Unit 1 Flashcards
What is an example of a totipotent cell?
- fertilized egg
How many germ layers do we have?
3
What is the bev bio mantra?
- find it move it block it
What does find it mean?
- where is gene expressed, does protein made stay in cell or diffuse
How does info move throughout the cell?
- info starts in the nucleus, transcription of RNA takes it out, ribosome carries it around
How are proteins made?
by the translation of mrna
What is genomic equivilance?
- 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
What are the protein tracking mechanisms?
- western blot
- immunohistochemistry
- immuno cytochemistry
What does a western blot look for?
if the protein is present
What does immunohistochemistry look for?
- antibody detects protein location from tissue sample
What does immunocytochemistry look for?
- analyzes a single cell
What are the RNA sequencing mechanisms?
- rna seq (total and sc)
- insituhybridization
What does RNA seq look for?
- says whats there, not where in the cell it is
What does insituhybridization look for?
- ## holes in cell then hybridizes by injecting to see where protein is coming from
What are housekeeping genes?
- genes transcribed and needed in all cells
What is an abbarent cell?
- when a cell turns on a gene they don’t need
- causes disease
What are the two opposing view points of developmental bio?
- epigenesis
- preformation
- onotgeny recapitulates phylogeny
What is epigenesis?
- everything is an embryo ( cells, tissues, organs) “de novo”
- Aristotle’s viewpoint
What is preformation?
- adult form homunculus is present in mini form
- leewevenhoeks view
- everything is pre-developed
What are metameric structures and metamerism?
- repetitive structures in development then goes to somites to structures like vertebrae
- type of pattern formation
What oes ontogeny recapitulates phylogeny mean?
- 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
What is ontogenesis?
- development of an individual organism
- anatomical structure, behavioral feature
- basically the stages of development
What is phylogeny?
- evolutionary development and diversification of a species, group of organisms, a feature of an organism
What does extant mean?
still alive, has extinct ancestors
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
What is temperospatial expression?
- where and when does something develop and show
What is differentiation?
- how does simple cells become complex
What is morphogenesis?
how do cells organize to form things
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
Are all evolutionary changes possible?
- not all beneficial but all possible
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
How do stem cells develop?
- if you put a stem cell in blood it will become blood stem cell
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
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
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
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
What is syncytial development?
- most insects and muscle cells
- karyokinesis but not cytokinesis
- gives cells multiple nuclei
- asymmetrically split
What are morphogens?
- molecuels that drive pattern formation
- usually secreted
- higher levels closer to what it was secreted from
-ex. biccoid
What is a feccund?
- capable of producing lots of offspring
What are the steps to the lifecycle?
- fertilization
- cleavage
- gastrulation
- organogenesis
- larval
- maturity
- gametogenesis
fat cows give out lucrative milk generously
What is fertiilization?
sperm + egg= 1 cell
What happens during clevage?
- cell goes from morula to blastula
What is the morula stage?
- cells in an organism are easily told apart from each other
What is the blastula stage?
- cavity for embro to develop is formed
What is reductive clevage?
- DNA synthesis goes through mitosis without cell synthesis
- membrane synthesis to fill in cell forms “lumps”
What is gastrulation?
- blastocoel to blastopore to ectoderm, mesoderm and endoderm
- allows us to divide animals into protostomes vs deuterosomes
What is a protostomes?
mouth formed first
What are deuterostomes?
- anal pore formed first
What happens during organogenesis?
- nervous system develops then head then body
- has an anterior primacy
- neural tube helps divide us into axis
What is anterior primacy?
- anterior side develops first
What is gametogenesis?
- organism is sexually mature
What are the human axis?
- anterior/ rostral
- posterior/ caudal
- lateral (r/l)
bilateral organisms have all 3 planes
What are the fate mapping techniques?
- vital dyes
- xenotransplantation
- transgenic DNA
What are vital dyes?
- dyes that won’t kill you
- persists through development
What is xenotransplantation?
- adds foreign DNA to see where it goes
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
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)
What are the type of epithelial cell to cell contacts?
- adherens junction
- tight junctions
- desmosomes
What do adherens junctions contain?
- cadherin, catenines, vinculin, actin
What is the function of adherens junctions?
- initiation and stabilization of cell to cell adhesion
- regulation of actin cytoskeleton
- intracellular signaling
- transcriptional regulation
What do tight junctions contain?
