Lecture 5

Question 1

DNA transposons are also powerful mutagens, T or F

Answer 1

T

Question 2

What specialised DNA polymerase enzyme is responsible for replication of telomeres

Answer 2

Telomerase

Question 3

What are the four different specialised sequences contained within chromosomes

Answer 3

Telomeres, centromeres, replication origins and kinetochores

Question 4

What happens to the original site from which the DNA transposon was initially excised from

Answer 4

It is repaired by DNA repair mechanisms

Question 5

Not all of the genetic information in eukaryotes is encoded in the nucleus, where else is some genetic information stored and how

Answer 5

Some genetic information is contained in the mitochondria and chloroplasts in the form of small circular chromosomes

Question 6

Each de-condensed chromosome occupies a specific region in the interphase nuclei, explain this phenomenon

Answer 6

As genes are transcribed the relative position of the chromosome in the nucleus changes. At interphase transcriptionally inactive regions of/chromosomes become localised at the periphery of the nucleus. In contrast, transcriptional activation of a gene is accompanied by movement of the gene towards the centre of the nucleus

Question 7

Explain the role of linker histones such as H1

Answer 7

Linker histones act as straps that connect the incoming and outgoing strands of DNA that wrap around the core nucleosome. This helps to stabilise the formation of the 30nm chromatin fibres

Question 8

Retrotransposons also move throughout the genome/chromosomes, T or F

Answer 8

F – retrotransposons never move. They act through RT converting RNA back to dsDNA at random points in the genome

Question 9

Define what is meant by a kinetochore

Answer 9

Protein complex that binds to the microtubules in the mitotic spindle

Question 10

Who discovered chromosomes in 1902

Answer 10

Sutton and Boveri

Question 11

What are the two constituent parts of each nuclear chromosome

Answer 11

Linear DNA molecule and proteins that confer specialised functions called chromatin

Question 12

Give an example of a specialised histone that mediates the attachment of the chromosome to the kinetochore inner plate

Answer 12

CENP-A

Question 13

During which specific stage of the cell cycle can chromosomes easily be distinguished

Answer 13

Metaphase of mitosis

Question 14

Telomeres define chromosome ends and maintain chromosome integrity, T or F

Answer 14

T

Question 15

Explain how the chromatin is indirectly linked to the microtubules during chromosome segregation

Answer 15

The CENP-A histone containing chromatin physically binds to the kinetochore inner plate. An interaction between the kinetochore inner and outer plates links this chromatin to the microtubules of the mitotic spindle

Question 16

What are alpha-satellite DNA repeats that are found within centromeres

Answer 16

Alpha-satellite DNA repeat sequences are repeat sequence elements around 170bps that act as specific binding sites for a set of specialised histones localised to centrometic sequences. These act as target interaction proteins for kinetochores

Question 17

Which type of transposons make up the majority of transposons

Answer 17

Retroviral retrotransposons

Question 18

How do retroviral retrotransposons act

Answer 18

Function via the production of an RNA intermediate

Question 19

What is the main benefit of carrying mobile genetic sequence information around

Answer 19

Acts as a genome shuffling mechanism that breaks up and reassembles the genome, providing new combinations of DNA sequences and facilitating rapid genomic evolution

Question 20

What is significant about the N-terminals of core histones

Answer 20

These project out from the nucleosome core and are free to interact with other proteins. These tails are rich in lysine residues and facilitate regulation of chromatin structure and function. They interact with proteins that effect the ability of the chromatin to be de-condensed, re-condensed and transcribed

Question 21

The organised representation of all of the chromosomes in a eukaryote at metaphase is canned the karyotype, T or F

Answer 21

T

Question 22

What is meant by the term transposon

Answer 22

Mobile genetic elements that can replicate themselves and jump around the genome

Question 23

DNA transposons make up the largest proportion of transposable DNA elements in the human genome, T or F

Answer 23

F – they only account for 5%

Question 24

What are the five main functions of chromatin

Answer 24

Packaging and unfolding DNA in the nucleus, control of DNA replication, repair and recombination, maintenance of chromosome integrity, governing chromosome segregation and the regulation of gene expression

Question 25

Describe the structure/composition and role of centromeres

Answer 25

Higher order repeat sequences that contain subsets of repeat sequences called alpha-satellites. Centromeres facilitate chromosome segregation during cell division

Question 26

Retrotransposons are abundant in invertebrate genomes, T or F

Answer 26

F – they are abundant in vertebrates

Question 27

What are the three types of transposons

Answer 27

DNA Transposons, Retroviral retrotransposons, Non-retroviral PolyA retrotransposons

Question 28

Structurally and in terms of proteins encoded by them, how are retrotransposons similar to retroviruses and what is a significant difference

