Chapter 11 & 12

Question 1

Both parental strands stay together after DNA replication

Answer 1

Conservative model

Question 2

The double-stranded DNA contains one parental and one daughter strand following replication

Answer 2

Semiconservative model

Question 3

Parental and daughter DNA are interspersed in both strands following replication

Answer 3

Dispersive model

Question 4

• Used isotope of nitrogen to change the weight of DNA N15 & N14
• demonstrated that the semi-conservative model is the best description of replication.

Answer 4

The Meselson-Stahl experiment

Question 5

the fundamental reaction by which DNA is synthesized

Answer 5

The addition of a deoxyribonucleotide to the 3’ end of a polynucleotide chain (the primer strand)

Question 6

DNA polymerase catalyzes DNA synthesis and requires _____, ____, ___

Answer 6

a DNA template, a primer, and all four dNTPs

Question 7

Chain elongation occurs in the _ direction by addition of one nucleotide at a time to the _ end

Answer 7

5’ to 3’; 3’

Question 8

As the nucleotide is added, the two terminal phosphates are cleaved off, released as _

Answer 8

pyrophosphate

Question 9

enzymes that catalyze synthesis of DNA polynucleotide chains
- depend on single-stranded template DNA
- can add free nucleotides only to the 3’-OH end of an existing polynucleotide (DNA or RNA)

Answer 9

DNA polymerases

Question 10

complex enzyme with ten subunits (called the holoenzyme)

• responsible for the 5’ to 3’ polymerization essential in vivo
• Its 3’ to 5’ exonuclease activity allows proofreading

Answer 10

DNA polymerase III

Question 11

• removes the RNA primer
• fills the resulting gaps with DNA

Answer 11

DNA polymerase I

Question 12

involved in various aspects of repair of damaged DNA

Answer 12

DNA polymerases I, II, IV, V

Question 13

binds to the origin of replication and is responsible for the initial steps in unwinding the helix

Answer 13

DnaA

Question 14

• binding further opens and destabilizes the helix
• separates the two DNA strands by breaking the hydrogen bonds between them
• generates positive supercoiling ahead of each replication fork

Answer 14

DnaB and DnaC /helicases

Question 15

• stabilize the open conformation
• bind to the separated DNA strands to keep them apart

Answer 15

Single-stranded binding proteins (SSBPs)

Question 16

travels ahead of the helicase and alleviates the supercoils

Answer 16

DNA gyrase

Question 17

• synthesized by DNA primase
• 10 to 12 nucleotides
• start/ prime DNA synthesis
• later removed and replaced with DNA

Answer 17

RNA primers

Question 18

the new complementary DNA strand synthesized continuously along the template strand toward the replication fork in the mandatory 5’ to 3’ direction

Answer 18

leading strand

Question 19

A discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each with a RNA primer and synthesized in a 5’ to 3’ direction away from the replication fork.

Answer 19

lagging strand

Question 20

DNA polymerases have 3’ to 5’ __ activity that allows proofreading

Answer 20

exonuclease

Question 21

prevents the core enzyme from falling off the template

Answer 21

Beta subunit sliding clamp

Question 22

keeps parental strands apart

Answer 22

single stranded binding proteins

Question 23

synthesizes RNA primer

Answer 23

primase

Question 24

replication in eukaryotic cells (3 reasons why its more complex than in prokaryotic)

Answer 24

• the chromosomes are linear
• the DNA is associated with proteins
• there is more DNA than prokaryotic cells

Question 25

Three DNA polymerases are involved in replication of nuclear DNA

Answer 25

DNA Pol a, d and e

Question 26

DNA polymerase involved in mitochondrial DNA replication

Answer 26

DNA polymerase gamma

Question 27

- synthesizes a short RNA-DNA hybrid -- 10 RNA nucleotides followed by 20-30 DNA nucleotides - used by DNA pol d or e for the elongation of the leading (e) and lagging (d) strands

Answer 27

DNA pol a/primase complex (Eukaryotic: formation of the primer)

Question 28

Pol a is replaced by Pol d for elongation of the lagging strand, and by Pol e for elongation of the leading strand (after the RNA-DNA hybrid is made)

Answer 28

polymerase switching

Question 29

- Provide Structural Integrity at Chromosome Ends but Are Problematic to Replicate - consist of long stretches of short repeating sequences - have a 3' overhang that is 12-16 nucleotides long - typically consist of several guanine and thymine nucleotides

Answer 29

Telomeres

Question 30

complete (nuclear) genetic information of a cell/organism

Answer 30

genome

Question 31

In_, genome is typically a single circular chromosome In _, genome refers to one complete set of nuclear chromosomes

Answer 31

bacteria; eukaryotes

Question 32

- a single nucleic acid molecule - much smaller than eukaryotic chromosomes

Answer 32

Bacterial and viral chromosomes

Question 33

only the centromeres are stained

Answer 33

C-banding

Question 34

due to differential staining along the length of each chromosome.

Answer 34

G-banding

Question 35

- Satellite DNA - Found tens of thousands to millions of times - Each copy is relatively short (a few nucleotides to several hundred in length)

Answer 35

highly repetitive DNA

Question 36

- tandem repeats and interspersed retrotransposons - Found a few hundred to a few thousand times - Includes genes for rRNA and histones, Origins of replication, and Transposable elements

Answer 36

middle repetitive DNA

Question 37

multiple copy genes, mini-satellites, microsatellites

Answer 37

tandem repeats

Question 38

SINEs and LINEs

Answer 38

interspersed retrotransposons

Question 39

Three types of DNA sequences are required for chromosomal replication and segregation

Answer 39

- Origins of replication (many) - Centromeres - Telomeres

Question 40

located between the centromeric and telomeric regions along the entire chromosome

Answer 40

genes (location)

Question 41

levels of eukaryotic chromatin compaction

Answer 41

naked DNA -> beads on a string-> solenoid-> loops-> radial loops->chromosome

Question 42

- the substance chromosomes are made of - complex of chromosomal DNA and protein (and specific RNAs)

Answer 42

chromatin

Question 43

histones and nonhistone proteins

Answer 43

chromatin proteins

Question 44

- Many proteins of different functions - present in chromatin - 5,000 - 10,000 encoded in the human genome - ex: DNA and RNA polymerases, DNA repair enzymes, transcription factors, kinetochore proteins, topoisomerases

Answer 44

nonhistone proteins

Question 45

- function in the compaction of DNA in the nucleus - synthesized at same time as DNA (S-phase) - small and basic (high content of arginine and lysine)

Answer 45

histones

Question 46

5 types of histones

Answer 46

- H1: occurs in different variants - H2A H2B H3 H4= nucleosomal or core histones, each present in the same number of molecules

Question 47

- the repeating structural unit within eukaryotic chromatin - composed of double-stranded DNA wrapped around an octamer of histone proteins - Beads on a string; 5 fold condensation

Answer 47

nucleosomes

Question 48

_ bp of DNA make 1.65 negative superhelical turns around the histone octamer

Answer 48

146

Question 49

- 40 fold condensation - nucleosomes wrapped into rings and stacked

Answer 49

solenoid

Question 50

- condensed and densely staining in interphase - genetically inactive - constitutive and factultative

Answer 50

heterochromatin

Question 51

constitutive heterochromatin

Answer 51

telomeres and centromeres

Question 52

facultative heterochromatin

Answer 52

can change to euchromatin

Question 53

- decondensed and only weakly staining in interphase - genetically active - replicated first in S phase

Answer 53

euchromatin