1
Q
What is an example of a totipotent cell?
A
- fertilized egg
2
Q
How many germ layers do we have?
A
3
3
Q
What is the bev bio mantra?
A
- find it move it block it
4
Q
What does find it mean?
A
- where is gene expressed, does protein made stay in cell or diffuse
5
Q
How does info move throughout the cell?
A
- info starts in the nucleus, transcription of RNA takes it out, ribosome carries it around
6
Q
How are proteins made?
A
by the translation of mrna
7
Q
What is genomic equivilance?
A
- all cells except RBCs and germ cells have same genetic info (blueprint and internal factors) material is just used differently
- each cell just transcribes different subsets of info
8
Q
What are the protein tracking mechanisms?
A
- western blot
- immunohistochemistry
- immuno cytochemistry
9
Q
What does a western blot look for?
A
if the protein is present
10
Q
What does immunohistochemistry look for?
A
- antibody detects protein location from tissue sample
11
Q
What does immunocytochemistry look for?
A
- analyzes a single cell
12
Q
What are the RNA sequencing mechanisms?
A
- rna seq (total and sc)
- insituhybridization
13
Q
What does RNA seq look for?
A
- says whats there, not where in the cell it is
14
Q
What does insituhybridization look for?
A
- ## holes in cell then hybridizes by injecting to see where protein is coming from
15
Q
What are housekeeping genes?
A
- genes transcribed and needed in all cells
16
Q
What is an abbarent cell?
A
- when a cell turns on a gene they don’t need
- causes disease
17
Q
What are the two opposing view points of developmental bio?
A
- epigenesis
- preformation
- onotgeny recapitulates phylogeny
18
Q
What is epigenesis?
A
- everything is an embryo ( cells, tissues, organs) “de novo”
- Aristotle’s viewpoint
19
Q
What is preformation?
A
- adult form homunculus is present in mini form
- leewevenhoeks view
- everything is pre-developed
20
Q
What are metameric structures and metamerism?
A
- repetitive structures in development then goes to somites to structures like vertebrae
- type of pattern formation
21
Q
What oes ontogeny recapitulates phylogeny mean?
A
- the current organism develops through the same way all their ancestors did before they became themselves
- same phases as the ancestral group
- embryonic development from fertilization to gestation or hatching (ontogeny) goes through stages of evolution from remote ancestors (phylogeny)
- human development started like chicken development is what they were getting at
22
Q
What is ontogenesis?
A
- development of an individual organism
- anatomical structure, behavioral feature
- basically the stages of development
23
Q
What is phylogeny?
A
- evolutionary development and diversification of a species, group of organisms, a feature of an organism
24
Q
What does extant mean?
A
still alive, has extinct ancestors
25
What is the most accurate way to identify an organism?
- protein sequencing
- because of evolution by DNA mutations, same dna sequence can mean different things through evolution
26
What is temperospatial expression?
- where and when does something develop and show
27
What is differentiation?
- how does simple cells become complex
28
What is morphogenesis?
how do cells organize to form things
29
How do cells know when to stop diving?
-cells have positional information about the sum of all cellular and molecular processes that tells a cell where it is
- gives symmetry
30
Are all evolutionary changes possible?
- not all beneficial but all possible
31
What is conditional development?
- reversible subject to time
- if you change it early enough it will, if not it wont
- you would change it by putting in a non-neutral environment
- aka regulative development
32
How do stem cells develop?
- if you put a stem cell in blood it will become blood stem cell
33
What is autonomous specification?
- cell has extra info so regardless of where they are it will become the original purposed cell
- extra info is gene products
34
Explain the yellow cresent?
- as cells divides only 1/2 the cells have it so maternal determinants get filtered out
- cell is yellow and red ombre
35
What is a blastomere?
- cell derived from reductive cleavage
- maternal determinants have different molecules and doesnt always happen early in development
- bc of blastomere and reductive division only giving 1/2 of the macho MRNA is asymmetrically inherited
- allows us to fate map what cells will become
36
What can the fate map depend on?
- position in embryo
- for the first few cell divisions your genome has no control over development, only mom's
37
What is syncytial development?
- most insects and muscle cells
- karyokinesis but not cytokinesis
- gives cells multiple nuclei
- asymmetrically split
38
What are morphogens?
