Exam 3, week 9: DNA and plasmids

what is a genome

all the genetic information that defines an organism

what are the parts of the genome

• chromosomes

• plasmids

• other elements

how many DNA chromosomes do microbial genomes usually consist of

one, but sometimes more

what composes proteins

20 different amino acids

what composes nucleic acids

five different nucleotides

what suggested that proteins were better suited to store large amounts of complex genetic information

their structural diversity

what was believed to contain the genetic material in chromosomes

proteins

what doesa structural gene produce

a functional RNA

what does a functional RNA encode for

a protein

what does a DNA control sequence regulate

the expression of a structural gene

what are examples of a DNA control sequence

promoter and enhancer

does the DNA control sequence encode for RNA

no

what are the two types of gene transfer

vertical and horizontal transmission

what is vertical transmission

from parent to child

what is horizontal transmission

transfer of small pieces of DNA from one cell to another

what is the distinction between genomes of a bacterium and a eukaryote

the presence of noncoding DNA

what percentage of the sequence in prokarytotic genomes consist of noncoding information

15%

in eukarytes, noncoding content makes up more than what percent of the genome

90%

bacterial and archaeal chromosomes range in what from size

106 kilobase pairs to 16,000 kilobase pairs

eukaryotic chromosomes range from what in size

2,900 kb to over 100,000,000 kb

the human genome is over what in size

3,000,000 kb

the simpler the organism the ____ its genome

smaller

a single gene can operate ____ of others

independently

what is a operon

genes in a unit

how are genes controlled

by a regulatory protein

bacteria pack their DNA into a series of loops or domains called the ____

nucleoid

what are the nucleoids of bacteria anchored by

histone-like proteins

what are positive supercoils

DNA is overwound

what is negative supercoils

DNA is underwound

eukaryotes, bacteria, and most archaea posses what type of supercoiled DNA

negatively

why do eukaryotes, bacteria, and most archaea possess negatively superoiled DNA

the two DNA strands are easier to separate as negatively supercoiled DNA

what are topoisomerases

enzymes that change DNA supercoiling

why does relaxation of supercoiled DNA need to occur

DNA replication and transciption

why does supercoiling of DNA occur

need supercoiling for packing of DNA

how does the DNA achieve the supercoiled state

• supercoils are introduced into chromosomes in a three-step mechanism

  • produce a double-strand break in the circular chromosome

  • pass an intact region of the DNA through the break

  • seal the ends to generate a twist in the chromosome

do type 1 topoisomerases have a single or multiple proteins

single proteins

do type 1 topoisomerases cleave one or both strands of DNA

one strand

what does type 1 topoisomerases do

relieves or unwinds supercoils

do type 2 topoisomerases have a single or multiple subunits

multiple subunits

do type 2 topoisomerases cleave one or both strands of DNA

both strands of DNA

what is an example of type 2 topoisomerases

DNA gyrase

what does type 2 topoisomerases do

adds negative supercoils in DNA

how does topoisomerase 1 supercoil DNA

• topoisomerase 1 cleaves one strand of a double helix, holds onto both ends, and passes the other interact strand through the break and re-ligates the strand

• the helix winds in this region, resulting in one less negative supercoil

how does type 2 tpoisomerases gyrase enzyme work

• grabs DNA

• introduces a double-strand break using ATP energy

• passes another part of the double helix through the break

• reseals the break. The end result is the introduction of a negative supercoil

what extrachromosomal DNA elements do genomes of some microbes have that replicate autonomously

plasmids and secondary chromosomes

what do plasmids and secondary chromosomes do to the genomes

adds various types of genes to the genome

what domains are plasmids found in

archaea, bacteria, and eukaryotic microbes

how does the size of plasmids compare to chromosomes

plasmids are smaller compared to chromosomes

what is the shape of the plasmids

circular

are plasmids negatively or positively supercoiled

negatively

what do plasmids contain

nonessential genes that often play critical roles in certain situations

do plasmids replicate dependently or independently of the host chromosome

independently

when are plasmids advantageous

• resistance to antibiotics and toxic metals

• pathogenesis

• symbiosis

what are the two ways that plasmids can replicate

• bidirectional replication

• rolling-cricle replication

what direction does replication occur in bidirectional replication

starts at a single origin and occurs in two directions simultaneously

what direction does replication occur in rolling-circle replication

starts a single origin and moves in only one direction

what do plasmids need to borrow from the host chromosome so that they can preform replication

replication machinery

what do plasmids already have so they they can preform replication

their own origin sequences and initiator proteins

how does rolling circle replication work

• RepA picks strand

• Host DNA polymerase 3 copies DNA

• the new DNA strand peels off of the original strand

• ssDNA is bound by single-stranded binding protein (SSB)

what are the strategies that plasmids employ to maintain themselves in the host cell

• carry genes whose functions benefit the host-microbe under certain conditions

• high-copy-number plasmids segregate randomly to daughter cells

• low-copy-number plasmids evolved dedicated partitioning systems that ensure both daughter cells receive copies of the plasmid

how are secondary chromosomes distinguished from plasmids

the secondary chromosomes carry at least one essential gene

what are genomes with multiple chromosomes composed of

a primary chromosomes and one or more smaller secondary chromosomes

what did secondary chromosomes envolve from

plasmids that captured one or more essential genes from the primary chromosome

why can a cell contain more than one plasmid, but it cannot be closely related genetically

plasmid incompatibility

how are plasmids affected that belong to the same incompatibility group with they are in the same cell

plasmids belonging to the same incompatibility group exclude each other from replicating in the same cell

are plasmids able to coexist with plasmids from other groups when they are in the same cell

yes

what do microorganisms in nature exist in

microbiomes

what is contained in a microbiome

numerous species

do microorganisms in nature exist as pure cultures

no

what is a microbiome

all of the microbes within a defined community

who was the first to isolate, sequence, and analyze DNA from complex environmental samples

Norman Pace

why did Norman Pace sequence 16S rRNA gene

it is highly conserved in microbes

what is the goal of the human microbiome project

is to characterize our gut, skin, and oral microbiomes

what view does characterizing a microbiome on the basis of a single gene provide of microbiome function

a limited view

what is a metagenome

all the genes in a community