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Flashcards in DNA Lecture 7 Deck (54):
1

This means a loss of native secondary structure (the helix changes to a random coil)

Denaturation

2

What causes denaturation?

What happens during denaturation?

Heat and pH

H bonds and base stacking are disrupted

3

Are covalent bonds broken during denaturation?

What happens after denaturation when the temperature or pH are returned to physiological range

No.

Rewinding or annealing to yield the exact duplex

4

The transition from the native (double helix) DNA to randomly coiled single chains can be monitored by following the change in UV absorbance at ____

Recall earlier DNA lectures that all nucleotide bases absorb UV light, with a strong absorption at or near _______

260nm

26nm

5

The absorbance of nucleotide bases is less in the double helical form than in the random coil form. This phenomenon is known as

Hypochromism

6

The midpoint of the curve on the absorbance vs. temperature figure is the

Melting Temperature (Tm)

7

This value corresponds to the midpoint of the transition from the double helix to a single stranded DNA in a random coil formation

Tm (Melting temperature

8

This is also defined as the temperature at 50% denaturation

Tm

9

Each species of DNA has a characteristic

Tm

10

Differences in Tm of different DNA molecules under various conditions provide information about factors contributing to double helix stability

Tm depends on 4 things..

1) pH
2) ionic strength
3) size
4) base composition of DNA

11

DNA molecules with higher _____ base pairs have higher Tm values

G-C

12

How many bonds to G-C base pairs have?

A-T?

Which form stronger van der Waals interactions between base pairs?

G-C: 3

A-T: 2

G-C (duh)

13

The free energies of formation are most favorable for ____ base pairs (more negative)

G--C

14

Higher salt concentration ___ Tm

Why?

Increases Tm

The double helix is stabilized

15

Salt ____ may reduce the repulsion between DNA chains by neutralizing the negative charge on the ______ groups

cations

phosphate

16

Purines and pyrimidines can exhibit spontaneous alterations in their covalent structure

The rate of these reactions is very low, but is physiologically significant because they can result in ____

Mutations

17

Alterations in DNA structure that produce permanent changes in genetic information

Mutation

18

Evidence suggests a link between aging, carcinogenesis, and the accumulation of mutations in an organism

!

19

Several nucleotide bases spontaneously lose the exocyclic amino groups in a ____ reaction

Deamination

20

In deamination, cytosine undergoes deamination to ______

It occurs in about 1*107 cytidine residues in 24 hours

Uracil

21

If DNA contained U rather than T, the cell would have a harder time recognizing those uracils which resulted from deamination of cytosine and starting a repair system

!

22

As U's paired with __, more permanent sequence changes would result; there would be a decreases in GC base pairs and an increase in ____ pairs in DNA

A

AU

23

Cytosine deamination could eliminate GC pairs over time and the genetic code

Thus, establishing T as one of the four bases in DNA was critical to the long term storage of genetic information

24

This is defined as hydrolysis of the N-B-glycosyl bond between a base and the pentose ring

It is more common for

Depurination

Purines

25

Up to 105 purines are lost from DNA in a 24 hour period under typical cell conditions

The resulting structure, where the base is lost on the ribose ring and replaced with a hydroxyl group, is called an

Depurination

Apurinic Residue

26

UV light can alter ____

bases

27

In the cell, adjacent pyrimidine bases in nucleic acids condense to form

Cyclobutane pyrimidine dimers

28

A second type of pyrimidine dimer, called a ____ can also result from UV light exposure

6-4 photoproduct

29

These type of rays can cause ring opening, fragmentation of bases and breaks in the covalent backbone of nucleic acid

X-rays and gamm rays (ionizing radiation)

30

It is estimated that UV and ionizing radiation are responsible for 10% of all DNA damage caused by environmental agents

!

31

These include nitrosamines from nitrate and nitrite salts used as preservatives in processed food to prevent bacterial growth. Used in very low levels.

Deaminating Agents

32

These include dimethylsulfate and can alter certain bases of DNA

Alkylating Agents

33

In this case, dimethylsulfate can methylate a guanine to yield O^6-methylguanine, which can't base pair with cytosine

Alkylating Agent

34

What is responsible for most oxidative DNA damage?

The cell has defense mechanisms to get rid of most of the ___ species

But some reactive ___ species don't get destroyed

The reactions that damage DNA are complex and include strand breaks, oxidation of deoxyribose and oxidation of the bases

Hydroxyl radicals

Oxygen

Oxygen

35

A linear polymer composed of four different nucleotides

The sugar component is ribose, different from DNA

RNA

36

In RNA there are four possible bases. Purines are

Pyrimidines are

The __ replaces thymine found in DNA

Adenine and guanine

Cytosine and uracil

Uracil

37

How do thymine and uracil differ?

Thymine has a methyl group on C5

38

The backbone of alternating pentose and phosphate groups in RNA is highly

Polar

39

RNA is sensitive to ____

In a test tube, RNA is rapidly hydrolyzed under alkaline conditions, but DNA is not

Why?

alkaline hydrolysis

I dunno...

40

This process forms cyclic 2', 3' monophosphates and then further hydrolizes them to yield 2' and 3' nucleoside monophosphates

Alkaline hydrolysis

41

Like DNA, RNAs are characterized by a strong absorption at about

As a result of resonance, all nucleotide bases absorb

260nm

UV light

42

In RNA, which tautomeric form of uracil predominates at pH=7.0?

Lactam Form

43

RNA typically exists as single or double strand?

The product of transcription of DNA is always a double or single stranded RNA

The single strand tends to assume a _______ handed helical conformation dominated by base stacking interactions

Which interaction is the strongest?

Single strand

Single stranded

Right handed

Purine-purine

44

Single strands of RNA will show base pairing in self-complimentary region in the molecule

RNA can also pair with complementary region of DNA or RNA. The strands are antiparallel as in DNA

!

45

One unusual different in RNA base pairing is that the base pairing between __ and ___ is fairly common

G and U

46

RNA 3‐D structures are complex and unique. There is no regular, secondary structure that serves as a reference point.

When complementary sequences are present, the double stranded structure that tends to exist is a __ form right handed double helix

A form right handed double helix

47

Breaks in regular A-form helix RNA caused by mismatched or unmatched bases in one or both strands are common. What can result?

Bulges or internal loops

48

What is the most common type of secondary structure in RNA?

What specific base sequence is often found at the end of hairpins?

Hairpins

UUGG

49

Can RNA form tertiary structures?

Yes.

50

____ bonds between non-Watson-Crick base pairs make structural contributions to the folding of RNA into its precise 3D structure

Hydrogen bonds

51

Have Z-forms of RNA been observed?

B-forms?

Yes in the lab

Nope.

52

Hydrolysis of nucleoside triphosphates provides

Chemical Energy

53

An important regulatory nucleotide is

Cyclic AMP

54

The phosphate group at the 5' hydroxyl of a ribonucleotide may have one or two additional phosphates attached, the resulting molecules are nucleoside mono,di, and triphosphates

!