Lecture 8: Nucleic Acids

Question 1

What are the 3 parts of a nucleotide?

Answer 1

Nitrogenous base
Pentose sugar
Phosphate groups

Question 2

Two types of nitrogenous bases

Answer 2

Purines

Pyrimidines

Question 3

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

Answer 3

N-B-glycosyl bond

Question 4

Purines

Answer 4

have two rings

A and G are purines

Question 5

Pyrimidines

Answer 5

have one ring

C and T are pyrimidines

Question 6

How many hydrogen bonds can GC pairs make?

Answer 6

3 hydrogen bonds

Question 7

How many hydrogen bonds can AT pairs make?

Answer 7

2 hydrogen bonds

Question 8

Characteristics of nitrogenous bases

Answer 8

weakly basic and hydrophobic

move inside the DNA molecule since hydrophobic

nitrogenous bases can tautomerize which is a potential problem

Question 9

Difference between ribonucleotides and nucleotides?

Answer 9

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

Question 10

How many phosphate groups do nucleotides have?

Answer 10

can vary

can have mono-, di-, or tri-

Question 11

2,3-cyclic monophosphate derivative

Answer 11

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

Question 12

When labeling sugars what is always 1’?

Answer 12

where the nitrogenous base is attached

Question 13

Phosphodiester linkage

Answer 13

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

Question 14

5’ end

Answer 14

has an unliked phosphate group

Question 15

3’ end

Answer 15

has an unliked 3’ OH

Question 16

Why is DNA more stable than RNA?

Answer 16

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

Question 17

Characteristics of DNA double helix

Answer 17

antiparallel and right-handed

has major and minor grooves

hydrophobic core on inner column

negatively charged phosphorous backbone

Question 18

A form of double helix

Answer 18

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

Question 19

Z form of double helix

Answer 19

left-handed helix

Question 20

B form of double helix

Answer 20

true form of double helix

right-handed and has major and minor grooves

Question 21

Palindrome sequence

Answer 21

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

palindromes can form different shaped structures such as a cruciform

Question 22

Mirror repeat

Answer 22

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

Question 23

RNA sequence

Answer 23

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

Question 24

How can DNA denature?

Answer 24

break down H-bonds through heat or changes in pH

Question 25

Hypochromic effect

Answer 25

absorbance decreases as you go from single stranded to double stranded DNA

there is a lower amount of light that can be absorbed

Question 26

What causes the hypochromic effect

Answer 26

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

Question 27

Hyperchromic effect

Answer 27

denatured DNA absorbs more light than double stranded DNA

going to a state that can absorb more light

Question 28

Tm

Answer 28

the temperature where 1/2 of DNA is single stranded

as you raise temperature, more DNA denatures and absorbance increases

Question 29

What happens when you have more GC pairs in a sequence?

Answer 29

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

Question 30

Relationship between GC and Tm?

Answer 30

positive linear trend

Question 31

Nanopore sequencing

Answer 31

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

Question 32

Depurination

Answer 32

purines can be hydrolyzed

leaves a nucleotide residue without a nitrogenous base

Question 33

Deamination

Answer 33

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)

Question 34

Thymine dimers

Answer 34

occur when cells recieve UV light

creates a kink in the DNA and trouble replicating

can often lead to cancer

Question 35

A hairpin can occur in palindromic sequences of DNA or RNA. What is the difference in these structures?

Answer 35

the RNA helix is in the A conformation

the DNA helix is in the B conformation

Question 36

Why is UV absorption reduced in double stranded helix?

Answer 36

base stacking in double strand reduces the amount of UV absorption

denaturing involved loss of base-stacking and UV absorption increases

Question 37

Where do you expect to find hairpins and loops?

Answer 37

near the promoter

these structure often contribute to transcription factors binding the promoter

Question 38

Changes made in the evolution of RNA to DNA

Answer 38

remove 2’ -OH for more stability
change uracil to thymine
make double stranded copy

Question 39

Other functions of nucleotides

Answer 39

electron carriers like NAD and FAD
energy source like ATP
Coenzyme A
signaling molecule like cAMP

Question 40

Why is the change from uracil to thymine important in DNA evolution?

Answer 40

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