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module 2 exam Flashcards

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1
Q

What is a hypothesis

A

A proposed explanation for a phenomenon

it needs to be testable

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2
Q

Correlation/Descriptive

A

Correlation/Descriptive not altering variables

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3
Q

Loss of Function

A

take it away & see if

outcome changes

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4
Q

Gain of Function

A

add it/change it & see if

outcome changes.

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5
Q

if a gene is
1. Expressed at right time and place
(correlation) – yes
• 2. Loss of Function – see expected phenotype
• 3. Gain of Function – don’t see expected
phenotype

A

the phenotype is not reliant on one gene

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6
Q

is a gene
1. Expressed at right time and place
(correlation) – yes
• 2. Loss of Function – don’t see expected
phenotype
• 3. Gain of Function – see expected phenotype

A

Redundancy more than one gene can do it

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7
Q

if a gene
1. Correlation – No
• 2. Loss of Function – don’t see expected
phenotype
• 3. Gain of Function – see expected phenotype

A

the gene can express the function but it does not normally doesnt

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8
Q

If embryos homozygous for a mutation in

gene limbless have no limbs

A 
A. Limbless	is	sufficient	
for	limbs	to	form	
B. Limbless is	required	
for	limbs to	form	
C. Both	A and	B
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9
Q

Evx1 function in limb development

A

Evx1 is required for lepidotrichia (bony ray) joint formation
– Lepidotrichia are part of the dermoskeleton of the fins
– Joint formation in the endoskeleton does not need Evx1 and is
genetically conserved with joint formaGon in mammalian limbs

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10
Q

Role of Evx1 in joint formation is ____ ________between zebrafish and
mammals

A

not conserved

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11
Q

. Developmental genes usually have conserved funcGons

in invertebrates and vertebrates which means

A

means these genes

probably had these funcGons in the bilaterian ancestor

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12
Q

Many of the important developmental genes were first

discovered in

A

Drosophila Melanogaster (fruit flies)

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13
Q

Most developmental genes are also implicated in

A

human developmental disorders, diseases and cancer

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14
Q

Embryology:

now called developmental bio

A

Understanding the development of animal form.

How eggs become embryos become adults

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15
Q

what are the 4 main stages of Development of a vertebrate embryo

A
  • Cleavage
  • Gastrulation
  • Neurulation
  • Organogenesis and Cell DifferenGaGon
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16
Q

Ini=al stages of Development in

vertebrates – are mainly

A

cell division. one cell becomes many

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17
Q

the most rapid increase in cell count occurs durning

A

clevage

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18
Q

when does the blastoderm form during development

A

cleavage

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19
Q

gastrulation signals the development of

A

3 germ layers and when cells start to involute

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20
Q

what are the 3 germ layers

A

Endoderm, Mesoderm,Ectoderm

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21
Q

How can you test whether a difference you

observe may be due to a genetic mutation

A 
Count	the	number	of	
progeny	from	a	maHng	
that	have	the	phenotype	
 Genotype	individuals	with	
phenotype	and	check	if	
they	have	the	mutaHon	
 Check	if	any	“unaffected	
individuals”	have	the	
mutaHon
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22
Q

What is a Transcription Factor?

A

Protein that binds DNA
and can either inhibit or
activate gene
transcripHon

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23
Q

What might zebrafish NOT be a good model

system for studying?

A

Cortical

development, becasue the spinal cord and brain stem are very similar in earlier stages in development

