Lecture 3

Question 0

what must have low mutiation rate to maintain speciese?

Answer 0

germ cells

Question 1

Most errors are corrected by

Answer 1

proofreading and DNA repair
post-relication repair mechanism

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

Question 2

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

Answer 2

somatic cells

Question 3

What synthesize DNA by catalyzing

Answer 3

DNA plymerase

Question 4

the following reaction is catalyzed

Answer 4

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

Question 5

How is the new DNA strand made?

Answer 5

template directed

Question 6

What must be seperated for replication?

Answer 6

two parental strands

Question 7

What does DNA replications require? 4 thins

Answer 7

dATP
dGTP
dCTP
dTTP

Question 8

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

Answer 8

DNA polymerase

Question 9

DNA feeds through the …. during replication

Answer 9

polemerase

Question 10

Both strands are …. replicated

Answer 10

simultaneously

Question 11

DNa plymerase can only synthesize DNA in the

Answer 11

5’ to 3’ direction

Question 12

synthesized continualsly

Answer 12

leading strand

Question 13

synthesized in segemnts

Answer 13

lagging strand

Question 14

The enzyme tightens its “fingers” around the active site…

Answer 14

which is easiest if the correct base pair is there

Question 15

exonucleolytic proofreading

Answer 15

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

Question 16

5 to 3 allows efficent error correction

Answer 16

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

Question 17

Laggin Strand Synthesis

Answer 17

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

Question 18

What joins the ends?

Answer 18

DNA ligase

Question 19

what does DNA helicase do?

Answer 19

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

Question 20

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

Answer 20

single- stranded DNA binding protein

Question 21

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

Answer 21

sliding clamp

Question 22

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

Answer 22

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

Question 23

mismatch repair

Answer 23

MutS binds to mismatch;

Mut: scans for the nick and triggers degradation of nicked strand

Question 24

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

Answer 24

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

Question 25

Type 1 Topoisomerases

Answer 25

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

Question 26

Type II topoisomerase

Answer 26

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

Question 27

Replication origins

Answer 27

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,

Question 28

Initiation of DNA replication in bacteria

Answer 28

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

Question 29

Eukaryotic DNA replication

Answer 29

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

Question 30

Origin of replication Yeast eukaryote | min requirements 3

Answer 30

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

Question 31

ORC interaction w/ ORI persists

Answer 31

throughout cell cycle

Question 32

protein that beind to from a ....

Answer 32

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

Question 33

Regulation of OR in Eukaryotes | In S phase,

Answer 33

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

Question 34

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

Answer 34

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

Question 35

ORI function depends critically on distanct sequences

Answer 35

also affects transcription | global effect of decondensing chromatin structure

Question 36

DNA requires not only DNA but

Answer 36

synthesis and assembly of new proteins

Question 37

histone proteins are synthesised in what phase

Answer 37

S phase

Question 38

What is needed to destabilize DNA histone interface?

Answer 38

chromatin remodeling proteins

Question 39

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

Answer 39

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

Question 40

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

Answer 40

they are added at random to complete complex

Question 41

What does the addition of hisones require?

Answer 41

Histone chaperones (chromatin assembly factors)

Question 42

What is the sliding clamp called that directs to DNA?

Answer 42

PCNA

Question 43

Patterns of Histone modification can be inherited

Answer 43

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

Question 44

End replication problem on lagging strand:

Answer 44

no place for RNA primer

Question 45

bacteria have cirular genome

Answer 45

eukakaryores have telomeres

Question 46

What is the special sequence at the end of eache chromosome

Answer 46

GGGTTA

Question 47

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

Answer 47

telomerase it's a protein and RNA combination

Question 48

What completes the telomerase replication of laggins strands?

Answer 48

``` 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 ```

Question 49

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

Answer 49

T-loops

Question 50

What cells have full complement of telomere repeats at birth?

Answer 50

somatic cells

Question 51

What retain full telomerase activity?

Answer 51

stem cells

Question 52

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

Answer 52

repeats are lost each genreation due to insufficient telomerase acitivity

Question 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

Answer 53

replicative senescence | may cause againg

Question 54

How many times do human fibroblasts divide before undergoing replicative senescence

Answer 54

60 times

Question 55

dyskeratosis congenita

Answer 55

carry mutant telomerase RNA gene