M2 L12: genome organization and organellar genetics

Question 1

3 reasons bacterial genomes are simpler than eukaryotic genomes

Answer 1

1) usually only 1 DNA molecule

2) fewer genes

3) less associated with proteins

Question 2

is bacterial DNA always dsDNA

Answer 2

yes

Question 3

char of viral genomes (size, molecule, strands, shape)

Answer 3

• smaller than eukaryotes
• DNA or RNA
• 1 or 2 strands
• circular or linear

Question 4

what region of the cell are bacterial genomes packaged in? membrane bound?

Answer 4

nucleiod region, not membrane bound

Question 5

what proteins are bacterial genomes associated with? what char do they have? why?

Answer 5

HU and H1

small and pos charged –> electrostatic interactions compact DNA

Question 6

how much do bacterial genomes compact compared to eukaryotes

Answer 6

not as much

Question 7

what are polytene chromosomes

Answer 7

specialized eukaryotic chromosomes (in Drosophila)

paired homologs in somatic cells

large and banded (1000-5000 parallel DNA strands) - can see during interphase

Question 8

what are the bands in polytene chrom

Answer 8

bands used to be thought as genes but there are actually many genes/band

Question 9

what are puffs in polytene chrom

Answer 9

localized uncoiling of DNA –> places of active transcription

Question 10

what do puffs tell us? puffs in different locations at different points in development?

Answer 10

puffs show what regions are transcriptionally active

different puffs at different times reflect the expression of different genes at different points in development

Question 11

what are lampbrush chrom

Answer 11

specialized eukaryotic chromosomes

common structure for meiotic chrom in vertebrate oocytes / some insect spermatocytes

Question 12

what is the structure of a lampbrush chrom? what does it tell us?

Answer 12

central axis with lateral loops

loops are areas that are transcriptionally active

Question 13

what are histones

Answer 13

proteins associated with DNA during all phases of cell cycle

organize DNA into repeating structures

Question 14

what amino acids are histones mostly made of? why?

Answer 14

arganine/lysine because they are positively charged –> allow histones to have electrostatic interactions with DNA

Question 15

4 observations that lead to the understanding of chromatin structure

Answer 15

1) endonuclease digestion –> multiples of 200bp

2) beads on a string (nucleosomes)

3) histone molecules

4) 147bp and nucleosome core particles

Question 16

explain the endonuclease/200bp observation of chromatin

Answer 16

endonuclease digestion of chromatin –> fragments are multiples of 200 bp (enzymatic degradation is not random, DNA can’t be cut in the 200bp intervals)

Question 17

explain the beads on a string observation of chromatin

Answer 17

imaging of chromatin shows “beads on a string” where the beads = nucleosomes (DNA wrapped around histones)
particle

Question 18

explain the 147bp and nucleosome core particle observation

Answer 18

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

Question 19

explain the histone octamer observation

Answer 19

histone octamers are made of 2 types of tetramers using 4 dif histone proteins (Tetramer 1 = 2H2As + 2H2Bs, tetramer 2 = 2H3s + 2H4s

Question 20

wrapping DNA around histones compacts DNA to ____ of its original length

Answer 20

1/3

Question 21

how does chromatin compact for cell division?

Answer 21

exact structures/method unknown

beads on a string structure condenses into a solenoid –> coiling and supercoiling –> highly compact chromosomes for mitosis and meiosis

Question 22

what’s euchromatin

Answer 22

DNA loosely wrapped around histones, transcriptionally active

Question 23

what’s heterochromatin

Answer 23

DNA tightly bound around histones, transcriptionally inactive

Question 24

how can chromatin states be changed

Answer 24

histone modification

Question 25

what is repetitive DNA? do eukaryotes have a lot? is it functional?

Answer 25

- 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)

Question 26

what percent of the human and s cerevisiae genomes code for proteins

Answer 26

2% and 70%

Question 27

are mito and chloro inheritance usually bi or uniparentally inherited?

