DNA replication and such

Question 1

nucleosides vs nucleotides

Answer 1

sides= sugar and base covalently linked

tides= when one or more phosphate attached to a nucleoside ATP, GTP

Question 2

which is biggest base

Answer 2

guanosine, adenosine, thymine and then cytosine

Question 3

why is ATP hydrolysis an exception to a chemistry rule

Answer 3

NORMALLY it takes energy to break bonds (endothermic), but with ATP breaking it releases energy bc of the repulision of the phosphates

Question 4

guanosine vs guanine

Answer 4

basically, if the bases end in “ine” this means they are nucleosides (no phosphate)

• be careful with this! guanosine, adenosine, cytidine, uridine

Question 5

describe sugar-phosphate backbone

Answer 5

3’ on the sugar links via a phosphodiester bond to the 5’ of the next sugar

Question 6

difference between thymine and uracil

Answer 6

both pyrimidines- thymine just has a methyl group atttached to the N-ring (both 2 c=o bonds, and 2 NH spots)

Question 7

purines and pyrimidines are aromatic heterocycles, what 4 criteria determine aromatic molecules

Answer 7

1. cyclic
2. planar
3. 4n + 2 rule o pi electrons
4. compound is conjugated - need atleast one unhybridized p-orbital for each atom in the ring- cant be sp3)

Question 8

base pairing and amount of H-bonds betwen

Answer 8

AT and GC

AT- 2 bonds

GC- three bonds (more stable and stronger)

Question 9

most DNA is

Answer 9

right handed helix called B-DNA

Question 10

B-DNA makes turns every??

Answer 10

3.4 nm, about every 10 base pairs

Question 11

left handed DNA is called

Answer 11

Z-DNA (more unstable- may happen if high GC content)

Question 12

Z-DNA makes turns every?

Answer 12

4.6 nm, 12 bases

Question 13

what can be used to denate DNA

Answer 13

heat, base pH, chemicals like formaldehyde and urea

• can reanneal DNA (brig back together) by slowly removing these conditions

Question 14

are histones basic or acidic proteins

Answer 14

basic ( means that they have a positive charge that allows them to interact with negative DNA)

Question 15

which histones form histone core

Answer 15

H2A, H2B, H3, H4 and H1 is the glue that pulls them all together

• about 200 bp in a nucleosome

Question 16

telomerase is more highly expressed in what kinda cells

Answer 16

rapidly dividing ones

Question 17

is there a set number of replications possible?

Answer 17

yes- this contributes to aging

Question 18

what is telomere sequence

Answer 18

TTAGGG ( the ending with high GC–> 3 H-bons is extremely strong to prevent unravelling )

Question 19

centromeres are high in

Answer 19

GC and are heterochromatin

Question 20

orgins of replications- which direction do they go in

Answer 20

both- to be more efficient

Question 21

In eukaryotes, replication forks move towards each other and create?

Answer 21

sister chromatids

Question 22

single stranded DNA - binding proteins

Answer 22

after helicase unwinds - they bind to prevent rebinding and to stop nucleases

Question 23

what enzyme, prevens/ fixes supercoiling

Answer 23

DNA topoisomerase

Question 24

what processes are 5’—>3’

Answer 24

pretty much all:

• DNA synth
• DNA repair
• RNA transcritption
• RNA translation

its just DNA polymerase reading that is 3–.5

Question 25

RNaseH

Answer 25

in eukaryotes this removes the RNA primers

Question 26

which polymerases begin synth of daughter strand?

Answer 26

prokaryotes- DNA poly 3

eukaryotes- DNA polymerase a,g,e

Question 27

to remove RNA primers

Answer 27

pro- DNA poly 1

euk- DNA poly g

Question 28

Five DNA polymerases in eukaryotes

Answer 28

a, B, y, g, e,

Question 29

DNA poly a, g. e

Answer 29

synth both leading and lagging strands

Question 30

DNA poly y

Answer 30

replicates mito DNA

Question 31

DNA poly B and e

Answer 31

DNA repair

Question 32

antioncogenes

Answer 32

tumour suppressor genes - normally function to stop tumour progression

Question 33

when proofreading what does DNA poly detect if somthing is wrong

Answer 33

H-bond unstability

• then looks at level of methylation–> more methylated = parent strand

Question 34

where is DNA mutations more likley and why?

Answer 34

in the laggin strand, bc ligase lacks proofreading mechanism

Question 35

G2 phase checkpoint checks for

Answer 35

mismatching - they detect and remove errors that occures during S phase

Question 36

how are thyamine dimers cut out

Answer 36

nucleotide excision repair - with excinuclease

Question 37

requirement for restriction sites

Answer 37

5’ to 3’ is identical antiparralell (palidromic)

for example:

5’ CAT 3’
3’ TAC 5’

Question 38

Genomic libraries vs cDNA (expression) libraries

Answer 38

genomic contai large fragments of DNA so they contain introns and exons

whereas cDNA is only the expresssed version bc it comes from mature mRNA

Question 39

PCR

Answer 39

DNa of interest is heater, denatureted, replicatied and then reannealed

• thermal stable DNA polymerase is used and comlimentary nucleotides added

Question 40

Southern Blot

Answer 40

used to detect the presense and quantity of various DNA strands in a sample. DNA cut by restriction enezymesand then seperated by gel electrophoresis

• DNA frag carefully transferred to a membrane, membrane then probed with varies ss DNA. Probe will bind to complementary- these are radiolabeled

so the point is that we to see if a gene of interest was in a sample

Question 41

DNA sequencing

Answer 41

the one where you add ddATP, ddCTP ect and when they get added the DNA strand stops , sepreate by gel electrophoresis

Question 42

transgene

Answer 42

when a cloned gene is introduced a fertilized agg or embryonic stem cells

• take fertalized egg out of mother, inject new gene, implant into foster mom, offspring will be transgenic

Important to note that this gene COEXISTS with their own copies of their gene - so this is usful for studying dominate genes