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Developmental Biology > Unit 1 > Flashcards

Unit 1 Flashcards

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1
Q

What is an example of a totipotent cell?

A
  • fertilized egg
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2
Q

How many germ layers do we have?

A

3

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3
Q

What is the bev bio mantra?

A
  • find it move it block it
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4
Q

What does find it mean?

A
  • where is gene expressed, does protein made stay in cell or diffuse
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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
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6
Q

How are proteins made?

A

by the translation of mrna

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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
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8
Q

What are the protein tracking mechanisms?

A
  • western blot
  • immunohistochemistry
  • immuno cytochemistry
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9
Q

What does a western blot look for?

A

if the protein is present

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10
Q

What does immunohistochemistry look for?

A
  • antibody detects protein location from tissue sample
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11
Q

What does immunocytochemistry look for?

A
  • analyzes a single cell
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12
Q

What are the RNA sequencing mechanisms?

A
  • rna seq (total and sc)
  • insituhybridization
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13
Q

What does RNA seq look for?

A
  • says whats there, not where in the cell it is
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14
Q

What does insituhybridization look for?

A
  • ## holes in cell then hybridizes by injecting to see where protein is coming from
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15
Q

What are housekeeping genes?

A
  • genes transcribed and needed in all cells
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16
Q

What is an abbarent cell?

A
  • when a cell turns on a gene they don’t need
  • causes disease
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17
Q

What are the two opposing view points of developmental bio?

A
  • epigenesis
  • preformation
  • onotgeny recapitulates phylogeny
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18
Q

What is epigenesis?

A
  • everything is an embryo ( cells, tissues, organs) “de novo”
  • Aristotle’s viewpoint
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19
Q

What is preformation?

A
  • adult form homunculus is present in mini form
  • leewevenhoeks view
  • everything is pre-developed
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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
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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
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22
Q

What is ontogenesis?

A
  • development of an individual organism
  • anatomical structure, behavioral feature
  • basically the stages of development
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23
Q

What is phylogeny?

A
  • evolutionary development and diversification of a species, group of organisms, a feature of an organism
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24
Q

What does extant mean?

A

still alive, has extinct ancestors

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25
Q

What is the most accurate way to identify an organism?

A
  • protein sequencing
  • because of evolution by DNA mutations, same dna sequence can mean different things through evolution
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26
Q

What is temperospatial expression?

A
  • where and when does something develop and show
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27
Q

What is differentiation?

A
  • how does simple cells become complex
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28
Q

What is morphogenesis?

A

how do cells organize to form things

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29
Q

How do cells know when to stop diving?

A

-cells have positional information about the sum of all cellular and molecular processes that tells a cell where it is
- gives symmetry

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30
Q

Are all evolutionary changes possible?

A
  • not all beneficial but all possible
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31
Q

What is conditional development?

A
  • 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
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32
Q

How do stem cells develop?

A
  • if you put a stem cell in blood it will become blood stem cell
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33
Q

What is autonomous specification?

A
  • cell has extra info so regardless of where they are it will become the original purposed cell
  • extra info is gene products
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34
Q

Explain the yellow cresent?

A
  • as cells divides only 1/2 the cells have it so maternal determinants get filtered out
  • cell is yellow and red ombre
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35
Q

What is a blastomere?

A
  • 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
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36
Q

What can the fate map depend on?

A
  • position in embryo
  • for the first few cell divisions your genome has no control over development, only mom’s
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37
Q

What is syncytial development?

A
  • most insects and muscle cells
  • karyokinesis but not cytokinesis
  • gives cells multiple nuclei
  • asymmetrically split
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38
Q

What are morphogens?

A
  • molecuels that drive pattern formation
  • usually secreted
  • higher levels closer to what it was secreted from
    -ex. biccoid
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39
Q

What is a feccund?

A
  • capable of producing lots of offspring
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40
Q

What are the steps to the lifecycle?

A
  • fertilization
  • cleavage
  • gastrulation
  • organogenesis
  • larval
  • maturity
  • gametogenesis

fat cows give out lucrative milk generously

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41
Q

What is fertiilization?

A

sperm + egg= 1 cell

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42
Q

What happens during clevage?

A
  • cell goes from morula to blastula
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43
Q

What is the morula stage?

