CH 7 Flashcards by Ahmed Yasser

Do plasmids and chromosomes mix?

the two forms of DNA do not mingle
Note: Plasmid: A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently.

How well did you know this?

Not at all

Perfectly

Codes for one protein

monocistronic

How well did you know this?

Not at all

Perfectly

codes for three proteins

polycistronic

How well did you know this?

Not at all

Perfectly

a group of genes that are regulated as a unit

regulon

How well did you know this?

Not at all

Perfectly

In a bacterial nucleoid what does a nick made in a single strand do to the nucleiod strand

supercoiling relaxes in the nicked strand
- relaxes only one loop

How well did you know this?

Not at all

Perfectly

enzymes involved with the topology (geometric properties) of dna

topoisomerase 1
topoisomerase 2

How well did you know this?

Not at all

Perfectly

what does type one topoisomerase do?

Topoisomerase I relaxes a negatively supercoiled DNA molecule by introducing a single-strand nick. Start with 5 and
end up with four negative supercoils
- Does not require energy

How well did you know this?

Not at all

Perfectly

what does type two topoisomerase do?

makes a double-strand break and makes negative super coiling
- requires energy (ATP)
- Ex: DNA gyrase

How well did you know this?

Not at all

Perfectly

what antibiotic attacks dna gyrases

quinolones, kill bacteria by targeting dna gyrase
cost: can produce connective tissue damage

How well did you know this?

Not at all

Perfectly

What is a nucleoid

a nucleoid consists of DNA arranged in loops w boundaries held up by histone-like anchoring proteins

How well did you know this?

Not at all

Perfectly

what is a negative supercoil

Releases strain of underwound dna

How well did you know this?

Not at all

Perfectly

what is a positive super coil

releases strain of overwound dna

How well did you know this?

Not at all

Perfectly

what is semiconservative replication

A replication bubble with two replication forks.
Replication is called “semiconservative” because one parental strand is conserved and inherited by each daughter cell genome. - It is called “bidirectional” because it begins at a fixed origin and progresses in opposite directions.

How well did you know this?

Not at all

Perfectly

Where does DNAATP bind to

origin of replication (oriC)

How well did you know this?

Not at all

Perfectly

what are the two primary DNA polymerases in bacteria

DNA polymerase 1 and 3

How well did you know this?

Not at all

Perfectly

What is DNA polymerase 3

Main polymerase in bacteria

How well did you know this?

Not at all

Perfectly

gap filling dna polymerase in bacteria

DNA polymerase 1

How well did you know this?

Not at all

Perfectly

what are okazaki fragments

Relatively short fragment of DNA synthesized on the lagging strand during DNA replication

How well did you know this?

Not at all

Perfectly

purpose of dna binding proteins

keep dna from hybridizing

How well did you know this?

Not at all

Perfectly

DNA replication occurs in what direction

5’ to 3’

How well did you know this?

Not at all

Perfectly

what is the purpose of helicase in dna replication

separates the strands of the double helix

How well did you know this?

Not at all

Perfectly

purpose of single stranded binding proteins in dna replication

stabilizing single-stranded regions

How well did you know this?

Not at all

Perfectly

Purpose of DNA gyrase in dna replication

keeps the dna from supercoiling

How well did you know this?

Not at all

Perfectly

Purpose of DNA polymerase 1 in dna replication

functions to fill DNA gaps that arise during DNA replication, repair, and recombination

How well did you know this?

Not at all

Perfectly

Purpose of primase in dna replication

synthesizing short RNA sequences that are complementary to a single-stranded piece of DNA, which serves as its template.

purpose of primer

serves to prime and lay a foundation for DNA polymerase

continuous synthesis of DNA occurs in what direction?

3' to 5' (leading strand)

discontinuous strand occurs in what direction

5' to 3' called the lagging strand which is completed in segments called okazaki fragments

purpose of DNA polymerase 3 in lagging strand

adds Okazaki fragments to the primer of lagging strand

Purpose of DNA ligase in DNA replication

glues fragments in dna replication together

DNA replication in prokaryotes video:

https://www.youtube.com/watch?v=HSoKeKV5ecs

Removing the RNA primer

The 3′-to-5′ exonuclease activity of Pol I or RNase H cleaves the RNA primer

What is the role of exonuclease?

act as proof-readers during DNA polymerisation in DNA replication, to remove unusual DNA structures that arise from problems with DNA replication fork progression, and they can be directly involved in repairing damaged DNA.

Purpose of XerCD in terminating replication of the chromosome

type 2 topoisomerases that pass linked chromosomes through each other to forme a catenane

Purpose of FtsZ

key in septum formation for chromosome segregation which leads to cell division

what is SimA

a protein that binds to FtsZ which prevents septum fromation

two categories of plasmids

1. high copy number plasmids- 50 to 700 copies of plasmid (lower molecular weight) 2. low copy number plasmid- 1 to 3 copies

what type of plasmids are non-conjugated

high ccopy number

what type of plasmids are conjugated

low copy number

how many basepairs per gene in plasmids

1000

PBR322 is a plasmid that is the basis for what?

used in genetic engineering

Plasmids reproduce by

rolling circle replication - some viruses use rolling circle to make concatimores to make opies of viruses

purpose of repA in rolling circle replication

binds to the origin of replication (ori) - nicks one strand of the dna and holds on to the 5' so that the 3' end can be used as a primer

purpose of DNA polymerase 3 in rolling circle replication

binds to 3' end primer to begin replication

rolling circle replication video:

https://www.youtube.com/watch?v=ZDqsojQ8A5k

what is the function of ParM in plasmids?

ParM is a prokaryotic actin carrier which provides the force to drive copies of the plasmids to opposite ends of rod shaped bacteria before cytokinesis

how was the ParM filament visualized

ParM filament was seen by combined phase-contrast and immunofluorescence microscopy

Key difference between prokaryote and eukaryote cells when it comes to genome structure

Prokaryotes: introns Eukaryotes: no introns

How many RNA polymerases do Bacteria have

one (RNAP)

Eukaryotes have how many RNA polymerases

three - one for transfer RNA - RNA polymerase 2 (mRNA) - RNA polymerase 3

Archea and eukaryotes share what when it comes to genome structure

- the TATA binding protein - TFB

Do bacterial antibiotics work on archea? and are there any pathogenic archea

No they do not - there are no pathogenic archea

Two ways to protect DNA

1. telomeres 2. looping of DNA

What E. coli pathogen strain kill humans

E. coli 0157

What are the three basic methods for DNA sequencing

- Sanger sequencing - pyro sequencing - illumina

compare and contrast between pyro and illumina sequenccing

- they both involve synthesis - pyro uses fire flies - illumina uses floreccent lable

what organism affects obesity in a positive way (makes people less obese)

christensenella

what are gnotobiotic mice

germ free mice

tow biological ways that obesity can be affected

1. herpes 2. gut-microbiome

Definition of metagenomics

metagenomics studies the collection of different organisms' genomes within a sample

definition of genomics

Genomics studies the genome of a single organism