DNA Manipulation and Replication

Question 1

RNA Structure

Answer 1

Consists of a ribose sugar and a phosphate group attached to the 5’ carbon. A nucleic acid base is attached to the 1’ carbon. RNA bases are AUCG.

Question 2

DNA Structure

Answer 2

Consists of a ribose sugar and a phosphate group attached to the 5’ carbon and a nucleic acid base attached to the 1’ carbon. DNA bases are ATCG.

Question 3

Purines

Answer 3

Consists of the bases G and A, which are two cyclic molecules linked together

Question 4

Pyrimidines

Answer 4

Consists of the bases C, T and U, which are single cyclic molecules.

Question 5

Phosphodiester bond

Answer 5

Bond between a phosphate group and the ribose sugars on either side, links two successive sugar molecules together. (Made up of two esther linkages).

Question 6

Esther Linkage

Answer 6

The bond between the O of the phosphate group and the carbons of the sugar

Question 7

Nucleotides can only be added to the

Answer 7

3’ end. Because the OH on the 3’ end can attack the high energy phosphate bond of the incoming nucleotide - causes synthesis

Question 8

Major groove

Answer 8

A wider, thicker section of double helix

Question 9

Minor Groove

Answer 9

A smaller, thinner section of double helix

Question 10

There are _____ bases per complete turn

Answer 10

10

Question 11

Bases are _______ and the backbone is ________

Answer 11

hydrophobic, hydrophilic

Question 12

Primary Structure of DNA

Answer 12

Order of bases in the DNA strand

Question 13

Watson, Crick, Wilkins

Answer 13

Determined the structure of DNA. Two DNA strands line up in an antiparallel manner, and twist to form a double helix

Question 14

Secondary Structure of DNA

Answer 14

Stabilized by complimentary base pairing and by ‘Base stacking’.

Question 15

Rosalind Franklin

Answer 15

Crystalography of DNA.

Question 16

Chargaff’s Rule

Answer 16

Found that the amount of guanine and is the same as the amount of cytosine, and the amount of adenine is the same as the amount of thymine. Decided they are bonded together. Through radioactive labeling.

Question 17

Pyrophosphate

Answer 17

2 phosphate groups removed from ATP releasing a lot of energy. Coupled with adding incoming nucleotides to the chain

Question 18

Forces stabilizing DNA

Answer 18

H-bonds
Hydrophobic, hydrophilic interactions
‘Base stacking’, or Van der Waals forces
Electrostatic interactions between bases

Question 19

Replication

Answer 19

Two strands of the parental duplex separate at the replication fork. Each parental strand serves as a template for the synthesis of a new daughter strand

Question 20

DNA replication is

Answer 20

Semiconservative

Question 21

Miselson and Staal

Answer 21

Used radioactive material to label and replicated DNA. Two bands were shown which proved that the process was semiconservative.

Question 22

Leading Strand

Answer 22

Can be replicated continuously in the 5’ to 3’ direction

Question 23

Lagging Strand

Answer 23

Is replicated in small segments discontinuously in the 5’ to 3’ direction

Question 24

Okasaki Fragments

Answer 24

Short segments produced on the lagging strand

Question 25

RNA Primase

Answer 25

Lays down primers to start replication, because DNA polymerase needs a free OH group to lay down nucleotides. The primers are removed by a different DNA polymerase

Question 26

Ligase

Answer 26

Ligates the Okasaki fragments together after primers have been removed.

Question 27

Helicase

Answer 27

Unwinds the parental DNA strands

Question 28

Topiosomerase II

Answer 28

Relieves the stress of unwinding - cuts strands of DNA, unwinds it, and sticks it back together

Question 29

Single-strand binding proteins

Answer 29

Stabilizes single strands of DNA, works next to helicase, protects the DNA when its unzipped as single strands

Question 30

DNA Polymerases

Answer 30

There are five, DNA polymerase I and III are the most important. I fills in gaps left by RNA primers and is involved with DNA repair, and III is the main player in replication and has proof-reading abilities. The rest are involved in proof-reading and repair.

Question 31

Replication bubble

Answer 31

Forms around the origin of replication, the replication fork proceeds in both directions from this area

Question 32

Origin of Replication

Answer 32

Eukaryotes have many, and they fuse together when they meet. Prokaryotes have one.

Question 33

Circular DNA

Answer 33

Still has a leading and lagging strand, replication starts at the origin and moves in both directions

Question 34

Telomerase

Answer 34

Contains an RNA template that allows the shortened 3’ end of the template strand to be restored by the addition of more telomere repeats. Present mostly in gametes and stem cells.

Question 35

Telomere

Answer 35

TAG repeating sequences on somatic cells. Needed because the lagging strand has a small section that goes unreplicated in eukaryotes.

Question 36

PCR

Answer 36

Polymerase Chain Reaction. Has three stages, denaturation, annealing and extension. Kary Mullis.

Question 37

Denaturation (PCR)

Answer 37

Solution containing DNA is heated to separate the DNA strands. Intention is to make large amounts of DNA

Question 38

Annealing

Answer 38

Solution is cooled, two primers anneal to their complimentary sequence on the strands of the template duplex

Question 39

Extension

Answer 39

DNA polymerase synthesizes new DNA strands by extending primers in a 5’ to 3’ direction

Question 40

Gel Electrophoresis

Answer 40

DNA molecules are separated by size. Larger molecules move more slowly. DNA moves from the minus end to the plus end

Question 41

Restriction enzymes

Answer 41

Cut DNA in set places, after identifying a specific 6 base sequences. Sticky end is when one end of the DNA cut is longer than the other. Blunt end is the opposite.

Question 42

Restriction Fragments

Answer 42

Pieces of bacterial DNA cut by restriction enzymes

Question 43

Southern Blot

Answer 43

DNA fragments are denatured and then transferred (blotted) onto filter paper. Then placed in a bag containing solution with a single-stranded labeled probe, which sticks to complimentary fragments by hybridization. Filter paper is then exposed to X-ray film. Purpose is to verify that a DNA fragment is what one thinks it is.

Question 44

Sanger Sequencing

Answer 44

Template strand is unknown, purpose is to determine nucleotide sequence. Creation of a daughter strand is stopped when a terminator is incorporated at the 3’ end. Each dideoxynucleotide is labeled with a different florescent dye, and we can find the sequence of daughter strand. Run through gel electro and a detector picks up on each dye as it exits.

Question 45

Recombinant DNA

Answer 45

Donor DNA and vector DNA are both cleaved with the same restriction enzyme, and joined together with DNA ligase. Can be inserted into bacterial population and uptaken through transformation.

Question 46

Gene Editing

Answer 46

Guide RNA binds with Cas9 protein and brings it to the target DNA and the target is cleaved. An exonuclease widens the gap in the target DNA. Editing template is used to repair this gap. Result is edited DNA.

Question 47

Dideoxynucleotide Terminator or Chain Terminator

Answer 47

Lacks an OH group that is needed to add additional nucleotides to the 3’ end. Terminates the creation of a DNA chain.

Question 48

DNA is read in the

Answer 48

3-5 direction

Question 49

DNA is replicated in the

Answer 49

5-3 direction

Question 50

Midochondria and Chloroplasts have…

Answer 50

Circular DNA