Nucleic Acids

Question 1

What are some functions of nucleic acids?

Answer 1

Information storage, information transmission, catalysis, regulation

Question 2

What 3 components make up a nucleotide?

Answer 2

Nitrogenous base, pentose sugar, phosphates

Question 3

What are the bases of nucleic acids made of? Are they acidic or basic?

Answer 3

Aromatic heterocyclic rings that are planar and rigid, and have hydrophobic faces with polar edges. They are weakly basic

Question 4

What is the difference between a purine and pyrimidine?

Answer 4

Purines are A and G and are a five membered ring fused to a six membered ring. Pyrimidines are C, T and U and are a 6 membered ring

Question 5

What is a nucleoside?

Answer 5

The base and the sugar ring, but no phosphates

Question 6

What is attached to each of the carbons in the 5 membered sugar ring?

Answer 6

The base is attached to the 1’ carbon. The 2’ carbon has an OH attached if the sugar is ribose, and an H if the sugar is deoxyribose. The 3’ carbon has an OH. The 4’ carbon is attached to the 5’ carbon. The 5’ carbon is attached to the phosphate

Question 7

What type of bonds join phosphates together in a nucleotide?

Answer 7

Phosphoanhydride bonds

Question 8

What type of bonds join nucleotides together?

Answer 8

Phosphodiester bonds

Question 9

Why do nucleic acid strands have directionality?

Answer 9

One end has a free 5’ phosphate and the other end has a free 3’ OH

Question 10

What are the Watson-Crick base pairs?

Answer 10

G-C and A-T

Question 11

Which direction does the DNA double helix turn?

Answer 11

Right handed

Question 12

Why is it important that the helix is held together by non-covalent interactions?

Answer 12

The helix needs to be disrupted for the information to be read and transcripted

Question 13

What is base stacking?

Answer 13

The hydrophobic faces of the bases stack up really close together and form hydrophobic interactions to get away from the water

Question 14

What is the difference between the major groove and the minor groove in DNA?

Answer 14

The major groove is deeper and wider than the minor groove

Question 15

How do DNA binding proteins tell the difference between the major and minor groove of DNA?

Answer 15

In the major groove, the edge that faces out looks different for each base pairing. An AT looks different from a TA and a CG looks different than a GC. In the minor groove, AT and TA look the same, and so does CG and GC

Question 16

Why is the ability to recognize the differences in the bases in the major groove important?

Answer 16

It allows proteins to read the sequence of the DNA without opening the helix, so they can bind in the right place

Question 17

How is DNA compacted into cells?

Answer 17

Supercoiling and looping (in prokaryotes) and binding to histones in eukaryotes

Question 18

What causes DNA to denature?

Answer 18

Heat, it disrupts the hydrogen bonds and the base stacking

Question 19

What happens to DNA when it is denatured?

Answer 19

Separates into single strands

Question 20

Why is it critical that DNA denaturation is reversible?

Answer 20

The helix needs to be melted and unwound for the information to be read, but that information still needs to be stored so it needs to go back to the more stable double helix once the information has been read

Question 21

What is hyperchromicity?

Answer 21

Monitoring the melting of DNA

Question 22

What is the transition temperature?

Answer 22

The temperature where half of the DNA is melted and half is still in the double helix

Question 23

How can we tell if a strand of DNA is denatured?

Answer 23

Double stranded DNA absorbs less UV light at 260 nm than single stranded DNA

Question 24

How can the sequence of DNA affect its transition temperature?

Answer 24

A sequence with more GC will have a higher melting point

Question 25

Why is RNA unable to form a double helix like DNA?

Answer 25

The 2' OH on the sugar ring

Question 26

What is RNA with enzymatic activity called?

Answer 26

Ribozymes

Question 27

How does RNA fold into hairpin structures?

Answer 27

Short regions with complementary base pairing within inverted repeat sequences

Question 28

Can RNA only use Watson-Crick base pairs?

Answer 28

No, it has more pairings as long as the hydrogen bonds line up. Can pair up G and U, G and A

Question 29

What bases can be found in RNA?

Answer 29

A,C,G, U mainly. Some contain modified bases and some have thymine

Question 30

Why is RNA less stable than DNA?

Answer 30

The 2' OH acts as an internal nucleophile that can assist base-catalyzed hydrolysis of a phosphodiester bond to form cyclic nucleotides that break apart the molecule

Question 31

What feature of nucleic acids allows DNA to be copied and transcribed into RNA?

Answer 31

Base complementarity

Question 32

What are the building blocks used in the synthesis of DNA?

Answer 32

dNTPs - deoxynucleotide triphosphates

Question 33

What are the building blocks used in the synthesis of RNA?

Answer 33

NTPs - nucleotide triphosphates

Question 34

When does a nucleotide become a nucleotide residue?

Answer 34

When the NTP has lost two of its phosphates from being attached to the growing nucleic acid chain

Question 35

What 3 things does DNA polymerase require to synthesize DNA?

Answer 35

A 3' OH, dNTPs, and a template strand

Question 36

Why does DNA polymerase require a primer to start synthesizing?

Answer 36

Needs a 3' OH to begin, can't start the strand without that

Question 37

Which strand of DNA contains the coding information?

Answer 37

The coding strand/sense strand

Question 38

What strand of DNA doesn't contain any coding information?

Answer 38

The template strand/anti-sense strand. It has complementary base pairing with the coding strand

Question 39

Which strand of DNA does the RNA transcript resemble?

Answer 39

The coding strand. The sequence is the same except that all T are replaced with U

Question 40

Which strand does RNA polymerase read to synthesize the RNA transcript? Which direction does it read it in?

Answer 40

The template strand is read in the 3' to the 5' direction, and the RNA is synthesized 5' to 3'

Question 41

What is the adaptor molecule that decodes the mRNA to determine which amino acid to add during translation?

Answer 41

tRNA, the one with the right anti-codon sequence is the one that will bind to the mRNA

Question 42

What is a tRNA with an amino acid attached called?

Answer 42

Amino-acyl tRNA

Question 43

What does the ribosome attach the growing peptide chain to when another amino acid is brought in?

Answer 43

The incoming tRNA with the correct anticodon for the next codon on the mRNA

Question 44

What are 8 possible changes to the structure of DNA that can cause mutations?

Answer 44

- Depurination - Deamination - Single or double strand breaks - Base oxidation - Thymine dimers - Bulky adduct - Base mismatch - Base alkylation

Question 45

What damage does UV radiation do to DNA?

Answer 45

Thymine dimers that distort the DNA double helix and stall replication

Question 46

What damage does ionizing radiation and free radicals do to DNA?

Answer 46

Cleavage of the DNA backbone, which causes strand breaks

Question 47

What damage does nitrous acid do to DNA?

Answer 47

Causes oxidative deamination and converts a cytosine to a uracil and an adenine to a hypoxanthine

Question 48

Why does DNA use thymine instead of cytosine?

Answer 48

So that DNA repair mechanisms can differentiate between a deaminated cytosine and something that is actually supposed to base pair with adenine