nucleotides and nucleic acids

Question 1

central dogma

Answer 1

dna-transcription-mrna-translation-protein

Question 2

functions of DNA

Answer 2

genetic code
storage within cell
accessibility for transcription
replication
meiosis
genome integrity

Question 3

purines

Answer 3

2 rings

adenine and guanine

Question 4

pyramidines

Answer 4

1 ring

cytosine, thymine, uracil

Question 5

nucleoside

Answer 5

base attached to 1’sugar
purine n9 attached to c1 sugar
pyramidine n1 attached to c1 sugar

Question 6

nucleotide

Answer 6

base + sugar + phosphate
purine n9 attached to sugar c1’
pyramidine n1 attached to sugar c1’

Question 7

polymeric structure of DNA and RNA

Answer 7

linear polymer formed by 3’5’ phosphodiester bonds
acidic (negatively charged) sugar phosphate backbone
written out in 5’ to 3’ direction
5’ end carries free phosphate
3’ end carries free hydroxyl

Question 8

DNA/RNA - resistant to hydrolysis?

Answer 8

DNA - hydrolysis resistant, used for long term info storage

RNA - hydrolysis vulnerable, used for temporary info storage

Question 9

chargaffs rules

Answer 9

for a particular species, [A]=[T], and [G]=[C]

Question 10

St Andrews cross in X-ray

Answer 10

indicates double helix
molecule is helical
meridian angle = 60 degrees

Question 11

watson and crick

Answer 11

2 antiparallel strands
specific base pairing
double helix dimensions
base pairing held together by h bonds

Question 12

G-C pairing

Answer 12

held by 3 H bonds

Question 13

A-T pairing

Answer 13

held by 2 H bonds

Question 14

structural stability of DNA

Answer 14

hydrophobic effect
hydrophobic bases inside
charged backbone outside

Question 15

features of the sugar phosphate backbone

Answer 15

negatively charged
targeted for non specific DNA binding
binding by positively charged proteins
e.g. histones package DNA in nucelosomes

Question 16

major groove

Answer 16

information rich
sequence specific DNA
sequence can be read w/o unwinding
exploited by Tf
22A wide

Question 17

minor groove

Answer 17

information poor
infrequently used for sequence recognition
binding typically alters DNA architecture
12A wide

Question 18

single stranded nucleic acid structures

Answer 18

attempt to satisfy watson crick base pairing
elaborate structures
mismatched base pairing
tertiary interactions

Question 19

semi conservative replication

Answer 19

strands separate

free complementary nucleotides attach to each strand producing two new strands of DNA

Question 20

3’5’ exonucleases

Answer 20

permit removal of incorrect nucleotides

Question 21

DNaB helicase

Answer 21

recruited by recruited by DnaA
loaded around ssDNA
ATPase dependent translocation

Question 22

stabilising nascent ssDNA

Answer 22

loaded onto ssDNA
ssDNA wrapped around SSB tetrameters
prevents secondary structure formation

Question 23

nascent ssDNA

Answer 23

ssDNA at the start of its lifespan

big potential

Question 24

relaxing DNA molecules

Answer 24

topisomerase 1 catalyses relaxation of supercoiled DNA
cleavage of 1 strand
passage of cut end under other strand
break is resealed

Question 25

topisomerase catalyses untangling of DNA duplexes

Answer 25

cleavage of both strands
pass duplex molecule through break
reseal break

Question 26

primase

Answer 26

RNA primer required for synthesis of DNA
provides initial free 3’-OH
DnaG primase synthesises RNA primer recruited by DnaB

Question 27

DNA polymerase 3

Answer 27

alpha core
exonuclease domain
proofreading and reduces error rate
sliding clamp -beta2 hole accomodates dsDNA and keeps polymerase 3 in contact w DNA

Question 28

trombone model

Answer 28

looping of lagging strand
lets go after adding 1000 nts
new loop formed
loop lengthens and shortens

Question 29

role of lagging strand

Answer 29

fills in gaps

Question 30

DNA polymerase 1

Answer 30

fills in gaps between fragments
5’-3’ exonuclease activity
removes RNA primer, synthesises DNA

Question 31

DNA ligase

Answer 31

catalyses phosphodiester formation

fills in ‘nicks’ between Okazaki fragments