A
  • cells in an organism are easily told apart from each other
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44
Q

What is the blastula stage?

A
  • cavity for embro to develop is formed
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45
Q

What is reductive clevage?

A
  • DNA synthesis goes through mitosis without cell synthesis
  • membrane synthesis to fill in cell forms “lumps”
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46
Q

What is gastrulation?

A
  • blastocoel to blastopore to ectoderm, mesoderm and endoderm
  • allows us to divide animals into protostomes vs deuterosomes
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47
Q

What is a protostomes?

A

mouth formed first

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48
Q

What are deuterostomes?

A
  • anal pore formed first
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49
Q

What happens during organogenesis?

A
  • nervous system develops then head then body
  • has an anterior primacy
  • neural tube helps divide us into axis
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50
Q

What is anterior primacy?

A
  • anterior side develops first
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50
Q

What is gametogenesis?

A
  • organism is sexually mature
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50
Q

What are the human axis?

A
  • anterior/ rostral
  • posterior/ caudal
  • lateral (r/l)
    bilateral organisms have all 3 planes
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51
Q

What are the fate mapping techniques?

A
  • vital dyes
  • xenotransplantation
  • transgenic DNA
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52
Q

What are vital dyes?

A
  • dyes that won’t kill you
  • persists through development
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53
Q

What is xenotransplantation?

A
  • adds foreign DNA to see where it goes
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54
Q

What is the transgenic method of fate mapping

A
  • adds foreign DNA
  • uses a constitutive gfp; green light that goes everywhere with foreign DNA
  • recipient can’t also have transgenic gfp
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55
Q

What are epithelial cells?

A
  • 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)
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55
Q

What are the type of epithelial cell to cell contacts?

A
  • adherens junction
  • tight junctions
  • desmosomes
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56
Q

What do adherens junctions contain?

A
  • cadherin, catenines, vinculin, actin
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57
Q

What is the function of adherens junctions?

A
  • initiation and stabilization of cell to cell adhesion
  • regulation of actin cytoskeleton
  • intracellular signaling
  • transcriptional regulation
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58
Q

What do tight junctions contain?

A
  • claudin, occludin, zona occludins, actin
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59
Q

What are the functions of tight junctions?

A
  • stronger junction
  • fence (prevents mixing of membrane proteins between apical and basolateral membranes )
    gate: controls paracellular passage of ions and solutes between cells
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60
Q

What does paracellular mean?

A

between cells

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61
Q

What are the functions of desmosomes?

A
  • still a tight and strong junction
  • in tissues that experience tight mechanical stress (cardiac muscle, bladder, skin)
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62
Q

What are the functions of the cell to ECM focal adhesions?

A
  • anchor cells using integrins to ECM
  • transduce mechanical forces
  • facilitates diffusion of regulatory signals
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63
Q

What do cell to ECM focal adhesions contain?

A
  • integrins, vinculin, talin, alpha-actinin, actin , ecm
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64
Q

where are cell to ecm focal adhesions found?

A
  • epithelial and mesenchymal cells
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65
Q

What are mesnchymal cells?

A
  • 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
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66
Q

what are the functions of mesenchymal cells?

A
  • 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
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67
Q

What kind of cytoskeleton do epithelial cells have?

A
  • actin based cortical cytoskeleton
  • quasi static
  • cell shape doesn’t change too much (snaps back into shape)
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68
Q

What does quasi-static mean?

A
  • slow change that maintains equillibrium
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69
Q

What kind of cytoskeleton do mesynchimal stem cells have?

A
  • actin based stress fiber network
  • very dynamic, cell shape changes
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70
Q

What is a primary protein structure?

A
  • linear sequence of AA making up polypeptide chains
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71
Q

What is a secondary protein structure?

A
  • local spatial conformation of backbone without side chains
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72
Q

What is a tertiary protien structure?

A
  • 3D interaction between AA side chains and backbone
  • fibrous protein
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73
Q

What is a fibrous protein?

A
  • tertiary protein
  • made of elaongated polypeptide chains forming filamentous structures
  • low H20 solubility
  • ex. intermediate filaments (keratin, vimentin) collagens, elsastins, fibrins
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74
Q

What is a quaternary protein structure?