Answer 28

Retrotransposons contain DNA sequences that code for envelope and capsid proteins just like retroviruses do. However, these proteins are usually defective but without preventing the replication capability of the retrotransposon

Question 29

Of what order can the telomeric repeat sequences at the ends of chromosomes be

Answer 29

Hundreds

Question 30

How do retrotransposons act in a similar way to retroviruses

Answer 30

They replicate via RNA intermediates and produce new DNA copies that integrate at new genomic locations. Retrotransposons self-encode the reverse transcriptase enzyme required for this mechanism

Question 31

Which technique is useful for visualising chromosomes in interphase nuclei

Answer 31

Chromosome painting

Question 32

Chromatin is a protein, T or F

Answer 32

T

Question 33

Describe the composition of the core nucleosomes which the DNA sequence wraps around

Answer 33

Core nucleosomes are proteins that consist of 8 distinct subunits called histones. The DNA sequence wraps twice around each core nucleosome

Question 34

What happens as a result of selective removal of linker histone H1 from the core nucleosome

Answer 34

Causes de-condensation of the chromatin during interphase that allows gene transcription

Question 35

The process of DNA transposon movement throughout the genome is also referred to as non-replicative transposition, T or F

Answer 35

T

Question 36

Which specialised sequence within chromosomes is the DNA sequence located at the ends of linear chromosomes and maintain chromosomal integrity

Answer 36

Telomeres

Question 37

What is meant by PolyA

Answer 37

The RNA transcript produced by the non-retroviral retrotransposon is poly-adenylated

Question 38

Describe the structure of the 10nm chromatin fibre

Answer 38

Single strand of DNA coiled around core nucleosomes

Question 39

What features define transposons and are the site for enzyme binding

Answer 39

Short simple sequence repeats that lie at each end of the transposon where transposase binds

Question 40

Alu and B1 are human non-retroviral retrotransposons, explain what is significant about these two transposable DNA sequences

Answer 40

They evolved from the same sequence element – 90million years ago. Alu and B1 originate from a single copy of the 7SL RNA gene

Question 41

What do telomeres consist of

Answer 41

Hexanucleotide repeat sequences that create a 3’ overhang in the linear chromosome

Question 42

More complex organisms have more protein coding genes and less non-protein-coding DNA, T or F

Answer 42

F – they contain more protein and non-protein encoding genes

Question 43

What is significant about the enzyme required by DNA transposons to move throughout the chromosome/genome

Answer 43

Transposase is encoded by the DNA transposon itself

Question 44

How do DNA transposons act

Answer 44

Transposase binds to the short simple repeat sequences that flank the transposon itself. These enzymes then induce double-stranded breaks in the DNA sequence to excise the gene from its initial location. This mobile intermediate produced is then able to move to a new location in the chromosome/genome and insert at a random locus

Question 45

What mechanism do DNA transposons move by

Answer 45

Cut-and-paste – without self-duplication

Question 46

Which specialised sequence within chromosomes is the DNA sequence at which the kinetochore assembles to mediate chromosome segregation at mitosis and meiosis

Answer 46

Centromeres

Question 47

Non-retroviral retrotransposons have expanded hugely in numbers during evolution of higher mammal genomes, T or F

Answer 47

T

Question 48

Which specialised sequence within chromosomes is the DNA sequence at which DNA replication is initiated

Answer 48

Replication origin

Question 49

What enzyme is required by DNA transposons in order to move throughout the genome in the way that they do

Answer 49

Transposase

Question 50

Describe the structure of the 30nm chromatin fibre

Answer 50

Causes by a supercoiling of the 10nm chromatin fibre into a superhelix

Question 51

Recall the specific DNA sequence found in telomeres

Answer 51

TTAGGG

Question 52

Give some examples of transposable DNA elements

Answer 52

Ac-Dc in maize, P-elements from flies and Tn3/Tn10 from E.coli

Question 53

Explain why non-retroviral PolyA retrotransposons are referred to as stripped down retrotransposons

Answer 53

They lack the envelope and capsid proteins encoded within the retrotransposon sequence

Question 54

The kinetochores consist of out and inner plate proteins, explain the different roles of these constituent parts

Answer 54

The kinetochore inner plates bind to alpha-satellite DNA and specific centromeric histones. The kinetochore outer plate proteins bind to protein components of the mitotic spindles such as microtubules

Question 55

Explain how the reverse transcriptase self-encoded by non-retroviral PolyA retrotransposons also acts as an endonuclease

Answer 55

As well as producing the new DNA copy of the RNA intermediate created from the non-retroviral retrotransposon, the RT self-encoded by it alsi creates a nick in the target DNA. This allows for the physical insertion of the newly synthesised DNA copy of the PolyA transcript into this cleavage site