3. Genome

Question 1

What is a proteome?

Answer 1

It refers to all of the different proteins that can be synthesized by an organism.

Question 2

What are the four types of DNA molecules that may be found in bacteria?

Answer 2

Chromosomes: must be found. Secondary chromosome, chromatid, plasmid: may or may not be found.

Question 3

What are the three types of DNA molecules that may be found in archaea?

Answer 3

Chromosome: must be found. Mini chromosome, plasmid: may or may not be found.

Question 4

How are bacterial chromosomes replicated?

Answer 4

DNA replication is initiated by proteins which bind add a specific nucleotide sequence called the origin of replication (oriC). DNA synthesis then proceeds in both directions and then and add a region opposite on the chromosome.

Question 5

How are bacterial plasmids replicated?

Answer 5

Like the chromosome, beginning at an origin of replication (oriV) and then DNA replication in two directions. There are also other mechanisms.

Question 6

What is a plasmid copy number?

Answer 6

The number of copies of the same plasmid molecule per cell. Greater than 20 copies per cell is considered a high copy number plasmid and one to five copies is considered a low copy number plasmid.

Question 7

Describe the DNA replication of archaea.

Answer 7

Some have a single chromosome with a single origin of replication like bacteria, but others have multiple origins per chromosome like eukarya.

Question 8

Describe the four types of plasmids.

Answer 8

Resistance plasmid: carry genes specifying proteins that allow resistance to antibiotics and other chemicals. Nutrition plasmids: carry genes that specify enzymes that allows organisms to use certain molecules as nutrients. Infection plasmids: carry genes which specify proteins that are required for the establishment of infections and animals and plants. Symbiosis plasmids: carry genes which specify proteins that are required for the establishment of symbiotic relationships with plants and animals.

Question 9

What is the size of an average protein coding gene?

Answer 9

1KB. Approximately 300 amino acids.

Question 10

Describe some aspects of protein in coding genes.

Answer 10

They dominate prokaryotic genomes, prokaryotic genes rarely overlap, prokaryotic genomes possess little non-gene DNA between non-overlapping genes.

Question 11

Describe the mRNA structure.

Answer 11

The five prime untranslated region carrying a ribosome binding site, 5 to 9 spacer nucleotides, the initiation or start codon, a sequence of nucleotides who’s number is divisible by three, one of three translation termination or stop codons and a three prime untranslated region.

Question 12

Describe the RNA polymerase that bacteria have.

Answer 12

It exists in two forms: the holoenzyme in the core enzyme. Core enzyme has four subunits: two alpha subunit and two beta subunits. In order to recognize and bind to the promoter sequence, the curtains I must associate with the fifth protein called the sigma subunit to form the holoenzyme.

Question 13

Describe intrinsic transcription termination.

Answer 13

RNA polymerase falls off the template strand when it pauses over a stretch of weekly each bonded A nucleotide pairs. RNA polymerase is pausing is associated with the formation of a stem loop structure in the mRNA but interacts with enzyme.

Question 14

Describe transcription of archaea.

Answer 14

Takes place in the cytoplasm and uses more accessory processing factors for translation initiation, elongation and termination like eukarya. Transcription is very similar to eukarya, basal protein transcription factors are used to allow the RNA polymerase to recognize the promoter.

Question 15

What are the two ways prokaryotes use for controlling polypeptide copy number?

Answer 15

Promoter strength and rate of mRNA degradation.

Question 16

How is mRNA degraded?

Answer 16

By ribonuclease enzymes. In some organisms, an endoribonuclease first binds to the triphosphorylated five prime end of an mRNA and catalyzes the hydrolysis of a down stream phosphodiester linkage that lies within an AU rich sequence. The ribonuclease then catalyzes repeated secondary cleavages of this mono phosphorylated RNA resulting in further fragmentation of the RNA. Additional exoribonuclease is working from the three prime end of the RNA fragments complete the decorative process using single ribo nucleotides. In other organisms, an exoribonuclease binds to the five prime end of the mRNA and then moves in the five prime to three prime direction degrading the mRNA into ribonucleotides.

Question 17

What does RNA pyrophosphorylase do?

Answer 17

Catalyzes the hydrolytic cleavage of a Phosphodiester linkage releasing pyrophosphate from a five prime triphosphorylated RNA to yield a five prime model phosphorylated RNA. It’s pizza in the process of the primary cleavage step.

Question 18

What are the three forms of genomic variation?

Answer 18

Spontaneous mutation, transposition, horizontal gene transfer.

Question 19

Why do base substitution mutations occur?

Answer 19

Tautomers

Question 20

Describe the proofreading of DNA polymerase.

