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The genome in general

A genome includes all the genetic information for a given species

Human genome: all the genetic information on the 22 autosomal plus the sex chromosomes (x and y)

In higher eukaryotes the genome is composed of mostly non coding regions. It is speculated that only 3-5% of DNA in humans actually codes for genes

1

What is a gene?

A gene is a sequence of DNA nucleotides

The sequence holds a "code" with all of the information needed to make protein or RNA, can code for more than one protein

Alleles are the "forms" of the gene- Found in physical location of chromosome- locus. DNA and genome are the same in all cells. Use switches to turn on and off genes, control of gene expression.

2

Non coding DNA

no information, does not code for proteins or RNA. However noncoding DNA Controls which genes are turned on or which proteins are translated

3

Simple representation of a gene

Promoter region- Series of base pairs. recognized by proteins so that it can be transcribed.


Protein coding region- most information carried in DNA. In protein coding regions: introns (non coding, found in genes, only transcribed ) exons (protein coding, will be translated)

4

Organism complexity

With 
increasing
 complexity
 there
 is
 an
 increase 
in
 the
 number 
of
 genes

5

Decreasing gene density

Larger genome, more genes, decreasing gene density (number of genes per number of base pairs)

6

Amount of DNA

DNA of bacterium is about 1000times as long as the length of the cell

The DNA of a human cell is about 100,000 times the cell diameter and consists of about 3 x 10^9 base pairs

Many plants have more DNA than humans. Polyploidy- entire genome is doubled during the evolutionary history of the plant

Size of genome does not indicate size of organism

7

Chromosomes

Linear array of genes, DNA wrapped around histone proteins to form nucleosomes

Each chromosome in a cell contains only one single DNA molecule

Circular in DNA but linear in eukaryotic cells

Circular DNA also found in mitochondria, chloroplasts and some viruses (endosymbiosis)

8

Centromere

In the center of the chromosome

9

Telomeres

End of chromosomes, Common microsatellite, has a sticky end complimentary to other telomeres. Chromosome fusion can result

10

Closely related species

May have different number of chromosomes due to fusion

Similar DNA sequences different chromosomal anatomy. Can cause a speciation event

11

Ape chromosomal arrangements

Overall DNA sequence very similar, but humans have one chromosome where apes have 2

12

Between the genes

Non coding regions and repetitive DNA

•  Satellite,
 minisatellite
 and
 microsatellite
 DNAs
 refer to repetitive sequences, reanneal more rapidly than a unique sequence of DNA - number of repeated, genetic fingerprint

Analysis of these sequences forms the basis for DNA fingerprinting and act as markers in complex genomes, many times being used for mapping other genes

Location of these repeated sequences can be determined using FISH with a repeat sequence as the probe

13

Hybridization

Hybridization can occur between two complimentary strands (don't have to be exactly complimentary)

If you have a mixture of Nucleic acid strands, those that are complimentary will anneal more readily

Temperature important- more GC higher temp needed

14

Probes

Can be used to find complimentary sequences in larger fragments by fluorescence



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Stringency

High stringency refers toast concentrations and temperatures that allow only perfectly complimentary sequences to hybridize

Low stringency refers to conditions that allow hybridization even when a number of mismatches are present, lower temperature

Heteroduplex- mismatched hybrid

16

Florence in situ hybridization

Double stranded DNA on slide treated with hot salt solution to denature it

Incubate with biotnylated probe, then wash to remove unhybridized DNA

Incubate with flourescently labeled avidin to reveal location of probe

Localization of satellite DNA

17

Where is highly repetitive DNA found?

Centromeres and telomeres

18

Diseases associated with repetitive DNA

Myotonic distrophy (non coding region)

Fragile x- tremors (non-coding region)- Repeats hang off chromosomes. At a certain length of tri nucleotide repeats the strand breaks off

Huntington's chorea (coding region) - Fewer than 36 repeats you don't develop the disease. The more repeats the more severe. Establishes well after maturity

19

Comparing genomes

Prokaryotes- no repetitive DNA, genes that are close to each other, very few introns

Eukaryotes- DNA concentrated at middle and end interspersed, interspersed genes, many introns within genes

20

Chloroplast genome

Encodes enzymes involved in photosynthesis

21

Mitochondrial genome

Get it from your mom

Genes that code for proteins in mitochondria for electron transport/ ATP production

22

Endosymbiotic theory

Original prokaryotic host cell with DNA engulfs aerobic bacteria

Photosynthetic bacteria become chloroplasts and the other bacteria become mitochondria

23

Lateral gene transfer- intercompartmental

Damage to the organelle membranes

Non-homologous end joining allows pieces of the DNA to enter the nuclear genome

24

Tracking DNA sequences through endosymbiosis

Photosynthetic bacterium ingested by eukaryote and by secondary endosymbiosis some alga was eaten and retained in eukaryotes. Can track it, similar DNA sequences

25

Packaging of DNA

DNA wraps around proteins called histones

Histones wrap around themselves twice and then form looped regions around a protein scaffold

These are found in a metaphase chromosome

Packaging is important because some parts of the DNA need to be available at certain times

26

Two models for chromatin structure (histones)

Solenoid

Zig zag

27

Histones have similarities

8 protein parts

N terminal tail and a histone fold

H2A and H2B dimer

H3H4 tetramer

28

Histone octamer

Two dimers and tetramer

High ionic concentrations, electrostatic interactions- Electrostatic interactions holds the DNA and the histomes together. Histomes have an overall positive charge

H1 is linker histone

Tails held by peptide bind, can be cut off with protease treatment

29

Protective nature of histones

Experiment: Nuclease will cut between the histomes- cuts linker dna 180 bp increments in histomes, discovered with nuclease. Does not cut DNA on histones

30

Nucleosomes

repeating structural element in chromosomes composed of histone proteins, fundamental packing units, natural unit that DNA in chromatin degrades to

31

Process of packaging

DNA (isolated patches)- add core histones

Nucleosomes (genes under active transcription)- add H1

30nm fiber (less active genes)- add scaffold proteins

Active chromosome (during interphase)- add more scaffold proteins

Metaphase chromosome (cell division)