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Molecules to Medicine Unit 1 > DNA > Flashcards

Flashcards in DNA Deck (76):
1

Mitochondrial DNA is passed down from the….

Mother

2

The shape of a nuclear chromosome

Linear

3

The shape of mitochondrial chromosome

Circular

4

The three units of DNA include:

1. deoxyribose 2. a nitrogen containing base 3. phosphate group

5

Purine base

Has two rings and includes adenine and guanine

6

Pyrimidine base

Has one ring and include thymine and cytosine

7

Ribose

Five carbon sugar which a hydroxyl group on the 2' position, repelling the negative charge in the phosphate group and making RNA less stable than DNA.

8

At what point on the 5-carbon sugar is the differentiating factor between DNA and RNA?

2'

9

At what point on the 5-carbon sugar is the phosphate group attached?

3' and 5'

10

Deoxyribose ribose

A 5-carbon sugar with a hydrogen on the 2' position

11

Deoxyribonucleoside

In DNA, purine or pyrimidine linked with deoxyribose, without a phosphate group

12

Ribonucleoside

In RNA, purine or pyrimidine linked with a ribose, without a phosphate group

13

Nucleotide

Composed of a base, a sugar and at least one phosphate. They are the monomer building block of DNA or RNA. POlymerize into long polynucleotide chains in the 5'-3' phosphodiester bonds formed between adjacent deoxyribose units.

14

Relative solubility of components of nucleotides.

A base is less soluble than a nucleoside which is less soluble than a nucleotide. Purine is less soluble than pyrimidine.

15

Gout/ Lesch Nyhan

Both diseases have a defect in enzymes making the bases build-up, There is especially an accumulation of purine due to its insolubility

16

What did Fred Griffith discover around WWI?

He characterized different strands of pneumonia - one with a capsule (which killed mice) and one without (which did not kill mice).

17

Describe the study of Avery, McCloud and McCarty.

They looked at the virulent strain and the non-vvirulent stain and observe that the non-virulent strain was transformed by the virulent strain.

18

What did Rosalind Franklin and Maurice Wilkins discover?

X-ray diffraction of moist DNA fibers showed a helical structure

19

What are the implications of Chargaff's rules?

Equal percentages of A/G and C/T in every cellular organism meaning there is base pairing!

20

Two strands of DNA intertwine in a _________ helix.

Right-handed

21

DNA strands' backbones are oriented ________ to one another.

Antiparallel

22

The base pairs are bonded by ___________.

Hydrogen bonding

23

If you count ________ base pairs, you will end up in the same position.

10

24

Name the factors which negate the repelling energy of the phosphate groups on the DNA helical structure. (3)

1. Hydrophobic interaction/ stacking energy between adjacent base pairs 2. Hydrogen bonding between complementary bases 3. Positive ions floating in the cells which neutralize the negative charge of the phosphate

25

Factors that affect DNA melting/ melting temperature.

1. Salt concentration 2.pH 3. DNA chain length 4. GC content

26

Methylation

The major covalent modification of human DNA is methylation of Cytocine, which occurs naturally, allowing enzymes to differentiate between the parent and daughter strans

27

Deamination

Deamination of bases is a major cause of mutation, sped up by nitrous acid. Water reacts with an amino group to release ammonia. This occurs spontaneously.

28

Deamination is an issue if it alters _________ to _________.

5-methylcytosine to thymine; but enzymes can recognize a difference in strands and remedy

29

Depurination

This causes the phosphate back to be sensitive to breakage

30

UV damage

Covalently links thymines, creating diner or kinks in the double helix

31

DNA intercalation

DNA intercalation occurs when ligands of appropriate size and chemical nature insert themselves in between base pairs. An example is doxorubicin.

32

Nucleoside analogs

Nucleoside analogs mimic actual nucleoside and are phosphorylated and incorporated into the growing DNA strand where they can act as chain terminators and stop DNA polymerase.

33

What does semi-concervative mean?

A newly replicated double helix contains one parental strand and one newly synthesized daughter strand.

34

Birectionality in DNA replication

Replication begins at a site of origin and simultaneously moves out in both directions

35

What are the three conserved features of the origin of replication?

1. They are unique DNA segments with multiple short repeats 2. They can be recognized by multimeric origin-binding proteins 3. They are usually rich in A/T base pairs

36

What is the function of origin binding proteins?

Origin binding proteins recognizes and binds to the origin of replication

37

In humans, the origin binding protein is called ________.

ORC

38

What is the function of single-strand binding proteins?

When helices unwinds the double-helix, single-strand binding proteins bind to each single strand of DNA, holding it in that conformation.