Answer 20

Prokaryotic DNA polymerases can detect mispaired nucleotides. Either alone or with the help of other proteins, they can remove the misplaced nucleotide and replace it before continuing on.

Question 21

Describe postsynthetic correction systems.

Answer 21

If an error escapes proofreading, all forms of life have evolved systems for correcting errors in completed duplex DNA. A key step is to identify which of the two strands is the mutated one.

Question 22

Define transposons.

Answer 22

Jeans or Jean sets that can move from one location to another by a process called transposition. They can move between any two regions of DNA within a cell.

Question 23

Describe transposon structure.

Answer 23

All transposons possess a transposase gene in coding the transposase enzyme that mediates the process of transposition, and inverted repeat sequences usually 10 to 50 base pairs in link define the ends and the identity of the transposon.

Question 24

Describe nonreplicative transposition.

Answer 24

Transposon’s moved locations in DNA characterized by short nucleotide sequence is about five base pairs in length called target sites. Part of the transposition process involves the duplication of the target site sequence. This results in the production of the direct repeat sequences always found on either side of transposon. When an enzyme breaks the sugar phosphate backbone at the target site, it does not do so at exactly the same position on both strands. As a result, single-stranded regions are left after the transposon is joined to the recipient DNA. These regions are copied by hosting any polymerase resulting in duplication of the target site. Host ligase seals the nick in the sugar phosphate back bone.

Question 25

Describe replicative transposition.

Answer 25

It has basically the same structure as non-replicative transposon except they possess a gene for an enzyme called resolvase and specific nucleotide sequence call the res site.

Question 26

Define horizontal gene transfer and list its mechanisms.

Answer 26

Obtaining genes from non-parental sources. There are five mechanisms in bacteria: transformation, transduction, conjugation, mobilization, and transduction-like gene transfer.

Question 27

Which horizontal gene transfer mechanisms are found in archaea?

Answer 27

Transformation, transduction, and conjugation. Two other mechanisms have been found that are uniquely archaeal. Different proteins involved in the transfer and different molecular mechanisms are used for these mechanisms as compared to bacteria.

Question 28

Describe the horizontal gene transfer mechanism called transformation.

Answer 28

Original usage: the transport of naked donor DNA from the environment changes the phenotype of the recipient progeny relative to the parent.
Modern usage: the transport of naked donor DNA from the environment into a recipient. The transport of the DNA may or may not change the genome, genotype, or phenotype of the recipient or its progeny.

Question 29

How does transformation work?

Answer 29

When bacteria die, they can lyse and released her DNA and other contacts into the environment where they can be taken up by other cells.

Question 30

What is the competent state?

Answer 30

It is the state that bacteria have to be in in order to transport DNA from the environment. In this state, proteins for the transport of DNA from the environment are synthesized. They will be referred to as competence proteins.

Question 31

Describe the transformation DNA uptake in firmicutes.

Answer 31

In the competent state, A type four pilus called a transformation pilus is synthesized. Donor DNA binds to the tip of this pilus, which retracts, conveying the DNA through the PG layers to a DNA binding protein in the cytoplasmic membrane. This protein is situated close to a protein with exonuclease activity specific for double stranded DNA and protein that transports single-stranded DNA through the cytoplasmic membrane. Energy is provided by ATP.

Question 32

Describe the transformation DNA uptake in proteobacteria.

Answer 32

It works like the DNA uptake in Firmicutes, except the DNA must pass through the outer membrane pilus usher proteins. The pore of the usher proteins might be wide enough to accommodate the pillar shaft and a single double stranded DNA if the DNA was threaded through the pore. The pilus pore may be wide enough to accommodate a pair of DNA double helices but not the pilus shaft at the same time. Pilus retraction only initiates transport across the outer membrane, but to finish the job, another protein located in the periplasm known to bind DNA has been implicated.

Question 33

Describe uptake sequences.

Answer 33

For transformation, in some bacteria, there is a nucleotide sequence dependency for double stranded DNA binding by the pilus.

Question 34

What is the fate of transported single stranded donor DNA?

Answer 34

The usual fate is to be degraded into nucleotides by nucleus is specific for single strand of DNA normally present in bacterial cells. Occasionally, single-stranded donor DNA fragments escape degradation because they interact with the protein RecA. If this happens, there is the potential for the donor DNA to become integrated into the recipient chromosome. It depends on whether the donor DNA and recipient chromosomal DNA share homology.

Question 35

Describe homologous recombination.

Answer 35

Homologous recombination is mediated by the RecA protein. Besides RecA, and enzymes with endonuclease and ligase activities are involved in the process.

Question 36

Describe the horizontal gene transfer mechanism called transduction.

