DNA Structure and Organization

Question 1

How is DNA’s sugar different?

Answer 1

no -OH on 2’ C

Question 2

Which base pairing is stronger and why?

Answer 2

G-C because it has 3 H bonds vs 2

Question 3

nucleoside

Answer 3

base+sugar

Question 4

nucleotide

Answer 4

base+sugar+phosphate

Question 5

Where are DTPs found?

Answer 5

everywhere

Question 6

Where are nucleosides found?

Answer 6

Transiently because they’re phosphorylated quickly

Question 7

What creates the double helix?

Answer 7

H bonding and base stacking

Question 8

A-DNA

Answer 8

dehydrated and condensed DNA

Question 9

B-DNA

Answer 9

normal helix

Question 10

Z-DNA

Answer 10

stressed form of DNA following transcription, goes reverse direction (counterclockwise)

Question 11

Why are there major and minor grooves in DNA?

Answer 11

H bonding

Question 12

The bacterial genome is compartmentalized by which 2 things?

Answer 12

nucleoid and genophore

Question 13

The genophore is compacted by what 2 things?

Answer 13

nucleoid associated proteins and supercoiling

Question 14

Which 5 proteins are involved in nuceloid formation?

Answer 14

HU, IHF, H-NS, FIS, SMC

Question 15

HU

Answer 15

protein that does DNA bending for nucleoid formation

Question 16

IHF

Answer 16

protein that does DNA bending for nucleoid formation

Question 17

H-NS

Answer 17

protein that binds to curved DNA and forms bridges for nucleoid formation

Question 18

FIS

Answer 18

protein that does significant DNA bending and increases DNA branching for nucleoid formation

Question 19

SMC

Answer 19

protein that condenses the genome for nucleoid formation

Question 20

Lateral gene transfer mechanisms

Answer 20

transformation, conjugation, transduction

Question 21

transformation

Answer 21

LGT from environment

Question 22

conjugation

Answer 22

LGT from bacteria

Question 23

transduction

Answer 23

LGT from bacteriophage

Question 24

2 hallmarks of gene flow

Answer 24

sequence identity in distantly related strains AND conservation of gene order and direction (synteny)

Question 25

The Black Queen hypothesis

Answer 25

Explains how obligate symbiotes form by gaining an energetic advantage by not having to produce a product which eventually results in gene loss

Question 26

gene loss by intrachromosomal recombination

Answer 26

recombination between similar sequences on the same DNA molecule can result in deletion between them

Question 27

gene family expansion steps

Answer 27

1. innovation (minor function becomes beneficial)
2. amplification (gene copy number increased to maximize benefit)
3. diversification (beneficial mutations increase activity of gene and original gene may be lost)

Question 28

Lenski experiment

Answer 28

Studies E. coli evolution by freezing samples every 500 generations and comparing them