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genomics- Stem Cells (unit 3) Flashcards

1
Q

goals of HGP

A
  • DNA based genetic testing for disease and carrier status

- pharmacogenetics for new drugs

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2
Q

shotgun sequencing

A

1) isolate DNA, sequence lots of it

2) use computer to line up short DNA sequences

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3
Q

genetics vs genomics

A 
genetics= single DNA molecule to one phenotype
genomics= multiple molecules- whole genome to metabolomics
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4
Q

transcriptomics

A

the genes expressed in a given cell type or environmental condition =analysis of transcripts- level of mRNA expressed
-uses micro assay and RNA sequencing

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5
Q

DNA microassay

A

high-throughput tech used in molecular bio and in medicine- allow the expression level of thousands of genes to be measured at the same time
=arrayed series of 1000s of microscopic DNA, each containing specific DNA sequence

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6
Q

Reverse transcriptase

A

enzyme that makes DNA copy (cDNA) of RNA molecule

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7
Q

cDNA

A

copy of mRNA

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8
Q

proteomics

A

large-scale analysis of proteins of the proteome; all the proteins in a cell or tissue
methods= immunoprecipitation or mass spec

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9
Q

interactome

A

which proteins interact (bind/ regulate expression) with which other proteins

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10
Q

protein networks

A

pairs of interacting proteins= identified by Y2H and other methods, can be linked together in networks

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11
Q

synthetic bio

A

using engineering principles and bio components to purposefully make up and modify organisms

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12
Q

biobricks

A

promoters, enhancers, operators, repressors, terminators, protein domains, enzymes, siRNAs, miRNAs, etc…

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13
Q

reporter genes

A

investigate gene expression patterns
LacZ with B gal
GFP used to label specific cells

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14
Q

chimeras

A

animals composed of cells from different genetic sources

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15
Q

microinjecting DNA

A

most common method used to produce transgenic farm animals (into fertilized egg)

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16
Q

pharming

A

using transgenic animals to produce drug compounds

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17
Q

somatic cell nuclear transfer

A

cloning method also used to add transgenes

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18
Q

transgenic plant methods (2)

A 
agrobacterium (uses gene plasmid into bacteria and then mix with plant cell, then plasmid will mix with chrom, and then screen for cells with trans gene)
gene gun (gold particles coated with DNA are shot at cell with gene gun and DNA incorporated into plant cell chromosome to screen for cells with transgene
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19
Q

Bt toxin

A

plant (transgenic) makes Bt toxin in inactive form, insect eats, insect converts to active form, and then dies… protecting future plant progeny

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20
Q

CRISPR

A

clustered regularly interspaced short palindromic repeats
-natural role= bacterial acquired immunity
immunization= 1) phage DNA sampled and 2) spacers are integrated between repeats = proteins incorporate phage DNA at Eds of repeats- recognizable

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21
Q

PAM

A

must be right upstream of match (N-GG)

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22
Q

natural role

A

1) bacteria have ability to acquire long-term immunity to threats they experience
2) widely spread through bacteria
3) many variants with differing proteins and mechanisms of action
4) similarities to RNAi suggest lab modification potential

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23
Q

RNA guided nuclease

A

nucleic acid can direct a nuclease to almost any sequence in any genome- and being able to break DNA at specific locations gives the ability to change DNA at any location
-allows creation of a DBS by Cas9 at almost any location which can be repaired by NHEJ or HDR

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24
Q

non homologous end joining (NHEJ)