- molecuels that drive pattern formation
- usually secreted
- higher levels closer to what it was secreted from
-ex. biccoid
39
What is a feccund?
- capable of producing lots of offspring
40
What are the steps to the lifecycle?
- fertilization
- cleavage
- gastrulation
- organogenesis
- larval
- maturity
- gametogenesis
| fat cows give out lucrative milk generously
41
What is fertiilization?
sperm + egg= 1 cell
42
What happens during clevage?
- cell goes from morula to blastula
43
What is the morula stage?
- cells in an organism are easily told apart from each other
44
What is the blastula stage?
- cavity for embro to develop is formed
45
What is reductive clevage?
- DNA synthesis goes through mitosis without cell synthesis
- membrane synthesis to fill in cell forms "lumps"
46
What is gastrulation?
- blastocoel to blastopore to ectoderm, mesoderm and endoderm
- allows us to divide animals into protostomes vs deuterosomes
47
What is a protostomes?
mouth formed first
48
What are deuterostomes?
- anal pore formed first
49
What happens during organogenesis?
- nervous system develops then head then body
- has an anterior primacy
- neural tube helps divide us into axis
50
What is anterior primacy?
- anterior side develops first
50
What is gametogenesis?
- organism is sexually mature
50
What are the human axis?
- anterior/ rostral
- posterior/ caudal
- lateral (r/l)
bilateral organisms have all 3 planes
51
What are the fate mapping techniques?
- vital dyes
- xenotransplantation
- transgenic DNA
52
What are vital dyes?
- dyes that won't kill you
- persists through development
53
What is xenotransplantation?
- adds foreign DNA to see where it goes
54
What is the transgenic method of fate mapping
- adds foreign DNA
- uses a constitutive gfp; green light that goes everywhere with foreign DNA
- recipient can't also have transgenic gfp
55
What are epithelial cells?
- skin cells, line intestine lungs, and blood vessels
- polarized and can preform different tasks on different surfaces
- tightly associated
- have sensory functions if ciliated
- have an absent or reduced intercellular matrix
- usually on basal lamina (ECM)
55
What are the type of epithelial cell to cell contacts?
- adherens junction
- tight junctions
- desmosomes
56
What do adherens junctions contain?
- cadherin, catenines, vinculin, actin
57
What is the function of adherens junctions?
- initiation and stabilization of cell to cell adhesion
- regulation of actin cytoskeleton
- intracellular signaling
- transcriptional regulation
58
What do tight junctions contain?
- claudin, occludin, zona occludins, actin
59
What are the functions of tight junctions?
- stronger junction
- fence (prevents mixing of membrane proteins between apical and basolateral membranes )
gate: controls paracellular passage of ions and solutes between cells
60
What does paracellular mean?
between cells
61
What are the functions of desmosomes?
- still a tight and strong junction
- in tissues that experience tight mechanical stress (cardiac muscle, bladder, skin)
62
What are the functions of the cell to ECM focal adhesions?
- anchor cells using integrins to ECM
- transduce mechanical forces
- facilitates diffusion of regulatory signals
63
What do cell to ECM focal adhesions contain?
- integrins, vinculin, talin, alpha-actinin, actin , ecm
64
where are cell to ecm focal adhesions found?
- epithelial and mesenchymal cells
65
What are mesnchymal cells?
- cells (especially immune cells) that need to move
- when epithelial cells become unanchored and can move they become mesenchymal (derived from epithelial cells)
- have a loss of cell to cell adhesion and have weakly interacting cell to ecm interactions (can't fully adhere but can grasp
- have a loss of apical basal polarity but a gain of front to pack polarity
- migratory and invasive
- loss of keratin expression but gain of vimentin expression
66
what are the functions of mesenchymal cells?
- capacity for self- renewal and proliferation (dividing)
- stem cells with capacity to differentiate into different cells
0 gives rise to embryonic germ layers (mesoderm and endoderm)
- gives rise to neural crest
67
What kind of cytoskeleton do epithelial cells have?
- actin based cortical cytoskeleton
- quasi static
- cell shape doesn't change too much (snaps back into shape)
68
What does quasi-static mean?
- slow change that maintains equillibrium
69
What kind of cytoskeleton do mesynchimal stem cells have?