Answer 36

Original usage: transfer of DNA from a donor to recipient mediated by a virus infection that result in a change in the phenotype of the recipient progeny relative to the parent.
Modern usage: the transfer of DNA from a donor to a recipient mediated by a virus infection. Transfer of the DNA may or may not change the genome, genotype, or phenotype of the recipient or its progeny.

Question 37

Describe viruses and and phages.

Answer 37

Viruses are kind of selfish genetic element. The viruses that infect bacteria and archaea are called phages. It seems that the only phage important in transduction are the so-called tailed double stranded DNA phage.

Question 38

Describe phage particle binding and receptors.

Answer 38

In order for phage particle to bind to a cell, there has to be a geometric and chemical fit between a molecule or structure on the page particle and a molecule or structure on the surface of a host cell. T4 phage particles bind to LPS. Some phage particles have a surface exposed enzyme that catalyzes the hydrolytic depolymerization of the sugars or amino acids that make up the capsule.

Question 39

What are the three genes phages need?

Answer 39

Hijack genes, structural genes, and egress genes.

Question 40

How do you phages play a role in transduction?

Answer 40

Sometimes, fragments of post chromosomal DNA become mistakenly packaged into capsules by page packaging proteins and phage particles with only host DNA are released into the environment.

Question 41

Describe the horizontal gene transfer mechanism conjugation.

Answer 41

It refers to the transfer of a plasmid from one prokaryote to another by cell to cell contact. Plasmids are a kind of selfish genetic element.

Question 42

Describe the plasmids used in conjugation.

Answer 42

Conjugative plasmid have DNA transfer or tra genes that encode transfer proteins required to mediate the conjugative transfer of plasmid DNA from one cell to another.

Question 43

Describe the pili used in conjugation.

Answer 43

And gram negative unicellular proteobacteria, initial contact between the donor and recipient is made with conjugation pili. The proteins that compose conjugation pili are specified by some of the tra genes of the conjugative plasmid in the donor.

Question 44

What is the conjugation bridge?

Answer 44

In conjugation, pili mediate a nonspecific interaction that is characterized by a loose association. This loose association is replaced with a tight one resistant forces when the cell surfaces of the donor and recipient are brought together and fuse, forming the conjugation bridge.

Question 45

How is the plasmid transported in conjugation?

Answer 45

Bacteria with conjugative F & P pili make a multiprotein DNA translocation apparatus which stretches from the innermembrane through the periplasm to the outer membrane. The transport DNA, a tra protein called relaxase enzymatically cleaves the sugar phosphate backbone of one plasmid strand and becomes covalently bonded to it’s five prime end. The complex stand binds to the coupling proteins of the apparatus and is transported out of the donor into the recipient.

Question 46

Describe conjugation in gram-positive unicellular firmicutes.

Answer 46

Not much is known, but they use PG hydrolases and don’t use pili. They use adhesins.

Question 47

What are mobilizable plasmids?

Answer 47

Plasmids that lack a tra operon can still be transferred by conjugation if they are present in the same donor cell with the conjugative plasmid.

Question 48

How can plasmids also be transferred from a donor to a recipient by transformation?

Answer 48

It is highly unlikely because DNA uptake and transformation is designed for linear DNA fragments. If a plasmid is integrated into a donor chromosome and a DNA fragment of which the plasma is a part of is taken up by a recipient, plasmid establishment is possible. After this, because plasma integration is reversible, if the plastic replicate in the recipient in my establish as a replicating molecule and the recipient. Another possibility is that it’s genes might be expressed while integrated in the recipient chromosome even if the plasma cannot replicate in the recipient.

Question 49

How can plasmids be transferred from a donor to a recipient by transduction?

Answer 49

Plasmid DNA can be packaged into phage capsids. The plasmid genes could’ve been in the chromosome of a donor, which is most likely, or it could’ve been in linear form, but that is unlikely.

Question 50

What are the three types of selfish genetic elements?

Answer 50

Plasmids, viruses, and transposons.

Question 51

What are some of the relationships between plasmids and its host?

Answer 51

Mutualistic symbiosis, cryptic plasmids a.k.a. commensals, and poison antidote plasmids.

Question 52

Describe lysogenic infection.

Answer 52

Virulent phages cause lytic infection while temperate phages cause either lytic or lysogenic infections. A lysogenic infection is one that does not immediately result in host cell lysis. Instead, the temperate page enters a dormant state inside the host cell called lysogeny. The dormant phage is called a prophage.

Question 53

Describe the restriction modification system.

Answer 53

Prokaryotes mark their own DNA by adding methyl groups to a base within a specific nucleotide sequence, called the recognition sequence. Prokaryotes also make an enzyme called a restriction endonuclease to destroy foreign DNA.