- claudin, occludin, zona occludins, actin
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
What does paracellular mean?
between cells
What are the functions of desmosomes?
- still a tight and strong junction
- in tissues that experience tight mechanical stress (cardiac muscle, bladder, skin)
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
What do cell to ECM focal adhesions contain?
- integrins, vinculin, talin, alpha-actinin, actin , ecm
where are cell to ecm focal adhesions found?
- epithelial and mesenchymal cells
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
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
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)
What does quasi-static mean?
- slow change that maintains equillibrium
What kind of cytoskeleton do mesynchimal stem cells have?
- actin based stress fiber network
- very dynamic, cell shape changes
What is a primary protein structure?
- linear sequence of AA making up polypeptide chains
What is a secondary protein structure?
- local spatial conformation of backbone without side chains
What is a tertiary protien structure?
- 3D interaction between AA side chains and backbone
- fibrous protein
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
What is a quaternary protein structure?
- multiple protein chains packaged closely
- globular protein
What is a globular protein?
- quaternary structure
- small and compact
- largest class in human body
- forms transcription factors, molecules and morphogens
- high H20 solubility
Xan a protein be globular and fibrous?
yes
- globular could become fibrous
What are the membrane associated proteins?
- integral proteins
- monotropic proteins
- extrinsic proteins
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
What are monotropic proteins?
- intracellular protein associating with 1 layer of lipid bilayer
- lipidphillic
- endoderm
What are extrinsic proteins?
- extracellular protein having a loose association with outer layer of lipid bilayer
- hydrophilic
- ectoderm
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
What is cell segregation?
- how tight cells come together to form outer and inner layer
- think of it like cell velcro
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
How do cadherens stick to the cortical cytoskeleton?
through catenins
- alpha gamma betta
What are the tree types of cadherins?
- epithelial
- placental
- neural
can all bind together
What are cadherins strengthened by?
calcium
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
How are mesenchymal cells aligned?
- less densly packed because they neeed to move
- basal lamina seperates E and M cells
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
What is juxtacrine signaling?
- cells close together communicate through hormones
- cells must be next to eachother
- needs ligand and receptor
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
What is a ligand?
- signaling proteins
What is up-regulation?
- need more of something, add more receptors
What is a nuclear receptor?
- ex/ estrogen estrogen pathway
- uses endocrine and paracrine receptors
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
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
What is an example of physical cells communicating?
- going to gym or getting a tan
What is a constitutive pathway?
always on
What is an example of juxtacrine signaling?
- Delta-Notch
Whata are examples of paracrine signaling?
- teceptor tyrosine kinase
- hedgehog
- WNT
- serine adn threonine and kinases
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
What does it mean that microtubules assemble in a semi-crystalized order?
- Beta on positive end
- alpha on negative end
What do colcemide and nacodazole do?
inhibit tubulin polymerization on microtubules
What does taxol do?
- stabilizes microtubules
- stops cell division
How does kenesin move on microtubules?
- moves on positive end
- anterograde movement (moves fowards)
How does dyenien move on microtubules?-
- on negative end
- retrograde movement, goes backwards
What do latrunculin and cytochalisin do?
inhibit actin polymerization
What does phalloidin do?
- stabilizes actin polymers
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
Describe intermediate filaments?
- made of keratin and vinculin
- shifted and antiparallel
What do gap junctions do?
- form channels to allow cell to cell communication
What is the central dogma of gene regulation?
- DNA to RNA to Protein
What can chemical modifications effect?
- DNA
- RNA
- Protein
What is a chemical modification to DNA?
cytosine methylation
What are chemical modifications to RNA?
- splicing
- poly adenylation
- 5’ capping
- adenine methylation
What are all protein modifications?
post translational modifications
What are the types of protein chemical modification?
- phosphorylation
- methylation
- acylation
- acetylation
- glycosylation
What is the difference between RNA and DNA?
- RNA has an extra O
What is spontaneous deamination?
- oxygen takes NH2 (amine) from cytosine and turns it to thymine
What is chromatin?
- made of protein and DNA and makes up eukaryotic chromosomes
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
What are nucelosomes?
- beads on a string
What is heterochromatin?
- darkly stained
- densely packed
- transcriptionally de-active
What is euchromatin?
- open chromatin
- loosely packed
- lightly stained
- transcriptionally active
- good chromatin
What does the nucleolus do?
