Weeks 4-5

Question 1

What is a bacteriophage and how do they reproduce?

Answer 1

= a bacterial virus, most abundant of any biological agent

• by infecting bacterial cells by injecting genetic material into bacterium
• can be lytic (T4) or lysogenic and lytic (lambda)

Question 2

What are prototrophs?

Answer 2

wild type bacteria that can grow on minimal media plate, i.e. can synthesize everything they need
themselves
(is a phenotype)

Question 3

What are auxotrophs?

Answer 3

mutant bacteria strains that lack certain enzymes which they cannot synthesize, so they need to be grown in complete media

Question 4

What is a prophage?

Answer 4

= inserted viral DNA in bacterial cell

Question 5

Lysogenic cycle

Answer 5

• phage DNA integrates into bacterial chromosome and becomes a prophage
• prophage is replicated as part of bacterial chromosome
• prophage may separate from chromosome and cell enters lytic cycle

Question 6

Gene transfer in Bacteria

Answer 6

• always unidirectional from donor cells to recipient cells

Question 7

Viral Genome

Answer 7

• very small and mostly linear but can be circular
• only about 300 genes
• the smaller the faster to replicate
• some viruses have RNA genome

Question 8

Bacterial Genome

Answer 8

• several million base pairs but smaller than eukaryotes
• circular
• additional genetic material in plasmids and episomes

Question 9

Plasmid

Answer 9

• small circular DNA, can replicate independently of bacterial chromosomes
• usually non-essential genes since plasmids can be lost but they are very mobile, often responsible for antibiotic resistance genes

Question 10

Episomes

Answer 10

• large circular DNA that can integrate into bacterial chromosome for replication or remain separate
• can consist of fertility factor, viral genomes, transposons, etc.

Question 11

Conjugation

Answer 11

• requires direct physical contact between two cells, form cytoplasmic bridge
• some DNA is transferred and replicates
• crossover in recipient cell leads to recombinant chromosome

Question 12

Transformation

Answer 12

• DNA fragments are taken up by a recipient cell

- crossover in bacterium leads to creation of recombinant chromosome

Question 13

Transduction

Answer 13

• virus attaches to bacterial cell and injects its DNA
• DNA is replicated, then bacterial cell lyses
• virus takes up some bacterial DNA with its own and carries it to next cell where it injects
• bacterial cell creates a recombinant chromosome from crossing over
• bacteriophage acts as a vector

Question 14

Which parasexual process in bacteria requires cell contact?

Answer 14

Conjugation

Question 15

Which parasexual process in bacteria is sensitive to DNase?

Answer 15

Transformation (b/c neither a bridge nor protected by bacteriophage)

Question 16

What is a competent bacterial cell?

Answer 16

• one that can take up free DNA (even from other species)

- essentially refers to permeability of the cell

Question 17

What is cotransformation?

Answer 17

• when multiple genes on same DNA fragment are taken up by recipient cell
• the closer together two genes are, the more likely that they will be taken up and transformed together
• therefore, can be used to map distance

Question 18

What is the fertility factor?

Answer 18

• an episome or plasmid
• it mediates conjugation
• F- is always recipient cell
• F+ can be a donor cell with F factor but not on bacterial chromosome (rather plasmid or episome)
• Hfr cell: when the F factor has been integrated into bacterial chromosome and this can also be a donor

Question 19

Generalized Transduction

Answer 19

= when a random fragment of bacterial DNA is packaged in the phage head by mistake

Question 20

Specialized Transduction

Answer 20

= when the prophage excises imprecisely from the chromosome and produces a phage chromosome that only contains the adjacent bacterial genes not entire bacterial genome

Question 21

3 Basic Components of nucleotides

Answer 21

1) Nitrogen containing bases (ATGCU)
2) Sugar (pentose - either deoxyribose or ribose)
3) Phosphate-diester bond (joins nucleotides)

Question 22

Which bases are purines?

Answer 22

Adenine and Guanine

Question 23

Which bases are pyrimidines?

Answer 23

Cytosine, Thymine, Uracil

Question 24

What forms the backbone of the helix?

Answer 24

sugar and phosphate

the bases face inward and base pair

Question 25

Which is most common DNA structure?

Answer 25

B DNA - right handed double helix (clockwise) with minor and major groove
- the two strands (always) have opposite chemical polarity (5’ and 3’ end)

Question 26

3 Levels of Structure of DNA?

Answer 26

Primary: repeating units of nucleotides
Secondary: right-handed double helix
Tertiary: supercoiled DNA in in vivo cells

Question 27

How does DNA become super-coiled?

Answer 27

• through topoisomerases = an enzyme that can add or remove turns from chromosome and induce or relief stress/tension

Question 28

Do bacteria have histones?

Answer 28

no, they are just coiled into little loops, called domains, each domain has supercoiling

Question 29

What do eukaryotic chromosomes consist of?

Answer 29

• one large linear molecule of DNA
• histone proteins (5), positively charged
• non-histone proteins

Question 30

What is chromatin?

Answer 30

= DNA + histones + proteins
- two types
Euchromatin: where most transcription takes place
Heterochromatin: highly condensed DNA (transcription and crossing over don’t really occur here)

Question 31

What is the first level of eukaryotic DNA packaging?

Answer 31

Nucleosomes
beads on a string: 146 bp of DNA wrapped as 1 3/4 turns around an octamer of histones
linker DNA in between (8-114 bp)

Question 32

Describe the nucleosome

Answer 32

• Octamer at nucleosome core consists of 2 H2a, 2 H2b, 2 H3 and 2 H4 histones
• Histone H1 is the 5th histone and acts as a clamp to keep DNA bound to octamer

Question 33

What is the 2nd level of packaging?

Answer 33

• 30nm chromatin fiber or solenoid
• nucleosomes stack together and are spaced by linker DNA
• Histone H1 stabilizes nucleosome fibre and contributes to 30nm chromatin fibre

Question 34

What is the 3rd level of packaging DNA?

Answer 34

= inter-phase chromosomes
looping of 30nm fibres is anchored at the base by certain proteins to a chromosome scaffold comprised mostly of non-histone proteins

Question 35

Least condensed state of DNA?

Answer 35

Interphase

Question 36

Most condensed state of DNA?

Answer 36

Metaphase during mitosis (allows for segregation without entanglement)