M2 L12: genome organization and organellar genetics Flashcards
3 reasons bacterial genomes are simpler than eukaryotic genomes
1) usually only 1 DNA molecule
2) fewer genes
3) less associated with proteins
is bacterial DNA always dsDNA
yes
char of viral genomes (size, molecule, strands, shape)
- smaller than eukaryotes
- DNA or RNA
- 1 or 2 strands
- circular or linear
what region of the cell are bacterial genomes packaged in? membrane bound?
nucleiod region, not membrane bound
what proteins are bacterial genomes associated with? what char do they have? why?
HU and H1
small and pos charged –> electrostatic interactions compact DNA
how much do bacterial genomes compact compared to eukaryotes
not as much
what are polytene chromosomes
specialized eukaryotic chromosomes (in Drosophila)
paired homologs in somatic cells
large and banded (1000-5000 parallel DNA strands) - can see during interphase
what are the bands in polytene chrom
bands used to be thought as genes but there are actually many genes/band
what are puffs in polytene chrom
localized uncoiling of DNA –> places of active transcription
what do puffs tell us? puffs in different locations at different points in development?
puffs show what regions are transcriptionally active
different puffs at different times reflect the expression of different genes at different points in development
what are lampbrush chrom
specialized eukaryotic chromosomes
common structure for meiotic chrom in vertebrate oocytes / some insect spermatocytes
what is the structure of a lampbrush chrom? what does it tell us?
central axis with lateral loops
loops are areas that are transcriptionally active
what are histones
proteins associated with DNA during all phases of cell cycle
organize DNA into repeating structures
what amino acids are histones mostly made of? why?
arganine/lysine because they are positively charged –> allow histones to have electrostatic interactions with DNA
4 observations that lead to the understanding of chromatin structure
1) endonuclease digestion –> multiples of 200bp
2) beads on a string (nucleosomes)
3) histone molecules
4) 147bp and nucleosome core particles
explain the endonuclease/200bp observation of chromatin
endonuclease digestion of chromatin –> fragments are multiples of 200 bp (enzymatic degradation is not random, DNA can’t be cut in the 200bp intervals)
explain the beads on a string observation of chromatin
imaging of chromatin shows “beads on a string” where the beads = nucleosomes (DNA wrapped around histones)
particle
explain the 147bp and nucleosome core particle observation
longer endonuclease digestion of chromatin –> 147bp fragments (147bp wrapped around histone octamer), DNA between histone octamers = linker DNA (associated w/ histone H1), histone octamer + 147bp = nucleosome core particle
explain the histone octamer observation
histone octamers are made of 2 types of tetramers using 4 dif histone proteins (Tetramer 1 = 2H2As + 2H2Bs, tetramer 2 = 2H3s + 2H4s
wrapping DNA around histones compacts DNA to ____ of its original length
1/3
how does chromatin compact for cell division?
exact structures/method unknown
beads on a string structure condenses into a solenoid –> coiling and supercoiling –> highly compact chromosomes for mitosis and meiosis
what’s euchromatin
DNA loosely wrapped around histones, transcriptionally active
what’s heterochromatin
DNA tightly bound around histones, transcriptionally inactive
how can chromatin states be changed
histone modification
what is repetitive DNA? do eukaryotes have a lot? is it functional?
- repetitive sequences
- eukaryotes have a lot
- most is nongenic (leftover from transposable elements - “jumping genes” that can replicate themselves and jump to other parts of genome)
what percent of the human and s cerevisiae genomes code for proteins
2% and 70%
are mito and chloro inheritance usually bi or uniparentally inherited?
uni
2 ways to get uniparental inheritance
1) one parent donates all organelles to zygote (one parent donates basically all cytoplasm)
2) selective destruction of organelles from one parent
is biparental cytoplasmic inheritance equal?
not always, one parent can donate more cytoplasm and organelles
what 4 things distinguish organellar inheritance from nuclear inheritance
1) cells have many types of organelles
2) cells can have multiples of each organelle
3) genome sizes/number of genes in organellar genomes vary widely
4) traits det by organellar genome also influenced by nuclear genome
who discovered polytene chromosomes
EG Balbiani
who discovered leaf variegation was inherited in a non-mendelian fashion
Edwin Bauer/Carl Correns
how is leaf color inherited
- offspring usually phenocopy mother (if green or white)
- if mother is variegated, offspring may be green, white, or variegated
what is heteroplasmy
when a cell has organelles with different genotypes (mutant and WT)
what is homoplasmy
when a cell has organelles that all have the same genotyoe (mutant or WT)
can a heteroplastic cell give rise to hetero and homoplastic cells? why/why not? what is the term for this?
