Chapter 5 Flashcards Preview

MCBL > Chapter 5 > Flashcards

Flashcards in Chapter 5 Deck (65):
1

What is a permanent change in a DNA sequence?

mutation

2

What is the mutation rate?

the rate at which mutations occur in the cell

3

What is a silent mutation?

a mutation that changes the codon but not the amino acid

4

what is the mutation rate of a bacteria?

one/10^6 generations
one nucleotide change per 10^9 nucleotide per generation

5

What are fibrinogens?

proteins that do not depend on the amino sequence for survival so, you can insert any AA in their sequence and they will survive. you can use them to calculate mutations in proteins

6

What is the mutation rate of eukaryotic proteins?

once every 200,000 years of a protein of 400 AA

7

What are two ways to measure mutation rates for eukaryotes?

measure the amino acid sequence for changes
measure the DNA sequence of a closely related species

8

What are germ cells?

reproductive cells of sexually reproducing organisms

9

What are somatic cells?

any cell that is not a sex cell

10

What does a high mutation rate in somatic cells cause?

cancer

11

How fast is DNA replicated?

1000 nucleotides per second

12

What is DNA templating?

using the complementary strand to copy a strand of DNA.

13

What is the enzyme that polymerizes the hydrogen bond between a nucleotide and its complementary nucleotide?

DNA polymerase
free nucleotides serve as its substrate

14

What is the nucleotide that polymerized into DNA by DNA polymerase?

deoxyribonucleoside triphosphate

15

What is semiconservative replication of DNA?

during replication the daughter DNA receive one old strand and one new strand

16

What is the replication fork?

it is the y shaped area in DNA that DNA polymerase continually synthesizes complementary strands of DNA

17

Which way is DNA synthesis on the strands of DNA?

From the 5` to the 3` direction

18

What are Okazaki fragments?

sequence of DNA that is synthesized on the lagging strand about 1000-2000 base pairs long that synthesized in the 5` to 3` direction. allows for 3`to 5` direction on the lagging strand

19

What is the leading strand?

the strand of DNA that synthesized continuously from 5` to 3`

20

What is the lagging strand?

the strand that has chain growth from 3`to 5` but synthesizes only 5` to 3`. this is accomplished by discontinuous backstitching

21

What does the first step in proofreading the DNA sequence?

The DNA polymerase
the correct nucleotide has a higher affinity for the polymerase. it is more energetically favorable.
before the nucleotide covalently binds the correct nucleotide, it finger tightens around the active sight. this is done readily with the correct nucleotide (it double checks base pair geometry before catalyzing the bind)

22

What is exonucleolytic proofreading?

when a DNA polymerase cleaves of a mismatch nucleotide at the 3`OH. and inserts the correct base. tho is done by a separate domain called the 3` to 5` proofreading exonuclease. requires a previous 3` OH end of the primer strand

23

What are the self correcting properties of DNA polymerase dependent on?

perfectly base paired primer terminus

24

Why doesn't RNA require a primer terminus?

because mistakes are not passed on to the next generation. Mistakes in RNA are 100000 times higher

25

What is DNA primase?

a enzyme that lays down a short RNA primer that DNA polymerase needs to start DNA replication

26

How long are the RNA primer?

10 nucleotides

27

how far apart are the RNA primers on the lagging strand?

100-200 nucleotides

28

What is DNA ligase?

they remove* the RNA primer and ligate the Okazaki fragments together on the lagging strand. by sealing a broken phosphosdiester bond

29

What is DNA helicase?

uses ATP to pry apsrt the helix of DNA at 1000nucleotide per second

30

What direction does DNA helicase unwinds double-stranded DNA?

in both directions

31

In which direction does the helicase have the predominant?

The DNA helicase that is unwinding in the 5` to 3` direction on the lagging strand

32

What are Single Strand DNA-binding proteins also called?

helix-destabilizing proteins.

33

What do Single Strand DNA-binding proteins do?

They stabilize the unwound single-stranded conformation
Straightens out the single strand on the lagging strand preventing short hair pins

34

What holds te DNA polymerase onto the DNA as it is moving on the strand?

sliding clamp

35

How does the sliding clam prevent DNA polymerase from falling off the strand of DNA?

one part of the clamp is attached to the back of DNA polymerase. the whole ring slides along

36

What does the assembly of the sliding need to bind to DNA polymerase?

a clamp loader uses ATP to bind the sliding clamp onto DNA polymerase

37

Where is the sliding clamp for the DNA polymerase?

for the lagging strand the sliding clamp is assembled on the RNA primer. a new clamp is used for every fragment it makes

38

Is the protein that synthesize DNA in one single complex?

yes, the DNA moves as if it was a cloth moving along a sewing machine.

39

What is the strand directed mismatch repair in prokaryotes?

The A in the GATC sequence is methylated not until some time after it is incorporated into new DNA. this way the new strand can be distinguished from the old strand if repair is needed
educes errors by 100 fold

40

What is the directed mismatch repair in eukaryotes?

instad of methylation the DNA strands have nicks to tell the new strand from the old strand

41

What are DNA Topoisomerase's?

it swivels DNA so it wouldn't wind because DNA forms a helix every 10 base pairs

42

How does Topoisomerase's add add to the DNA?

They break the phosphodiester bond in a reversible reaction. it covalently links itself to phosphate in DNA

43

What does Topoisomerase 1 does?

Cleaves the phosphodiester bond and uses the bond opposite on the nick as a swivel point. Any tension will unwind the DNA in the opposite direction. use the energy in the phosphodiester bond to reseal the bond. doesn't use add. energy

44

What does Topoisomerase 2 does?

it binds to DNA strands that are crossed over each other. binds to both strands. uses ATP
1)breaks double helix reversibly
2)the second to cross through the gate
3)reseals break and dissociates from DNA

45

What is the mutation rate of DNA before proofreading?

10^5

46

What are the exonuclease activity of pol I?

5`-3` exonuclease (removes nucleotides)
3`-5` exonuclease (proofreading)

47

what is the exonuclease activity of pol II?

3`-5` exonuclease

48

What is the exonuclease activity of Pol III (holoenzyme)?

3`-5` exonuclease activity

49

What are the subunits of holoenzyme Pol III?

Catalytic core of three subunits - alpha - epsilon-pmega
Clamp subunits - Beta Beta - for processivity
Clamp loader - Y complex
assembly subunits Theta theta

50

What are does the catalytic core of the holoenzyme do?

alpha-polymerase activity
epsilon - exonuclease activity
omega- not well defines

51

What are the steps of DNA replication?

Unwinding by of DNA by helicase
stabilization by SSB and topoisomerases
primer sythesis by primase
leading and lagging strand synthesis
removal of RNA primer
sealing gaps by ligase

52

Which polymerase removes the RNA primer?

DNA pol I

53

What is the protein for dnaA?

initiator protein

54

what is the protein for dnaB?

Helicase

55

what is the protein for dnaG

primase

56

What is the protein for polA?

Polymerase I

57

What is the protein for polB?

polymerase II

58

what is the protein for dnaE?

polymerase III

59

What resyricts the size of okazaki fragments in eukaryotes?

nucleosomes

60

What are the DNA polymerases in mammals?

poly alpha (primase)
poly ?
poly epsilon

61

Which polymerase in mammals is used for the lagging strand?

poly ?

62

Which polymerase in mammals is used for the leading strand?

poly epsilon

63

What degrades RNA ?

RNaseH

64

how long are Okazaki fragments in mammals?

0.1-0.2 Kb

65

How long is Okazaki fragments in E. coli?

1- 2 Kb

Decks in MCBL Class (70):