Macromolecules

Question 1

Central dogma of biology

Answer 1

DNA - RNA - protein

Question 2

the primary sequence of proteins is held together by

Answer 2

covalent bonds

Question 3

X Ray diffraction data

Answer 3

Rosalind Franklin

Question 4

4 bases of DNA

Answer 4

• Adenine, Guanine, Thymine, Cytosine
• A,G purines
• T, C pyrimidines

Question 5

nucleoside

Answer 5

base + sugar

Question 6

nucleotide

Answer 6

• base + sugar + phosphate

- phosphate addition to the 5’ carbon of ribose sugar

Question 7

Base pairs

Answer 7

• Cytosine always base pairs with Guanosine - 3 H bonds

- Adenosine always base pairs with Thymidine - 2 H bonds

Question 8

When DNA is polymerized

Answer 8

• a triphosphate nucleotide is hydrolyzed between the first and second phosphate, and the resulting monophosphate is added to the hydroxy group on the 3’ carbon of the ribose sugar of the preceding molecule.

Question 9

all bases of DNA linked through

Answer 9

• phosphodiester bond

- backbone of DNA

Question 10

complimentary

Answer 10

• each base in the DNA will bind to its complimentary base on the other strand

Question 11

anti-parallel

Answer 11

• the complimentary strained of 5’ - 3’ is 3’ - 5’

Question 12

Conformations

Answer 12

• the only one we worry about is B DNA

Question 13

B DNA

Answer 13

• right handed double helix

- 10 base pairs per turn

Question 14

Double Stranded DNA conformation

Answer 14

• oriented with the bases facing inward and the phosphodiester bonds exposed
• the planes of the bases stack on top of one another due to hydrophobic interactions

Question 15

The two grooves

Answer 15

• major groove

- minor groove

Question 16

Nuclear packing

Answer 16

• the first step in compacting the DNA is the introduction of supercoils
• bacterial DNA is made with negative supercoiling

Question 17

Topoisomerase 1

Answer 17

• can relieve negative supercoils by nicking one strand of DNA.
• the nick is then sealed without the need for ATP bc energy stored in P-bond is conserved.

Question 18

gyrase

Answer 18

• introduces negative supercoils in an ATP dependent manner

- requires breaking and re-sealing both strands of DNA

Question 19

DNA proteins

Answer 19

• bacteria lack histones, but contain histone-like proteins which will compact DNA further
• IHF
• HU
• H-NS

Question 20

DNA replication in all organisms is

Answer 20

• semi-conservative

- one old strand, one newly synthesized strand

Question 21

All DNA polymerases

Answer 21

• polymerize in the 5’ to 3’ direction
• requires a pre-existing 3’ hydroxyl primer
• add nucleotides to the 3’ -OH strand

Question 22

The replication fork

Answer 22

• leading strand replication - with fork

- lagging strand replication - away from rep fork - make in chunks - Okazaki fragments

Question 23

Pre-priming

Answer 23

• separating the DNA strands
• forming the replication bubble to allow access to the DNA polymerase complex
• occurs at origin of replication and proceeds in both directions
• contains several A+T regions called A- boxes

Question 24

A boxes

Answer 24

• target for DnaA
• about 20 DnaA molecules bind to A-box which then recruit DnaC and DnaB (helicase) then bind the DNA and hold it in the “open” complex

Question 25

Unwinding

Answer 25

• DNA unwound by helicase
• single stranded DNA kept unwound by single stranded binding proteins and protected from nuclease
• unwinding DNA introduces positive supercoils ahead of the replication fork, which must be relieved by DNA gyrase

Question 26

Priming

Answer 26

• Primase synthesizes the RNA primer on the sand, which can then be extended by the DNA polymerase
• leading strand only requires 1 primer
• lagging strand requires primer a lot

Question 27

B-clamp loading

Answer 27

• the clamp moves along the DNA and increases its processivity
• the leading strand only loads once and stays attached
• the lagging strand clamp must load at every Okazaki fragment

Question 28

Synthesis

Answer 28

• DNA synthesis catalyzed by DNA pol III
• leading strand synthesis occurs continuously
• lagging strand synthesis continues until the polymerase encounters the 5’ end of the RNA primer, when it dissociates

Question 29

Proofreading

Answer 29

• Most errors fixed during DNA synthesis
• The DnaQ subunit of the pol III holoenzyme can recognize base mis-matches and cause the polymerase to stall and remove the mis-match via the 3’ - 5’ exonuclease activity
• pol III then inserts the correct base

Question 30

Replacing the primer

Answer 30

• DNA pol I removes the RNA primer and replaces it with DNA

- the nick is then sealed via DNA ligase

Question 31

Termination

Answer 31

• the chromosome contains Ter sequences which only allow replication to occur in one direction.

Question 32

Tus protein

Answer 32

• DNA is bound by the Tus protein such that it is bent
• A DNA rep fork that approaches from the right will halt, however a fork that approaches from the left can proceed terminating DNA synthesis.

Question 33

Chromosome separation

Answer 33

• after termination, the two DNA strands are connected or are concatamers
• The XerC and XerD recombinases bind at the dif locus an resolves the concatamers
• makes a double strand break in the DNA and pass the other strand though, like gyrase

Question 34

Partitioning

Answer 34

• evidence indicates the oriC region of the chromosomes will start to partition because replication is completed.
• Par and Muk bind and walk the chromosomes along the MreB cytoskeleton to the end of the cell.