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Biochemistry > DNA Lecture 7 > Flashcards

DNA Lecture 7 Flashcards

1
Q

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

A

Denaturation

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2
Q

What causes denaturation?

What happens during denaturation?

A

Heat and pH

H bonds and base stacking are disrupted

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3
Q

Are covalent bonds broken during denaturation?

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

A

No.

Rewinding or annealing to yield the exact duplex

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4
Q

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 _______

A

260nm

26nm

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5
Q

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

A

Hypochromism

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6
Q

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

A

Melting Temperature (Tm)

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7
Q

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

A

Tm (Melting temperature

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8
Q

This is also defined as the temperature at 50% denaturation

A

Tm

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9
Q

Each species of DNA has a characteristic

A

Tm

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10
Q

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

Tm depends on 4 things..

A

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

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11
Q

DNA molecules with higher _____ base pairs have higher Tm values

A

G-C

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12
Q

How many bonds to G-C base pairs have?

A-T?

Which form stronger van der Waals interactions between base pairs?

A

G-C: 3

A-T: 2

G-C (duh)

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13
Q

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

A

G–C

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14
Q

Higher salt concentration ___ Tm

Why?

A

Increases Tm

The double helix is stabilized

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15
Q

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

A

cations

phosphate

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16
Q

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 ____

A

Mutations

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17
Q

Alterations in DNA structure that produce permanent changes in genetic information

A

Mutation

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18
Q

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

A

!

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19
Q

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

A

Deamination

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20
Q

In deamination, cytosine undergoes deamination to ______

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

A

Uracil

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21
Q

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

A

!

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22
Q

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

A

AU

23
Q

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

A

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

24
Q

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

It is more common for

A

Depurination

Purines

25
Q

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

A

Depurination

Apurinic Residue

26
Q

UV light can alter ____

A

bases

27
Q

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

A

Cyclobutane pyrimidine dimers

28
Q

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

A

6-4 photoproduct

29
Q

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

A

X-rays and gamm rays (ionizing radiation)

30
Q

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

A

!

31
Q

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

A

Deaminating Agents

32
Q

These include dimethylsulfate and can alter certain bases of DNA

A

Alkylating Agents

33
Q

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

A

Alkylating Agent

34
Q

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

A

Hydroxyl radicals

Oxygen

Oxygen

35
Q

A linear polymer composed of four different nucleotides

The sugar component is ribose, different from DNA

A

RNA

36
Q

In RNA there are four possible bases. Purines are

Pyrimidines are

The __ replaces thymine found in DNA

A

Adenine and guanine

Cytosine and uracil

Uracil

37
Q

How do thymine and uracil differ?

A

Thymine has a methyl group on C5

38
Q

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

A

Polar

39
Q

RNA is sensitive to ____

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

Why?

A

alkaline hydrolysis

I dunno…

40
Q

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

A

Alkaline hydrolysis

41
Q

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

As a result of resonance, all nucleotide bases absorb

A

260nm

UV light

42
Q

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

A

Lactam Form

43
Q

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?

A

Single strand

Single stranded

Right handed

Purine-purine

44
Q

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

A

!

45
Q

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

A

G and U

46
Q

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

A form right handed double helix

47
Q

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

A

Bulges or internal loops

48
Q

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

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

A

Hairpins

UUGG

49
Q

Can RNA form tertiary structures?

A

Yes.

50
Q

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

A

Hydrogen bonds

51
Q

Have Z-forms of RNA been observed?

B-forms?

A

Yes in the lab

Nope.

52
Q

Hydrolysis of nucleoside triphosphates provides

A

Chemical Energy

53
Q

An important regulatory nucleotide is

A

Cyclic AMP

54
Q

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

A

!

Biochemistry (27 decks)

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