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BIOL332 > The Nature of Genetic Material > Flashcards

The Nature of Genetic Material Flashcards

1
Q

What carries a human genome?

A

23 chromosomes + mtDNA

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2
Q

How do we talk about genomes?

A

Haploid Way

***Means we have 2 copies per genome
- Always refer to genome as haploid set of genetic material

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3
Q

Genome

A

Haploid set of genetic material

***Means we have 2 copies per genome

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4
Q

How do we visualize chromosomes?

A

Geimsa dye staining + Microscopy + Sorting

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5
Q

Steps for visualizing chromosomes

A
  1. Isolate cells
  2. Stain with Dye
  3. Splash on slide
  4. Organized by person into karyotype
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6
Q

Karyotype

A

Image of organized chromosomes - refers to individuals complete set of chromosomes ALSO refers to the image of a persons organized chromosomes

Ex. 46XX or 46XY (humans have 23 pairs of chromosomes = 46 total)

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7
Q

Who makes Karyotpes

A

Cytogenetics
***Isolate blood –> Grow cells for cell replication –> Isolate chromsomes

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8
Q

Cytogenetics

A

Detect and interoret chromosomal abnormalities
***Often world in hospital + often part of prenatal testing (look at neonatal fluid)

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9
Q

Making Karyotypes

A

Cells are collected –> Cells are then grown for a little while to initiate DNA replication –> Chromosomes are analyzed

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10
Q

Reproductive Genetic Tesing

A
  1. Prenatal Testing
  2. Preimplantation genetic diagnosis
    ***Looks at babies cells
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11
Q

Prenatal Testing

A
  1. Amniocentesis (16 weeks) – very invasive
  2. Chorionic vili sampling (11 weeks) – very invasive
  3. Maternal Blood testing (9 weeks)
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12
Q

Maternal Blood tesing

A

Less invasive prenatal testing
***Do karytype from blood testing

- Newer
- Blood smear 
- Pregnanet mom = has DNA from developing fetus --> can seperate them and anylzye
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13
Q

Preimplantation genetic diagnosis

A

Can only done with IVF –> fertilzie egg –> get blastocyte –> use mircotweezers –> get 1 cell –> Get genetics of cell –> choose zygote to implant

***More recent with CRSIPR becaise can edit genome

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14
Q

Curved Chromosomes

A

Doesn’t actually mean anything – just a way it fell on a slide
***When lkayrotyoe is done = blood cells in pippete and drop on slide and then they splatter = can lead to weird –> take pic and it might be curved because it landed curved

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15
Q
A

A – Telomere –> End of chromsomes
B – Eurochromatin
C – centromere
D – heterochromatin
E – Chromatid
F – Stister Chromatids

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16
Q

Eurochromatin Vs. heterochromatin

A

***Both banding pattersn
Eurochromatin – Light band
Heterochromatin – Dark band

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17
Q

Counting Number of Chromsomes

A

Count by the number of centromeres

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18
Q

Chromatd Counting

A

Example:
1 chromatid = 1 chromosome

Sister chromatids = 2 chromatids; 1 chromosome

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19
Q

Sister Chromatids

A

Replicated Chromatids
***Still 1 chromosome

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20
Q

Describing Chromsomes by Position of Centromere

A

Metacentric vs. Submetacentric vs. Acrocentric vs. telecentric

Metacentric – In the center
Submetacentric – Off but not too off
Acrocentric – very off center
Telocentric – at the end

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21
Q

Centromere

A

Proteins that bind to DNA to hold sister chromatids together
- Helps traffick chromsomes thorugh division
- Located in differnet places

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22
Q

Ways of describing chromosomes

A
  1. Size
  2. position of centromere
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23
Q

Telecentric in humans

A

There are no telecentric in humans

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24
Q

Human chromsomes

A

22 pairs of autosomes (non-sex)
1 Pair of sex chromosomes

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25
Q

What is seen in most karyotypes

A

Replicated pair of chromosomes – replicated pair of sister chromatids

***Karyotype – get pair of sister chromatids

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26
Q

Cohesions

A

Hold together sister chromatids together during mitosis

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27
Q

Seperation at the end of chromosomes

A

Only when cells under-go DNA replication – Seen in Karyotype because get bettwer pic if induce replication = get pair of sister chromatids in karyotypes

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28
Q

Type of DNA in Chromsomes

A

dsDNA – each Chromatid = dsDNA

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29
Q

Replication schematic

A
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30
Q

Homologous Chromosomes

A

One paternal + One Maternal

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31
Q

Normal State of Chromosomes

A

Not normally replicated homogougous chrosmomes with sister chromatids – only replicated if undergoing replications

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32
Q

Diploid

A

Have 2 homologous chromsomes (one maternal + One paternal)

***We are dilpoid

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33
Q

Haploid Number (N)

A

N –> Number of unique chromsomes in a set

Example – humans = 23

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34
Q

Ploidy

A

Number of comeplete sets of chromoeomes

***Number of copies

Example – humans = Diploid (2 sets)