A
  • multiple protein chains packaged closely
  • globular protein
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75
Q

What is a globular protein?

A
  • quaternary structure
  • small and compact
  • largest class in human body
  • forms transcription factors, molecules and morphogens
  • high H20 solubility
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76
Q

Xan a protein be globular and fibrous?

A

yes
- globular could become fibrous

77
Q

What are the membrane associated proteins?

A
  • integral proteins
  • monotropic proteins
  • extrinsic proteins
78
Q

What are integral proteins?

A
  • having domains that pass through both layers of lipid bilayer (plasma membrane)
  • can be single or multiple pass integral proteins
  • ecto and endoderm
79
Q

What are monotropic proteins?

A
  • intracellular protein associating with 1 layer of lipid bilayer
  • lipidphillic
  • endoderm
80
Q

What are extrinsic proteins?

A
  • extracellular protein having a loose association with outer layer of lipid bilayer
  • hydrophilic
  • ectoderm
81
Q

what does surface tension do?

A
  • 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
Q

What is cell segregation?

A
  • how tight cells come together to form outer and inner layer
  • think of it like cell velcro
83
Q

how doe cell segregation work?

A
  • cadherins on one cell adhere to cadherens on another cell which are attached to the cortical-actin cytoskeleton at adherens junction
84
Q

How do cadherens stick to the cortical cytoskeleton?

A

through catenins
- alpha gamma betta

85
Q

What are the tree types of cadherins?

A
  • epithelial
  • placental
  • neural
    can all bind together
86
Q

What are cadherins strengthened by?

A

calcium

87
Q

How do cadherins relate to cell segregation?

A
  • 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
Q

How are mesenchymal cells aligned?

A
  • less densly packed because they neeed to move
  • basal lamina seperates E and M cells
89
Q

How are cells stabilized?

A
  • 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
Q

What is juxtacrine signaling?

A
  • cells close together communicate through hormones
  • cells must be next to eachother
  • needs ligand and receptor
91
Q

What is paracrine signaling?

A
  • 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
Q

What is a ligand?

A
  • signaling proteins
93
Q

What is up-regulation?

A
  • need more of something, add more receptors
94
Q

What is a nuclear receptor?

A
  • ex/ estrogen estrogen pathway
  • uses endocrine and paracrine receptors
95
Q

What do morphogens cause?

A
  • 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
Q

What are enhancer elements?

A
  • 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
Q

What is an example of physical cells communicating?

A
  • going to gym or getting a tan
98
Q

What is a constitutive pathway?

A

always on

99
Q

What is an example of juxtacrine signaling?

A
  • Delta-Notch
100
Q

Whata are examples of paracrine signaling?

A
  • teceptor tyrosine kinase
  • hedgehog
  • WNT
  • serine adn threonine and kinases
101
Q

What are some key characteristics of microtubules

A
  • 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
Q

What does it mean that microtubules assemble in a semi-crystalized order?

A
  • Beta on positive end
  • alpha on negative end
103
Q

What do colcemide and nacodazole do?

A

inhibit tubulin polymerization on microtubules

104
Q

What does taxol do?

A
  • stabilizes microtubules
  • stops cell division
105
Q

How does kenesin move on microtubules?

A
  • moves on positive end
  • anterograde movement (moves fowards)
106
Q

How does dyenien move on microtubules?-

A
  • on negative end
  • retrograde movement, goes backwards
107
Q

What do latrunculin and cytochalisin do?

A

inhibit actin polymerization

108
Q

What does phalloidin do?

A
  • stabilizes actin polymers
109
Q

What is actin really important for on microtubules?

A
  • cell migration like epithelial to mesenchymal transition
  • globular to fibrous actin transition extends cell and allows cell movement
110
Q

Describe intermediate filaments?

A
  • made of keratin and vinculin
  • shifted and antiparallel
111
Q

What do gap junctions do?

A
  • form channels to allow cell to cell communication
112
Q

What is the central dogma of gene regulation?

A
  • DNA to RNA to Protein
113
Q

What can chemical modifications effect?

A
  • DNA
  • RNA
  • Protein
114
Q

What is a chemical modification to DNA?

A

cytosine methylation

115
Q

What are chemical modifications to RNA?

