ch14: DNA structure and function

Question 1

structure of DNA

Answer 1

nucleic acid (polymer of nucleotides)
nucleotide (5-carbon sugar; either deoxyribose or ribose)
phosphate group
nitrogenous base (A,G,C,T/U)

Question 2

which nitrogenous bases are pyrimidines (one ring)

Answer 2

cytosine, thymine and uracil

Question 3

which nitrogenous bases are purines (two rings)

Answer 3

adenine and guanine

Question 4

what is a primer

Answer 4

a short nucleic acid sequence that provides a starting point for DNA synthesis

Question 5

DNA strand structure is a

Answer 5

polymer of nucelotides

Question 6

what is a phosphodiester backbone

Answer 6

a repeating sugar-phosphate unit that is joined by a phosphodiester bond

Question 7

where is the base connected on the 5-carbon sugar

Answer 7

1’ sugar

Question 8

chain of nucleotides has an orientation of

Answer 8

5’-to-3’ (fifth carbon connected to the third carbon by phosphodiester bond)

Question 9

double helix

Answer 9

• 2 anti-parallel strands (run in opposite directions)
• bases protrude into center held together by base pairing (hydrogen bonds)
• major and minor grooves (DNA-interacting proteins can fit in these grooves to “read” specific DNA sequences)
• bases stuck on top of each other

Question 10

G forms — bonds withs C

Answer 10

3 hydrogen

Question 11

A forms —- bonds with T

Answer 11

2 hydrogen

Question 12

equal bond distances gives

Answer 12

consistent diameter of helix

Question 13

Why do you think it’s
important that the
phosphodiester bonds in
the DNA backbone are
covalent (strong) bonds,
and the bonds between the
bases are hydrogen (weak)
bonds?

Answer 13

if you break a phosphodiester bond, it damages the DNA, which causes mutations and all other kinds of problems. but you need those weak hydrogen bonds so that DNA mechanisms can break those bonds in order to copy the DNA into RNA for replication

Question 14

what does “complementarity of bases” mean

Answer 14

each strand is a template for the opposite base

Question 15

requirements of DNA replication

Answer 15

• something to copy (parental DNA strand)
• something to do the copying (enzymes; DNA polymerase and other enzymes)
• building blocks to make the copy (nucleotide triphosphates)

Question 16

process of DNA replication

Answer 16

1) initiation: beginning of replication
2) elongation: new strands of DNA are synthesized by DNA polymerase
3) termination: replication is terminated

Question 17

DNA is copied by

Answer 17

DNA polymerase

Question 18

how is DNA copied by DNA polymerase (4)

Answer 18

-it matches existing DNA bases with complementary nucleotides and links them
-adds new bases to the 3’ end of the existing strand
-synthesizes in 5’-to-3’ direction
-requires a primer (usually RNA)

Question 19

prokaryotic replication (4)

Answer 19

-single circular molecule of DNA
-replication begins at one origin of replication
-helicase unwinds DNA
-DNA replication proceeds in both directions around the chromosome

Question 20

helicase

Answer 20

clamp onto and unwind DNA

Question 21

DNA shape in prokaryotes and eukaryotes

Answer 21

prokaryotes: in circular form
eukaryotes: wrapped around histones

Question 22

supercoiling

Answer 22

unwinding DNA in one area will increase tension in the rest of the strand (one complete helical turn=one supercoil)

Question 23

unwinding DNA causes

Answer 23

torsional strain

Question 24

topoisomerase

Answer 24

unwinds DNA to prevent supercoiling (one called DNA gyrase is used in replication)

Question 25

replication is

Answer 25

semidiscontinous (unwinds a little then lets go to prevent too much tension)

Question 26

partial opening of helix forms

Answer 26

replication forks

Question 27

DNA primase

Answer 27

RNA polymerase that makes RNA primer (RNA will later be removed and replaced with DNA)

Question 28

DNA polymerase III

Answer 28

main replication enzyme

Question 29

DNA polymerase I

Answer 29

has 5’-to3’ exonuclase activity (acts on lagging strand to remove primers and replace them with DNA)

Question 30

DNA polymerase II

Answer 30

involved in DNA repair processes

Question 31

leading strand

Answer 31

-synthesized continuously from a single initial primer
-strand extended by DNA polymerase III

Question 32

processivity

Answer 32

subunit of DNA polymerase III forms “sliding clamp” to keep it attached to the DNA template

Question 33

clamp loader

Answer 33

loads clamp onto DNA

Question 34

DNA primase

Answer 34

produces an RNA primer for each okazaki fragment

Question 35

DNA polymerase III

Answer 35

synthesizes DNA from each RNA primer

Question 36

DNA polymerase I

Answer 36

removes all RNA primers and replaces them with DNA

Question 37

DNA ligase

Answer 37

seals the DNA backbone

Question 38

okazaki fragments

Answer 38

short sections of DNA formed at the time of discontinuous synthesis of the lagging strand during replication of DNA; allows for the synthesis of both the daughter strands required for cell division

Question 39

primose

Answer 39

all the proteins involved in DNA synthesis (primase, helicase, clamp loader)

Question 40

where does termination of replication happen

Answer 40

occurs at a specific site roughtly opposite of the origin of replication

Question 41

what does termination of replication do

Answer 41

cuts two daughter molecules that are intertwined like a ring; the chromosomes are unlinked by DNA gyrase