39

What is the function of primase?

DNA polymerase cannot initiate synthesis of new strand without RNA primer, which is formed by copying of the parental DNA strand.

40

DNA polymerase I

DNA Pol I performs the cleanup function in prokaryotes. DNA Pol I mediates replacement of RNA primers

41

DNA polymerase III

In prokaryotes, DNA polymerase III is the major replication enzyme because is has a sliding clamp, giving it higher processivity.

42

In eukaryotes, _____________ synthesizes the first 20 deoxyribonucleotides in eukaryotes after the RNA primer and is then swapped for __________ for the lagging strand and __________ for the leading strand.

DNA Pol α; Pol δ;Pol ε

43

What is the sliding clamp called in humans?

PCNA

44

What is the sliding clamp called in E. Coli?

Beta-clamp

45

What is the function of Gyrase?

In prokaryotes, relieves torsional strain

46

What is the function of Topoisomerase?

In eukaryotes, relieves torsional strain

47

What is the function of Telomerase?

Telomerase has reverse transcriptase activity and carries its own RNA template in order to restore the ends of chromosomes (telomeres) in human cancer and stem cells.

48

The leading strand is formed by continuous copying of the parental strand that runs 3' to 5' ________ the replication fork.

Towards

49

The lagging strand is formed by discontinuous copying of the parental strand that runs 3' to 5' __________ from the replication fork.

Away

50

What are the two main components which contribute to the fidelity of replication in polymerase activity?

1. The ability to form hydrogen bonds between with bases A and T and G and C 2. Common geometry of the A and T and G and C basepairs

51

DNA damage repair is __________ meaning if one repair mechanism fails, there are back-up options.

Redundant

52

What causes oxidative damage to DNA?

Oxidative damages to bases are caused by reactive oxygen species that are generated during normal cell metabolism

53

What is base alkylation?

Chemical alteration to a base; which can cause a point mutation

54

What is depurination or depyrimidination?

Loss of a base

55

What is base deamination?

Loss of an amine group which can cause a point mutation

56

What are the two changes in DNA structure which interferes with replication and transcription?

DNA strandbreaks and Inter/Intra strand crosslinks

57

What is a point mutation?

Substitution of one base for another

58

What is an insertions?

Additions of one or more nucleotides within a DNA sequence.

59

What is a deletion?

Removal of one or more nucleotides from a DNA sequence.

60

What is nucleotide excision repair?

NER removes DNA lesion that distort the DNA structure and block transcription.

61

What are the two types of nucleotide excision repair?

1. Global genome NER which recognizes distorting DNA lesion in any region of the genome 2. transcription-coupled NER which recognizes distorting lesion in regions that are actively transcribed

62

What is base excision repair?

BER removes DNA lesions that are missed by the NER process but do not necessarily block polymerase function or distort the DNA structure.

63

Glycosylases are required in __________. They recognize a specific type of altered base and flips the altered base of the helix and removes the damaged base.

Base excision repair

64

What are the two types of double-stranded break repairs?

1. Non-homologous end joining (NHEJ): required no sequence homology 2. Homologous recombination: required extensive sequence homology between broken ends and template DNA

65

What is the function of endonuclease in excision repair?

Mediates cutting of the phosphodiester backbone flanking the damaged nucleotide

66

What is the pair of homologous protein kinases central to lesion detection?

ATM and ATR, which are recruited to the site of DNA damage and initiate the recruitment of downstream proteins.

67

What are the five sources of DNA double-strand breaks?

1. Naturally during Meiosis 2. During generation of immune diversity (VDJ) 3. During DNA replication, when the replication fork encounters a nick in one template strand 4. During insertion of retrovirus 5. From ionizing radiation in the environment

68

Double stranded breaks are sensed by __________ and ___________ kinases.

ATM and ATR

69

Positively, Imprecise repair by NHEJ contributes to ___________

Antibody diversity

70

NHEJ is __________, ____________, and __________

Fast, relatively inaccurate, not sequence dependent

71

Homologous recombination can only occur during _________ and _________ of the cell cycle

S; G2

72

Homologous recombination requires____________

The nearly identical DNA strands of the unbroken sister chromatid

73

Different resolution of _______________ can lead to exchange of genetic information between the two chromosomes undergoing HR

Holliday junction

74

The formation of ___________ is an essential feature of meioses which can lead to gene conversion of crossing over

Holliday junction

75

Failure to repair a double-stranded break will lead to cell death. This is exploited by __________

Cancer therapy drugs such as bleomycin which causes double-stranded breaks

76

What is resection?

Resection is processing in homologous recombination in which broken ends are processed to expose single-strand ending in 3' OH