DNA Lecture 7

Question 1

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

Answer 1

Denaturation

Question 2

What causes denaturation?

What happens during denaturation?

Answer 2

Heat and pH

H bonds and base stacking are disrupted

Question 3

Are covalent bonds broken during denaturation?

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

Answer 3

No.

Rewinding or annealing to yield the exact duplex

Question 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 _______

Answer 4

260nm

26nm

Question 5

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

Answer 5

Hypochromism

Question 6

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

Answer 6

Melting Temperature (Tm)

Question 7

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

Answer 7

Tm (Melting temperature

Question 8

This is also defined as the temperature at 50% denaturation

Answer 8

Tm

Question 9

Each species of DNA has a characteristic

Answer 9

Tm

Question 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..

Answer 10

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

Question 11

DNA molecules with higher _____ base pairs have higher Tm values

Answer 11

G-C

Question 12

How many bonds to G-C base pairs have?

A-T?

Which form stronger van der Waals interactions between base pairs?

Answer 12

G-C: 3

A-T: 2

G-C (duh)

Question 13

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

Answer 13

G–C

Question 14

Higher salt concentration ___ Tm

Why?

Answer 14

Increases Tm

The double helix is stabilized

Question 15

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

Answer 15

cations

phosphate

Question 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 ____

Answer 16

Mutations

Question 17

Alterations in DNA structure that produce permanent changes in genetic information

Answer 17

Mutation

Question 18

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

Answer 18

!

Question 19

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

Answer 19

Deamination

Question 20

In deamination, cytosine undergoes deamination to ______

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

Answer 20

Uracil

Question 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

Answer 21

!

Question 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

Answer 22

A

AU

Question 23

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

Answer 23

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

Question 24

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

It is more common for

Answer 24

Depurination

Purines

Question 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

Answer 25

Depurination Apurinic Residue

Question 26

UV light can alter ____

Answer 26

bases

Question 27

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

Answer 27

Cyclobutane pyrimidine dimers

Question 28

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

Answer 28

6-4 photoproduct

Question 29

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

Answer 29

X-rays and gamm rays (ionizing radiation)

Question 30

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

Answer 30

!

Question 31

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

Answer 31

Deaminating Agents

Question 32

These include dimethylsulfate and can alter certain bases of DNA

Answer 32

Alkylating Agents

Question 33

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

Answer 33

Alkylating Agent

Question 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

Answer 34

Hydroxyl radicals Oxygen Oxygen

Question 35

A linear polymer composed of four different nucleotides The sugar component is ribose, different from DNA

Answer 35

RNA

Question 36

In RNA there are four possible bases. Purines are Pyrimidines are The __ replaces thymine found in DNA

Answer 36

Adenine and guanine Cytosine and uracil Uracil

Question 37

How do thymine and uracil differ?

Answer 37

Thymine has a methyl group on C5

Question 38

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

Answer 38

Polar

Question 39

RNA is sensitive to ____ In a test tube, RNA is rapidly hydrolyzed under alkaline conditions, but DNA is not Why?

Answer 39

alkaline hydrolysis I dunno...

Question 40

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

Answer 40

Alkaline hydrolysis

Question 41

Like DNA, RNAs are characterized by a strong absorption at about As a result of resonance, all nucleotide bases absorb

Answer 41

260nm UV light

Question 42

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

Answer 42

Lactam Form

Question 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?

Answer 43

Single strand Single stranded Right handed Purine-purine

Question 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

Answer 44

!

Question 45

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

Answer 45

G and U

Question 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

Answer 46

A form right handed double helix

Question 47

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

Answer 47

Bulges or internal loops

Question 48

What is the most common type of secondary structure in RNA? What specific base sequence is often found at the end of hairpins?

Answer 48

Hairpins UUGG

Question 49

Can RNA form tertiary structures?

Answer 49

Yes.

Question 50

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

Answer 50

Hydrogen bonds

Question 51

Have Z-forms of RNA been observed? B-forms?

Answer 51

Yes in the lab Nope.

Question 52

Hydrolysis of nucleoside triphosphates provides

Answer 52

Chemical Energy

Question 53

An important regulatory nucleotide is

Answer 53

Cyclic AMP

Question 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

Answer 54

!