A
  • splicing
  • poly adenylation
  • 5’ capping
  • adenine methylation
116
Q

What are all protein modifications?

A

post translational modifications

117
Q

What are the types of protein chemical modification?

A
  • phosphorylation
  • methylation
  • acylation
  • acetylation
  • glycosylation
118
Q

What is the difference between RNA and DNA?

A
  • RNA has an extra O
119
Q

What is spontaneous deamination?

A
  • oxygen takes NH2 (amine) from cytosine and turns it to thymine
120
Q

What is chromatin?

A
  • made of protein and DNA and makes up eukaryotic chromosomes
121
Q

What are the steps to Chromatin modification?

A
  • 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
Q

What are nucelosomes?

A
  • beads on a string
123
Q

What is heterochromatin?

A
  • darkly stained
  • densely packed
  • transcriptionally de-active
124
Q

What is euchromatin?

A
  • open chromatin
  • loosely packed
  • lightly stained
  • transcriptionally active
  • good chromatin
125
Q

What does the nucleolus do?

A
  • makes Rrna and Trna
  • transcriptionally active
126
Q

Does all chromatin look the same?

A

no, different based on cell type bc different genes are transcribed in different cell

127
Q

what do core histones create?

A
  • histone octomer
128
Q

What do histone tails do?

A
  • make the chromatin more accessible to transcription factors or restrict access to chromatin
  • site of post-translational modifications that alter chromatin
129
Q

What do histones face?

A
  • lots of negative selective pressure
130
Q

What does it mean if the histone tail is methylated?

A
  • its closed
  • condensed nucleosome
131
Q

What does it mean that histones make chromatin more accessible?

A
  • open chromatin, expose euchromatin
132
Q

What does it mean histones make chromatin less accessible?

A
  • close off chromatin
  • heterochromatin usage
133
Q

What do histone post translational modifications create?

A
  • open chromatin
  • uncondensed nucleosome?
134
Q

What are the histone post translational modifications?

A

-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
Q

Is dna methylation and methylation of histones the same?

A
  • no
136
Q

What is the RTK pathway?

A
  • binding
  • homodimer
  • phosphorylation cascade
  • tyrosine kinase hyper activated
  • TK phosphorylated and activated
  • protein goes to target
137
Q

What is the Jak-stat RTK pathway?

A
  • ligand
  • receptor
  • Jak
  • Stat Dimerization
  • transcription
138
Q

What is the RTK signal transduction cascade?

A
  • Ligand
  • RTK
  • GEF
    _ RAS
    _ RAF
  • MEK
  • ERK
  • Transcription Factor
  • Transcription
    ( RAF to MEK to ERK is kinase cascade)
    (GEF is guanine exchange factor)
139
Q

What is the ligand in the hedgehog pathway?

A

hedgehog

140
Q

What is the receptor in the hedgehog pathway?

A

patched

141
Q

What is the co-receptor in the hedgehog pathway?

A

smoothened

142
Q

What is the effector in the hedgehog pathway?

A

gli

143
Q

What happens in the hedgehog pathway if there is no transcription of hedgehog repressive genes ?

A
  • smoothened repressed
144
Q

What happes in the hedgehog pathway if there is transcription of hedgehog-repressive genes?

A

smoothened is de-repressed and activates gli

145
Q

Where does hedgehog and WNT occur?

A

on cillium protrusions from cell
- involves microtubukes protruding from centriol

146
Q

What is the canonical pathway of WNT?

A
  • WNT
  • Frizzled/ LRP5
  • Disheveled
  • GSK3
  • Beta catenin
  • Transcription
147
Q

What is the ligand in the WNT Pathway?

A

WND

148
Q

What is the receptor in the WNT Pathway?

A

frizzled

149
Q

What is the co-activator in the WNT pathway?

A
  • disheveled
150
Q

What is the effector in the WNT Pathway?

A

B-catenin

151
Q

Where si B-catenin when there is no WNT?

A
  • destruction complex
  • then phosphorylated and ubiquinated
  • then no transcription
152
Q

What happens when WNT is bound?

A
  • gene is expressed
153
Q

What are non-canonical pathways ?