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35
Q

Counting total chromosomes

A

Count the number of centromeres

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36
Q

Chromoeome math

A

of each type of chomosome (Ploidy #)X N = Total # of chromosomes

N = How many different kinds of chromsome

Example – Humans –> 2N=46

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37
Q

Example Chromosome Math

A
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38
Q

Chromosome haploid Number and PLoidy in species

A

Chromoosome haploid number (N) and Ploidy are specific to species

***Stays the same within species

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39
Q

Number of chromoromes and complexity

A

No rule for how many chromosome an organism has –> in 1950s there was a guess that the number of chromsomes correlates to complexity BUT turns out that this is not true – no correlation

***Organismal complexity is NOT correlated with N, Ploidy, Or number of genes

40
Q

C- value

A

Amount of nucelur DNA in gamete (halpoid) irrespective of ploidy
- Number of chromsomes + length of DNA = correspondes to complexity – NOT TRUE
***Was originally hypothesized to be a measure of gene capacity (THIS WAS WRONG)

41
Q

Issue with genes

A

Genomes are much longer than cells BUT they need to fit inside

Math:
1 bp = 3.4 A = 3.4 X 10^-10
Human genome = 3 Billion BP/cell
37.2 triullion cells/body
END – 3.79 X 10^13 emters of DNA in body

***The DNA in your body can wrap around the globe 9,475,000 times

Other example – A prokaryote genomes is 34,000 tiumes longer than an avergae bacteria

42
Q

Genome packaging in prokaryotes

A

Genome packaging in Prokaryites is less organize than in Eukaryites
***Bacteria condesing DNA – not well organized in prokaryotes

43
Q

Nuceloid

A

Region that contains condensed DNA/protein complexes attaches to unner memebrane

  - Condensed region of DNA + Proteins -- have center with Nucleiod asscoiated proteins
44
Q

Nuceloid Assciated proteins

A

Bind to repatatiuve sequences to form loops of supercoilled DNA
***10,000 BP/loop
- Loop in DNA –> Loppes = DNA held together ay center by NAPs
- Bind chromsomes tigether to fit in nucleiod

45
Q

Microdomains

A

Loop domains – help to condense bacterial chromosomes

46
Q

Issue with NAPs

A

Doesn’t condense DNA enough = need to do supercoiling

47
Q

Supercoiling

A

Helps package DNA into smaller spaces

48
Q

Process of supercoiling

A

Just keeps winding – when it keeps winding it wants to condense all together –> loops in on self to reelive the tension of winding

***Wind a lot = then we get supercoiling – Keep winding = it wants to compact

***Enzymes = wind DNA NOT actually coiling it

49
Q

Bacterial DNA

A

Circular – winds a lot = then we get supercoiling –> it wants to compact

***Enzymes = wind DNA NOT actually coil it

50
Q

Topisomerases

A

Enzymes that overwind DNA and underwind dsDNA
***They don’t actually compact DNA just overwind it

- Sits on top of DNA
51
Q

What facilitates Supercoiling

A

Facilitated by enzymes – Topisomerases

52
Q

Types of Topisomerases

A

have one that overwinds in the Positive direction and one that underwinds in the negative direction

Positive = over winds
Negitive = underwinds

53
Q

Isomers

A

Different forms of the same thing

54
Q

Why wind in positive vs. negitive

A

Don’t know why go in positive or negitive BUT most of coiling is in the positive in bacteria

55
Q

Drugs + Topisomerase

A

Drugs that inhibit Topisomerase are one type of chemotheraputic agnge
**Prevents the cell from replacating because to divide they need to replicate
**Especially used in lung cancer

56
Q

DNA in bacteria

A

DNA is spilling out

57
Q

Eukaryotic genes fitting in cells

A

Supercoiling isn’t enough = need to use Histones

58
Q

Eukaryotic genome packaging

A

Very organized – uses Histones

59
Q

Eukaryotic genes fitting in cells process

A

dsDNA = wraps around histone complex –> get nucleosome –> Wraps around Histone li7 and and 1 histone that anchors it –> get 30 nm fiber

dsDNA –> Nuleosome –> 30 nm fiber

60
Q

Shape of Histone

A

Octomer

61
Q

Nucleosome

A

A single histone/DNA complex
***the fundemantal Subunit of chromatin
dsDNA wrapped around histones

62
Q

Fundamental Subunit of chromatin

A

Nucleosome

63
Q

5 histone proteins

A

H2A, H2B, H3, H4 –> forms an octomer
H1 = acts as a clamp

***Makes up nucleosome?

64
Q

DNA wrapped around octomer

A

DNA – (145-147 BP) –> wrapped around the octomer 1.65 times

65
Q

Forming DNA fibers

A

nucleosome –> 30 nm fiber –> 350 nm loops –> 250nm fibers + 700 nm fibers

66
Q

350 nm loops

A

30 nm lopps = wrapp around by proteins

67
Q

Pointing to line in chromosome

A

Technically pointing at many genes – very low resultion

68
Q

700 nm fiber + 250 nm fiber

A

Fiber that you see on chromsome level

69
Q

Banding pattern matching

A

Banding pattern = same between matched chromsomes in karyotypes

70
Q

Cytogentic banding Nomenclature

A

Chromsome # –> Arm –> Band # –> band within band number…

Example – 3P2 –> 3P22 –> 3P22.1

71
Q

P arm vs. Q arm

A

P = short arm (contains P telemorere)
Q = Longer arm (Q telomere)

***Seperated by centromere

Nomenclature – Chromsome #P/Q

72
Q

Do 2 different people have the same banding pattern on Chromosomes?

