topic 3: molecular basis of inheritance

Question 1

who were the two scientists that produced the double-helical model for DNA structure?

Answer 1

James Watson and Francis Crick

Question 2

what year was the double-helical structure of DNA discovered?

Answer 2

1953

Question 3

describe the structure of DNA

Answer 3

• 2 antiparallel sugar-phosphate backbones
• the nitrogenous base pairs are in the molecule’s interior

Question 4

what is Chargaff’s rule?

Answer 4

in any species, there is an equal number of A and T bases, and an equal number of G and C bases

Question 5

which of the nitrogenous bases are purines, and which are pyrimidines?

Answer 5

purines: adenine, guanine (two-carbon nitrogen ring bases)
pyrimidines: thymine, cytosine (one-carbon nitrogen ring bases)

Question 6

there are ___ hydrogen bonds between A and T, and ___ hydrogen bonds between C and G

Answer 6

2, 3

Question 7

in what direction do the two helices of DNA run?

Answer 7

in an anti-parallel manner

Question 8

monomers of DNA are known as

Answer 8

nucleotides

Question 9

what does each DNA nucleotide consist of?

Answer 9

• a nitrogenous base
• a pentose sugar (deoxyribose)
• a phosphate group

Question 10

what is a nucleoside?

Answer 10

nitrogenous base + pentose sugar
(excluding the phosphate group)

Question 11

describe eukaryotic DNA molecules

Answer 11

• consist of 2 polynucleotide strands that spiral around an imaginary axis forming a double helix
• anti-parallel strands: each strand runs in an opposite direction to the other (3’ –> 5’ and 5’ –> 3’)
• sugar-phosphate backbone is on the outside
• the nitrogenous bases form hydrogen bonds in a complementary fashion:
• A - T, C - G
• the 2 strands are complementary: knowing one sequence, we can derive the other

Question 12

how are nucleotides connected to create a polymer?

Answer 12

in a 3’ to 5’ phosphodiester bond
- between the 3’ -OH group of the sugar molecule of one nucleotide and the 5’ -phosphate group of the second nucleotide

Question 13

explain the difference between bacterial chromosomes and eukaryotic chromosomes

Answer 13

bacterial chromosomes:
- double-stranded circular DNA molecule associated with a small amount of protein
- DNA is supercoiled in the nucleoid

eukaryotic chromosomes:
- double-strand linear DNA molecules associated with a large amount of proteins (histones)
- located in the nucleus
- consist of chromatin
- chromosomes are packed and supercoiled in different levels in order to fit into the nucleus

Question 14

what is chromatin?

Answer 14

DNA + histones (proteins)

Question 15

what is the diameter of the DNA double helix?

SOS

Answer 15

2 nm

Question 16

what is the diameter of a nucleosome?

SOS

Answer 16

10 nm

Question 17

what are the levels of chromatin packing in a eukaryotic chromosome?

SOS

Answer 17

1. DNA, double helix (2 nm)
2. DNA comes together with the histones to create nucleosomes (10 nm)
3. nucleosomes are wrapped around themselves (to form 30 nm fibers)
4. looped domains – the fibers form loops to fit in the nucleus (300 nm)
5. the condensed metaphase chromosome (2 chromatids, each 700 nm)

Question 18

how are nucleosomes made?

Answer 18

DNA is wrapped twice around a set of eight proteins – histone octamer

Question 19

what are the diameters of each step of chromatin packing?

SOS

Answer 19

• DNA double helix: 2 nm
• DNA + histones: 10 or 11 nm (depending on histone 1)
• nucleosomes wrapped around themselves: 30 nm fibers
• looped domaines: 300 nm
• metaphase chromatids: 700 nm each
• metaphase chromosome: 1400 nm or 1.4 μm

Question 20

what is the structure of a nucleosome?

Answer 20

• each nucleosome consists of 8 histone molecules
• (H2A, H2B, H3, H4) x 2
• +ds DNA (168 base pairs)
• with histone one

Question 21

what is histone 1 (H1)?

Answer 21

• located between the nucleosome (NOT part of the octamer core)
• role: stabilizes the interaction between DNA and nucleosomal histones

Question 22

(1) what is the diameter and (2) how many base pairs is DNA with and without histone 1?

Answer 22

• without H1: 146 base pairs, 10 nm
• with H1: 168 base pairs, 11 nm

Question 23

what is euchromatin?

Answer 23

• ACTIVE FORM
• loosely packed chromatin
• enables replication and transcription
• enables gene expression

Question 24

what is heterochromatin?

Answer 24

• INACTIVE FORM
• highly condensed chromatin
• inhibits replication and transcription
• inhibits gene expression

Question 25

at what stage of the cell cycle is chromatin (1) in the form of euchromatin and (2) in the form of heterochromatin?

Answer 25

• euchromatin: during interphase
• heterochromatin: during mitosis

Question 26

explain why the forms of chromatin occur at their respective phases of the cell cycle

Answer 26

• gene expression occurs during interphase, therefore chromatin has to be in its active form (euchromatin)
• during mitosis, the cell is actively undergoing cell division (no gene expression) so the inactive form of chromatin is present

Question 27

what are the two exceptions (structures) of chromosomes that are ALWAYS in heterochromatin form?

Answer 27

• centromeres and telomeres
• these two structures are always in heterochromatin form because they have structural roles (are not transcribed/translated)

Question 28

what are the chemical modifications histones can undergo that results in changes in gene expression?

Answer 28

• methylation
• acetylation

Question 29

what could be a consequence of histone modification?