Answer 27

uni

Question 28

2 ways to get uniparental inheritance

Answer 28

1) one parent donates all organelles to zygote (one parent donates basically all cytoplasm) 2) selective destruction of organelles from one parent

Question 29

is biparental cytoplasmic inheritance equal?

Answer 29

not always, one parent can donate more cytoplasm and organelles

Question 30

what 4 things distinguish organellar inheritance from nuclear inheritance

Answer 30

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

Question 31

who discovered polytene chromosomes

Answer 31

EG Balbiani

Question 32

who discovered leaf variegation was inherited in a non-mendelian fashion

Answer 32

Edwin Bauer/Carl Correns

Question 33

how is leaf color inherited

Answer 33

- offspring usually phenocopy mother (if green or white) - if mother is variegated, offspring may be green, white, or variegated

Question 34

what is heteroplasmy

Answer 34

when a cell has organelles with different genotypes (mutant and WT)

Question 35

what is homoplasmy

Answer 35

when a cell has organelles that all have the same genotyoe (mutant or WT)

Question 36

can a heteroplastic cell give rise to hetero and homoplastic cells? why/why not? what is the term for this?

Answer 36

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

Question 37

effect of heteroplasmy on inheritance

Answer 37

many mito diseases have variable penetrance and expressivity bc they require a threshold amount of mutated organelles to express the phenotype

Question 38

why do mito diseases usually require a high fraction of mutated mito? example?

Answer 38

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

Question 39

why are mito diseases usually more severe in males? example?

Answer 39

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

Question 40

what organism demonstrates uniparental inheritance via destruction?

Answer 40

chlamydomonas only keep chloro from mt+ parent, selectively degrate chloro from mt- parent

Question 41

who discovered first mutation in chloroplast gene using chlamydomonas? how?

Answer 41

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-

Question 42

do saccharomyces have uni or biparental mito inheritance?

Answer 42

biparental

Question 43

what are "petites" in saccharomyces

Answer 43

individuals with a mutation where they do not have functional mitochondria --> can only get ATP from fermentation --> don't grow as large

Question 44

what are the 3 types of petite mutations?

Answer 44

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

Question 45

char of organelle genomes (size, shape, content)

Answer 45

- wide range in kbp - wide range in number of genes ^^(mito more variable than chloro) - linear or circular - encode own rRNA and tRNA

Question 46

how flexible is organelle wobble bp compared to nuclear? mininum tRNAs for mito and chloro?

Answer 46

organelle is more flexible mito 22 chloro 30-35

Question 47

why are organellar genomes so variable

Answer 47

their genes can integrate into nuclear genome

Question 48

what's neofunctionalization

Answer 48

organellar genes integrate into nuclear genome --> the proteins don't localize back to original organelle

Question 49

why is the tree of life a web, not a tree?

Answer 49

bacterial sequences spread through all eukaryotic genomes (reticulartion/horizontal gene movement not shown by trees)

Question 50

what do mito most closely resemble

Answer 50

alpha-proteobacteria

Question 51

what are the most recent ancestors of choro

Answer 51

cyanobacteria

Question 52

what is secondary endosymbiosis

Answer 52

eukaryote acquires photosynthetic eukaryote

Question 53

5 pieces evidence for endosymbiosis

Answer 53

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

Question 54

what are the 2 hypothesis fro origin of eukaryotes? which is right and how do we know?

Answer 54

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

Question 55

what are plastids? what are examples of nonphotosynthetic plastids? what's the purpose of keeping nonphotosynthetic plastids?

Answer 55

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

Question 56

Suppose endonuclease digestions of chromatin of a new eukaryotic species yielded fragments of 500 bp and multiples thereof. How would you interpret this?

Answer 56

About 500 bp is wound around histones, so you can’t cut those regions, but you can cut in between them.

Question 57

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?

Answer 57

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.