- actin based stress fiber network
- very dynamic, cell shape changes
70
What is a primary protein structure?
- linear sequence of AA making up polypeptide chains
71
What is a secondary protein structure?
- local spatial conformation of backbone without side chains
72
What is a tertiary protien structure?
- 3D interaction between AA side chains and backbone
- fibrous protein
73
What is a fibrous protein?
- tertiary protein
- made of elaongated polypeptide chains forming filamentous structures
- low H20 solubility
- ex. intermediate filaments (keratin, vimentin) collagens, elsastins, fibrins
74
What is a quaternary protein structure?
- multiple protein chains packaged closely
- globular protein
75
What is a globular protein?
- quaternary structure
- small and compact
- largest class in human body
- forms transcription factors, molecules and morphogens
- high H20 solubility
76
Xan a protein be globular and fibrous?
yes
- globular could become fibrous
77
What are the membrane associated proteins?
- integral proteins
- monotropic proteins
- extrinsic proteins
78
What are integral proteins?
- having domains that pass through both layers of lipid bilayer (plasma membrane)
- can be single or multiple pass integral proteins
- ecto and endoderm
79
What are monotropic proteins?
- intracellular protein associating with 1 layer of lipid bilayer
- lipidphillic
- endoderm
80
What are extrinsic proteins?
- extracellular protein having a loose association with outer layer of lipid bilayer
- hydrophilic
- ectoderm
81
what does surface tension do?
- surgace shrinks and minimizes surface area
- measured as resistance to deformation when a force is applied
- plays a roll in cell segregation, but not most of it
82
What is cell segregation?
- how tight cells come together to form outer and inner layer
- think of it like cell velcro
83
how doe cell segregation work?
- cadherins on one cell adhere to cadherens on another cell which are attached to the cortical-actin cytoskeleton at adherens junction
84
How do cadherens stick to the cortical cytoskeleton?
through catenins
- alpha gamma betta
85
What are the tree types of cadherins?
- epithelial
- placental
- neural
can all bind together
86
What are cadherins strengthened by?
calcium
87
How do cadherins relate to cell segregation?
- density of cadherins on cell surgace affect sorting
- more cadherins create more surface tension and make it harder to pull apart
- more cadherins of 1 type means that that cadherin group goes to the middle
88
How are mesenchymal cells aligned?
- less densly packed because they neeed to move
- basal lamina seperates E and M cells
89
How are cells stabilized?
- basal lamina binds using focal adhesions in adherins junction to keep epithelial cells in place
- focal adhesion associates with cortical actin cytoskeleton
- integrin helps with binding
90
What is juxtacrine signaling?
- cells close together communicate through hormones
- cells must be next to eachother
- needs ligand and receptor
91
What is paracrine signaling?
- long distance, diffuses throughout
- like a cell tower but antenna = receptor to get signal and must have receptor
- needs a ligand and a receptor
92
What is a ligand?
- signaling proteins
93
What is up-regulation?
- need more of something, add more receptors
94
What is a nuclear receptor?
- ex/ estrogen estrogen pathway
- uses endocrine and paracrine receptors
95
What do morphogens cause?
- concentration gradient
- activates gene expression in a gradient because if there are more ligands binding = more showing gene
= - cells closer to the source typically have more enhancers
96
What are enhancer elements?
- bind to transcription factor to interact with RNA polymerase to accelerate transcription of that gene
- more enhancers = more transcription
- ligand binding to receptor causes signal transduction cascade
- gene transcription happens in nucleus
- cells closer to the source typically have more enhancers
97
What is an example of physical cells communicating?
- going to gym or getting a tan
98
What is a constitutive pathway?
always on
99
What is an example of juxtacrine signaling?
- Delta-Notch
100
Whata are examples of paracrine signaling?
- teceptor tyrosine kinase
- hedgehog
- WNT
- serine adn threonine and kinases
101
What are some key characteristics of microtubules
- polarized
- assemble in semi crystalized order
- kinesin and dyesin move on them
- actin is globular on the + end of the tubule but fibrous on the - end
102
What does it mean that microtubules assemble in a semi-crystalized order?
- Beta on positive end
- alpha on negative end
103
What do colcemide and nacodazole do?
inhibit tubulin polymerization on microtubules
104
What does taxol do?
