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Yr 2 - EMS > Genome Anatomy > Flashcards

Genome Anatomy Flashcards

1
Q

What makes DNA good for storage?

A

Structure - far more stable

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2
Q

What sugar is DNA based off?

A

2’-deoxyribose

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3
Q

How does structure of RNA differ? How does this affect its

A

Has an OH on 2’ carbon –> chemically unstable Used instead for transient information transfer

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4
Q

In what direction is DNA and RNA synthesised?

A

In a 5’ to 3’

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5
Q

Does the sense or anti sense strand end up in the mRNA?

A

Sense –> this is the strand that would usually be written out for a gene

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6
Q

What is chromatin? What is a nucleosome?

A

Chromatin: Chromatin is the material that makes up a chromosome that consists of DNA and protein. The major proteins in chromatin are proteins called histones.

Nucleosome: The fundamental subunit of chromatin. Each nucleosome is composed of a little less than two turns of DNA wrapped around a set of eight proteins called histones

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7
Q

What is a chromatid?

A

1/2 of a replicated chromosome. Prior to cell division, chromosomes are copied and identical chromosome copies join together at their centromeres. Each strand of one of these chromosomes is a chromatid. Joined chromatids are known as sister chromatids.

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8
Q

What is the core of a nucleosome?

A

A histone octamer –> a set of 8 proteins

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9
Q

What is the centromere?

A

Narrowing near centre of chromosome where mitotic spindle is attached

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10
Q

What separates the short from the long arm of the chromosome?

A

Centromere

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11
Q

What is the short and long arm of the chromosome referred to respectively?

A

Short - (p) Long (q)

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12
Q

What is a telomere (tel)?

A

A region of repetitive nucleotide sequences at each end of a chromosome e.g. qtel / ptel

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13
Q

What is function of telomere?

A

Protects the end of the chromosome from deterioration or from fusion with neighbouring chromosomes

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14
Q

What is a chromosome ideogram?

A

Provide a schematic representation of chromosomes. They are used to show the relative size of the chromosomes and their characteristic banding patterns.

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15
Q

What is the maximum resolution achievable in the human genome using ideograms?

A

About 850 bands

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16
Q

What is typically used to describe location of genetic variants / genetic features?

A

Chromosome coordinates

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17
Q

What is haploinsufficiency?

A

Haploinsufficiency describes the situation where having only a single functioning copy of a gene is not enough for normal function, so that loss‐of‐function mutations cause a dominant phenotype.

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18
Q

Are all autosomes haploinsufficient?

A

Yes

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19
Q

What is exempt from haploinsufficiency?

A

X chromosome - Only one working copy is necessary/sufficient for normal expression of the gene’s function. The functional allele of a haplosufficient gene is dominant. The non-functional allele of a haplosufficient gene is recessive.

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20
Q

What are the pseudoautosomal regions?

A

Homologous sequences of nucleotides on the X and Y chromosomes

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21
Q

What does the term ‘x-unique’ refer to?

A

Many genes are unique to the X chromosome, but genes in the pseudoautosomal regions are present on both sex chromosomes.

X-unique genes are unique only to the X chromosome. This means males are hemizygous for most genes on sex chromosomes (has only one member of a chromosome pair or chromosome segment rather than the usual two)

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22
Q

What does hemizygous mean? Does this feature in males or females?

A

Hemizygous is a condition in which only one copy of a gene or DNA sequence is present in diploid cells.

Males are hemizygous for most genes on sex chromosomes, having only one X and one Y chromosome.

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23
Q

What makes up the majority of the Y chromosome?

A

Heterochromatin

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24
Q

What is heterochromatin?

A

a tightly packed form of DNA

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25
Q

There are only a few unique genes on the Y chromosome. What is the most important one?

A

SRY –> sex determining region

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26
Q

What is SRY responsible for?

A

Testes formation

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27
Q

Does the number of chromosomes remain constant thoughout the life cycle of a cell? Does the DNA content?

A

Yes

No –> replication (4n), separation

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28
Q

What are sister chromatids?

A

Identical copies formed by the DNA replication of a chromosome, joined together by a centromere. Is ‘one-half’ of the duplicated chromosome.

4n

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29
Q

How are sister chromatids formed?

A

Chromosome replicates (2n becomes 4n)

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30
Q

What then happens to sister chromatids?

A

Separate at mitosis

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31
Q

What proportion of our genome is non coding DNA?

A

>90%

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32
Q

What is mitochrondrial DNA? Where is it found?

A

The small circular chromosome found inside mitochondria (powerhouse of cell)

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33
Q

Describe difference in location between nuclear and mitochondrial DNA?

A

Nuclear DNA is located within the nucleus of eukaryote cells while mitochondrial DNA is located in the mitochondria in cytoplasm

34
Q

How many genes does the mitochondrial DNA contain?

A

37

35
Q

Describe difference in structure between mitochondrial and nuclear DNA

A

Circular vs linear

36
Q

How is mitochondrial genome inherited?

A

Maternal (oocyte) inheritance –> passed on in cytoplasm of oocyte

37
Q

What 2 sequences can the human genome be broken down into?

A
  1. Single-copy sequences (non-repetitive)
  2. Repetitive sequences
38
Q

How do single-copy and repetitive sequences differ?

A

Single-copy sequences are unique and are translated and code for proteins

Repetitive sequences are not translated (typically non-coding)

39
Q

Are genes single-copy sequences or repetitive?

A

Single-copy (are translated)

40
Q

What 2 main types can repetitive sequences be subdivided into?

A
  1. Satellite DNA
  2. Interspersed repeats
41
Q

What does satellite DNA consist of?

