DNA Structure & Replication

Question 1

Conservative model of DNA replication

Answer 1

Parental DNA strand creates a separate identical daughter strand. There is no sharing between the two.

Question 2

Semiconservative DNA replication

Answer 2

The parental DNA splits in half and creates two daughter DNAs that share one half a new strand, one half old strand.

Question 3

Dispersive DNA replication

Answer 3

The parental DNA splits into two collection of pieces which are filled with new DNA pieces. All daughter strands contain bits and pieces of the parental strand.

Question 4

Meselson-Stahl “The Most Beautiful Experiment”

Answer 4

In 1958, Matthew Meselson and Frank Stahl figured out which of the three models of DNA replication was correct using heavy N15 labeled DNA and N14 amino acids. They then put the DNA in a centrifuge with test tubes to see what pattern would arise.

Question 5

Nucleophile attack

Answer 5

When a strongly electronegative atom such as oxygen attacks, a less electronegative atom

Question 6

Hydrolysis reaction

Answer 6

When a nucleophile is part of a water molecule

Question 7

Gamma phosphoryl

Answer 7

What is attacked in ATP hydrolysis and results in ADP + P1

Question 8

Nucleophilic substitution

Answer 8

The three prime oxygen in a DNA backbone attacks the alpha phosphoryl group of the incoming dNTP

Question 9

DNA polymerase III

Answer 9

Holds base pairs in place and creates the correct chemical environment so that synthesis reaction can occur. The hand thing.

Question 10

DNA polymerase palm

Answer 10

The active site and the proofreading site

Question 11

DNA polymerase fingers

Answer 11

Grip incoming dNTP and create a 90° bend in template DNA

Question 12

DNA polymerase thumb

Answer 12

Interacts with newly synthesized DNA to stabilize the primer and maintains contact with the primer. It also stabilizes DNA and increases processivity.

Question 13

Processivity

Answer 13

The rate at which we can add nucleotides, the rate of replication

Question 14

Kinetic pause

Answer 14

Allows for time to move from active site to proofreading site

Question 15

Replication fork

Answer 15

The active area of DNA were replication takes place

Question 16

Leading strand

Answer 16

The piece of DNA that is being replicated in a continuous manner

Question 17

Lagging strand

Answer 17

The piece of DNA that is being replicated in a discontinuous manner

Question 18

Okazaki fragment

Answer 18

The peace of DNA that is replicated onto the lagging strand

Question 19

Topoisomerase

Answer 19

The protein that is used to untwist helical DNA, it relieves overwhelmed DNA making sure it is ready to be opened up. It does this by making a small cut in one of the two DNA strands then resealing it

Question 20

Helicase

Answer 20

The protein that opens up DNA for replication. It uses ATP to break the hydrogen bonds between DNA.

Question 21

Beta sliding clamp

Answer 21

The protein attached to polymerase III that increases processivity and allows replication to speed up in a controlled way

Question 22

DNA polymerase I

Answer 22

The polymerase that removes RNA primers in the processing of DNA after replication

Question 23

SSB or single-stranded binding protein

Answer 23

Protects the part of the lagging strand that’s not being replicated yet. Keeps DNA from attaching to itself

Question 24

Clamp loader

Answer 24

Uses ATP to attach the beta clamp to DNA to help increase processivity

Question 25

DNA primase

Answer 25

Places in RNA primer so that DNA has a 3’ location to build from

Question 26

RNA primer

Answer 26

Provides a 3’ location so that DNA replication can happen as DNA must be built 3’ to 5’

Question 27

DNA ligase

Answer 27

Seals the nick in the DNA backbone left behind after polymerase I replaces RNA primers with DNA

Question 28

DNA and RNA composition

Answer 28

Phosphate, pentos sugar, nitrogenous base

Question 29

Nucleoside

Answer 29

Just the base and a sugar

Question 30

Nucleotide

Answer 30

The base, sugar and five prime phosphate in a DNA structure

Question 31

Pyrimidine

Answer 31

Uracell, cytosine, and thymine

Question 32

Purine

Answer 32

Adenine, and guanine

Question 33

DNA consists of

Answer 33

A pento sugar, a phosphate, and a nitrogenous base

Question 34

What are the four DNA nucleotides?

Answer 34

Deoxyadenosine, deoxyguanosine, deoxythymidine, deoxycytidine

Question 35

Phosphodiester bond

Answer 35

The phosphate that is bonded between two pinto sugars in the DNA backbone

Question 36

Chromosome

Answer 36

Higher order structures of DNA and protein

Question 37

Chromatin

Answer 37

A region of DNA and its associated proteins

Question 38

DNAase I

Answer 38

A nuclease that digests unprotected DNA

Question 39

Heterochromatin

Answer 39

Highly condensed, gene poor, transcriptionally inactive sections of DNA

Question 40

Euchromatin

Answer 40

Less condensed, Gene rich, transcriptionally active sections of DNA

Question 41

Chromatin remodeling complexes or CRCs

Answer 41

ATP dependent, multi-protein complexes that catalyze nucleosome sliding, exchange, and transfer. Allow us to change the histone core. Their primary use is to alter structure.