- stabilizes microtubules
- stops cell division
105
How does kenesin move on microtubules?
- moves on positive end
- anterograde movement (moves fowards)
106
How does dyenien move on microtubules?-
- on negative end
- retrograde movement, goes backwards
107
What do latrunculin and cytochalisin do?
inhibit actin polymerization
108
What does phalloidin do?
- stabilizes actin polymers
109
What is actin really important for on microtubules?
- cell migration like epithelial to mesenchymal transition
- globular to fibrous actin transition extends cell and allows cell movement
110
Describe intermediate filaments?
- made of keratin and vinculin
- shifted and antiparallel
111
What do gap junctions do?
- form channels to allow cell to cell communication
112
What is the central dogma of gene regulation?
- DNA to RNA to Protein
113
What can chemical modifications effect?
- DNA
- RNA
- Protein
114
What is a chemical modification to DNA?
cytosine methylation
115
What are chemical modifications to RNA?
- splicing
- poly adenylation
- 5' capping
- adenine methylation
116
What are all protein modifications?
post translational modifications
117
What are the types of protein chemical modification?
- phosphorylation
- methylation
- acylation
- acetylation
- glycosylation
118
What is the difference between RNA and DNA?
- RNA has an extra O
119
What is spontaneous deamination?
- oxygen takes NH2 (amine) from cytosine and turns it to thymine
120
What is chromatin?
- made of protein and DNA and makes up eukaryotic chromosomes
121
What are the steps to Chromatin modification?
- starts with nucleosome's
- histone modification makes nucleosomes into solenoid
- domiain organization makes solenoid into scaffold loop
- mitotic condensation makes scaffoled loop into chromosome
122
What are nucelosomes?
- beads on a string
123
What is heterochromatin?
- darkly stained
- densely packed
- transcriptionally de-active
124
What is euchromatin?
- open chromatin
- loosely packed
- lightly stained
- transcriptionally active
- good chromatin
125
What does the nucleolus do?
- makes Rrna and Trna
- transcriptionally active
126
Does all chromatin look the same?
no, different based on cell type bc different genes are transcribed in different cell
127
what do core histones create?
- histone octomer
128
What do histone tails do?
- make the chromatin more accessible to transcription factors or restrict access to chromatin
- site of post-translational modifications that alter chromatin
129
What do histones face?
- lots of negative selective pressure
130
What does it mean if the histone tail is methylated?
- its closed
- condensed nucleosome
131
What does it mean that histones make chromatin more accessible?
- open chromatin, expose euchromatin
132
What does it mean histones make chromatin less accessible?
- close off chromatin
- heterochromatin usage
133
What do histone post translational modifications create?
- open chromatin
- uncondensed nucleosome?
134
What are the histone post translational modifications?
-phosphorylation
-acetylation
- methylation with active lysine
- methylation with repressive lysine
- methylation with arginine
- ubiquitylation
- all different because different chromatin binding sites have affinities for different proteins
135
Is dna methylation and methylation of histones the same?
- no
136
What is the RTK pathway?
- binding
- homodimer
- phosphorylation cascade
- tyrosine kinase hyper activated
- TK phosphorylated and activated
- protein goes to target
137
What is the Jak-stat RTK pathway?
- ligand
- receptor
- Jak
- Stat Dimerization
- transcription
138
What is the RTK signal transduction cascade?
- Ligand
- RTK
- GEF
_ RAS
_ RAF
- MEK
- ERK
- Transcription Factor
- Transcription
( RAF to MEK to ERK is kinase cascade)
(GEF is guanine exchange factor)
139
What is the ligand in the hedgehog pathway?
hedgehog
140
What is the receptor in the hedgehog pathway?
patched
141
What is the co-receptor in the hedgehog pathway?
smoothened
142
What is the effector in the hedgehog pathway?
gli
143
What happens in the hedgehog pathway if there is no transcription of hedgehog repressive genes ?
- smoothened repressed
144
What happes in the hedgehog pathway if there is transcription of hedgehog-repressive genes?
smoothened is de-repressed and activates gli
145
Where does hedgehog and WNT occur?
on cillium protrusions from cell
- involves microtubukes protruding from centriol
146
What is the canonical pathway of WNT?
