Lecture 8: Nucleic Acids Flashcards

1
Q

What are the 3 parts of a nucleotide?

A

Nitrogenous base
Pentose sugar
Phosphate groups

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2
Q

Two types of nitrogenous bases

A

Purines

Pyrimidines

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3
Q

What type of bond links the nitrogenous base to the pentose sugar?

A

N-B-glycosyl bond

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4
Q

Purines

A

have two rings

A and G are purines

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5
Q

Pyrimidines

A

have one ring

C and T are pyrimidines

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6
Q

How many hydrogen bonds can GC pairs make?

A

3 hydrogen bonds

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7
Q

How many hydrogen bonds can AT pairs make?

A

2 hydrogen bonds

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8
Q

Characteristics of nitrogenous bases

A

weakly basic and hydrophobic

move inside the DNA molecule since hydrophobic

nitrogenous bases can tautomerize which is a potential problem

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9
Q

Difference between ribonucleotides and nucleotides?

A

ribonucleotides have an -OH group at the 2; position on the pentose sugar

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10
Q

How many phosphate groups do nucleotides have?

A

can vary

can have mono-, di-, or tri-

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11
Q

2,3-cyclic monophosphate derivative

A

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

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12
Q

When labeling sugars what is always 1’?

A

where the nitrogenous base is attached

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13
Q

Phosphodiester linkage

A

5’ Phosphate attaches itself to 3’ pentose sugar on another nucleotide

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14
Q

5’ end

A

has an unliked phosphate group

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15
Q

3’ end

A

has an unliked 3’ OH

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16
Q

Why is DNA more stable than RNA?

A

The 2’ -OH of RNA makes it easily hydrolyzable in alkaline conditions

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17
Q

Characteristics of DNA double helix

A

antiparallel and right-handed

has major and minor grooves

hydrophobic core on inner column

negatively charged phosphorous backbone

18
Q

A form of double helix

A

right-handed but doesn’t have major and minor grooves

19
Q

Z form of double helix

A

left-handed helix

20
Q

B form of double helix

A

true form of double helix

right-handed and has major and minor grooves

21
Q

Palindrome sequence

A

in DNA, looks the same if we read the sequences backwards or forwards

palindromes can form different shaped structures such as a cruciform

22
Q

Mirror repeat

A

sequence that is flipped and repeated on the same side of the strand

23
Q

RNA sequence

A

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

24
Q

How can DNA denature?

A

break down H-bonds through heat or changes in pH

25
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
26
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
27
Hyperchromic effect
denatured DNA absorbs more light than double stranded DNA going to a state that can absorb more light
28
Tm
the temperature where 1/2 of DNA is single stranded as you raise temperature, more DNA denatures and absorbance increases
29
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
30
Relationship between GC and Tm?
positive linear trend
31
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
32
Depurination
purines can be hydrolyzed leaves a nucleotide residue without a nitrogenous base
33
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)
34
Thymine dimers
occur when cells recieve UV light creates a kink in the DNA and trouble replicating can often lead to cancer
35
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
36
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
37
Where do you expect to find hairpins and loops?
near the promoter these structure often contribute to transcription factors binding the promoter
38
Changes made in the evolution of RNA to DNA
remove 2' -OH for more stability change uracil to thymine make double stranded copy
39
Other functions of nucleotides
electron carriers like NAD and FAD energy source like ATP Coenzyme A signaling molecule like cAMP
40
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