COCKBURN 1

Question 1

what is a model organism

Answer 1

a non human species that is used to study a specific phenomenon or disease

Question 2

why do we use model organisms?

Answer 2

we cannot experiment on humans so we need to learn from other organisms that mimic specific aspects of human biology and are comparatively easy to work with
can be used for forward and reverse genetics

Question 3

what is forward genetics

Answer 3

there is a phenotype, an observable characteristic that is different, and we figure out which genes regulate those differences

Question 4

what is reverse genetics

Answer 4

mutate a gene/multiple genes and observe the effect of that on the phenotype

Question 5

what are the eukaryotic organisms most commonly used?

Answer 5

S.cerevisiae (yeast)
C.elegans
d.melanogaster (fruit fly)
danio rerio (zebrafish)
mus musculus (mouse mouse)

put in order of decreasing ease to grow and increasing similarity to humans

Question 6

what are characteristics of s.cerevisiae

Answer 6

eukaryotic, unicellular fungus
generation time; 2-3 hours (till next generation is reproductively able)
can exist as haploid or diploid
can reproduce sexually or asexually
can be frozen and revived

Question 7

what is the life cycle of s.cerevisiae

Answer 7

can be haploid or diploid
haploid yeast can do asexual reproduction by budding
alpha and a are the 2 mating types
can mate to make a diploid cell, which can also do budding
when conditions are hard diploid cell can become haploid by meiosis

Question 8

what are the advantages of using haploid yeast?

Answer 8

only one copy of each gene, easy to see what happens when you change it

Question 9

what are characteristics of C.elegans?

Answer 9

invertebrate animal, multicellular
generation time: 3 days, can make 300 progeny
extremely simple, translucent (easy to see inside)
can trance the fate of each cell (1090 total)
two sexes: male and hermaphrodite
can be frozen and revived

Question 10

how do the two sexes of c.elegans reproduce?

Answer 10

hermaphrodites can self fertilise to make clones of themselves
can also breed with males to make mostly hermaphrodites, but also some males

Question 11

what is the life cycle of c.elegans

Answer 11

embryo goes through multiple larval stages (L1, L2, L3, L4) till it is a reproductive adult (this all takes about 3 days), and then it ages
an alternative life cycle is if there is crowding starvation or high temperatures at the L1 stage it can go into a dauer state (smaller) and then after several months it can go to L4 and then grow to an adult

Question 12

what are the characteristics of d.melanogaster

Answer 12

invertebrate animal, multicellular
similar to humans in terms of body organisation, digestive tract, nervous system, excretion, muscles, circulation, skeleton
generation time: 10 days, 100 progeny
share 75% of human disease causing genes
very well studied

Question 13

what are the characteristics of danio rerio

Answer 13

vertebrate animal, multicellular
generation time: 2-3 months, 200 eggs
optically translucent embryos and larvae (can be seen with light microscope)
relatively simple and inexpensive to maintain, but you need a whole water system
easily treated with small molecules for drug and toxicity screens because it is all in water

Question 14

what are the characteristics for mus musculus?

Answer 14

vertebrate animal
generation time: 3 months, 2-12 pups
small, easy to house
commonly used to study human biology and perform preclinical testing
not always the perfect models

Question 15

why do we study unique phenomena

Answer 15

study these unique mechanisms to then maybe apply their unique phenomena to humans

Question 16

what are some emerging organisms that are being studied for their unique features?

Answer 16

axolotls can regenerate limbs
planaria can regenerate everything, no matter where they are cut

Question 17

what are the basics of forward genetic screens

Answer 17

perturb lots of genes (randomly or systematically)
look for a specific phenotype
figure out which gene you mutated

Question 18

how do temperature sensitive mutants work?

Answer 18

permissive temperatures give normal polypeptide folding and the wild type phenotype
restrictive temperatures lead to unfolding/misfolding and proteolysis or aggregation, decreased amount of active protein and yields to temperature sensitive (TS) phenotype

Question 19

how is replica plating done to isolate TS mutants?

Answer 19

mutate the yeast
put them on a master plate
put it on sterile velveteen
velveteen with imprint of all colonies
make one plate on high temp and one plate on low temp
at low temp all colonies grow
at high temps mutates do not grow, you can go back to the plate and figure out which plates those were

Question 20

what were the conclusions of mutating cdc1

Answer 20

cdc 1 mutants arrest in G1 phase
cdc1 encodes for a cell wall which is needed to expand

Question 21

what are the findings of mutating cdc2

Answer 21

arrest in S phase
cdc2 codes for part of DNA polymerase 3

Question 22

what are the findings of mutating cdc3

Answer 22

stop in mitosis
divide but do not separate, no cytokinesis
cdc3 codes for septin, involved in cytokinesis

Question 23

what can the fact that yeast can go from haploid to diploid be used for?

Answer 23

can be used to perform complementation
used to test whether two mutants strains have mutations in the same gene

Question 24

how is a yeast genomic DNA library made?

Answer 24

yeast double stranded DNA is cleaved with restriction nucleases to make thousands of genomic DNA fragments
DNA fragments are inserted into plasmids to make recombinant DNA
introduce into bacteria to make the library

Question 25

how is the mutant gene identified

Answer 25

introduce different plasmids into yeast and test which plasmids rescue the mutant
sequence the plasmids that rescue to identify the yeast gene responsible for a phenotype

Question 26

how is the mutant gene identified when investigating human genes

Answer 26

introduce different cDNAs into yeast, test which plasmids rescue the mutant
sequence cDNAs that rescue to identify the human gene responsible for a phenotype

Question 27

what type of embryogenesis do c.elegans show?

Answer 27

invariant embryogenesis

Question 28

what does invariant embryogenesis mean for c.elegans?

Answer 28

every embryo develops with the same pattern of divisions and migrations
adult worms have exactly 959 cells generated in the exact same way
very useful when performing genetic screens to understand development

Question 29

how many cells form during c.elegans embryogenesis and how many die?

Answer 29

1090 cells form
131 die during embryogenesis, leaving 959 cells at adult age