A

YES – Logical because in karyotype you see the mom and dad chromsomes and match them by banding pattern –> Two different people gave you each BUT you can still match them up by banding pattern because everyone has the same banding pattern

***All individuals in the same species = have the same banding pattern

73
Q

Banding pattern in species

A

All individuals in the same species have the same banding pattern –> very evolutionary conserved
***Know very evolutionarily conversed because have similar banding patterns to other species

74
Q

Things to notice in karyotype

A
  1. Trisomy (Annuploidy)
  2. It you have two chromsomes aligned that look different

Example – In image – Chromsome 6 = the banding pattern looks different
- Area that the person woudl look at because there is abnormality

75
Q

FISH

A

Flourecent in-situ hybridization – A DNA or RNA probe (5-10 kb in length) complementary to a specific region of the genome is hydridized to chromsomes

USE: Used to visulaize specific regions of genome – typically used when abnormalities are suspected

76
Q

Purpose of FISH

A

Allows for fine-grained information from chromosome visualization
- Can look at specific gene on chromsome
- Might look at abnormal region seen in Karyotype
- FISH = can identofy differences in base pair order

77
Q

RNA/DNA probe

A

5-10 kb in length – complementary to sequence of interest in region of genome

78
Q

Extra use of FISH

A

Can be used to make probes so all chromsomes has different probes in different colors = “chromosome paintaing”
- Each chromsome is labeled differentley

79
Q

Chromosomal Painting

A

FISH techqniue – simulatenously probes for sequences alomg each chromsome – labes each one a diffreent color

Example –image
- Chromosme 6 (HAS MUTATION) = Has white band (weird region) – shows that it should normally be on chromsome 9 (because chromsome 9 is white)
***This is all we know about the weird abnormality – limit of karyotyoe

80
Q

Use of Karyotype

A

Gives us information on where to look deeoer

81
Q

What does genome look like inside of a cell?

A

They are organized – very ordered (often order in the same way)

**Chromomes occupy specific terrotories within the nucelus
**We know from chromsome paninting using FISH inside a cell

82
Q

Why are chromsomes so organized on cell?

A

Likey allows for specific interactions between different chromsomes

***Could allow something on chromsome 3 to affect something on chromsome 20

83
Q

Genomes in cells

A

Genomes are dynamic – genomes are opening and closing all of the time

***Sometimes our cells need to “see” the DNA in uncondensed form – regions of genomes will condense and de-condense at different times

84
Q

When is DNA NOT condensed

A

DNA replication + gene expression (Transcription and translation)

85
Q

Genome

A

The complete haploid set of genetic material in a virus, cell, or organelle

***The word genome can be contect specific

86
Q

Genome counting

A

Virus – 1 genome

Bacteria – 1 genome

Animal cell – 2 genomes (Nucleus + Mitocindria)

Plant cell – 3 genomes (Nucleus + Mitocondria + Chloroplast)

87
Q

Eukaryotic genomes

A
  1. 10 Mb - >100,000 Mb
  2. Contained in organelles
    • Nucleus – multiple linear chromsomes + multiple copies of each chromsomes
    • Mitochondria – 12kb-2400 kb –> cicular
    • Chloroplast – 120kb-170 kb –> Circular
88
Q

Eukaryotic Nuclear genome

A

Multiple linear Chromoeomes + multiple copies of each chromsome

89
Q

Shape of mitochondria + Chrloplast DNA in Eukaryotes

A

Circular

90
Q

Viruses

A

Infectious particles comprised of a genome surrounded by a protein coat

91
Q

Viral Genomes

A
  • 2000 - 1 Million BP of RNA or DNA
    • Linear or circular
    • Single-stranded OR double stranded OR segmented
92
Q

Viral genome invasion

A

Viral genomes frequently invade the genomes of other organisms

93
Q

Prokaryotes Genomes

A
  • 1 Chromsome of DNA
    • 0.5 - 12 Mb
      - Circular
    • Found in Nuceloid
    • Haploid
94
Q

Plasmids

A

Types of Prokaryotes genomes – small circles of DNA
- 1 - 200 kbp
- Autonomously replicating
- NOT present in all bacteria

95
Q

Where are plasmids found?

A

Found in some prokryotes (NOT present in all bacteria) + are sometimes found in Eukaryotes cells
***Plasmids in Eukaryotic cells = not often considered when people use the term genome

BIOL332 (25 decks)

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