Ch. 6 DNA and RNA Structure Flashcards
What are the roles of nucleotides in cells (3)?
Nucleotides form nucleic acids, are in energy related molecules (ATP, GTP, NAD⁺, NADP⁺, FAD), and are in signaling molecules (cAMP, cGMP).
Why is the presence of an OH group on the 2’ carbon of ribose of note?
It makes ribonucleotides more reactive and therefore less stable.
What effect does the sugar identity have on the backbone of nucleic acids?
The slightly different ring conformation of ribose vs deoxyribose affects DNA and RNA backbones.
What are nucleotides linked by and what does this linkage produce?
Nucleotides are linked by phosphodiester bonds to form nucleic acids. This linkage produces a 5’ → 3’ direction.
What should you assume the direction of an unlabeled nucleotide sequence is?
Assume the left is 5’ and the right is 3’.
Is the phosphate-sugar backbone hydrophobic or hydrophilic, and what does this allow for?
The phosphate-sugar backbone is hydrophilic and H-bonds to water.
What does the 2’ OH of RNA do that DNA does not?
The 2’ OH of RNA allows it to rapidly hydrolyze in certain conditions; DNA does not.
What does the presence of RNA’s 2’OH mean for storage?
RNA is “temporary” while DNA is more “permanent”.
Are bases hydrophobic or hydrophilic, and what does this allow them to do?
Bases are hydrophobic and associate more closely with each other putting them in the same plane. This is called hydrophobic stacking.
How do bases interact with each other?
Bases of one nucleic acid can interact with the bases of another nucleic acid through base pairing. Base pairing is via H-bonds (A=T and C≡G).
How does DNA usually exist in the cell?
It is usually a right-handed double helix with consistent featues.
What are the consistent features of the DNA right-handed double helix in cells (4)?
- Major and minor groove present in helix
- Antiparallel and complementary strands that allow for replication
- ~10 bases per turn
- Hydrophobic stacking of bases and various noncovalent forces make the double helix very stable
Why is the DNA helix flexible (4)?
The helix is flexible due to bond rotation, thermal fluctuation, localized unpairing of strands, and other factors.
What is the Watson and Crick form of the DNA helix?
The B-form. It is the most stable under physiological conditions.
What are the two variant forms of DNA?
A form DNA and Z form DNA.
How to these variant forms of DNA differ from B form (broadly and 4)?
They very in helix diameter, bases per turn, base tilt, sugar structure, and more.
What is the structure of A form DNA (4)?
It is a right-handed helix, a wider helix than B form, the base pairs are more tilted, and the major grooves are deeper while the minor grooves are shallower?
When and where does A form DNA occur?
A form DNA occurs in dehydration conditions, but is NOT known to occur in cells.
What is the structure of Z form DNA (3)?
It is a left handed helix, has a zig-zag backbone pattern, and has more bases per turn.
What causes Z form DNA?
It is caused by certain base pairs.
Where does Z form DNA occur?
It is normally found in certain parts of a chromosome, but the function is unclear.
What are A tracts?
A base sequence pattern in DNA that cause DNA bending.
What are DNA palindromes?
A base sequence pattern that are the same forwards and backwards. They serve as protein recognition sites.
What are inverted repeats?
A base sequence pattern that has inverted repeats that are complementary and lead to secondary structure.
Where are inverted repeats normally found?
They are more common in RNA, but can occur in both RNA and DNA.
What can the secondary structure formed by these base sequence patterns do?
They can inhibit transcription, translation, etc.
What is the structure of RNA and what can it lead to?
RNA is single stranded, but regions of the strand can base pair to form secondary structure.
What orientation will base paired regions of RNA have?
Base paired regions of RNA will be antiparallel.
If RNA secondary structure produces a helix, what form will it be?
RNA will usually be an A form helical structure because of the ribose ring structure and OH group.
What odd base pairing can occur in RNA due to ribose’s properties?
RNA can have A=A pairing and G=U pairing.
What does the structure of RNA (odd base pairing and secondary structure, etc.) result in?
As a result, there is greater structural variety of RNA, which allows for the many functions of RNA.
How can double stranded nucleic acids be denatured? Renatured?
Double strands can be denatured (melted) by heat or pH. They can renature (anneal) when returned to physiological conditions.
What does higher GC DNA mean?
Higher GC DNA denatures at higher temperatures because there are more H-bonds.
What kinds of duplexes can form upon renaturation (annealing)?
RNA duplexes and RNA:DNA duplexes can form.
List the melting temperatures of the following from lowest to highest… dsRNA, dsDNA, and RNA:DNA hybrids.
Lowest… dsDNA
Intermediate… RNA:DNA hybrids
Highest… dsRNA
How can nucleic acids of different species hybridize?
The nucleic acids of different species can hybridize IF they are complementary, and will indicate that similar sequences are present.
What does hybridization allow for research wise?
Hybridization allows for the detection of a gene’s DNA or RNA in a species using a labeled probe.
How does hybridization work in a lab?
It utilizes gel electrophoresis to separate fragments, transfers the nucleic acid to a membrane, and allows the labeled probe to base pair to a nucleic acid in the membrane.
What is southern blotting?
A hybridization technique that is used to detect DNA.
What is northern blotting?
A hybridization technique that is used to detect RNA.
What do spontaneous changes in nucleotides lead to?
Nucleotides can undergo spontaneous changes that lead to mutations.
How does deamination of cytosine effect cells?
The deamination of cytosine produces uracil. This might occur ~100 times a day in a cell. This is likely why DNA evolved to use thymine, because the presence of uracil indicates an error.
What is base methylation?
It is the addition of a methyl group to a base. It is common and related to regulating gene expression.
