Chapter 10 Flashcards
amount of DNA in a haploid cell
C-value
amount of DNA not correlated with complexity
C- value Paradox
Lungfish have how many time the DNA of humans
40x
the first genome sequencing
bacteriophage MS2 ( RNA virus)
- 1.8 terabases of data — 16 human genomes’ worth — per three-day run
- 18,000 human genomes per year. Each genome 30x
- Machine is $1,000,000, –but genome ~$1,000
Illumina HiSeqX
- Connects to a computer through USB
- Uses Nanopore technology - draw DNA through a small hole
- Each chip would be about $1000
- Can’t handle big genomes yet
Oxford Nanopore MinION
C-value paradox
- Even though about the same number of genes in organisms
- Larger % noncoding in Eukaryotes
move sections of DNA around, - may drive and increase in genome size over time
transposons
selection for replication speed, small cell size, and energetic efficiency may favor reductions in size over time
transposons
- Evolutionary history
- Drosophila has lots of active transposons
- Humans had them in past, but few active now
balance of these forces leads to C-value paradox
Increase in DNA leads to increase in…
cell size
number of protien -coding genes
G-values
does not appear correlated with complexity
G-value Paradox
it is all about the regulatory genes
G-value Paradox
Bind to specific regions of DNA in order to regulate when where and to what degree specific genes are expressed
-Transcription factors
often act upon another
Transcription factors
Degree of regulatory control of non-coding regions
Increase # regulatory elements with C-value
One protein-coding gene ≠ one protein
G-value Paradox
put the exons together in different ways
- can increase the diversity of an organisms functional proteins
alternative splicing
-humans: more alternative spliced genes and more introns than nematodes
changes to newly transcribed RNA
Posttranscriptional modification
- pre-mRNA
- Alternatively spliced mRNA
- Different protein isoforms
steps of alternative splicing
RNA or DNA
Single linear, set of linear, or circular chromosomes
The Viral Genome
Compact – RNA up to 30kb
Few proteins
DNA to 1mb
The Viral Genome
May have overlapping, but same reading frame genes
Or different reading frames
The Viral Genome
is a single-stranded positive-sense RNA virus with a genome composed of a single linear chromosome
SARS Coronavirus Single Stranded RNA
Single Stranded, Segemented RNA
Influenza B virus
circular double-stranded DNA
Hepatitus B
. Viruses employ both methods of coding for multiple proteins using a single region of the genome.
- read in same fram but start and stop in different places
2. read in a different frame
Bateria and Archaea
Prokaryotic Genomes
Single, circular chromosome – 1 copy
Are exceptions to circular and 1 copy
Prokaryotic Genomes
85%-95% protein coding
Prokaryotic Genomes
Usually no introns (in rRNA or tRNA)
Few pseudogenes
Prokaryotic Genomes
Used to be viruses
Prophages
Can vary in different strains
Prophages
Can impart virulence to bacteria
Prophages
Can no longer replicate, but still work
Prophages
Small, nonessential circular DNA
Plasmids
Code for additional function – often resistance to antibiotics
And their own replication
Plasmids
prokaryotes are almost all _____ no____
genes
junk
have the smallest geomes
symbionts
-parasites are larger
Moving genetic material from one cell to another
HGT
phage packages bacterial DNA instead of its own
Transduction (HGT)
bacteria takes up free DNA
food
acquired in DNA repair
generate variability
Transformation ( HGT )
– plasmids pass, some even code for conjugation Sometimes called bacterial sex Not once a generation Not by species Donor does not receive DNA
Conjugation (HGT)
E. coli K-12 harmless enteric strain
E. coli O157:H7 a pathogen that causes bloody diarrhea and (in some) hemolytic uremic syndrome which causes kidney failure
Virulence from HGT
May reduce fitness – evolved for other reasons in other places
But may increase fitness
HGT
Open new evolutionary pathways
Can obtain genes from other species
HGT
Enterococcus faecalis not limited to variation within its species
Obtained antibiotic resistance genes from soil bacteria
HGT
Evolves rapidly
Translocations, inversions, deletions, etc.
