Lecture 3 Flashcards Preview

Undeleted > Lecture 3 > Flashcards

Flashcards in Lecture 3 Deck (56):
0

Most errors are corrected by

proofreading and DNA repair
post-relication repair mechanism

only 1 mistake every 10^9 base pair, 3 nucleotides every cell division

1

what must have low mutiation rate to maintain speciese?

germ cells

2

What needs to have low mutation rates to avoid uncontrolled proliferation/ cancer?

somatic cells

3

What synthesize DNA by catalyzing

DNA plymerase

4

the following reaction is catalyzed

DNAn residues + dNTP ---> (DNAn+1 residues + P2O7^4-

5

How is the new DNA strand made?

template directed

6

What must be seperated for replication?

two parental strands

7

What does DNA replications require? 4 thins

dATP
dGTP
dCTP
dTTP

8

What needds a primer with a 3' -OH to begin?

DNA polymerase

9

DNA feeds through the .... during replication

polemerase

10

Both strands are .... replicated

simultaneously

11

DNa plymerase can only synthesize DNA in the

5' to 3' direction

12

synthesized continualsly

leading strand

13

synthesized in segemnts

lagging strand

14

The enzyme tightens its "fingers" around the active site...

which is easiest if the correct base pair is there

15

exonucleolytic proofreading

takes place immediatly after incorrect bases is added
DNA plymerease requries a perfectly paired 3; terminus
3' to 5' exonuclease clips off unpaired residues at 3' primer terminus

16

5 to 3 allows efficent error correction

when a high energy bond is cleaved, provides energy for plymerization of that bond.
if it went the other direction, there would not be sufficent energy

17

Laggin Strand Synthesis

backstitching process
DNA PRIMASE synthesizes an 10nt long RNA primer to rpime DNA synthesis.
RNA primer is erased by RNAseH and replaced with DNA; DNA ligase joins the ends

18

What joins the ends?

DNA ligase

19

what does DNA helicase do?

unwinds DNA
protein with 6 identical subunits uses AT hydrolyses
cuases confomational change

20

helps stabalize DNA, prevents hairpins, base pairing, allows DNA polimerase to still read and put in new

single- stranded DNA binding protein

21

keep DNA polymerase on DNA when moving; releses when double stranded DNA is encountered

sliding clamp

22

what pust the sliding clamp onto a primer template junction??

clamp loader
with laggins strand clamp loader is always present since it is procuding DNA in segments and the sliding clamp needs to continually be put bakc on

23

mismatch repair

MutS binds to mismatch;
Mut: scans for the nick and triggers degradation of nicked strand

24

How does it know if it is fixing the new strand or the old strnad?

it fixes the non methalated strand, which is the new strand... this is E coli

25

Type 1 Topoisomerases

makes a single cut on one strand in the phosphodiester bond
thermodynamically favorable process
allows to remove tention and spin around
resealing is rapid

26

Type II topoisomerase

makes double stranded break in DNA
1. brekas on double stranded helix reversibly to create gate
2. causes second strand to pass through
3. reseals break and dissociates
can seperate "decatenate" 2 interlocked DNA circules
can prevent severe tangling problems

27

Replication origins

rich in A-T based pairs
bacteria-inition is only pt, only when sufficent nutrients, refractory periord for new strands to be metholated, 2 replication forks do all of it
euarkyotes- need more than 1 origin,

28

Initiation of DNA replication in bacteria

initiator protein binds to specific site in ORI froming complex
Complex attracts DNA helicase + helicase loader
helicase is placed around a SS DNA exposed by assembly of complex
helicase loader remains engaged until helicase properly loaded
Helicase unwinds DNA so primase can make RNA primer on leading strand; remaining proteins assemble to create 2 replication formks w complexes moving in opposite direction w respect to the ORI

29

Eukaryotic DNA replication

only occurs during S phase, 8 hours
done in clusters 20-80
heterochromatin is late replicating

30

Origin of replication Yeast eukaryote
min requirements 3

binding site for ORC
A-T rich stretch for easy unwinding
binding site for proteins that thelp attract ORC(origin of replication complex)

31

ORC interaction w/ ORI persists

throughout cell cycle

32

protein that beind to from a ....

prereplicative complex and regulates origin acitivity
done by helicase and helicase loading proteins, Cdc6 and Cdt1

33

Regulation of OR in Eukaryotes
In S phase,

activated Cdks lead to
-dissociation of helicase loading proteins
-activation of helicase
-unwinding of DNA
- loading of DNA polymerase, etc.

34

Regulation in eukaryotes of ORC
prevent assembly of new ORC until next M phase resets cycle

single chance to form in G1 when Cdk activity is low
second window for pre-replicative complexes to be activated and disassembles in S phase when Cdks activity is high

35

ORI function depends critically on distanct sequences

also affects transcription
global effect of decondensing chromatin structure

36

DNA requires not only DNA but

synthesis and assembly of new proteins

37

histone proteins are synthesised in what phase

S phase

38

What is needed to destabilize DNA histone interface?

chromatin remodeling proteins

39

As replication fork passes through chromatin, histone octamer breaks into;

-an H3-H4 tetramer, distributed randombly to daughter duplexes
- 2 H2A-H2B dimers which are released from the DNA

40

H2A/H2B dimers are 1/2 old and 1/2 new

they are added at random to complete complex

41

What does the addition of hisones require?

Histone chaperones (chromatin assembly factors)

42

What is the sliding clamp called that directs to DNA?

PCNA

43

Patterns of Histone modification can be inherited

some contain only parental histones, some only new but most are hybrids of new and old.
parental patterns of histone modification are spread through reader-writer complexes
epigentic inheritance responsibility

44

End replication problem on lagging strand:

no place for RNA primer

45

bacteria have cirular genome

eukakaryores have telomeres

46

What is the special sequence at the end of eache chromosome

GGGTTA

47

What enzyme relenishes these sequences by elongating parental strand in 5' to 3' direction using an RNA template on the enzyme

telomerase it's a protein and RNA combination

48

What completes the telomerase replication of laggins strands?

DNA plymerase, using extension as template
This mechanism(plus a 5' nuclease) ensures 3' end is longer, leaving a protruding SS end that loops back and tucks into the repeat

49

structures protect ends and distinguishes them from broken ones that need to be repaired

T-loops

50

What cells have full complement of telomere repeats at birth?

somatic cells

51

What retain full telomerase activity?

stem cells

52

Each chromosome end in a given cell contains variable # of telomere repeats depending on age

repeats are lost each genreation due to insufficient telomerase acitivity

53

after many generations, daughter cells will have defective chromosomes and stop dividing; in this way the cell's lifetime is regulated to guard against cancer

replicative senescence
may cause againg

54

How many times do human fibroblasts divide before undergoing replicative senescence

60 times

55

dyskeratosis congenita

carry mutant telomerase RNA gene