Bacterial Replication and Transcription 5.1

Question 1

Flow of genetic information in any cell depends on ?

Answer 1

central dogma

1) replication- copy DNA
2) transcription- convert DNA to RNA
3) translation- convert RNA into protein format

Question 2

what do retroviruses do? exception for what?

Answer 2

encode an enzyme with the ability for reverse transcription via reverse transcriptase
*exception to central dogma

Question 3

reverse transcriptase does what?

Answer 3

conversion of RNA information into DNA format

Question 4

purpose of promotor?

Answer 4

regulates the flow of information from DNA to RNA (in both Pro and Euk)

Question 5

Describe prokaryote genes

Answer 5

1) contiguous coding regions
2) upstream regulatory regions
3) transcription leads to a polycistronic RNA message- one RNA that contains several coding regions

Question 6

describe eukaryote genes

Answer 6

1) exons= regions that code for genes
2) introns= extra DNA between exons
3) regulatory regions (regions that do NOT code for protein that regulate transcription)

Question 7

exons vs introns

Answer 7

exons= used
introns= not used..... not sure how to remember this, but stop flipping them

Question 8

Regardles of species, DNA ALWAYS has these characteristics?

Answer 8

1) polydeoxyribose-phosphate backbone
2) purine and pyrimidines hydrogen bonded to complementary base pairs
3) antiparallel; coding 5’ to 3’
4) double stranded supercoil

Question 9

What is unique characteristics to Pro DNA?

Answer 9

1) circular

2) nuclear regions celled “nucleoid”

Question 10

double stranded DNA in its simplest form is alpha or beta and contains what grooves per tuern?

Answer 10

alpha

*contains major and minor groove per turn

Question 11

hydrogen bonds in DNA can be broken with? reannealled with?

Answer 11

broken with heat

*renealled with cooling

Question 12

DNA absobrs light best at what wavelength?

Answer 12

260 nm

Question 13

does single or double standed DNA absorb more light?

Answer 13

single

Question 14

as DNA melts, does its light absorbance increase or decrease?

Answer 14

increase

Question 15

Each dsDNA has a melting temperature proportional to the amount of?

Answer 15

G:C bonds in the strand

*greater the amount of G:C; greater the MP will be

Question 16

what is the nucleoid? contains?

Answer 16

nuclear region in Pro. (bc Pro has no membraned nucleus protecting its DNA)
*contains chromosomes, plasmids, and genetic exchange

Question 17

chromosome? E. coli has how many?

Answer 17

single, haploid (one copy), supercoiled, structure in nucleoid area is composed of double stranded circular DNA-
*E. coli has ~4.7 million bases

Question 18

what are plasmids?

Answer 18

extrachromosomal elements

*may contain information for virulence factors or antibiotic resistance factors

Question 19

Genetic exchange occurs at the nucleoid through what 3 processes?

Answer 19

conjugation
transformation
transduction

Question 20

What does Class 1 topoisomerases do?

Answer 20

introduce single stranded breaks for supercoiling

Question 21

What does Class 2 topoisomerases do?

Answer 21

introduce double strand breaks to supercoil DNA

Question 22

what enzyme supercoils DNA?

Answer 22

gyrase (both topoisomerase 2 help)

Question 23

What are 3 antibiotics commonly used to inhibit gyrase?

Answer 23

Nalidixic acid, Ciprofloxacin, novobiocin

Question 24

Remember: DNA gyrase = _____ = creates supercoil

Answer 24

topoisomerase 2

Question 25

supercoiled DNA forms ___ held together by proteins? point of proteins?

Answer 25

domains * proteins prevent the entire NA from uncoiling when one domain is nicked/uncoiled (which is necessary for replication and transcription)

Question 26

Cutting of DNA with restriction enzymes leads to?

Answer 26

"sticky ends" which are complementary but unbound ends

Question 27

purpose of modification and restriction enzymes?

Answer 27

used to analyze DNA, cuts foreign DNA

Question 28

modification and restriction enzymes will cut and WILL NOT cut what? why?

Answer 28

will cut unmethylated sequences | *will NOT cut methylated sequences bc that indicates the bacterias own DNA! Bacteria methylate their DNA for protection

Question 29

Where do modification and restriction enzymes cut DNA at? derived from?

Answer 29

will cut DNA at specific palindromic sequences | *derived from bacteria

Question 30

The CRISPR region is bascally a?

Answer 30

*memory bank* of nucleus acid sequences that have come into the bacterial cell

Question 31

Describe how CRISPR work? what protein additionally helps destroy invading DNA?

Answer 31

1) copy of nucleis acid info stored within genome of bacteria 2) the DNA is transcribed when the bacterial cell is under attack by virus 3) the cut CRISPR RNA seeks out invading viral DNA 4) CRISPR and Cas protein bind 5) together destroy invading DNA

Question 32

what does semiconservative mean?

Answer 32

Both strands of the DNA helix serve as templates for the synthesis of two new strands

Question 33

Semiconservative DNA replication requires what 6 enzymes?

Answer 33

``` DNA polymerases helicase primase ligase Gyrase(topoisomerase II) topoisomerase I ```

Question 34

DNA polymerases, in general, do what?

Answer 34

attaches nucleotides

Question 35

helicase

Answer 35

1) binds to DNA near replication fork | 2) unwinds or splits open the double helix replication fork

Question 36

primase

Answer 36

makes short RNA starter chains

Question 37

ligase

Answer 37

1) links DNA molecules into single structure | 2) completes replication

Question 38

Gyrase(topoisomerase II

Answer 38

promotes supercoiling

Question 39

topoisomerase I

Answer 39

relaxes supercoiled DNA

Question 40

DNA replication ALWAYS progresses what direction? (3 facts)

Answer 40

5' to 3' occurs on both strands simultaneously occurs in both directions

Question 41

DNA polymerases require a primer to couple the? Primer composed of?

Answer 41

DNA oligonucleotides | *This primer is composed of RNA

Question 42

DNA replication starts at?

Answer 42

origin of replication

Question 43

New DNA synthesis occurs at?

Answer 43

growing forks and proceeds bidirectionally

Question 44

DNA synthesis progresses in the 5′ to 3′ direction continuously=____ strand or in pieces= _____ stand

Answer 44

``` continous= leading strand discontinuous= lagging strand ```

Question 45

How long does it take to complete one round of replication?

Answer 45

40 minutes

Question 46

How often do new replication initiation occur?

Answer 46

every 20 minutes

Question 47

Initiation of DNA synthesis precedes cell ___?

Answer 47

division | *Multiple growing forks may be initiated in a cell before complete septum formation and cell division

Question 48

Why is there a leading and lagging strand?

Answer 48

because replication is bidirectional

Question 49

leading vs lagging strand

Answer 49

- -Leading strand synthesis moves towards replication fork (continuous) - -Lagging strand synthesis moves away from replication fork (discontinuous)

Question 50

Each newly opened single strand is | stabilized by?

Answer 50

single-strand binding proteins

Question 51

DNA polymerase I

Answer 51

1) removes RNA primers 2) fills gaps in DNA 3) involved in DNA repair-also has proofreading

Question 52

DNA polymerase III

Answer 52

proffreading** recognizes mismatches and redoes mistakes | **reduces mutations