Bacterial genome
plot one genome against another
Syntenic plots
If straight 45° line, no changes
Angles occur for inversions
Syntenic plots
compare the gene order of two different strains or species, providing a picture of the genomic reorganization that has occurred.
Syntenic dot plots
indicates the relative positions along the chromosome of homologous genes in two genomes
Syntenic dot plot
Little is protein coding
Most are transposons and introns
The Eukaryotic Genome
move around the genome
Transposable elements
excise original DNA and reinsert it elsewhere
jumps and the original is lost
conservative transposons
Make a copy and reinsert
-DNA trasposons with DNA intermediate
Nonconservative transposons
RNA back to DNA
- type of nonconservative transposons
- line-1 elements
retrotransposons
encode enzymes necessary to catalyze own movement
autononomous transposons (LINE-1)
most common transposon at human genome
LINE-1
long interspersed elements
Most are decayed
~100 retain transposon ability
Occasional causes of disease
LINE-1 Elements (L1)
Can cause nonhomologous regions of DNA to pair
LINE-1 Elements (L1)
Short interspersed elements
Nonautonomous
SINE elements
Rely on machinery of autonomous trasposons
SINE elements
Most inactive
Have to be inserted by chance adjacent to right flanking sequences
SINE elements
act for own survival
Selfish genetic elements (SINE)
- In bacteria, can get to other cells via plasmids
- In eukaryotes, can move to other chromosomes to ensure survival
- May have evolved from retroviruses that lost the ability to form a protein coat
SINE Elements
Can cause problems if inserted in or near critical genes
-SINE Elements
Can generate mutation
SINE Elements
Cause ectopic recombination – separate chromosomes cross over
SINE Elements
May copy adjacent DNA as well – gene duplication
SINE Elements
Many, with multiple origins of replication – because of length
chromosome
attachment sites for kinetochore proteins
centromere
Discreet regions of satellite repeats for 100’s of kb interspersed w/transposons
Chromosome
Marked by DNA packaging protein = centromeric histone (CenH3)
Chromosome
among fastest evolving DNA
CenH3 and other proteins involved in packaging rapidly evolving
Centromeric DNA
Only one of 4 cells becomes egg
Rest are polar bodies
Centromeric Drive
Selection favors mutations of centromere that increases chance of chromosome segregating with oocyte
Centromeric Drive
Increase repeats to provide targets for microtubules
-Meitotic Drive
Centromeric Drive
But might cause problems like nondisjunction
Centromeric Drive
Could quickly lead to speciation
Centromeric Drive
Extended regions of short repeats at ends of chromosomes
Telomeres
DNA polymerase only in 3’ to 5’ direction
Would truncate 3’ end of chromosome
Ends would truncate by 100 bp per replication
Telomeres
extends 3’ end by adding repeat (TTAGGG in vertebrates)
Telomeres
encodes a domain (module)
exon
Proteins can evolve rapidly by recombining different domains
Exon shuffling
problems with this could increase size of genome site for transposons
Exon shuffling
– key protein in pathogenesis of Mycoplasma in birds
Sialidase
Transcription factors
Immune Function
Formation of gametes
Sensory Function
positive selection, important
Structural genes
Functional genes
Cellular
Biosynthesis
purifying selection, not important
When there is selection for an allele, nearby genes get moved en mass:
genetic hitchhiking
Not enough time to break up the block if recently selected for
Haplotype Blocks
Scan genome for these blocks to determine which gene is selected for
Haplotype Blocks
Lactose tolerance into adulthood
long blocks
no tolerance
short blocks
contain promotor at RNA polymerize that can lead to alternative splicing, translation regulation, and there impact is high in stressful conditions
SINE
BIOLUMINESING
SINE
Genes are moves around on chromosomes because of
transposons
