduction and Lysogenic conversion
vertical gene transfer
Transfer of genes from an organism or cell to its offspring.
Flow of information from gene to protein is based on a ______ _______
Triplet code series of non overlapping three nucleotide words
How many core enzymes are in each polymerase?
Two
Helicases
Unwinds double stranded DNA
Photolyase
Uses visible light energy to separate UV-induced pyrimidine dimers
When is AraC active in arabinose operon?
When arabinose is absent; prevents transcription.
When is AraC inactive in Arabinose Operon?
When arabinose is present; breaks AraC protein that holds loop together
Lysogenic cell
a bacterial cell containing a prophage
Conjugation
a copy of F factor is transferred into the recipient and does not integrate into host chromosome donor genes usually not transferred F factor codes for sex pilus -Type IV secretion system that makes contact between cells plasmid is replicated by rolling circle method
Archaea
also has circular DNA but may have more than one origin of replication
silent mutation
change nucleoside sequence of codon but not the encoded amino acid.
What is DNA polymerase made out of?
complex of 10 proteins 3 proteins form the core enzyme
Polyribosome
complex of mRNA with several ribosomes
Nonsense mutation
converts sense codon to a stop codon.
HFr Conjugation
donor HFr cell has F factor integrated into its chromosome Donor genes are transferred to recipient cell Complete copy of F factor usually not transferred Gene transfer can be clockwise or counterclockwise
What component of bacterial RNA polymerase begins transcription?
only holoenzyme
Lysogeny
phage DNA enters into the bacterial chromosome but does not cause lytic cycle to occur
What advantage do eukaryotes have with splicing?
provides for more than one polypeptide; increase in transcriptome diversity allows several proteins to be made from one gene.
What is the purpose of a promoter?
recognition or binding site for RNA polymerase functions to orient polymerase
Topoisomerase
relaxes supercoiling ahead of the replication fork; separates DNA circles at the end of DNA replication breaks one strand of DNA to relieve tension from rapid unwinding of double helix and prevents supercoiling
Frameshift mutation
results from insertion or deletion of one or two basepairs in the coding region of the gene.
Plasmids
small autonomously replicating DNA molecules that can exist independently or, as episomes, integrate reversibly into host chromosome.
Single strand DNA- binding proteins
stabilize single stranded DNA and prevent it from reforming double helix that has been separated by helicase
DNA Primase
synthesizes of RNA primer
Prophage
this is what a phage is called when all that remains of it is DNA.
What does DNA gyrase do?
topoisomerase also introduces negative supercoiling to help compact bacterial chromosome
Transformation
uptake of naked DNA by a competent cell followed by incorporation of DNA into the recipient cells genome.
