DNA Lecture 7 Flashcards
This means a loss of native secondary structure (the helix changes to a random coil)
Denaturation
What causes denaturation?
What happens during denaturation?
Heat and pH
H bonds and base stacking are disrupted
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
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
The absorbance of nucleotide bases is less in the double helical form than in the random coil form. This phenomenon is known as
Hypochromism
The midpoint of the curve on the absorbance vs. temperature figure is the
Melting Temperature (Tm)
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
This is also defined as the temperature at 50% denaturation
Tm
Each species of DNA has a characteristic
Tm
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
DNA molecules with higher _____ base pairs have higher Tm values
G-C
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)
The free energies of formation are most favorable for ____ base pairs (more negative)
G–C
Higher salt concentration ___ Tm
Why?
Increases Tm
The double helix is stabilized
Salt ____ may reduce the repulsion between DNA chains by neutralizing the negative charge on the ______ groups
cations
phosphate
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
Alterations in DNA structure that produce permanent changes in genetic information
Mutation
Evidence suggests a link between aging, carcinogenesis, and the accumulation of mutations in an organism
!
Several nucleotide bases spontaneously lose the exocyclic amino groups in a ____ reaction
Deamination
In deamination, cytosine undergoes deamination to ______
It occurs in about 1*107 cytidine residues in 24 hours
Uracil
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
!
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
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
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
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
UV light can alter ____
bases
In the cell, adjacent pyrimidine bases in nucleic acids condense to form
Cyclobutane pyrimidine dimers
A second type of pyrimidine dimer, called a ____ can also result from UV light exposure
6-4 photoproduct
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)
It is estimated that UV and ionizing radiation are responsible for 10% of all DNA damage caused by environmental agents
!
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
These include dimethylsulfate and can alter certain bases of DNA
Alkylating Agents
In this case, dimethylsulfate can methylate a guanine to yield O^6-methylguanine, which can’t base pair with cytosine
Alkylating Agent
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
A linear polymer composed of four different nucleotides
The sugar component is ribose, different from DNA
RNA
In RNA there are four possible bases. Purines are
Pyrimidines are
The __ replaces thymine found in DNA
Adenine and guanine
Cytosine and uracil
Uracil
How do thymine and uracil differ?
Thymine has a methyl group on C5
The backbone of alternating pentose and phosphate groups in RNA is highly
Polar
RNA is sensitive to ____
In a test tube, RNA is rapidly hydrolyzed under alkaline conditions, but DNA is not
Why?
alkaline hydrolysis
I dunno…
This process forms cyclic 2’, 3’ monophosphates and then further hydrolizes them to yield 2’ and 3’ nucleoside monophosphates
Alkaline hydrolysis
Like DNA, RNAs are characterized by a strong absorption at about
As a result of resonance, all nucleotide bases absorb
260nm
UV light
In RNA, which tautomeric form of uracil predominates at pH=7.0?
Lactam Form
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
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
!
One unusual different in RNA base pairing is that the base pairing between __ and ___ is fairly common
G and U
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
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
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
Can RNA form tertiary structures?
Yes.
____ bonds between non-Watson-Crick base pairs make structural contributions to the folding of RNA into its precise 3D structure
Hydrogen bonds
Have Z-forms of RNA been observed?
B-forms?
Yes in the lab
Nope.
Hydrolysis of nucleoside triphosphates provides
Chemical Energy
An important regulatory nucleotide is
Cyclic AMP
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
!