A

no b-catenin

154
Q

What are the possible outcomes of the non-canonical pathways

A
  • Ca2+ release and up regulation
  • cytoskeletal changes
  • transcription
  • genomic and non-genomic effects
155
Q

What are the steps to the smad pathway?

A
  • TGF b superfamily ligand
  • receptor 2
  • receptor 1
  • smad activation
  • smad dimerization
  • new transcription
  • activation
156
Q

What is the receptor in the smad pathway?

A
  • serine tirosine kindase
    (dimer of dimers)
157
Q

What is the ligand in the smad pathway?

A

lots of them

158
Q

What is the effector in the smad pathway?

A
  • smad 2/3
  • smad 1/5
159
Q

What is the co-effector in the smad pathway?

A

smad 4

160
Q

What is TFG B

A

tumor growth factor
activates smad pathway

161
Q

What is translated?

A

mrna

162
Q

What are the stepts to RNA processing and stability?

A
  1. gene has RNAP binded and regulated by transcription factors and enhancers
  2. copy of DNA strand into RNA.
  3. splicing
    4 MRNA processed
  4. translation
163
Q

What must the gene have to be regulated by transcription factors and enhancers?

A
  • open and accesible histone tail
164
Q

What is splicing?

A
  • 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
Q

What is the GU AG rule?

A
  • start to stop of intron
166
Q

Where are promoters located?

A

anywhere

167
Q

Why do trancription factors alter chromatin?

A
  • to allow transcription of chromatin and displace histones
168
Q

What are mediators?

A
  • bridges to link enhancers to promoters
  • important for gene expression
169
Q

What is a cis-enhacer?

A
  • on gene that is going to be activated
  • recognized by splicosome
170
Q

What is a trans-acting factor?

A
  • binds to enhancer on gene
  • part of splicosome
171
Q

What are enhancers described as?

A
  • modular and cooperative
  • can work together
172
Q

What are silencer elements?

A
  • attenuate gene expression and lower the amount of gene as well as saying when and where it is expressed
173
Q

What are the RNA processing methods?

A
  • capping on 5’
  • polyandenylation of 3’
  • splicing
174
Q

What does polyadenylation do?

A
  • regulates RNA stability
  • longer poly-A-tail is more stable
175
Q

What does capping do?

A
  • closing off sequence
176
Q

What is alternative splicing?

A
  • can cut different parts out of same sequence
177
Q

What are the forms of post-translational control?

A
  • hormonal activation
  • ribosome heterogeneity
  • protein translational contral miRNA
  • localisation of MRNAs
178
Q

What is ribosome heterogeniety?

A
  • not all ribosomea are = there are mutations that effet them
179
Q

What are the microRNA steps?

A
  • drsoha
  • dicer
  • risk
  • if imperfect complimentary= repression
  • if perfect complimentary= degradation
180
Q

What are the forms of mRNA localization?

A
  • diffusion and local anchoring
  • localize protection of MRNA (protects poly-A-tail)
  • active transport along cytoskeleton
181
Q

How does everyone start off?

A

bi-potential, has mullerian duct and wolfien duct

182
Q

What are barr bodies?

A
  • in all females
  • second x is silenced
183
Q

How many chromosomes do all people have?

A

44 chromosomes + 2 sex chromosomes

184
Q

What are mesonephros?

A
  • middle kidney of embryos . source of hematopoeitic stem cells and male sex organs
185
Q

What is the genital ridge?

A
  • thickening of mesoderm on medial edge of mesonephros
186
Q

What is a bipotential gonad?

A
  • ruminant tissue from genital ridge
  • derives ovaries and testes
187
Q

What happens at 8 weeks development?

A
  • xx wolfien disappears
  • xy mullerien disappears
188
Q

What happens at 20 weeks?

A
  • egg cells are covered by somatic cells called nurse cells
  • sperm cells are covered by netowrk forming tubes
189
Q

What do males need?

A

-SRY
- SOX 9
- FGF9

190
Q

What do females need?

A
  • WNT and RSPO4
191
Q

What are cell autonomous mutations?

A
  • affects cell harboring mutation
  • transcription factors
192
Q

What are cell non-autonomous mutations?

A
  • affect cells around mutated cell
  • secretions
193
Q
A

Developmental Biology (3 decks)

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