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Prokaryotic Molecular Genetics > DNA Structure > Flashcards

Flashcards in DNA Structure Deck (36):

What are some of the general characteristics that differ bacteria from eukaryotes?

-DNA forms an tangle known as a nucleid;which contains no membrane and is not bound to proteins.
-Contain plasmids; small loops of DNA that can be transmitted from cell to cell which can allow for special properties such as antibacterial resistance.
-Contain a cell wall but no nucleus as in eukaryotes.


What is the difference between the cell wall of gram-positive and Gram-negative bacteria?

Some of the key differences are as follows:
-Peptidoglycan is present in high amounts in gram positive whereas gram negative contain only a few layers.
- the peptidoglycan in gram negative bacteria is between two layers of the cellular membrane
-The S-layer is directly attached to the outer membrane.
-Lipoprotiens are attached to the polysaccharide whereas have no lipoproteins present.


What are the 3 medically relevant Gram-negative cocci?

- cause a sexually transmitted disease (Neisseria gonorrhoeae),

- a meningitis (Neisseria meningitidis),

-respiratory symptoms (Moraxella catarrhalis).


what are the medically relevant bacilli that are gram negative?

Respiratory problems: Hemophilus influenzae, Klebsiella pneumoniae, Legionella pneumophila, Pseudomonas aeruginosa

Urinary problems: Escherichia coli, Proteus mirabilis, Enterobacter cloacae, Serratia marcescens

Gastrointestinal problems: Helicobacter pylori, Salmonella enteritidis, Salmonella typhi.


What does Chargaff's Rule State?

The amounts of A = T, G = C, purines = pyrimidines


What are the four nucleotides that form the composition of DNA?

adenine, cytosine, thymine, or guanine


What is the key difference between ribose and deoxyribose?

Ribose; at the 2nd carbon there is a hydroxyl group attached

Deoxyribose; at the second carbon only a hydrogen is attached


What is the structure of DNA and how is it liked together?

-DNA is a double-stranded helix with antiparallel strands
-the nucleosides in each strand are held together by phosphodiester bonds
-while the bases are held tightly together busing hydrogen bonds


What is the central dogma of biology and how is it accomplished ?

-The central dogma of DNA states that the flow of genetic information flows from DNA-RNA-protiens. which can be divided or restated as DNA replication,Transcription,and Translation


What is the responsibility of DNA helicase?

DNA gyros relaxes the DNAby introducing positive supercoils, while helicase unwinds the double stranded helix by introducing negative supercoils into the strand and thus creating the replication fork.


What us the responsibility of the single stranded binding proteins during DNA replication?

The responsibility of the the single stranded binding proteins in DNA replication is to make the template available and thus keep the two strands from reforming the bond during DNA replication.


What does RNA primase do in DNA replication? Why is this step important and how does it accomplish this?

RNA primase catalyzes the synthesis of short RNA primers to which nucleotides are added and thus Thymine is replaced by Uricil in the fragment. This is important because without this short piece of RNA, DNA replication will not occur.


What is the difference in primary responsibilities of DNA polymerase I and DNA polymerase III?

The chief responsibility of DNA polymerase III is extend the DNA strand in the 5'-3' direction creating the newly synthesized DNA strand. While DNA polymerase I degrades the RNA primer and fills in the gaps by replacing the strand and replacing uricil with thymine. Both have the ability to proofread.


What is the activity is caused by DNA ligase?

Joins the DNA fragments into a continuos daughter strands during DNA replication and DNA repair.


What are Nucleases and how do they function?

Nucleases are enzymes that degrade DNA strands by breaking the phosphodiester bonds holding the nucleotides together. They function as either 5' or 3' exonucleases.


In what direction is DNA synthesized?

DNA is synthesized in the 5'-3' direction.


How are the leading and lagging strand synthesized in DNA replication?

The leading strand is continuous in replication as the lagging strand is synthesized in fragments known as the Okazaki fragments. During this process RNA polymerase adds a short fragment of RNA prior to each fragment that is synthesized. Which is then replaced by DNA polymerase I after DNA polymerase III has synthesized the short fragment of DNA in the 5'-3' direction. Lastly the enzyme ligase ligates the fragments together creating a continuous strand of DNA


What is the Cell Division Cycle?

