Nuclei Acid Structure and Chromosomes

Question 1

how are nucleic acids formed?

Answer 1

5’-P is esterified by 3’-OH of another nucleotide to form a phosphodiester bond

Question 2

what results from the nature of phosphodiester bonds?

Answer 2

• DNA and RNA have polarity/non-symmetrical bond

Question 3

what direction is DNA written in?

Answer 3

5’ to 3’ direction

Question 4

how are nucleic acids named?

Answer 4

• name bases using one letter code in 5’ to 3’ direction

Question 5

what observations helped solve the structure of DNA? (4)

Answer 5

1. Franklin: X-ray image suggested double helix structure
2. Chargott rules: A = T =/= G = C
3. Donohue: A-T (2-H bonds) and G-C (3-H bonds) can form H-bonds
4. Furberg: bases are at right angles to sugars

Question 6

what is the orientation and composition of the DNA helix? (2)

Answer 6

• DNA is a right handed double helix

- composed of polynucleotide chains

Question 7

define how the DNA strands are complementary (2)

Answer 7

• A pairs with T; G pairs with C

- the sequence of one strand determines the sequence of the other

Question 8

define how the DNA strands are anti-parallel

Answer 8

• the DNA strands run in opposite directions

- one is 5’ -> 3’ and the second is 3’ -> 5’

Question 9

what are the two ways that describe how DNA strands are oriented with each other? (2)

Answer 9

• the 2 DNA strands are complementary

- the 2 stands are anti-parallel

Question 10

what components of DNA are on the outside/inside?

Answer 10

• sugar phosphate backbone is on the outside - - the bases are on the inside of the helix

Question 11

how are bases oriented to the DNA helix axis?

Answer 11

• bases are almost perpendicular to the helix axis

Question 12

how much are DNA bases separated by?

Answer 12

• separated by 3.4 A

Question 13

how long is the repeating DNA helix section and how many bases are in each turn of these repeating DNA helixes? (2)

Answer 13

• repeats itself every 34 A

- 10.5 bases per turn of helix

Question 14

what is the diameter of the DNA helix?

Answer 14

• 20 A

Question 15

what are the three known forms of DNA?

Answer 15

1. B-DNA
2. A-DNA
3. Z-DNA

Question 16

what is the form of carbon in the sugars of B-DNA?

Answer 16

• C-2’ form of sugar

Question 17

how is B-DNA generally characterized? (3)

Answer 17

• hydrated DNA
• most abundant form of DNA
• geometry describes “relaxed state” of DNA

Question 18

how is A-DNA generally characterized?

Answer 18

• dehydrated DNA that is essentially a squished version of B-DNA

Question 19

how is Z-DNA generally characterized?

Answer 19

• unstable and transient, making it hard to isolate or study

Question 20

what forces hold DNA together? (4)

Answer 20

1. H-bonds between bases (A-T, C-G)
2. stacking of bases
3. hydrophobic interactions
4. electrostatic repulsion of phosphates

Question 21

how do proteins access DNA bases? (2)

Answer 21

• major groove

- minor groove

Question 22

what groove do proteins interact with more often and why?

Answer 22

• major groove because more functional groups are exposed here

Question 23

how do proteins interacts with DNA?

Answer 23

• via H-bonds between size chains of amino acids and bases

Question 24

what are the characteristics of RNA? (2)

Answer 24

• usually single stranded, but some parts can be double stranded
• can have very complex structure

Question 25

DNA denaturation

Answer 25

- separation of DNA strands

Question 26

how can DNA be denatured? (2)

Answer 26

- increasing temperature (easiest) | - changing pH

Question 27

what determines the melting temperature of DNA?

Answer 27

- the temperature where half of the DNA molecule is single stranded

Question 28

DNA renaturation

Answer 28

- previously denatured strands will reanneal to form original DNA molecule if conditions are reverted back to normal

Question 29

linking number (2)

Answer 29

- how many times strands are wrapped around each other | - changing the linking number in DNA will create supercoils

Question 30

overwinding DNA (2)

Answer 30

- positive supercoils | - increase in the linking number

Question 31

underwinding DNA (2)

Answer 31

- negative supercoils | - decreases linking number

Question 32

topoisomerase

Answer 32

- enzymes that change topology/linking number of DNA

Question 33

whats are some of topoisomerases' functions (2)

Answer 33

- primary way of packing DNA for bacteria's circular genomes - implication in DNA replication and transcription where separation of strands creates supercoils that need to be resolved

Question 34

type I topoisomerases (2)

Answer 34

- change linking number by +/- 1 | - does not require ATP

Question 35

how do type I topoisomerases function? (3)

Answer 35

1. make a ss break in DNA using tyrosine as a catalyst 2. pass second strand through ss break 3. reseal ss break

Question 36

type II topoisomerases (2)

Answer 36

- change linking number by +/- 2 | - require 2 molecules of ATP

Question 37

how do type II topoisomerases function? (3)

Answer 37

- making ds break - pass dsDNA fragment through dsDNA break - broken DNA is re-ligated and 2nd DNA segment is released

Question 38

bacterial DNA gyrase

Answer 38

- type of type II topoisomerase that decreases linkage number by 2

Question 39

how is DNA packaged in bacteria? (2)

Answer 39

- circular genome with supercoils created by topoisomerases | - histone-like proteins help DNA supercoiling

Question 40

how is DNA packaged in eukaryotes? (2)

Answer 40

- DNA forms complex with proteins to form chromatin | - chromatin is further packaged into chromosomes

Question 41

nucleosomes (2)

Answer 41

- basic unit of chromatin | - made up of DNA "wrapped" around histones

Question 42

histones (2) - composition - function of composition

Answer 42

- contain high percentage of basic amino acids, lysine and arginine - lys and arg allow electrostatic interactions to form between histones and negatively charge DNA