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DMD 5242 > DNA/DNA synthesis (complete) > Flashcards

DNA/DNA synthesis (complete) Flashcards

1
Q

What is on the 5’ end of a DNA strand

A

a free phosphate

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2
Q

What is on the 3’ end of a DNA strand

A

an OH

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3
Q

In which direction are nucleic acids named

A

5’ to 3’

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4
Q

are the two strand of a double stranded DNA parallel or antiparallel

A

antiparallel

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5
Q

what kind of bonds exist between bases that are on opposite DNA strands

A

hydrogen bonds

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6
Q

The DNA helix is right or left handed

A

right

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7
Q

What is the shape of the pyramidines

A

a six carbon ring

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8
Q

what is the shape of the purines

A

a six carbon ring bound to a five carbon ring

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9
Q

Which bases are pyrimidines

A

Cytosine
Thymine
Uracil

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10
Q

Which bases are purines

A

Adenine

Guanine

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11
Q

What is the structure of cytosine

A

a pyrimidine with -NH2

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12
Q

What is the structure of Thymine

A

a pyrimidine with -CH3

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13
Q

What is the structure of Uracil

A

a pyrimidine without -NH2 or -CH3

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14
Q

What is the structure of Adenine

A

the purine without the carbonyl

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15
Q

what is the structure of guanine

A

purine with the carbonyl

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16
Q

What is a nucleoside

A

a sugar and a base

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17
Q

what is a nucleotide

A

a sugar, base and phosphate group

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18
Q

What are the three parts of a nucleotide

A

sugar
base
phosphate group

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19
Q

how many phosphates can be on a nucleotide

A

0-3 (nucleoside if it has 0)

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20
Q

What is the difference between the sugar of DNA and RNA

A

the c-2 location has an OH in RNA

the c-2 location just has an H in DNA

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21
Q

Which of the Bases (A, T, G, C, U) bind together

A

A–T (in DNA)
C–G
A–U (in RNA)

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22
Q

how many hydrogen bonds are between A–T

A

two

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23
Q

how many hydrogen bonds are between C–G

A

three

24
Q

what kind of bonds connect nucleotides together

A

phosphodiester bonds

25
Q

which part of DNA is hydrophilic, which part is hydrophobic

A 
the backbone  (sugar and phosphate) is hydrophilic
the bases are hydrophobic
26
Q

What are the two types of Grooves in DNA

A

major and minor

27
Q

why are major and minor grooves significant

A

because enzymes likely enter and act upon the DNA through the major grooves

28
Q

Where is the new phosphodiester bond created when two nucleotides bind together

A

it is formed between the phosphate group off of the 5-C of one nucleotide, to the 3-C of the next

29
Q

which base pairs are harder to separate A–T or C–G

A

C–G because they have one more H bond between them

30
Q

what three things can denature DNA

A
  1. Heat
  2. pH changes
  3. DNA replication
31
Q

What did Hershey and Chase discover

A

that it was the DNA, not the protein, that held the genes

32
Q

What are histones

A

proteins that help condense DNA into chromosomes

33
Q

What did Meselson and Stahl discover

A

that DNA synthesis is semi conservative

34
Q

what does it mean that DNA synthesis is semi conservative

A

That for each generation of DNA made, there is one new strand and one old strand.

35
Q

at the replication fork is DNA synthesis bidirectional

A

yes

36
Q

What are the two types of strands in DNA synthesis

A

a leading strand

a lagging strand

37
Q

in which direction is DNA synthesized

A

5’ to 3’

38
Q

does DNA synthesis require a primer

A

yes

39
Q

does DNA synthesis have high or low processivity

A

high

40
Q

is DNA synthesis fairly accurate (doesn’t make many mistakes)

A

It is very very accurate

41
Q

What are the 7 enzymes used in DNA synthesis

A
  1. DNA-A
  2. DNA helicase
  3. Single stranded DNA binding protein
  4. Topoisomerase
  5. primase
  6. DNA polymerase
  7. ligase
42
Q

What is the function of DNA-A

A

it creates the replication bubble, begins to denature DNA

43
Q

What is the function of helicase

A

to continue to denature DNA (after DNA-A), unzips the double stranded DNA

44
Q

What is the function of single stranded DNA binding protein

A

to make sure that the two single strands of DNA in the replication fork done reanneal

45
Q

What is the function of Topoisomerase

A

to release the tension on the DNA coil that is caused by helicase unwinding the double strand (it cuts, untwists, and puts the strands back together)

46
Q

What is the function of primase

A

it lays down an RNA primer so that DNA polymerase can do it’s work

47
Q

what is the function of DNA polymerase

A

replicates DNA (brings the Bases into place and forms a new DNA strand)

48
Q

what is the function of ligase

A

links unconneced strands of the new DNA together

49
Q

What are the different types of DNA polymerase we talked about

A

DNA polymerase 1

DNA polymerase 3

50
Q

What does DNA polymerase 1 do

A
  1. removes RNA primer and puts DNA in it’s place
  2. proofreading
  3. regular polymerase activity
51
Q

What does DNA polymerase 3 do

A
  1. Most of the polymerase activity is done with #3

2. it also does proofreading

52
Q

Why does DNA polymerase 3 do most of the DNA synthesizing

A

because it is the fastest, and the most processive

53
Q

what does processivity measure

A

how many nucleotides can be added before the enzyme dissociates

54
Q

what are the two sites of DNA polymerase 1

A 
polymerase active site
Exonuclease site (proofreading)
55
Q

what are the two ways DNA polymerase can remove bases

A

5’–>3’ removes RNA primers

3’–>5’ removes misincorporated bases

56
Q

What are the differences between the leading and lagging strand

A

leading strand:
one long molecule
single RNA primer
adds 5’–>3’ moving toward the replication fork

lagging strand:
many short (okazaki) fragments
many RNA primers
adds 5’ –>3’ moving away from the replication fork

DMD 5242 (10 decks)

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