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BIOL 303 > CH 7 > Flashcards

CH 7 Flashcards

1
Q

Do plasmids and chromosomes mix?

A

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.

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2
Q

Codes for one protein

A

monocistronic

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3
Q

codes for three proteins

A

polycistronic

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4
Q

a group of genes that are regulated as a unit

A

regulon

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5
Q

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

A

supercoiling relaxes in the nicked strand
- relaxes only one loop

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6
Q

enzymes involved with the topology (geometric properties) of dna

A
  1. topoisomerase 1
  2. topoisomerase 2
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7
Q

what does type one topoisomerase do?

A

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

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8
Q

what does type two topoisomerase do?

A

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

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9
Q

what antibiotic attacks dna gyrases

A

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

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10
Q

What is a nucleoid

A

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

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11
Q

what is a negative supercoil

A

Releases strain of underwound dna

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12
Q

what is a positive super coil

A

releases strain of overwound dna

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13
Q

what is semiconservative replication

A
  • 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.
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14
Q

Where does DNAATP bind to

A

origin of replication (oriC)

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15
Q

what are the two primary DNA polymerases in bacteria

A

DNA polymerase 1 and 3

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16
Q

What is DNA polymerase 3

A

Main polymerase in bacteria

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17
Q

gap filling dna polymerase in bacteria

A

DNA polymerase 1

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18
Q

what are okazaki fragments

A

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

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19
Q

purpose of dna binding proteins

A

keep dna from hybridizing

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20
Q

DNA replication occurs in what direction

A

5’ to 3’

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21
Q

what is the purpose of helicase in dna replication

A

separates the strands of the double helix

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22
Q

purpose of single stranded binding proteins in dna replication

A

stabilizing single-stranded regions

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23
Q

Purpose of DNA gyrase in dna replication

A

keeps the dna from supercoiling

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24
Q

Purpose of DNA polymerase 1 in dna replication

A

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

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25
Q

Purpose of primase in dna replication

A

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

26
Q

purpose of primer

A

serves to prime and lay a foundation for DNA polymerase

27
Q

continuous synthesis of DNA occurs in what direction?

A

3’ to 5’ (leading strand)

28
Q

discontinuous strand occurs in what direction

A

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

29
Q

purpose of DNA polymerase 3 in lagging strand

A

adds Okazaki fragments to the primer of lagging strand

30
Q

Purpose of DNA ligase in DNA replication

A

glues fragments in dna replication together

31
Q

DNA replication in prokaryotes video:

A

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

32
Q

Removing the RNA primer

A

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

33
Q

What is the role of exonuclease?

A

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.

34
Q

Purpose of XerCD in terminating replication of the chromosome

A

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

35
Q

Purpose of FtsZ

A

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

36
Q

what is SimA

A

a protein that binds to FtsZ which prevents septum fromation

37
Q

two categories of plasmids

A
  1. high copy number plasmids- 50 to 700 copies of plasmid (lower molecular weight)
  2. low copy number plasmid- 1 to 3 copies
38
Q

what type of plasmids are non-conjugated

A

high ccopy number

39
Q

what type of plasmids are conjugated

A

low copy number

40
Q

how many basepairs per gene in plasmids

A

1000

41
Q

PBR322 is a plasmid that is the basis for what?

A

used in genetic engineering

42
Q

Plasmids reproduce by

A

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

43
Q

purpose of repA in rolling circle replication

A

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

44
Q

purpose of DNA polymerase 3 in rolling circle replication

A

binds to 3’ end primer to begin replication

45
Q

rolling circle replication video:

A

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

46
Q

what is the function of ParM in plasmids?

A

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

47
Q

how was the ParM filament visualized

A

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

48
Q

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

A

Prokaryotes: introns
Eukaryotes: no introns

49
Q

How many RNA polymerases do Bacteria have

A

one (RNAP)

50
Q

Eukaryotes have how many RNA polymerases

A

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

51
Q

Archea and eukaryotes share what when it comes to genome structure

A
  • the TATA binding protein
  • TFB
52
Q

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

A

No they do not
- there are no pathogenic archea

53
Q

Two ways to protect DNA

A
  1. telomeres
  2. looping of DNA
54
Q

What E. coli pathogen strain kill humans

A

E. coli 0157

55
Q

What are the three basic methods for DNA sequencing

A
  • Sanger sequencing
  • pyro sequencing
  • illumina
56
Q

compare and contrast between pyro and illumina sequenccing

A
  • they both involve synthesis
  • pyro uses fire flies
  • illumina uses floreccent lable
57
Q

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

A

christensenella

58
Q

what are gnotobiotic mice

A

germ free mice

59
Q

tow biological ways that obesity can be affected

A
  1. herpes
  2. gut-microbiome
60
Q

Definition of metagenomics

A

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

61
Q

definition of genomics

A

Genomics studies the genome of a single organism

BIOL 303 (26 decks)

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