yes because organelle partitioning is random - mutant and WT organelles can go to different daughter cells or a mix of both can go into the daughters
replicative segregation
effect of heteroplasmy on inheritance
many mito diseases have variable penetrance and expressivity bc they require a threshold amount of mutated organelles to express the phenotype
why do mito diseases usually require a high fraction of mutated mito? example?
the WT mito can complement the mutants –> individuals can still do cell respiration
MERRF: myoclonic epilepsy with ragged red fibers - 85% mutant –> no effect, 96% mutant shows mutant phenotype
why are mito diseases usually more severe in males? example?
since mito are inherited through the female parent, male mito are a dead end –> NS can’t act on mutations bc they are not inherited
LHON: leber’s hereditary optic neuropathy (affects more males) –> vision loss and heart complications
what organism demonstrates uniparental inheritance via destruction?
chlamydomonas only keep chloro from mt+ parent, selectively degrate chloro from mt- parent
who discovered first mutation in chloroplast gene using chlamydomonas? how?
ruth sager
reciprocal crosses with mt+ and mt- parent, had different parent by str resistant –> offspring str resistant when mt+ parent was str resistant but not mt-
do saccharomyces have uni or biparental mito inheritance?
biparental
what are “petites” in saccharomyces
individuals with a mutation where they do not have functional mitochondria –> can only get ATP from fermentation –> don’t grow as large
what are the 3 types of petite mutations?
segregational: in nuclear genome (WT x petite = 2 WT, 2 petite)
neutral: petite lacks most or all mito DNA (WT x petite = 4 WT)
suppressive: petite have deletions in mito genome (WT x petite = 4 petite)
- 2 possibilities:
1) mutated mito replicate faster than WT
2) mito genomes recombine so all genomes have mutations
char of organelle genomes (size, shape, content)
- wide range in kbp
- wide range in number of genes
^^(mito more variable than chloro) - linear or circular
- encode own rRNA and tRNA
how flexible is organelle wobble bp compared to nuclear? mininum tRNAs for mito and chloro?
organelle is more flexible
mito 22
chloro 30-35
why are organellar genomes so variable
their genes can integrate into nuclear genome
what’s neofunctionalization
organellar genes integrate into nuclear genome –> the proteins don’t localize back to original organelle
why is the tree of life a web, not a tree?
bacterial sequences spread through all eukaryotic genomes (reticulartion/horizontal gene movement not shown by trees)
what do mito most closely resemble
alpha-proteobacteria
what are the most recent ancestors of choro
cyanobacteria
what is secondary endosymbiosis
eukaryote acquires photosynthetic eukaryote
5 pieces evidence for endosymbiosis
1) mito and chlroo both double membranes like bacteria
2) mito and choro sim size to bacteria
3) organellar genomes packaged similar to bacterial genomes and are not associated with histones
4) transcription/translation machinery for mito and chloro more sim to bacteria than euk nuclear machinery
5) protein coding seq for mito and chloro more sim to bac than euk/arch
what are the 2 hypothesis fro origin of eukaryotes? which is right and how do we know?
1) nucleus then endosymbiosis –> expect SOME euk to NOT have mito
2) endosymbiosis then nucleus –> expect ALL euk to HAVE mito
- endosymbiosis then nucleus bc all eukaryotes have mito
- used to think giardia didn’t have mito, actually have mitosomes which have 2 membranes but not their own genome
- don’t have their own genome bc all important genes migrated to nuclear genome –> used to be mito like structures
what are plastids? what are examples of nonphotosynthetic plastids? what’s the purpose of keeping nonphotosynthetic plastids?
platids = organelles from endosymbiosis of cyanobacteria
chromoplasts and apicoplasts cannot do photosynthesis
plasmodium causes malaria (has nonphotosynthetic apicoplast for other biochem pathways) –> malaria drugs target the apicoplast
Suppose endonuclease digestions of chromatin of a new eukaryotic species yielded fragments of 500 bp and multiples thereof. How would you interpret this?
About 500 bp is wound around histones, so you can’t cut those regions, but you can cut in between them.
If pollen from a variegated branch fertilizes an ovule from a white branch, what is the result? What is the result of the reciprocal cross? What explains this difference?
White, but the reciprocal could be variegated, white, or green. Leaf color is determined by the chloroplast genome and is derived maternally, so the offspring phenocopy the female parent when it is homoplasmic. If the female parent is heteroplasmic, the offspring’s phenotype depends on what chloroplast genome(s) the offspring receives. This is because of replicative segregation in meiosis.
