The Nature of Genetic Material Flashcards
What carries a human genome?
23 chromosomes + mtDNA
How do we talk about genomes?
Haploid Way
***Means we have 2 copies per genome
- Always refer to genome as haploid set of genetic material
Genome
Haploid set of genetic material
***Means we have 2 copies per genome
How do we visualize chromosomes?
Geimsa dye staining + Microscopy + Sorting
Steps for visualizing chromosomes
- Isolate cells
- Stain with Dye
- Splash on slide
- Organized by person into karyotype
Karyotype
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)
Who makes Karyotpes
Cytogenetics
***Isolate blood –> Grow cells for cell replication –> Isolate chromsomes
Cytogenetics
Detect and interoret chromosomal abnormalities
***Often world in hospital + often part of prenatal testing (look at neonatal fluid)
Making Karyotypes
Cells are collected –> Cells are then grown for a little while to initiate DNA replication –> Chromosomes are analyzed
Reproductive Genetic Tesing
- Prenatal Testing
- Preimplantation genetic diagnosis
***Looks at babies cells
Prenatal Testing
- Amniocentesis (16 weeks) – very invasive
- Chorionic vili sampling (11 weeks) – very invasive
- Maternal Blood testing (9 weeks)
Maternal Blood tesing
Less invasive prenatal testing
***Do karytype from blood testing
- Newer - Blood smear - Pregnanet mom = has DNA from developing fetus --> can seperate them and anylzye
Preimplantation genetic diagnosis
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
Curved Chromosomes
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
A – Telomere –> End of chromsomes
B – Eurochromatin
C – centromere
D – heterochromatin
E – Chromatid
F – Stister Chromatids
Eurochromatin Vs. heterochromatin
***Both banding pattersn
Eurochromatin – Light band
Heterochromatin – Dark band
Counting Number of Chromsomes
Count by the number of centromeres
Chromatd Counting
Example:
1 chromatid = 1 chromosome
Sister chromatids = 2 chromatids; 1 chromosome
Sister Chromatids
Replicated Chromatids
***Still 1 chromosome
Describing Chromsomes by Position of Centromere
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
Centromere
Proteins that bind to DNA to hold sister chromatids together
- Helps traffick chromsomes thorugh division
- Located in differnet places
Ways of describing chromosomes
- Size
- position of centromere
Telecentric in humans
There are no telecentric in humans
Human chromsomes
22 pairs of autosomes (non-sex)
1 Pair of sex chromosomes
What is seen in most karyotypes
Replicated pair of chromosomes – replicated pair of sister chromatids
***Karyotype – get pair of sister chromatids
Cohesions
Hold together sister chromatids together during mitosis
Seperation at the end of chromosomes
Only when cells under-go DNA replication – Seen in Karyotype because get bettwer pic if induce replication = get pair of sister chromatids in karyotypes
Type of DNA in Chromsomes
dsDNA – each Chromatid = dsDNA
Replication schematic
Homologous Chromosomes
One paternal + One Maternal
Normal State of Chromosomes
Not normally replicated homogougous chrosmomes with sister chromatids – only replicated if undergoing replications
Diploid
Have 2 homologous chromsomes (one maternal + One paternal)
***We are dilpoid
Haploid Number (N)
N –> Number of unique chromsomes in a set
Example – humans = 23
Ploidy
Number of comeplete sets of chromoeomes
***Number of copies
Example – humans = Diploid (2 sets)
Counting total chromosomes
Count the number of centromeres
Chromoeome math
of each type of chomosome (Ploidy #)X N = Total # of chromosomes
N = How many different kinds of chromsome
Example – Humans –> 2N=46
Example Chromosome Math
Chromosome haploid Number and PLoidy in species
Chromoosome haploid number (N) and Ploidy are specific to species
***Stays the same within species
Number of chromoromes and complexity
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
C- value
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)
Issue with genes
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
Genome packaging in prokaryotes
Genome packaging in Prokaryites is less organize than in Eukaryites
***Bacteria condesing DNA – not well organized in prokaryotes
Nuceloid
Region that contains condensed DNA/protein complexes attaches to unner memebrane
- Condensed region of DNA + Proteins -- have center with Nucleiod asscoiated proteins
Nuceloid Assciated proteins
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
Microdomains
Loop domains – help to condense bacterial chromosomes
Issue with NAPs
Doesn’t condense DNA enough = need to do supercoiling
Supercoiling
Helps package DNA into smaller spaces
Process of supercoiling
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
Bacterial DNA
Circular – winds a lot = then we get supercoiling –> it wants to compact
***Enzymes = wind DNA NOT actually coil it
Topisomerases
Enzymes that overwind DNA and underwind dsDNA
***They don’t actually compact DNA just overwind it
- Sits on top of DNA
What facilitates Supercoiling
Facilitated by enzymes – Topisomerases
Types of Topisomerases
have one that overwinds in the Positive direction and one that underwinds in the negative direction
Positive = over winds
Negitive = underwinds
Isomers
Different forms of the same thing
Why wind in positive vs. negitive
Don’t know why go in positive or negitive BUT most of coiling is in the positive in bacteria