A

mistakes are made- insertions and deletions randomly occur

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25
homology dependent repair (HDR)
depends on source of homology sequence -if HDR occurs over NHEJ, if a truly homologous sequence is used, then it will be cut again and again until NHEJ causes indel
26
gene drive
makes modifications to descendants as well as individual- DNA inherited from their other parent= changed as well - the gene drive gene changes the other allele - dont follow mendelian inheritance patterns because GD copy overrides wild type copy in heterozygotes
27
gene drive limitations
for GD to spread through a pop, must be used on sexually reproducing species with relatively short generation time -for GD to convert entire pop- must be 100% effective
28
cellularization
cell membranes form around each nucleus
29
pole cells
will become the germ line
30
blastoderm
a flat, hollow ball of ~6000 cells | predetermined cell type from specific pattern of gene expression in their part of embryo
31
polarity
directional info available to cells
32
segmentation genes
determine early stages of pattern formation
33
4 classes of segmentation genes
coordinate (maternal effect) genes gap genes pair-rule genes segment polarity genes
34
coordinate (maternal effect) genes
determine the anterior posterior// dorsal- ventral axes in embryo
35
gap genes
establish the next level of spatial organization and are expressed in contiguous sets of segments- broad regions in which subsequent development takes place- when gap genes are mutated, segments that require the gene don't develop
36
pair rule genes
expressed in alternating segments- refine the pattern set up by the coordinate and gap genes- establish unique pattern of expression in every segment
37
segment polarity genes
determine the anterior and posterior side of each segment- create spatial differentiation within each segment- regulate each other
38
bicoid gene
transcription factor that turns on the genes that produce the fly head and thorax
39
maternal effect lethal
inheritance pattern of coordinate genes | -early development depends on mother's genome
40
zygotic genes
developmental genes that function in the embryo- interpret and respond to the positional info laid out in egg by MEG
41
maternal effect genes
genes required for females to be able to form functional oocytes- the pattern set up by mom determines where the next set of genes will turn on= expression of gap genes depends on the amount of bicoid and nanos protein in that cell
42
gastrulation
process of movement and infolding of embryonic cells in early animal embryos- after the early synchronized rounds of cell division, the cells migrate in sheets to form the gastrula
43
imaginal discs
adult body parts are generated in metamorphosis here - signals from ecdysone (hormone) regulate this process
44
Hox gene
enables development of adult body plan from patterns set up in embryo= transcription factors which influence anatomical development
45
homeotic mutation
causes transformation of one body segment into another
46
paracrine signaling
signaling molecule that has traveled a short distance and affected nearby cells
47
autocrine signaling
signaling molecule that affects the same cell which secretes it
48
endocrine signaling
signaling molecule is secreted by cells in a gland and can travel a long distance in the body
49
anchor cell
signals to development of the vulva * cells will default to anchor cell, unless told not to- either VU or AC - signals to vulval precursor cells (VPC) using EGF signal
50
LIN 12
receptor and LAG2= signal that determines which cell will be AC -the cell that expresses more LAG2 will be anchor cell- the LIN12 cells receive the signals
51
ligand
signaling molecule, usually method of growth factors (paracrine)
52
receptor
protein that biochemically binds to the ligand
53
kinase
an enzyme that phosphorylates another protein
54
kinase cascase
a series of kinases that pass a signal from the receptor through the sequential phosphorylation reactions
55
stem cell characteristics
- unspecialized - capable of long term self-renewal - give rise to specialized cells through differentiation
56
potency
ability to differentiate to different cell types
57
totipotent SCs
differentiate into any of the embryonic or extra-embryonic (placenta) cell types- only exist during first few cell divisions in embryogenesis
58
pluripotent SCs
differentiate into any cell type (or tissue layer- ectoderm, mesoderm, or endoderm) contained within embryo- can be isolated from inner cell mass (ICM)
59
multipotent SCs
differentiate into closely related cell types (same tissue layer)- they are partly differentiated and exist in adult tissues
60
blastocyst
hollow structure in early development (embryonic) that contains the inner cell mass (ICM)
61
inner cell mass (ICM)
cells give rise to embryonic tissues | -extract and give growth factors to keep undifferentiated
62
teratoma
tumor with all cell types (from embryonic SCs improperly injected)
63
adult stem cell
partly differentiated cell found among differential cells in a tissue or organ, can renew itself and can differentiate to yield the major specialized cell types of the tissue/ organ - primary role= maintain and repair the tissue in which they're found - multipotent, oligopotent, or unipotent- limited degrees of potency - signals from surrounding cells maintain the SCs in their undifferentiated, quiescent state- in injury state, SCs are stimulated to divide and differentiate
64
induced pluripotent SCs
de-differentiation of adult cells- revert a differentiated cell to primordial stem cell state

Genetics (5 decks)

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