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Genes, Genomes and Biomedical Implications > DNA Organisation and Packaging > Flashcards

DNA Organisation and Packaging Flashcards

1
Q

What happens during interphase?

A
  • the cell is actively expressing genes
  • DNA is replicated
  • chromosomes are duplicated
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2
Q

What happens once DNA replication is complete?

A

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

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3
Q

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

A

telomere, replication origin and centromere

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4
Q

What does each chromosome have?

A

multiple origins of replication, one centromere, and two telomeres

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5
Q

What do origins of replication do?

A

initiate replication bubbles

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6
Q

What are replication bubbles?

A

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

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7
Q

When do origins of replication activate?

A

S phase

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8
Q

What do DNA binding proteins do?

A

package DNA into a compact and less fragile form

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9
Q

What is the net result of DNA packaging?

A

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

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10
Q

What is chromatin?

A

DNA complexed with histones

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11
Q

What are histones?

A

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

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12
Q

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

A

by digestion of the linker DNA with a nuclease

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13
Q

What is the nucleosome protein core made up of?

A

2 pairs of H2A, H2B, H3 and H4

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14
Q

What does each core histone contain?

A
  • N-terminal tail which can be covalently modified
  • a histone fold region
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15
Q

How do the histone heterodimers form tetramers?

A

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

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16
Q

How do histone pairs form heterodimers?

A

α helices loop into the histone folds

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17
Q

What do H1 histones do?

A

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

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18
Q

Give examples of histone modifications

A
  • methylation
  • acetylation
  • phosphorylation
  • ubiquitination
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19
Q

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

A
  • 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
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20
Q

What does the histone code hypothesise?

A

DNA transcription is in part regulated by covalent histone tail modifications

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21
Q

Where is heterochromatin mostly found?

A

centromeres and telomeres

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22
Q

What is active euchromatin?

A

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

23
Q

What is inactive euchromatin?

A

the intermediate compaction form that is transcriptionally inactive

24
Q

What does higher order chromatin compaction produce?

A

solenoids

25
Q

What are solenoids?

A

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

26
Q

What are lampbrush chromosomes?

A

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

27
Q

Where is most DNA in chromosomes?

A

condensed in the chromomeres on the axis

28
Q

What are chromosome puffs?

A

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

29
Q

How are interphase chromosomes folded?

A

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

30
Q

When will individual loops decondense in interphase chromosomes?

A

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

31
Q

What is alpha satellite?

A

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

32
Q

What does the kinetochore of an alpha satellite consist of?

A

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

33
Q

What are telomeres?

A

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

34
Q

Why is telomerase used?

A

to ensure that no crucial gene sequences are lost in replication

35
Q

What are T loops?

A

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

36
Q

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

A

silent information regulator (Sir) proteins

37
Q

What do Sir proteins do?

A

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

38
Q

What does deacetylation by Sir2 help to do?

A

create new binding sites on nucleosomes for more Sir protein complexes

39
Q

What are gene families?

A

genes related by DNA sequence that likely arose from duplications

40
Q

What are the different modes of genetic innovation?

A
  • intragenic mutation
  • gene duplication
  • DNA segment shuffling
41
Q

What are paralogous sequences?

A

homologous sequences separated by a gene duplication event

42
Q

What are orthologous genes?

A

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

43
Q

Give examples of genome elements other than genes

A
  • retrotransposons
  • DNA-only transposons
  • duplications
  • simple repeats
  • gene regulatory elements
44
Q

What are LINEs and SINEs?

A

nonretroviral retrotransposons

45
Q

What do LINEs encode?

A

endonucleases and reverse transcriptases

46
Q

What are LINEs and SINEs biased towards respectively?

A
  • LINEs = AT rich regions
  • SINEs = GC rich regions
47
Q

What are the 2 methods of transposition?

A
  1. cut-and-paste mechanism
  2. copy-and-paste mechanism
48
Q

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

A

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

49
Q

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

A

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

50
Q

What is a pseudogene?

A

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

51
Q

What are pseudogenes most often derived from?

A

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

52
Q

What are the 8 steps of LINEs propagation?

A
  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
53
Q

What is mtDNA?

A

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

54
Q

What is the organisation of mtDNA in humans?

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

Genes, Genomes and Biomedical Implications (15 decks)

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