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24
Q

What controls which cells express /turn on a particular gene

A

Regulatory DNA
elsewhere in the
genome

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25
what is the order of stages of development
Cleavage-> Gastrulation-> Neurulation-> Organogenesis and Cell Differentiation
26
Neurulation forms when (2 way)
top layer curling up to make a tube | cells come together to make a soild mass then it opens in the middle
27
neural crest is only fond in
vertebrates
28
what is the neural crest responsible for making
the CNS, cartilage and bones, connective tissue, pigment cells, neurons and ganglia, PNS
29
Staes in developmental biology for animals are made
to have a set standard for objective criteria
30
transcription factors bind to __________ to turn gene expression on
enhancers
31
Promoter
region of regulatory DNA that is needed for the polymerase to bind and a gene to be transcribed. Located just 5’ of the coding region
32
Enhancer
region of regulatory DNA that regulates when and where (in which cell types) a gene to turned on/expressed. Usually binds transcription factors.
33
Enhancers (regulatory DNA) can occur
5' or 3' in gene, in introns, or far away from the gene
34
Easy way to make a transgenic line
cell specific enhancer-> put with a basal promoter-> selected proteins in specific cells
35
How do cells become different from one | another during embryo development
Start to express different developmental genes • Expression of these genes is tightly controlled - so specific genes are expressed only at the right time and place
36
Developmental Genes are (3)
• Small percentage of total number of genes. • Usually transcription factors or components of signal transduction pathways. • Widely conserved across animal phyla.
37
Tissue specific expression is often | regulated by tissue specific enhancers
Enhancers that regulate expression in different cell types or at different time points: ʻcis-regulatory elementsʼ
38
We can see which cells genes are turned on | in by looking at
RNA or Protein expressions
39
situ hybridization – labels
mRNA
40
what are the steps of situ hybridization
``` - Make labeled complement copy of RNA (so will bind to endogenous mRNA) - Hybridize so it enters cells. - Wash - so it is washed out of all cells where the RNA of interest is not present - Detect label with an antibody and a color reaction ```
41
Gene Expression by Microarray steps
``` 1. Isolate RNA samples. Synthesize labeled copies. (probes) 2. Hybridize labeled probe with cDNA microarray on a chip 3. scan the chip 4. analyze the data ```
42
Gene Expression by RNA-seq | like Figure 6A in paper
use big sequencing machines to sequence all the RNA, it is the most commonly used method because it takes less resources and time
43
Gene Expression by RNA-seq steps
Isolate RNA samples. Synthesize DNA copies. (in to a microcentrifuge tube) 2. Sequence on a high throughput sequencer
44
to see id genes are present in protein expression we would use __________ techniques
``` Immunohistochemistry or Antibody Staining( Need an antibody to the specific protein • Detect antibody with a color reaction) ```
45
just looking for is the gene is expressed or not is a
correlation experiment
46
Random mutagenesis -
look for embryonic mutant phenotypes and then identify (clone) the gene responsible • Starts with the loss-of-function data!
47
steps of random mutagenesis
1. treat with a chemical in sprems or male zebrafish to alter dna 2. mate until you find the phenotype
48
famous random mutagenesis study is from
Mutations affecting segment number and polarity in Drosophila. (1980) Nüsslein-Volhard C, Wieschaus E
49
Developmental Genes often involved in different embryonic patterning processes So mutant phenotypes are often
pleiotropic
50
Notch gene is important for (in fruit flies)
organizing wing growth, pattering the eye,regulating where joints form in leg
51
Hh(hedgehog) involved in
``` Involved in: CNS development limb development eye development muscle development ```
52
Two main ways of finding genes | involved in embryonic development
Look for genes expressed at the right time and place (correlation) and then analyse their function (gain-offunction and loss-of-function experiments). • Random mutagenesis - look for embryonic mutant phenotypes and then identify (clone) the gene responsible
53
Gene expressed at the right time and place ( embryonic development) PRO
we know what gene we are looking at.
54
Gene expressed at the right time and place ( embryonic development) CON
this is just a correlation. We donʼt know that it functions in the process we are interested in. It might do something else - gene that have not been discovered might play an important role like expression patterns
55
Random mutagensis PRO
Mutant phenotype shows us what the gene is required for. So we know it functions in a specific process that we are interested in
56
Random mutagensis CON
1)We donʼt know what the gene is. To understand how it works - usually need to identify (or “clone”) the gene and see what sort of a protein it encodes for 2)Genes could be redundant, 3)takes long time
57
Notch Signaling is involved in
In Zebrafish Notch signaling is required for trunk neural crest to form (including pigment cells)
58
``` BMP Signaling Important for (4) ```
1) Gastrulation 2) Specification of Ectoderm (at the expense of Neurectoderm) 3) Bone Formation (Bone Morphogenetic Protein) 4) Patterning of Nervous System
59
``` Hedgehog Signaling Important for (5) ```
1) Nervous system patterning 2) Specification of muscle cells 3) A-P polarity in limbs (limb patterning) 4) Correct spacing of the eyes 5) Somite shape (in zebrafish at least)
60
Mutations in Shh and Hh pathway genes can cause (4)
holoprosencephaly& Basal Cell Carcinoma & Brain Tumours & other disorders
61
Developmental genes usually have conserved functons | in invertebrates and vertebrates - means these
genes | probably had these functions in the bilaterian ancestor

bio 305 (2 decks)

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