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Microbio lecture > Chapter 7 > Flashcards

Chapter 7 Flashcards

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1
Q

Most bacteria and archaea have circular chromosomes

A

Some have linear or a mix of circular and linear chromosomes

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2
Q

Genomes vary in size

A

• Bacteria and archaea ~130 to 14,000 kilobase pairs (kb)
• Eukaryotic: 2,900 kb (Microsporidia) to 100,000,000 kb
(flowering plants); 3,000,000 kb (human)

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3
Q

Bacteria and archaea have very little noncoding DNA

DNA that does not encode proteins

A

Typically less than 15%
• Many eukaryotes have large amounts of noncoding
DNA (humans: over 90%)

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4
Q

gene

A

info composed of a sequence of DNA nucleotides

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5
Q

monocistronic RNA

A

A gene can operate independently of other genes

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6
Q

operon

A

gene 1 gene 2 gene 3 instead of just one gene.

• Creates a polycistronic RNA

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7
Q

promotor

A

DNA control sequence that launch RNA synthesis

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8
Q

regulon

A

genes and operons at diff positions in the chromosome that have a unified biochemical purpose

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9
Q

DNA function depends on its chemical

structure

A

• DNA is made of 4 different nucleotides linked by phosphodiester

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10
Q

purines

A

A, G (bycyclic, double ringed form)

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11
Q

Pyrimidines

A

T, C, U (monocyclic, single ringed form)

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12
Q

hydrogen bonding between bases

A
  • A – T

* G – C

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13
Q

dna double helix grooves

A
  • Major groove
  • Minor groove
  • Provide DNA-binding proteins access to nucleotides
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14
Q

DNA must be compacted to

A

fit into cell-into the nucleoid

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15
Q

histone like proteins

A

DNA ends must be tethered to form supercoils

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16
Q

• Supercoils are introduced by

A
  • Cleaving both strands at one site
  • Passing intact part of molecule b/w end of the cut site
  • Reconnecting the free ends
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17
Q

Nucleoids of bacteria and most archaea are

A

negatively supercoiled (underwound) – easier to separate during transcription

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18
Q

topoisomerases

A

Enzymes that change DNA supercoiling

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19
Q

topoisomerases type I

A

single proteins that cleave one strand of a double helix

• unwind/relieve supercoils

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20
Q

topoisomerases type II

A

multiple subunits that cleave both strands of DNA molecule
• Introduce negative supercoils
• DNA gyrase

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21
Q

DNA gyrase complex (example of Topoi. II) is a

A

tetramer composed of two GyrA and two GyrB subunits

• GyrA is ATP-dependent

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22
Q

Quinolone antibiotics

A

target type II topoisomerases (do not affect eukaryotic topoisomerases)
• Stabilize the complex in which DNA gyrase is covalently attached to DNA
• Creates a physical barrier that blocks DNA replication

