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CMMB 343 > M2 Wong > Flashcards

M2 Wong Flashcards

1
Q

3 Different Periods

A

B Period
- birth period

Replication “C” Period
- initiation, elongation, termination

“D” Period
-division period

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2
Q

Plasmids

A
  • nonessential
  • circular or linear
  • double stranded
  • rep. does not link to cell cycle
  • can majorly influence host
  • small
  • exist as “free dna” in cytoplasm
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3
Q

R Plasmid

A

Resistance Plasmid
- confers resistance to antibiotics or other growth inhibitors

encodes proteins that either protect cell or inactivate antibiotic

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4
Q

Exonuclease

A
  • cuts off the extra nucleotides at the end of a sequence

- binds to the end of DNA and starts to digest from there

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5
Q

Which form of DNA is dominant

A

CIRCULAR

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6
Q

Advantages of Circular Form

A
  1. Smaller length
  2. resistance to exonuclease
  3. less complicated replication
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7
Q

E. Coli
(Gene Count + Protein encoding genes)

Facts.

A

4.6 x 10^6 bp OR 4623 x 10^3 kb GENES

4288 protein encoding genes

  • circular
  • double stranded
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8
Q

Vibro Cholera

A

2 CC
crts to start replication of 2nd chromosome
(dimer –> monomer conformational change)
replication finishes at the same time
on chromosome is bigger than the other

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9
Q

Viruses

A

Bacteria
Single or Double strand
Unable to replicate without a host cell

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10
Q

Nitrosopumilus

A

First ammonia oxidizing (nitrifying) archeaon known

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11
Q

How many protein encoding genes in human genome?

A

20,000

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12
Q

Minimum number of possible genes for a viable cell

A

250-300

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13
Q

Advantages of Divided Genome

A
  1. Faster replication

2. Increased genome size = can specialize for fitness

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14
Q

3 divided genome examples

A 
Burkholderia Cepacia (3-4 CC)
Agrobacterium Tumefaciens (1LC + 1CC)
Borrelia Burgdorferi (1LC + 17-22 C/L plasmids)
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15
Q

In Bacterial chromosomes: What percentage of genes code for PROTEINS

A

75-90%

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16
Q

In Bacterial chromosomes: What percentage of genes code for tRNA or rRNA

A

0.8%

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17
Q

In Bacterial chromosomes: What percentage of genes code for Regulation

A

3-10%

18
Q

How many operon copies for Mycoplasma Pneumonie

A

1 Copy

Generational time = 24 hours

19
Q

How many operon copies for E.Coli

A

7 Copies

Generational time = 20 minutes

20
Q

How many copies of Clostridium Paradoxum

A

15 Copies

Generational time = 16 minutes

21
Q

Nucleoid

A
  • bacterial chromosomes are compacted into this
  • ~1600 fold
  • 50-500 dynamic loops
  • supercoiled by gyrase
22
Q

E. Coli = Average Size of Coding Sequence

A

951 bp

23
Q

E. Coli = Average Intergenic Region

A

118bp

24
Q

Largest coding sequence

A

7149 bp

25
Q

Genes that code for:
METABOLISM
TRANSPORT
UNKNOWN

A 
METABOLISM = 21%
TRANSPORT = 10%
UNKNOWN = 38%
26
Q

4 Categories of Gene Organization

A
  1. genes with relation functions (grouped with operons)
  2. equal gene numbers on each strand
  3. Many highly expressed genes are transcribed in the same way DNA replicates
  4. Highly expressed genes closer to OriC
27
Q

How many prokaryotic genomes have been sequenced?

A

115

28
Q

Bradyrhizobium Japonicum

A

8317 Genes

ORF and gene count graph

29
Q

5 Bacteria Strains

A 
E. Coli K12 (FL)
Mycoplasma (P)
Sorangium Cellulosum (FL)
Strain HTCC 2181 (FL)
Nasuia (E)
30
Q

3 Archaeal Strains

A

Thermoplasma (P)
Methanosarcina (FL)
Nanoarchaeum Equitans (FL)

31
Q

Smallest non-symbiotic bacterial genome

A

Mycoplasma -
580 kb
470 ORF

32
Q

Smallest non-symbiotic archaeal genome

A

Nanoarcheaum -
490 kb
522 ORF

33
Q

Smallest FL genome BACTERIA

A

HTCC 2181 -
1304 kb
1354 ORF

34
Q

Smallest FL genome ARCHAEA

A

Thermoplasma -
1564 kb
1509 ORF

35
Q

As ORFs Increase, what gene functions change (list order)

A
  1. Transcription
  2. Signal Transduction
  3. Energy Metabolism
  4. DNA replication
  5. Translation
36
Q

Bacteria: 2 Major types of TE

A
  1. Insertion Sequences

2. Transposons

37
Q

INSERTION SEQUENCE (IS)

A
  • IR (10-50bp)
  • up to 1000 nucleotides
  • small segments of DNA
  • only protein encoded is transposase
38
Q

How many TE in Prokaryotes and Eukaryotes

A 
Prokaryotes = 10 - 20 / cell
Eukaryotes = >100 / cell
39
Q

What is the rare event that mutation might occur

A

1 X 10^-5 OR 10^-7

40
Q

6 biological consequences cause by jumping of TE

A
  1. Deletion
  2. Inversion
  3. Polar Effect
  4. Turning on previously repressed genes
  5. Gene Inactivation (insertional mutagenesis)
  6. Gene Translocation
41
Q

Insertional Mutagenesis

A
  • biological consequence of TE jumping
  • genes can be disrupted/inactivated by transposons
    a. essential genes
    b. non-essential genes
    c. conditional essential
    d. redundant essential

CMMB 343 (5 decks)

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