A

Large blocks of repetitive sequences (heterochromatin) at specific locations

42
Q

Where are interspersed repeats found?

A

Scattered throughout genome

43
Q

What is transcription?

A

Information in strand of DNA is copied into RNA

44
Q

What is translation?

A

Turning RNA into protein

45
Q

Where does translation occur?

A

Cytoplasm

46
Q

Gene structure

A
47
Q

What are introns?

A

A portion of a gene that does not code for amino acids so is not expressed –> have to be removed from primary RNA transcript by splicing

48
Q

What is splicing governed by?

A

Specific sequences at junctions between exons and introns –> splice doner and splice acceptor sites

49
Q

What is the TATA box?

A

Promoter sequence –> specifies to other molecules where transcription begins

50
Q

What is alternative splicing?

A

A process by which exons or portions of exons or noncoding regions within a pre-mRNA transcript are differentially joined or skipped, resulting in multiple protein isoforms being encoded by a single gene

51
Q

What is exon skipping?

A

A form of alternative splicing

Certain exons are skipped resulting in various forms of mature mRNA

52
Q

What is mutually exclusive exon choice?

A

A form of alternative splicing where only one of two or more candidate exons is spliced into the mature mRNA isoform

53
Q

What does alternative splicing give rise to?

A

2 different proteins which are identical at end terminal regions but differ in small domain in centre

54
Q

What are pseudogenes?

A

Nonfunctional segments of DNA that resemble functional genes

55
Q

How do psuedogenes come about?

A

Unnecessary copies of functional genes, either directly by DNA duplication or indirectly by reverse transcription of an mRNA transcript

56
Q

What are processed genes?

A

Intronless copies of other genes, usually remote from the parent gene.

57
Q

How do processed genes come about?

A

Copies of messenger RNAs have been reverse transcribed into DNA and inserted into the genome

58
Q

What is reverse transcription and where is it commonly seen?

A

Te reverse process of the normal transcription in which the RNA template is copied to form a cDNA molecule in retroviruses (e.g. HIV)

59
Q

Are processed genes functional or non-functional?

A

Mostly non-functional

60
Q

What is satellite DNA?

A

Large blocks found at centromeres consisting of heterochromatic chromosomal regions –> simple tandemly repeated sequences

61
Q

What is genetic polymorphism?

A
  • The inheritance of a trait controlled by a single genetic locus with two alleles, in which the least common allele has a frequency of about 1% or greater.
  • Genetic polymorphism is a difference in DNA sequence among individuals, groups, or populations.
62
Q

What type of DNA is alphoid DNA?

A
  • A type of satellite DNA found at centromeres
  • 171-bp repeat unit
63
Q

What is alphoid DNA required for biologically?

A

The assembly of the centromere

64
Q

What is FISH?

A
  • A molecular cytogenetic technique that uses fluorescent probes that bind to only those parts of a nucleic acid sequence with a high degree of sequence complementarity
  • Detects and localises the presence or absence of specific DNA sequences on chromosomes
  • FISH can also be used to detect and localise specific RNA targets (mRNA, lncRNA and miRNA) in cells, circulating tumor cells, and tissue samples
65
Q

Why is FISH able to be used with alphoid DNA?

A

Repeat unit sequence shows chromosome specific sequence variation

66
Q

How does FISH work?

A

The first step is to prepare short sequences of single-stranded DNA that match a portion of the gene the researcher is looking for. These are called probes. The next step is to label these probes by attaching one of a number of colors of fluorescent dye.DNA is composed of two strands of complementary molecules that bind to each other like chemical magnets. Since the researchers’ probes are single-stranded, they are able to bind to the complementary strand of DNA, wherever it may reside on a person’s chromosomes. When a probe binds to a chromosome, its fluorescent tag provides a way for researchers to see its location.

67
Q

How are alphoid probes generated?

A

Generated from repetitive sequences found in the middle of each chromosome

68
Q

How does the dispersion of interspersed repeats differ from satellite DNA?

A

Scattered around the genome, not in large blocks

69
Q

What is the most widespread of the interspersed repeats?

A

Alu repeat which is a member of SINE family (short interspersed nuclear element)

70
Q

How much of your genome is composed of Alu repeats?

A

5%

71
Q

What is retrotransposition?

A

Insertion of DNA sequences mediated by an RNA intermediate

72
Q

How are Alu repeats dispersed?

A

By retrotransposition

73
Q

What is the difference between repetitive and single-copy DNA?

A

Single-copy: a unique sequence that code for proteins and undergoes transcription.

Repetitive: the sequence that has repeated sequences of nucleotides in the DNA and that don’t code for proteins.

74
Q

Where is single-copy DNA found?

A

In exons or euchromatin

75
Q

Where is repetitive DNA found?

A

In introns or the heterochromatin

76
Q

What is the difference between satellite and interspersed DNA?

A

Interspersed nuclear fragments, including MIRs and LINEs, are distributed throughout the genome, whereas satellite sequences are clustered in discrete areas (e.g. centromeres)

77
Q

What is alternative splicing? What is its function?

A

Alternative splicing is a process that enables mRNA to direct synthesis of different protein variants that may have different cellular functions or properties. It occurs by rearranging the pattern of intron and exons that are joined by splicing to alter the mRNA coding sequence.

78
Q

What is alphoid DNA and where is it found?

A

A complex family of repetitive DNA sequences found in the centromeric heterochromatin of human chromosomes.

79
Q

Alphoid vs Alu?

A

Alu - interspersed

Alphoid - satellite

80
Q

What are retrotransposons?

A

Retrotransposons copy and paste themselves into different genomic locations by converting RNA back into DNA through the process reverse transcription

Yr 2 - EMS (60 decks)

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