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23
Q

DNA replication is divided into 3 phases

A

initiation, elongation, termination

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24
Q

DNA REPLICATION initiation

Study These Flashcards
A

unwinding of helix and loading DNA polymerase

25
DNA REPLICATION elongation
addition of deoxyribonucleotides to growing DNA chain, followed by proofreading
26
DNA REPLICATION termination
the DNA duplex is duplicated, the negative supercoils are restored, and key sequences of new DNA are methylated
27
replication begins at
origin (oriC) (245-bp), replicates bidirectionally.
28
In E. coli, initiation is activated by | inhibited by
- protein DnaA | - SeqA
29
DNA methylation controls timing of SeqA binding | IN E COLI INITIATION
• Deoxyadenosine methylase (Dam) attaches CH3 to N-6 position of A in sequence GATC • lag b/w synthesis of new DNA and methylation • Origin is temporarily hemimethylated (only one strand is methylated) • SeqA has high affinity for hemimethylated origin sequence • Binding of SeqA prevents another initiation event until sequence is fully methylated
30
Binding of DnaA to the origin facilitates melting and initiates formation of the replisome
5 DnaA bind in E. coli, 15 for B. subtilis
31
Another round of replication can only begin after
1. Origin is fully methylated 2. SeqA dissociates 3. DnaA-ATP concentration rises
32
dna helicase
DnaB
33
Dna helicase holder
DnaC
34
(initiation) replisome
Two DNA polymerase III, DNA primase (DnaG), and | helicase (DnaB)
35
(elongation) E. coli contains 5 DNA polymerase proteins
Pol I to Pol V • 5’-to-3’ direction • Only Pol III and Pol I participate directly
36
(elongation) DNA Pol III
* Alpha subunit – DNA synthesis * Epsilon subunit – DnaQ – proofreading * Other subunits also involved in improving accuracy
37
(elongation) leading strand
synthesized continuously
38
(elongation) lagging strand
– synthesized discontinuously in pieces (Okazaki fragments)
39
(elongation) single-stranded DNA-binding proteins (SSBs) approx every
during lagging strand ssDNA is protected from degradation • approx. every 1000 bases new RNA primers are synthesized by DnaG
40
(elongation) Lagging strand left with patches
of RNA primers
41
(elongation) DNA Pol I 5’-to-3’ exonuclease activity or | RNaseH
cleaves RNA primers • RNaseH recognizes RNA-DNA hybrids uses 3’-OH end as a primer to fill in the gap • uses dna ligase
42
(elongation) DNA ligase with energy from NAD
forms the phosphodiester bond
43
(termination) A series of terminator sequences | stops replication
* 10 ter sequences in E. coli | * One set stops the CW replicating polymerases, one set for the CCW.
44
Tus – terminus utilization substance
binds to ter sequences and stops DnaB helicase activity
45
(termination) catenane
Replicated chromosomes appear as linked rings | • XerC and XerD cut and rejoin
46
plasmids ``` found? usually need can contribute to ____ bw cells ```
• Plasmids are extragenomic DNA molecules -Smaller than chromosomes • Found in archaea, bacteria, and eukaryotic microbes • Usually circular -Typically negatively supercoiled • Need host proteins to replicate -Replication not tied to chromosome replication • Can contribute to the physiology of the cell -Antibiotic resistance • Transmitted between cells -Conjugation
47
two replication methods IN PLASMIDS- bidirectional and - RepA- - RepA holds - RepA recruits
• Rolling-circle – unidirectional - RepA-replication initiator binds origin and nicks 1 strand - RepA holds onto 5’-phosphate of nicked strand while 3’-OH is primer for DNA polymerase - RepA recruits helicase to unwind DNA and SSBs bind - Nicked strand is rejoined by RepA
48
In some cases it is just by chance
that the daughter cell inherits a plasmid.
49
high-copy plasmids
(50-700 copies per cell) have a high probability that each daughter cell will have at least one plasmid
50
low-copy plasmids
* Ex plasmid R1 in Salmonella uses genes parC, parM, and parR * ParR-parC forms complex with the plasmid * ParM protein is an actin-like filament – attaches to ParR-parC and pushes plasmid copies to opposite ends of cell
51
plasmids carry
genes beneficial to the host survival in a specific environment (e.g. antibiotic resistance)
52
restriction sites
Restriction endonucleases cleave unfamiliar DNA - Palindromic sequences; 4-6 bases in length - Cleave the phosphodiester backbones of opposite strands - Create blunt or staggered (“sticky”) ends
53
Cloning
* Stanley Cohen and Herb Boyer * “cut and paste” cloning * Restriction cloning
54
Sanger sequencing Uses Specific
• Uses a DNA synthesis w/ ddNTP (stops elongation) • Specific ratio of dideoxy- to normal deoxynucleotides = elongation stopping at diff points in DNA sequence -Creates different lengths of DNA
55
Sanger sequencing –(number of bp)
1,000 bp in a few hours
56
Sequencing by synthesis
``` 600 gigabases (Gb) per run • 1 Gb = 1 billion bases (Human genome ~3 Gb) • Depending on Illumina system and settings, one run can take 1 day – 1 week ```
57
enhancer
drives transcription in eukaryotic promoters. function at large distances from gene.
58
extreme thermophiles- reverse dna gyrase
introduces positive supercoils.

Microbio lecture (12 decks)

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