Nucleotides and Nucleic Acids

Question 1

Nucleic Acid

Answer 1

The polymer of nucleotides, sugar + base + phosphate, DNA/RNA

Question 2

DNA

Answer 2

Double helix containing genetic information

Question 3

RNA

Answer 3

Responsible for protein synthesis

Question 4

Nucleotide

Answer 4

Base + sugar + phosphate

Question 5

Nucleoside

Answer 5

Base + sugar

Question 6

Deoxynucleoside

Answer 6

Nucleotide with a deoxyribose sugar

Question 7

Base

Answer 7

Adenine, Guanine, Cytosine, Thymine, Uracil

Question 8

Purines

Answer 8

Adenine, Guanine

Question 9

Pyrimidines

Answer 9

Thymine, Cytosine, Uracil

Question 10

Anti-Parallel

Answer 10

2 biopolymers that run parallel to each other but with opposite directionality

Question 11

Kb

Answer 11

Kilobase - the unit of measurement equal to 1000 base pairs of DNA or nucleotides in RNA

Question 12

Oligonucleotide

Answer 12

Short DNA or RNA molecules (<50)

Question 13

B-DNA

Answer 13

Right-handed double helix (most common)

Question 14

Stacking Interactions

Answer 14

The primary stabilizing force of DNA

• Van der Waals
• Hydrophobic forces

Question 15

Melting Temperature (DNA)

Answer 15

The temperature at which half of the DNA strands are in the random coil or single-stranded state

Question 16

Denaturation

Answer 16

Destroy the characteristic properties of a macromolecule by heat, acidity, etc

Question 17

Renaturation

Answer 17

Reconstruction of protein/nucleic acid that has been denatured such that molecules resume normal function

Question 18

Anneal

Answer 18

Recombine DNA in double-stranded form following separation from heat

Question 19

Draw Uracil

Answer 19

Check Structures Sheet

Question 20

Draw Thymine

Answer 20

Check Structures Sheet

Question 21

Draw Cytosine

Answer 21

Check Structures Sheet

Question 22

Draw Adenine

Answer 22

Check Structures Sheet

Question 23

Draw Guanine

Answer 23

Check Structures Sheet

Question 24

Draw Ribose

Answer 24

Check Structures Sheet

Question 25

Draw Deoxyribose

Answer 25

Check Structures Sheet

Question 26

Where is N Located on a Base?

Answer 26

Odd numbers (1,3,7,9)

Question 27

Where Do Bases Link to Sugar?

Answer 27

``` Pyrimidines = link to sugar C1' from N1 Purines = link to sugar C1' from N9 ```

Question 28

Naming Nucleosides

Answer 28

Pyrimidines = end in idine Purines = -ine -> -osine If the sugar is deoxyribose, put deoxy in front

Question 29

Phosphoester

Answer 29

Link carbon to a phosphate group

Question 30

Phosphodiester

Answer 30

Link two different carbons to one phosphate group

Question 31

Phosphoanhydrides

Answer 31

Link two phosphates to each other

Question 32

Properties of the Backbone in DNA/RNA

Answer 32

Consistent negative charge | Polar

Question 33

Is the DNA or RNA Backbone more Polar?

Answer 33

The RNA backbone is more polar because of the 2'OH group on the ribose sugar

Question 34

Why is RNA More Susceptible to Alkaline Hydrolysis?

Answer 34

Because of the 2'OH group on the ribose sugar

Question 35

Is DNA or RNA more Stable?

Answer 35

DNA

Question 36

What are the Forces Involved in Stacking Interactions?

Answer 36

Hydrophobic effect Van der Waals Forces Ionic interactions

Question 37

Chargaff's Rule

Answer 37

A=T and G=C Helps to deduce base composition Maintains the diameter in DNA double helix

Question 38

How is B-form DNA stabilized?

Answer 38

Primarily base stacking (Van der Waals and hydrophobic forces) Hydrogen bonding -AT = 2 H-bonds -GC = 3 H-bonds

Question 39

Why is it Important for DNA to be Stabilized by Non-Covalent Forces?

Answer 39

Covalent bonds are rigid and would not allow DNA to function Non-covalent bonds are strong enough to hold DNA together but attractive forces can be weakened to adapt to environmental changes

Question 40

B-form DNA Structure

Answer 40

Strands are anti-parallel with an overall right-handed twist Hydrophobic core and polar exterior Bases largely excluded from H2O = stabilizes H-bonds Sugar and phosphate exposed to H2O H-bonds in pairing interactions Base pairs are complements of each other Has grooves

Question 41

Function of Grooves

Answer 41

There are functional groups on the edge of base pairs that are exposed to water - important for proteins that must bind to dsDNA and read a sequence - major grooves have enough space for an alpha protein to bind

Question 42

RNA vs DNA sequence

Answer 42

RNA is single-stranded, DNA is double-stranded RNA contains uracil, DNA contains thymine RNA contains ribose, DNA contains deoxyribose

Question 43

What Causes the Denaturation of dsDNA

Answer 43

Disruption of non-covalent forces | -separates two paired strands

Question 44

DNA Melting

Answer 44

Goes from double-stranded to denatured single-stranded Absorbance changes as DNA melts = base stacking changes -ssDNA has a higher absorbance than dsDNA

Question 45

What is Tm?

Answer 45

The midpoint of melting and is a characteristic of the base composition and solvent conditions

Question 46

Hyperchromicity

Answer 46

High absorbance (ssDNA)

Question 47

Hypochromicity

Answer 47

Low absorbance (dsDNA)

Question 48

Renaturation

Answer 48

Reformation of dsDNA so it regains its native conformation - proper base pairing - nucleation and zippering

Question 49

Why do GC pairs have stronger base stacking interactions than AT pairs?

Answer 49

GC pairs are bigger and wider Therefore, AT pairs denature more readily Higher GC content results in elevated Tm

Question 50

How does Changing pH Affect Tm?

Answer 50

Affects the protonation state of DNA

Question 51

Draw a pH-Tm Graph

Answer 51

See Cheat Sheet

Question 52

How does Changing [Salt] Affect Tm?

Answer 52

Ions shield negative charges on phosphate backbone Low salt decreases Tm = destabilizes double helix High salt elevates Tm = stabilizes double helix

Question 53

RNA Melting

Answer 53

2x the H-bonds = higher Tm than DNA | ss + ds mixture