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module 2 exam Flashcards

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Biology 101 flashcards
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
Q

what is the order of stages of development

A

Cleavage-> Gastrulation-> Neurulation-> Organogenesis and Cell Differentiation

26
Q

Neurulation forms when (2 way)

A

top layer curling up to make a tube

cells come together to make a soild mass then it opens in the middle

27
Q

neural crest is only fond in

A

vertebrates

28
Q

what is the neural crest responsible for making

A

the CNS, cartilage and bones, connective tissue, pigment cells, neurons and ganglia, PNS

29
Q

Staes in developmental biology for animals are made

A

to have a set standard for objective criteria

30
Q

transcription factors bind to __________ to turn gene expression on

A

enhancers

31
Q

Promoter

A

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
Q

Enhancer

A

region of regulatory DNA that regulates when and where (in which cell types) a gene to turned on/expressed. Usually binds transcription factors.

33
Q

Enhancers (regulatory DNA) can occur

A

5’ or 3’ in gene, in introns, or far away from the gene

34
Q

Easy way to make a transgenic line

A

cell specific enhancer-> put with a basal promoter-> selected proteins in specific cells

35
Q

How do cells become different from one

another during embryo development

A

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
Q

Developmental Genes are (3)

A

• Small percentage of total number of genes.
• Usually transcription factors or components of
signal transduction pathways.
• Widely conserved across animal phyla.

37
Q

Tissue specific expression is often

regulated by tissue specific enhancers

A

Enhancers that regulate
expression in different cell types
or at different time points:
ʻcis-regulatory elementsʼ

38
Q

We can see which cells genes are turned on

in by looking at

A

RNA or Protein expressions

39
Q

situ hybridization – labels

A

mRNA

40
Q

what are the steps of situ hybridization

A 
- 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
Q

Gene Expression by Microarray steps

A 
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
Q

Gene Expression by RNA-seq

like Figure 6A in paper

A

use big sequencing machines to sequence all the RNA, it is the most commonly used method because it takes less resources and time

43
Q

Gene Expression by RNA-seq steps

A

Isolate RNA samples.
Synthesize DNA copies. (in to a microcentrifuge tube)
2. Sequence on a high throughput sequencer

44
Q

to see id genes are present in protein expression we would use __________ techniques

A 
Immunohistochemistry
or
Antibody Staining( Need an antibody to the
specific protein
• Detect antibody with a color reaction)
45
Q

just looking for is the gene is expressed or not is a

A

correlation experiment

46
Q

Random mutagenesis -

A

look for embryonic mutant
phenotypes and then identify (clone) the gene
responsible
• Starts with the loss-of-function data!

47
Q

steps of random mutagenesis

A
  1. treat with a chemical in sprems or male zebrafish to alter dna
  2. mate until you find the phenotype
48
Q

famous random mutagenesis study is from

A

Mutations affecting segment number and polarity
in Drosophila. (1980)
Nüsslein-Volhard C, Wieschaus E

49
Q

Developmental Genes often
involved in different embryonic
patterning processes
So mutant phenotypes are often

A

pleiotropic

50
Q

Notch gene is important for (in fruit flies)

A

organizing wing growth, pattering the eye,regulating where joints form in leg

51
Q

Hh(hedgehog) involved in

A 
Involved in:
 CNS development
 limb development
 eye development
 muscle development
52
Q

Two main ways of finding genes

involved in embryonic development

A

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
Q

Gene expressed at the right time and place ( embryonic development) PRO

A

we know what gene we are looking at.

54
Q

Gene expressed at the right time and place ( embryonic development) CON

A

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
Q

Random mutagensis PRO

A

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
Q

Random mutagensis CON

A

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
Q

Notch Signaling is involved in

A

In Zebrafish
Notch signaling is required for trunk neural crest to form
(including pigment cells)

58
Q 
BMP Signaling
Important for (4)
A

1) Gastrulation
2) Specification of Ectoderm (at the expense of Neurectoderm)
3) Bone Formation (Bone Morphogenetic Protein)
4) Patterning of Nervous System

59
Q 
Hedgehog Signaling
Important for (5)
A

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
Q

Mutations in Shh and Hh pathway genes can cause (4)

A

holoprosencephaly& Basal Cell Carcinoma
& Brain Tumours
& other disorders

61
Q

Developmental genes usually have conserved functons

in invertebrates and vertebrates - means these

A

genes

probably had these functions in the bilaterian ancestor

bio 305 (2 decks)

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