Drugs + Topisomerase
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
DNA in bacteria
DNA is spilling out
Eukaryotic genes fitting in cells
Supercoiling isn’t enough = need to use Histones
Eukaryotic genome packaging
Very organized – uses Histones
Eukaryotic genes fitting in cells process
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
Shape of Histone
Octomer
Nucleosome
A single histone/DNA complex
***the fundemantal Subunit of chromatin
dsDNA wrapped around histones
Fundamental Subunit of chromatin
Nucleosome
5 histone proteins
H2A, H2B, H3, H4 –> forms an octomer
H1 = acts as a clamp
***Makes up nucleosome?
DNA wrapped around octomer
DNA – (145-147 BP) –> wrapped around the octomer 1.65 times
Forming DNA fibers
nucleosome –> 30 nm fiber –> 350 nm loops –> 250nm fibers + 700 nm fibers
350 nm loops
30 nm lopps = wrapp around by proteins
Pointing to line in chromosome
Technically pointing at many genes – very low resultion
700 nm fiber + 250 nm fiber
Fiber that you see on chromsome level
Banding pattern matching
Banding pattern = same between matched chromsomes in karyotypes
Cytogentic banding Nomenclature
Chromsome # –> Arm –> Band # –> band within band number…
Example – 3P2 –> 3P22 –> 3P22.1
P arm vs. Q arm
P = short arm (contains P telemorere)
Q = Longer arm (Q telomere)
***Seperated by centromere
Nomenclature – Chromsome #P/Q
Do 2 different people have the same banding pattern on Chromosomes?
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
Banding pattern in species
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
Things to notice in karyotype
- Trisomy (Annuploidy)
- 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
FISH
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
Purpose of FISH
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
RNA/DNA probe
5-10 kb in length – complementary to sequence of interest in region of genome
Extra use of FISH
Can be used to make probes so all chromsomes has different probes in different colors = “chromosome paintaing”
- Each chromsome is labeled differentley
Chromosomal Painting
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
Use of Karyotype
Gives us information on where to look deeoer
What does genome look like inside of a cell?
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
Why are chromsomes so organized on cell?
Likey allows for specific interactions between different chromsomes
***Could allow something on chromsome 3 to affect something on chromsome 20
Genomes in cells
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
When is DNA NOT condensed
DNA replication + gene expression (Transcription and translation)
Genome
The complete haploid set of genetic material in a virus, cell, or organelle
***The word genome can be contect specific
Genome counting
Virus – 1 genome
Bacteria – 1 genome
Animal cell – 2 genomes (Nucleus + Mitocindria)
Plant cell – 3 genomes (Nucleus + Mitocondria + Chloroplast)
Eukaryotic genomes
- 10 Mb - >100,000 Mb
- Contained in organelles
- Nucleus – multiple linear chromsomes + multiple copies of each chromsomes
- Mitochondria – 12kb-2400 kb –> cicular
- Chloroplast – 120kb-170 kb –> Circular
Eukaryotic Nuclear genome
Multiple linear Chromoeomes + multiple copies of each chromsome
Shape of mitochondria + Chrloplast DNA in Eukaryotes
Circular
Viruses
Infectious particles comprised of a genome surrounded by a protein coat
Viral Genomes
- 2000 - 1 Million BP of RNA or DNA
- Linear or circular
- Single-stranded OR double stranded OR segmented
Viral genome invasion
Viral genomes frequently invade the genomes of other organisms
Prokaryotes Genomes
- 1 Chromsome of DNA
- 0.5 - 12 Mb
- Circular - Found in Nuceloid
- Haploid
- 0.5 - 12 Mb
Plasmids
Types of Prokaryotes genomes – small circles of DNA
- 1 - 200 kbp
- Autonomously replicating
- NOT present in all bacteria
Where are plasmids found?
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
