DNA Organisation and Packaging

Question 1

What happens during interphase?

Answer 1

• the cell is actively expressing genes
• DNA is replicated
• chromosomes are duplicated

Question 2

What happens once DNA replication is complete?

Answer 2

the cell can enter M phase, when mitosis occurs, and the nucleus is divided into two daughter nuclei

Question 3

What are the 3 DNA sequences required to produce a eukaryotic chromosome?

Answer 3

telomere, replication origin and centromere

Question 4

What does each chromosome have?

Answer 4

multiple origins of replication, one centromere, and two telomeres

Question 5

What do origins of replication do?

Answer 5

initiate replication bubbles

Question 6

What are replication bubbles?

Answer 6

short unwound regions of DNA formed by the helicase moving along the DNA strand

Question 7

When do origins of replication activate?

Answer 7

S phase

Question 8

What do DNA binding proteins do?

Answer 8

package DNA into a compact and less fragile form

Question 9

What is the net result of DNA packaging?

Answer 9

each DNA molecule is packaged into a mitotic chromosome that is 10000 times shorter than its extended length

Question 10

What is chromatin?

Answer 10

DNA complexed with histones

Question 11

What are histones?

Answer 11

positively charged proteins that form H bonds with the DNA backbone, which coils around the nucleosomal histones

Question 12

How can the protein core of a nucleosome be released from chromatin?

Answer 12

by digestion of the linker DNA with a nuclease

Question 13

What is the nucleosome protein core made up of?

Answer 13

2 pairs of H2A, H2B, H3 and H4

Question 14

What does each core histone contain?

Answer 14

• N-terminal tail which can be covalently modified
• a histone fold region

Question 15

How do the histone heterodimers form tetramers?

Answer 15

an H3-H4 tetramer forms the scaffold of the octamer onto which two H2A-H2B dimers are added

Question 16

How do histone pairs form heterodimers?

Answer 16

α helices loop into the histone folds

Question 17

What do H1 histones do?

Answer 17

package nucleosomes into even tighter arrays by guiding DNA entry and exit from the complex and by neutralising the DNA negative charge

Question 18

Give examples of histone modifications

Answer 18

• methylation
• acetylation
• phosphorylation
• ubiquitination

Question 19

What are the 3 classes of enzymes involved in histone modification?

Answer 19

• writers add groups e.g. acetylase
• erasers remove groups e.g. deacetylase
• readers identify the modification and alter gene activity and protein production e.g. chromodomain

Question 20

What does the histone code hypothesise?

Answer 20

DNA transcription is in part regulated by covalent histone tail modifications

Question 21

Where is heterochromatin mostly found?

Answer 21

centromeres and telomeres

Question 22

What is active euchromatin?

Answer 22

least condensed transcriptionally active chromatin form that accounts for ~10% of DNA

Question 23

What is inactive euchromatin?

Answer 23

the intermediate compaction form that is transcriptionally inactive

Question 24

What does higher order chromatin compaction produce?

Answer 24

solenoids

Question 25

What are solenoids?

Answer 25

nucleosomes that are folded up and stacked, forming a helix connected by bent linker DNA which positions sequential nucleosomes adjacent to one another in the helix with the H1 proteins facing toward the centre

Question 26

What are lampbrush chromosomes?

Answer 26

the largest known chromosome that contain loops of decondensed chromatin and are highly active in gene expression

Question 27

Where is most DNA in chromosomes?

Answer 27

condensed in the chromomeres on the axis

Question 28

What are chromosome puffs?

Answer 28

diffuse swellings along the regularly banded arms of polytene chromosomes that mostly arise from the decondensation of a single chromosome band

Question 29

How are interphase chromosomes folded?

Answer 29

into a series of looped domains condensed into a 30nm fibre

Question 30

When will individual loops decondense in interphase chromosomes?

Answer 30

when the cell requires direct access to the DNA packaged into these loops brought about by chromatin modifying enzymes or proteins

Question 31

What is alpha satellite?

Answer 31

the major repeated DNA element of primate centromeres that is AT-rich and flanked by centric heterochromatin

Question 32

What does the kinetochore of an alpha satellite consist of?

Answer 32

an inner and outer plate, formed by a set of kinetochore proteins

Question 33

What are telomeres?

Answer 33

regions of repetitive DNA sequences at the ends of chromosomes (GGGTTA in humans)

Question 34

Why is telomerase used?

Answer 34

to ensure that no crucial gene sequences are lost in replication

Question 35

What are T loops?

Answer 35

the protruding 5' end of elongated telomere DNA that tucks into the duplex DNA of the telomeric repeat sequence

Question 36

What are the under-acetylated histones bound by in heterochromatin?

Answer 36

silent information regulator (Sir) proteins

Question 37

What do Sir proteins do?

Answer 37

promote the formation of heterochromatin at telomeres, rDNA, and other silent loci through deacetylation of histone N-terminal tails

Question 38

What does deacetylation by Sir2 help to do?

Answer 38

create new binding sites on nucleosomes for more Sir protein complexes

Question 39

What are gene families?

Answer 39

genes related by DNA sequence that likely arose from duplications

Question 40

What are the different modes of genetic innovation?

Answer 40

- intragenic mutation - gene duplication - DNA segment shuffling

Question 41

What are paralogous sequences?

Answer 41

homologous sequences separated by a gene duplication event

Question 42

What are orthologous genes?

Answer 42

genes in different species that evolved from a common ancestor by speciation that normally retain the same function in the course of evolution

Question 43

Give examples of genome elements other than genes

Answer 43

- retrotransposons - DNA-only transposons - duplications - simple repeats - gene regulatory elements

Question 44

What are LINEs and SINEs?

Answer 44

nonretroviral retrotransposons

Question 45

What do LINEs encode?

Answer 45

endonucleases and reverse transcriptases

Question 46

What are LINEs and SINEs biased towards respectively?

Answer 46

- LINEs = AT rich regions - SINEs = GC rich regions

Question 47

What are the 2 methods of transposition?

Answer 47

1. cut-and-paste mechanism 2. copy-and-paste mechanism

Question 48

What happens in the cut-and-paste mechanism of transposition?

Answer 48

transposase cuts dsDNA to remove a transposon from one genomic site then it is integrated into the traget site

Question 49

What happens in the copy-and-paste mechanism of transposition?

Answer 49

a ds insertion sequence circle transposition intermediate is generated from the donor site by replication and proceeds to integrate into a suitable dsDNA target

Question 50

What is a pseudogene?

Answer 50

a segment of DNA that structurally resembles a gene but is not capable of coding for a protein

Question 51

What are pseudogenes most often derived from?

Answer 51

genes that have lost their protein-coding ability due to accumulated mutations that have occurred over the course of evolution

Question 52

What are the 8 steps of LINEs propagation?

Answer 52

1. transcription 2. translation 3. nick host DNA 4. reverse transcription 5. RNase H removes RNA 6. single strand ligation 7. nick second host DNA strand 8. DNA pol fills in second strand

Question 53

What is mtDNA?

Answer 53

mostly circular 16.5kb maternally inherited DNA that clusters as nucleoids and lacks histones

Question 54

What is the organisation of mtDNA in humans?

Answer 54

- 2 rRNA - 22 tRNA - 13 protein-coding sequences