Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Microbio lecture > Chapter 7 > Flashcards

Chapter 7 Flashcards

1
Q

Most bacteria and archaea have circular chromosomes

A

Some have linear or a mix of circular and linear chromosomes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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%)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

gene

A

info composed of a sequence of DNA nucleotides

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

monocistronic RNA

A

A gene can operate independently of other genes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

operon

A

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

• Creates a polycistronic RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

promotor

A

DNA control sequence that launch RNA synthesis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

regulon

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

DNA function depends on its chemical

structure

A

• DNA is made of 4 different nucleotides linked by phosphodiester

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

purines

A

A, G (bycyclic, double ringed form)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Pyrimidines

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

hydrogen bonding between bases

A
  • A – T

* G – C

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

dna double helix grooves

A
  • Major groove
  • Minor groove
  • Provide DNA-binding proteins access to nucleotides
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

DNA must be compacted to

A

fit into cell-into the nucleoid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

histone like proteins

A

DNA ends must be tethered to form supercoils

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Nucleoids of bacteria and most archaea are

A

negatively supercoiled (underwound) – easier to separate during transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

topoisomerases

A

Enzymes that change DNA supercoiling

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

topoisomerases type I

A

single proteins that cleave one strand of a double helix

• unwind/relieve supercoils

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

topoisomerases type II

A

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

DNA replication is divided into 3 phases

A

initiation, elongation, termination

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

DNA REPLICATION initiation

A

unwinding of helix and loading DNA polymerase

25
Q

DNA REPLICATION elongation

A

addition of deoxyribonucleotides to growing DNA chain, followed by proofreading

26
Q

DNA REPLICATION termination

A

the DNA duplex is duplicated, the negative supercoils are restored, and key sequences of new DNA are methylated

27
Q

replication begins at

A

origin (oriC) (245-bp), replicates bidirectionally.

28
Q

In E. coli, initiation is activated by

inhibited by

A
  • protein DnaA

- SeqA

29
Q

DNA methylation controls timing of SeqA binding

IN E COLI INITIATION

A

• 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
Q

Binding of DnaA to the origin facilitates melting and initiates formation of the replisome

A

5 DnaA bind in E. coli, 15 for B. subtilis

31
Q

Another round of replication can only begin after

A
  1. Origin is fully methylated
  2. SeqA dissociates
  3. DnaA-ATP concentration rises
32
Q

dna helicase

A

DnaB

33
Q

Dna helicase holder

A

DnaC

34
Q

(initiation) replisome

A

Two DNA polymerase III, DNA primase (DnaG), and

helicase (DnaB)

35
Q

(elongation) E. coli contains 5 DNA polymerase proteins

A

Pol I to Pol V
• 5’-to-3’ direction
• Only Pol III and Pol I participate directly

36
Q

(elongation) DNA Pol III

A
  • Alpha subunit – DNA synthesis
  • Epsilon subunit – DnaQ – proofreading
  • Other subunits also involved in improving accuracy
37
Q

(elongation) leading strand

A

synthesized continuously

38
Q

(elongation) lagging strand

A

– synthesized discontinuously in pieces (Okazaki fragments)

39
Q

(elongation) single-stranded DNA-binding proteins (SSBs)

approx every

A

during lagging strand ssDNA is protected from degradation
• approx. every 1000 bases new RNA primers are
synthesized by DnaG

40
Q

(elongation) Lagging strand left with patches

A

of RNA primers

41
Q

(elongation) DNA Pol I 5’-to-3’ exonuclease activity or

RNaseH

A

cleaves RNA primers
• RNaseH recognizes RNA-DNA hybrids
uses 3’-OH end as a primer to fill in the gap
• uses dna ligase

42
Q

(elongation) DNA ligase with energy from NAD

A

forms the phosphodiester bond

43
Q

(termination) A series of terminator sequences

stops replication

A
  • 10 ter sequences in E. coli

* One set stops the CW replicating polymerases, one set for the CCW.

44
Q

Tus – terminus utilization substance

A

binds to ter sequences and stops DnaB helicase activity

45
Q

(termination) catenane

A

Replicated chromosomes appear as linked rings

• XerC and XerD cut and rejoin

46
Q

plasmids

found? 
usually 
need 
can contribute to 
\_\_\_\_ bw cells
A

• 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
Q

two replication methods IN PLASMIDS- bidirectional and

  • RepA-
  • RepA holds
  • RepA recruits
A

• 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
Q

In some cases it is just by chance

A

that the daughter cell inherits a plasmid.

49
Q

high-copy plasmids

A

(50-700 copies per cell) have a high probability that each daughter cell will have at least one plasmid

50
Q

low-copy plasmids

A
  • 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
Q

plasmids carry

A

genes beneficial to the host survival in a specific environment (e.g. antibiotic resistance)

52
Q

restriction sites

A

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
Q

Cloning

A
  • Stanley Cohen and Herb Boyer
  • “cut and paste” cloning
  • Restriction cloning
54
Q

Sanger sequencing

Uses
Specific

A

• 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
Q

Sanger sequencing –(number of bp)

A

1,000 bp in a few hours

56
Q

Sequencing by synthesis

A 
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
Q

enhancer

A

drives transcription in eukaryotic promoters. function at large distances from gene.

58
Q

extreme thermophiles- reverse dna gyrase

A

introduces positive supercoils.

Microbio lecture (12 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions