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Flashcards in Macromolecules Deck (34):
1

Central dogma of biology

DNA - RNA - protein

2

the primary sequence of proteins is held together by

covalent bonds

3

X Ray diffraction data

Rosalind Franklin

4

4 bases of DNA

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

5

nucleoside

base + sugar

6

nucleotide

- base + sugar + phosphate
- phosphate addition to the 5' carbon of ribose sugar

7

Base pairs

- Cytosine always base pairs with Guanosine - 3 H bonds
- Adenosine always base pairs with Thymidine - 2 H bonds

8

When DNA is polymerized

- 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.

9

all bases of DNA linked through

- phosphodiester bond
- backbone of DNA

10

complimentary

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

11

anti-parallel

- the complimentary strained of 5' - 3' is 3' - 5'

12

Conformations

- the only one we worry about is B DNA

13

B DNA

- right handed double helix
- 10 base pairs per turn

14

Double Stranded DNA conformation

- 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

15

The two grooves

- major groove
- minor groove

16

Nuclear packing

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

17

Topoisomerase 1

- 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.

18

gyrase

- introduces negative supercoils in an ATP dependent manner
- requires breaking and re-sealing both strands of DNA

19

DNA proteins

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

20

DNA replication in all organisms is

- semi-conservative
- one old strand, one newly synthesized strand

21

All DNA polymerases

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

22

The replication fork

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

23

Pre-priming

- 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

24

A boxes

- 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

25

Unwinding

- 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

26

Priming

- 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

27

B-clamp loading

- 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

28

Synthesis

- 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

29

Proofreading

- 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

30

Replacing the primer

- DNA pol I removes the RNA primer and replaces it with DNA
- the nick is then sealed via DNA ligase

31

Termination

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

32

Tus protein

- 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.

33

Chromosome separation

- 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

34

Partitioning

- 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.