Genomes Flashcards
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.
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
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
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)
Organism complexity
With increasing complexity there is an increase in the number of genes
Decreasing gene density
Larger genome, more genes, decreasing gene density (number of genes per number of base pairs)
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
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)
Centromere
In the center of the chromosome
Telomeres
End of chromosomes, Common microsatellite, has a sticky end complimentary to other telomeres. Chromosome fusion can result
Closely related species
May have different number of chromosomes due to fusion
Similar DNA sequences different chromosomal anatomy. Can cause a speciation event
Ape chromosomal arrangements
Overall DNA sequence very similar, but humans have one chromosome where apes have 2
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
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
Probes
Can be used to find complimentary sequences in larger fragments by fluorescence
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
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
Where is highly repetitive DNA found?
Centromeres and telomeres
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
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
Chloroplast genome
Encodes enzymes involved in photosynthesis
Mitochondrial genome
Get it from your mom
Genes that code for proteins in mitochondria for electron transport/ ATP production
Endosymbiotic theory
Original prokaryotic host cell with DNA engulfs aerobic bacteria
Photosynthetic bacteria become chloroplasts and the other bacteria become mitochondria
Lateral gene transfer- intercompartmental
Damage to the organelle membranes
Non-homologous end joining allows pieces of the DNA to enter the nuclear genome
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
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
Two models for chromatin structure (histones)
Solenoid
Zig zag
Histones have similarities
8 protein parts
N terminal tail and a histone fold
H2A and H2B dimer
H3H4 tetramer
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
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
Nucleosomes
repeating structural element in chromosomes composed of histone proteins, fundamental packing units, natural unit that DNA in chromatin degrades to
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)