- WNT
- Frizzled/ LRP5
- Disheveled
- GSK3
- Beta catenin
- Transcription
147
What is the ligand in the WNT Pathway?
WND
148
What is the receptor in the WNT Pathway?
frizzled
149
What is the co-activator in the WNT pathway?
- disheveled
150
What is the effector in the WNT Pathway?
B-catenin
151
Where si B-catenin when there is no WNT?
- destruction complex
- then phosphorylated and ubiquinated
- then no transcription
152
What happens when WNT is bound?
- gene is expressed
153
What are non-canonical pathways ?
no b-catenin
154
What are the possible outcomes of the non-canonical pathways
- Ca2+ release and up regulation
- cytoskeletal changes
- transcription
- genomic and non-genomic effects
155
What are the steps to the smad pathway?
- TGF b superfamily ligand
- receptor 2
- receptor 1
- smad activation
- smad dimerization
- new transcription
- activation
156
What is the receptor in the smad pathway?
- serine tirosine kindase
(dimer of dimers)
157
What is the ligand in the smad pathway?
lots of them
158
What is the effector in the smad pathway?
- smad 2/3
- smad 1/5
159
What is the co-effector in the smad pathway?
smad 4
160
What is TFG B
tumor growth factor
activates smad pathway
161
What is translated?
mrna
162
What are the stepts to RNA processing and stability?
1. gene has RNAP binded and regulated by transcription factors and enhancers
2. copy of DNA strand into RNA.
3. splicing
4 MRNA processed
5. translation
163
What must the gene have to be regulated by transcription factors and enhancers?
- open and accesible histone tail
164
What is splicing?
- exons coded introns cut out making nuclear RNA
- must be very specific not interrupting reading frame
- allows us to get more protein combos in a cell
165
What is the GU AG rule?
- start to stop of intron
166
Where are promoters located?
anywhere
167
Why do trancription factors alter chromatin?
- to allow transcription of chromatin and displace histones
168
What are mediators?
- bridges to link enhancers to promoters
- important for gene expression
169
What is a cis-enhacer?
- on gene that is going to be activated
- recognized by splicosome
170
What is a trans-acting factor?
- binds to enhancer on gene
- part of splicosome
171
What are enhancers described as?
- modular and cooperative
- can work together
172
What are silencer elements?
- attenuate gene expression and lower the amount of gene as well as saying when and where it is expressed
173
What are the RNA processing methods?
- capping on 5'
- polyandenylation of 3'
- splicing
174
What does polyadenylation do?
- regulates RNA stability
- longer poly-A-tail is more stable
175
What does capping do?
- closing off sequence
176
What is alternative splicing?
- can cut different parts out of same sequence
177
What are the forms of post-translational control?
- hormonal activation
- ribosome heterogeneity
- protein translational contral miRNA
- localisation of MRNAs
178
What is ribosome heterogeniety?
- not all ribosomea are = there are mutations that effet them
179
What are the microRNA steps?
- drsoha
- dicer
- risk
- if imperfect complimentary= repression
- if perfect complimentary= degradation
180
What are the forms of mRNA localization?
- diffusion and local anchoring
- localize protection of MRNA (protects poly-A-tail)
- active transport along cytoskeleton
181
How does everyone start off?
bi-potential, has mullerian duct and wolfien duct
182
What are barr bodies?
- in all females
- second x is silenced
183
How many chromosomes do all people have?
44 chromosomes + 2 sex chromosomes
184
What are mesonephros?
- middle kidney of embryos . source of hematopoeitic stem cells and male sex organs
185
What is the genital ridge?
- thickening of mesoderm on medial edge of mesonephros
186
What is a bipotential gonad?
- ruminant tissue from genital ridge
- derives ovaries and testes
187
What happens at 8 weeks development?
- xx wolfien disappears
- xy mullerien disappears
188
What happens at 20 weeks?
- egg cells are covered by somatic cells called nurse cells
- sperm cells are covered by netowrk forming tubes
189
What do males need?
-SRY
- SOX 9
- FGF9
190
What do females need?
- WNT and RSPO4
191
What are cell autonomous mutations?
- affects cell harboring mutation
- transcription factors
192
What are cell non-autonomous mutations?
- affect cells around mutated cell
- secretions
193
Developmental Biology
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