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.