M2 Wong

Question 1

3 Different Periods

Answer 1

B Period
- birth period

Replication “C” Period
- initiation, elongation, termination

“D” Period
-division period

Question 2

Plasmids

Answer 2

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

Question 3

R Plasmid

Answer 3

Resistance Plasmid
- confers resistance to antibiotics or other growth inhibitors

encodes proteins that either protect cell or inactivate antibiotic

Question 4

Exonuclease

Answer 4

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

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

Question 5

Which form of DNA is dominant

Answer 5

CIRCULAR

Question 6

Advantages of Circular Form

Answer 6

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

Question 7

E. Coli
(Gene Count + Protein encoding genes)

Facts.

Answer 7

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

4288 protein encoding genes

• circular
• double stranded

Question 8

Vibro Cholera

Answer 8

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

Question 9

Viruses

Answer 9

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

Question 10

Nitrosopumilus

Answer 10

First ammonia oxidizing (nitrifying) archeaon known

Question 11

How many protein encoding genes in human genome?

Answer 11

20,000

Question 12

Minimum number of possible genes for a viable cell

Answer 12

250-300

Question 13

Advantages of Divided Genome

Answer 13

1. Faster replication

2. Increased genome size = can specialize for fitness

Question 14

3 divided genome examples

Answer 14

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

Question 15

In Bacterial chromosomes: What percentage of genes code for PROTEINS

Answer 15

75-90%

Question 16

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

Answer 16

0.8%

Question 17

In Bacterial chromosomes: What percentage of genes code for Regulation

Answer 17

3-10%

Question 18

How many operon copies for Mycoplasma Pneumonie

Answer 18

1 Copy

Generational time = 24 hours

Question 19

How many operon copies for E.Coli

Answer 19

7 Copies

Generational time = 20 minutes

Question 20

How many copies of Clostridium Paradoxum

Answer 20

15 Copies

Generational time = 16 minutes

Question 21

Nucleoid

Answer 21

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

Question 22

E. Coli = Average Size of Coding Sequence

Answer 22

951 bp

Question 23

E. Coli = Average Intergenic Region

Answer 23

118bp

Question 24

Largest coding sequence

Answer 24

7149 bp

Question 25

Genes that code for: METABOLISM TRANSPORT UNKNOWN

Answer 25

``` METABOLISM = 21% TRANSPORT = 10% UNKNOWN = 38% ```

Question 26

4 Categories of Gene Organization

Answer 26

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

Question 27

How many prokaryotic genomes have been sequenced?

Answer 27

115

Question 28

Bradyrhizobium Japonicum

Answer 28

8317 Genes | ORF and gene count graph

Question 29

5 Bacteria Strains

Answer 29

``` E. Coli K12 (FL) Mycoplasma (P) Sorangium Cellulosum (FL) Strain HTCC 2181 (FL) Nasuia (E) ```

Question 30

3 Archaeal Strains

Answer 30

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

Question 31

Smallest non-symbiotic bacterial genome

Answer 31

Mycoplasma - 580 kb 470 ORF

Question 32

Smallest non-symbiotic archaeal genome

Answer 32

Nanoarcheaum - 490 kb 522 ORF

Question 33

Smallest FL genome BACTERIA

Answer 33

HTCC 2181 - 1304 kb 1354 ORF

Question 34

Smallest FL genome ARCHAEA

Answer 34

Thermoplasma - 1564 kb 1509 ORF

Question 35

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

Answer 35

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

Question 36

Bacteria: 2 Major types of TE

Answer 36

1. Insertion Sequences | 2. Transposons

Question 37

INSERTION SEQUENCE (IS)

Answer 37

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

Question 38

How many TE in Prokaryotes and Eukaryotes

Answer 38

``` Prokaryotes = 10 - 20 / cell Eukaryotes = >100 / cell ```

Question 39

What is the rare event that mutation might occur

Answer 39

1 X 10^-5 OR 10^-7

Question 40

6 biological consequences cause by jumping of TE

Answer 40

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

Question 41

Insertional Mutagenesis

Answer 41

- 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