Lecture 8: Nucleic Acids Flashcards
What are the 3 parts of a nucleotide?
Nitrogenous base
Pentose sugar
Phosphate groups
Two types of nitrogenous bases
Purines
Pyrimidines
What type of bond links the nitrogenous base to the pentose sugar?
N-B-glycosyl bond
Purines
have two rings
A and G are purines
Pyrimidines
have one ring
C and T are pyrimidines
How many hydrogen bonds can GC pairs make?
3 hydrogen bonds
How many hydrogen bonds can AT pairs make?
2 hydrogen bonds
Characteristics of nitrogenous bases
weakly basic and hydrophobic
move inside the DNA molecule since hydrophobic
nitrogenous bases can tautomerize which is a potential problem
Difference between ribonucleotides and nucleotides?
ribonucleotides have an -OH group at the 2; position on the pentose sugar
How many phosphate groups do nucleotides have?
can vary
can have mono-, di-, or tri-
2,3-cyclic monophosphate derivative
has phosphate in a cyclic structure at bottom of pentose sugar
Forms by ribonucleotide 2’ -OH group attacking the phosphate group to hydrolyze a phosphodiester bond
when add water can get either 2’ or 3’ phosphate
When labeling sugars what is always 1’?
where the nitrogenous base is attached
Phosphodiester linkage
5’ Phosphate attaches itself to 3’ pentose sugar on another nucleotide
5’ end
has an unliked phosphate group
3’ end
has an unliked 3’ OH
Why is DNA more stable than RNA?
The 2’ -OH of RNA makes it easily hydrolyzable in alkaline conditions
Characteristics of DNA double helix
antiparallel and right-handed
has major and minor grooves
hydrophobic core on inner column
negatively charged phosphorous backbone
A form of double helix
right-handed but doesn’t have major and minor grooves
Z form of double helix
left-handed helix
B form of double helix
true form of double helix
right-handed and has major and minor grooves
Palindrome sequence
in DNA, looks the same if we read the sequences backwards or forwards
palindromes can form different shaped structures such as a cruciform
Mirror repeat
sequence that is flipped and repeated on the same side of the strand
RNA sequence
RNA is said to be single stranded
has many complementary sequences that can base pair with its self through intramolecular pairing
RNA has no 1 simple secondary structure
How can DNA denature?
break down H-bonds through heat or changes in pH
Hypochromic effect
absorbance decreases as you go from single stranded to double stranded DNA
there is a lower amount of light that can be absorbed
What causes the hypochromic effect
Single stranded DNA can move an excited electron that absorbs light to the aqueous outer environment
Double stranded DNA has a hydrophobic interior that can not move excited electrons to the outer environment
Hyperchromic effect
denatured DNA absorbs more light than double stranded DNA
going to a state that can absorb more light
Tm
the temperature where 1/2 of DNA is single stranded
as you raise temperature, more DNA denatures and absorbance increases
What happens when you have more GC pairs in a sequence?
you have more H-bonds which makes it harder to denature the double strand
Tm raises since it takes longer for 1/2 of DNA to denature, requires higher temp
Relationship between GC and Tm?
positive linear trend
Nanopore sequencing
As a sequence of DNA moves down a pore, we can get information about which nucleotide is in the pore
Monitor a current that is moving through a pore
The current will change depending on which nucleotide is in the pore
Can read both the sense and antisense strand
Depurination
purines can be hydrolyzed
leaves a nucleotide residue without a nitrogenous base
Deamination
removal of an amine
changes cytosine to uracil (DNA repair mechanisms often detect)
changes 5-methylcytosine can be deaminated to form thymine (repair mechanisms do not often detect)
Thymine dimers
occur when cells recieve UV light
creates a kink in the DNA and trouble replicating
can often lead to cancer
A hairpin can occur in palindromic sequences of DNA or RNA. What is the difference in these structures?
the RNA helix is in the A conformation
the DNA helix is in the B conformation
Why is UV absorption reduced in double stranded helix?
base stacking in double strand reduces the amount of UV absorption
denaturing involved loss of base-stacking and UV absorption increases
Where do you expect to find hairpins and loops?
near the promoter
these structure often contribute to transcription factors binding the promoter
Changes made in the evolution of RNA to DNA
remove 2’ -OH for more stability
change uracil to thymine
make double stranded copy
Other functions of nucleotides
electron carriers like NAD and FAD
energy source like ATP
Coenzyme A
signaling molecule like cAMP
Why is the change from uracil to thymine important in DNA evolution?
now, DNA can detect when cytosine is deaminated to uracil
in RNA, uracil is supposed to be there, so cannot pick. up on this mutation