Born => Grows => Division


What is cell division?

The process by which the larger cell (mother cell) splits into 2 Daughter cells.


What is the generation time or division time?

The division or generation time is the amount of time that passes from when the cell is born to when the cell has divided into daughter cells.


What is the structure in which the bacterial chromosome is carried?

The bacterial Chromosome is carried as a single double-stranded mostly found in the circular form although some can be linear, where the DNA genome contains all the necessary "housekeeping" genes.


Is DNA replication synthesized using the Semiconservative model,Conservative, or Dispersive?

DNA is synthesized using the semiconservative model of DNA replication.


How is Chromosomal DNA packaged in the cell?

The chromosome is packaged using supercoiling and a DNA binding protein core. DNA is normally negatively supercoiled . Leaving the final package involving at least 60 loops around a central protein core.


What is the bacterial nucleotide?

The bacterial nucleotide is the chromosomal DNA packaged into its final packaging form involving the DNA loops and central protein core.


What is the enzyme that is usually involved in supercoiling?

The enzyme Gyrase.


What are the 2 main gyrases found?

-topoisomerase I - carries out positive supercoiling

-topoisomerase II- carries out negative supercoiling.


How is initiation of the chromosomal replication begin?

-Replication always begins at oriC

-DnaA binds to the oriC sequence

-DnaA multimer complexes with ATP causes melting of an AT rich region to which another protein (DnaB/DnaC/ATP complex) can then bind.

• oriC site must be methylated for initiation of replication.

• Methylation of new DNA occurs up to 10 minutes after synthesis and is important in allowing proof reading enzymes to distinguish between new and old.


After chromosomal initiate, chromosomal replication at the replication fork proceeds by what mechanisms?

-Topoisomerase I (gyrase) relaxes strands

-DnaB (helicase) opens strand and acts as guide
for primase on both strands

-Single strand binding proteins keep strand apart during the
replication process

-Primase synthesis primer sequences that are used
by DNA polymerase III

-DNA polymerase III extends strands only in 5’ 3’ direction, thus one strand is continuous and one is in short fragments (Okazaki fragments)


How is termination accomplished during chromosomal replication?

-Replication continues until the replication fork enters a region of the chromosome called Ter.

• This area contains multiple symmetrically arranged sites for trapping the replication fork.

• The two sites called:
– terA, Inhibits the fork counterclockwise moving
– terB. Inhibits the fork clockwise moving direction
clockwise moving direction fork pass through terA and stop in terB and vice-versa

• There is a protein associated with terA & terB that inhibits helicase activity.

• One replication fork will stall, the other will stop as soon as it meets the stalled fork.


How is Chromsomal replication ligated? And how is this process similar to the way chromosomal replication of the lagging strand?

The RNA primer is then removed and the gap filled in by DNA polymerase I and DNA ligase join the fragments forming one continuous strand.

• The lagging strand with the short fragments are treated in the same way using DNA polymerase I to remove the RNA primer and fill up the gap, then DNA ligase join them up .

• Topisomerase II restores negative supercoiling to new strands.


What is the partitioning of the chromosome?

The process by which the distribution of one mother cell to each of the two daughter cells. Which is accomplished using the Par system and Muk proteins.


What does the Par system include and how is it initiated?

-ParA; ATPase activity
-ParB; binds to ParS site on the DNa
-ParS site

-Where ParA and ParB bind to the parS site and helps to direct the
plasmids to the daughter cells


what are Muk proteins?

they form the sliding filament and help pull the chromosome apart. In a process similar to myosin.


how is the dimerization resolved in the chromosome?

-Resolution of Dimerized chromosomes uses the Xer site-specific recombination system which is composed of: XerC and XerD and site on the 2 dif. sites.

-the Xer proteins promote recombination between the 2 dif sites of the dimerized chromosomes


How is Decatenation accomplished?

Decatenation: Type II topoisomerase (Topo IV) removes the interlinks between the daughter DNAs


How is Condensation of the chromosome accomplished

-Condensation: Formation of supercoil DNA occupy a smaller space
Condensins: Proteins that bind DNA in two different places, folding it into large loops
Structural maintenance of the chromosome (SMC0) from B. subtilis and MukB from E. coli.