Ch. 10 and 12 (DNA Structure and Replication)

Question 1

describe the structure of DNA

Answer 1

Two COMPLEMENTARY and ANTIPARALLEL complementary nucleotide strands that form a double helix

Question 2

what is the “central dogma”?

Answer 2

DNA –> RNA –> PROTEIN
DNA (transcription) –> RNA (translation) –> PROTEIN

• all information used to instruct the development of an organism is housed in the DNA
• theres way more info in DNA than we can ever use at any one time

Question 3

what is the primary structure of DNA?

Answer 3

string of nucleotides joined together by phosphodiester linkages/bonds
(DNA is a “polymer”)

Question 4

what is the secondary structure of DNA?

Answer 4

DNA’s stable 3 dimensional structure (watson and crick’s helical structure)

Question 5

what is the tertiary structure of DNA?

Answer 5

complex packing of DNA into chromosomes

Question 6

what makes up a nucleotide?

Answer 6

5 CARBON SUGAR
contains either ribose (RNA) or deoxyribose (DNA)
-both are pentose sugars, 5 carbons numbered 1’-5’
-ribose (has hydroxyl group on 2’ carbon - OH)
-deoxyribose (has H group on 2’ carbon)

NITROGENOUS BASE
purines and pyrimidines (attach to the 1’ carbon of the pentose sugar)

PHOSPHATE GROUP
(attach to 5’ carbon of pentose sugar)
-phosphates are negatively charged, accumulate negative charges on DNA molecules

Question 7

what are purines?

Answer 7

• 2 ring structure
• Adenine + Guanine

“pure as gold”

Question 8

what are pyrimidines?

Answer 8

• 1 ring structure
  Cytosine + Thymine (dna) + Uracil (rna)

“Cut The Pyramid”

Question 9

in which way does DNA grow?

Answer 9

always 5’ –> 3’

covalent bonds between 5’ phosphate of one nucleotide and 3’ carbon of next nucleotide

Question 10

how many bonds to A-T nitrogenous base pairs have?

Answer 10

2 hydrogen bonds

Question 11

how many bonds do G-C nitrogenous base pairs have?

Answer 11

3 hydrogen bonds

Question 12

what do phosphodiester linkages do?

Answer 12

connects 5’ phosphate with 3’ OH (forms phosphodiester backbone)

Question 13

what is the difference between hydrogen and covalent bonds?

Answer 13

covalent bonds (like gluing together) stronger, phosphodiester backbone

hydrogen bonds (like magnets) weaker, allow separation of DNA strands

Question 14

how many amino acids are there to make up proteins?

Answer 14

20

Question 15

what did Edwin Chargaff find?

Answer 15

the amounts of the four bases of DNA varied between species, but their ratios did not
“Chargaff’s rule”
- # G = # C
- # A = # T

Question 16

what are dNTP’s?

Answer 16

“deoxyribonucleotide triphosphates”

• building blocks of DNA
• 3 phosphates (alpha, beta, and gamma)
• alpha binds, beta and gamma are lost

Question 17

how are dNTP’S added to a growing strand of DNA?

Answer 17

they are added to the free 3’-OH by “DNA polymerases”
always 5’ –> 3’
NEVER ADD TO 5’
ALWAYS ADD TO 3’

Question 18

what are some requirements of DNA replication?

Answer 18

1. high fidelity (no errors)
2. once and only once per cell cycle (avoid re-replication)
3. complete (entire genome must be copied)

Question 19

define “semiconservative” replication

Answer 19

• the way we replicate our DNA
• each strand serves as a template
• each of the original strands remain intact
• each DNA molecule is half (semi) conserved during replication
• each new strand is half original/half new
• replicates BIDIRECTIONALLY

Question 20

define “origin of replication”

Answer 20

• different spots on chromosomes where you begin DNA synthesis
• origin of replication is recognized by the “origin recognition complex” (ORC)

Question 21

how many origins of replication do bacteria have? eukaryotes?

Answer 21

eukaryotes - multiple origins of replication (need to replicate fast enough for large/complex organism)
bacteria - one origin of replication

Question 22

what does DNA helicase do?

Answer 22

opens up the double helix of DNA, begins unwinding

Question 23

what are single stranded binding proteins?

Answer 23

hold open the DNA and keep it form closing in on itself so replication can occur (naturally wants to close in on itself, doesn’t like to be single stranded)

Question 24

what is a topoisomerase?

Answer 24

relaxes the torsion caused by unwinding of DNA

gyrase in bacteria

Question 25

what is primase?

Answer 25

special kind of RNA polymerase used only in DNA replication

-synthesizes primers (small RNA’s, 10-12 nucleotides long)

Question 26

what do primers do?

Answer 26

short stretches of RNA 10-12 nucleotides long
prime DNA stretches to allow for DNA syntheses
(make leading/lagging strands)

-gets a 3’ OH ready for DNA polymerase to add onto

Question 27

what does DNA polymerase do?

Answer 27

• carries a 5’ –> 3’ exonuclease activity

- eats away RNA primers, replaces them with real DNA

Question 28

what does DNA ligase do?

Answer 28

every time primer segment gets eaten away by DNA polymerase, fills in breaks in sugar backbone
-fills in “nicks”

Question 29

what is significant about the helical structure of DNA?

Answer 29

forms major and minor grooves
-keeps DNA rungs with consistent widths
-(ex. checkpoints sense when there is a bulge, incorrect base pairing, imperfect helical shape)
DNA IS VERY STABLE
major groove usually houses more proteins because it is bigger

Question 30

what did Griffith discover? how?

Answer 30

the principle of transformation
isolated 2 strains of strep and injected into mice
1. rough (type IIR) non virulent
2. smooth (type IIIS) virulent

injected heat killed IIIS into mice and the mice lived!
injected heat killed IIIS with IIR = mice died
dead IIIS regenerated itself when mixed with living IIR

Question 31

what did Avery, McCloud, and McCarty discover?

Answer 31

they discovered that the “transforming principle” is DNA

-only DNA has the ability to transform

Question 32

telomere shortening

Answer 32

usually associated with age
-telomeres shorten over time,may eat away important DNA as telomeres become shorter due to years and years of DNA replication