Answer 29

• gene silencing (inhibition of gene expression)
• could result in diseases (ex: cancer)
• hypo-acetylation of histones causes a condensed or closed chromatin structure, disabling gene expression

Question 30

what is histone acetylation?

Answer 30

• converts heterochromatin into euchromatin
• ACTIVATES chromatin, ACTIVATES gene expression
• loss of histone (+) charge due to acetylation weakens their interactions with DNA (-) charge

Question 31

what is histone deacetylation?

Answer 31

• INACTIVATES chromatin
• converts it into heterochromatin
• restores (+) charge of histone –> strengthens their interaction with DNA

Question 32

what are the enzymes responsible for (1) histone acetylation and (2) histone de-acetylation?

Answer 32

• histone acetyl-transferases (HAT): is responsible for histone acetylation
• histone deacetylases (HDAC): is responsible for histone deacetylation

Question 33

what is the semiconservative model of replication?

Answer 33

when a double helix replicates, each daughter molecule will have 1 old strand (derived or conserved from the parent) and 1 newly synthesized strand

Question 34

replication begins at special sites called _____, and are separated opening up a _____

Answer 34

• origins of replication
• replication “bubble”

Question 35

what type of replication does the DNA double helix undergo?

Answer 35

• bidirectional replication: replication proceeds in both directions from each origin until the entire molecule is copied

Question 36

compare prokaryotic and eukaryotic origins of replication

Answer 36

prokaryotic:
- circular DNA, only 1 origin of replication
- replication is bidirectional

eukaryotic:
- linear DNA, several replication origins
- replication is also bidirectional

Question 37

what is the replication fork?

Answer 37

a Y shaped region at the end of each replication bubble where new DNA strands are elongating

Question 38

what are helicases?

Answer 38

enzymes that untwist the double helix at the replication forks

Question 39

what is topoisomerase?

Answer 39

enzyme that corrects “overwinding” of replication forks by breaking, shriveling, and rejoining DNA strands

Question 40

what are single-strand binding proteins used for?

Answer 40

protein that binds and stabilizes single-stranded DNA until it can be used as a template

Question 41

what enzyme fixes the action of helicases?

Answer 41

topoisomerase

Question 42

what is DNA polymerase used for?

Answer 42

enzymes that catalyze the elongation of new DNA at a replication fork

Question 43

what are the two limitations of DNA polymerases?

Answer 43

1. they can only add nucleotides to a pre-existing nucleotide chain (cannot add from scratch)
2. they can only add nucleotides in the 5’ –> 3’ direction (not the other way around)

Question 44

what 2 things does DNA polymerase require?

Answer 44

• a primer
• a DNA template strand

Question 45

what is used to fix the DNA polymerase limitation of only adding nucleotides to a pre-existing chain?

Answer 45

a short RNA primer has a free 3’ end that serves as the starting point for synthesis of the new DNA strand by DNA polymerase

Question 46

what is primase?

Answer 46

the enzyme that synthesizes a short RNA primer from scratch using parental DNA as a template

Question 47

where does each nucleotide being added to a growing DNA strand come from?

Answer 47

a nucleoside triphosphate (NTP)

Question 48

what will the 2 phosphate groups (from NTP) leave the reaction as?

Answer 48

pyrophosphate

Question 49

what are nucleoside analogues?

Answer 49

• drugs that have a modified 3’ -OH group, as a N3 group
• block replication, as cells think it is a nucleoside triphosphate, but the next nucleotide cannot bind to the N3 group

Question 50

give an example of a nucleoside analogues

Answer 50

• an example is AZT (azido-deoxy-thymidine)
• blocks replication due to modified 3’ -OH group
• an anti-retroviral drug (given to HIV patients)
• also given to cancer patients

Question 51

which DNA polymerase is responsible for synthesis of the leading strand?

Answer 51

DNA polymerase III

Question 52

how is the leading strand synthesized?

Answer 52

• DNA polymerase III copies the 3’ - 5’ strand
• synthesizes a leading strand continuously in the 5’ –> 3’ direction
• 2 leading strands per bubble are made

Question 53

since DNA polymerase cannot add nucleotides in the 3’ to 5’ direction, what does this cause?

Answer 53

the lagging strand

Question 54

how is the lagging strand synthesized?

Answer 54

• to copy the 5’ - 3’ strand, DNA polymerase III must work in the direction AWAY from the replication fork (5’ to 3’)
  1. primase: synthesizes short RNA primers
  2. DNA polymerase III: synthesizes discontinuously what are known as Okazaki fragments by adding DNA nucleotides to each primer
  3. DNA polymerase I: degrades RNA primers, replaces with DNA nucleotides
  4. DNA ligase: joins DNA fragments to the subsequent Okazaki fragments

Question 55

what problem does DNA polymerase create after many rounds of replication?

Answer 55

• the replication machinery does not provide a way to complete the 5’ ends
• repeated rounds of replication produce shorter DNA molecules

Question 56

why are only eukaryotic chromosomes affected by this DNA polymerase limitation?

Answer 56

because prokaryotes have circular DNA

Question 57

what are telomeres?

Answer 57

• the ends of eukaryotic chromosomes
• they protect chromosomal ends from erosion, degradation, and recombination with other chromosomes
• since they have a structural role, they do not get transcribed/translated

Question 58

is DNA shortening preventable?

Answer 58

no, telomeres only postpone the shortening of DNA but do not prevent it

Question 59

what is shortening of telomeres (or DNA) connected to?

Answer 59

aging