- makes Rrna and Trna
- transcriptionally active
Does all chromatin look the same?
no, different based on cell type bc different genes are transcribed in different cell
what do core histones create?
- histone octomer
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
What do histones face?
- lots of negative selective pressure
What does it mean if the histone tail is methylated?
- its closed
- condensed nucleosome
What does it mean that histones make chromatin more accessible?
- open chromatin, expose euchromatin
What does it mean histones make chromatin less accessible?
- close off chromatin
- heterochromatin usage
What do histone post translational modifications create?
- open chromatin
- uncondensed nucleosome?
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
Is dna methylation and methylation of histones the same?
- no
What is the RTK pathway?
- binding
- homodimer
- phosphorylation cascade
- tyrosine kinase hyper activated
- TK phosphorylated and activated
- protein goes to target
What is the Jak-stat RTK pathway?
- ligand
- receptor
- Jak
- Stat Dimerization
- transcription
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)
What is the ligand in the hedgehog pathway?
hedgehog
What is the receptor in the hedgehog pathway?
patched
What is the co-receptor in the hedgehog pathway?
smoothened
What is the effector in the hedgehog pathway?
gli
What happens in the hedgehog pathway if there is no transcription of hedgehog repressive genes ?
- smoothened repressed
What happes in the hedgehog pathway if there is transcription of hedgehog-repressive genes?
smoothened is de-repressed and activates gli
Where does hedgehog and WNT occur?
on cillium protrusions from cell
- involves microtubukes protruding from centriol
What is the canonical pathway of WNT?
- WNT
- Frizzled/ LRP5
- Disheveled
- GSK3
- Beta catenin
- Transcription
What is the ligand in the WNT Pathway?
WND
What is the receptor in the WNT Pathway?
frizzled
What is the co-activator in the WNT pathway?
- disheveled
What is the effector in the WNT Pathway?
B-catenin
Where si B-catenin when there is no WNT?
- destruction complex
- then phosphorylated and ubiquinated
- then no transcription
What happens when WNT is bound?
- gene is expressed
What are non-canonical pathways ?
no b-catenin
What are the possible outcomes of the non-canonical pathways
- Ca2+ release and up regulation
- cytoskeletal changes
- transcription
- genomic and non-genomic effects
What are the steps to the smad pathway?
- TGF b superfamily ligand
- receptor 2
- receptor 1
- smad activation
- smad dimerization
- new transcription
- activation
What is the receptor in the smad pathway?
- serine tirosine kindase
(dimer of dimers)
What is the ligand in the smad pathway?
lots of them
What is the effector in the smad pathway?
- smad 2/3
- smad 1/5
What is the co-effector in the smad pathway?
smad 4
What is TFG B
tumor growth factor
activates smad pathway
What is translated?
mrna
What are the stepts to RNA processing and stability?
- gene has RNAP binded and regulated by transcription factors and enhancers
- copy of DNA strand into RNA.
- splicing
4 MRNA processed - translation
What must the gene have to be regulated by transcription factors and enhancers?
- open and accesible histone tail
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
What is the GU AG rule?
- start to stop of intron
Where are promoters located?
anywhere
Why do trancription factors alter chromatin?
- to allow transcription of chromatin and displace histones
What are mediators?
- bridges to link enhancers to promoters
- important for gene expression
What is a cis-enhacer?
- on gene that is going to be activated
- recognized by splicosome
What is a trans-acting factor?
- binds to enhancer on gene
- part of splicosome
What are enhancers described as?
- modular and cooperative
- can work together
What are silencer elements?
- attenuate gene expression and lower the amount of gene as well as saying when and where it is expressed
What are the RNA processing methods?
- capping on 5’
- polyandenylation of 3’
- splicing
What does polyadenylation do?
- regulates RNA stability
- longer poly-A-tail is more stable
What does capping do?
- closing off sequence
What is alternative splicing?
- can cut different parts out of same sequence
What are the forms of post-translational control?
- hormonal activation
- ribosome heterogeneity
- protein translational contral miRNA
- localisation of MRNAs
What is ribosome heterogeniety?
- not all ribosomea are = there are mutations that effet them
What are the microRNA steps?
- drsoha
- dicer
- risk
- if imperfect complimentary= repression
- if perfect complimentary= degradation
What are the forms of mRNA localization?
- diffusion and local anchoring
- localize protection of MRNA (protects poly-A-tail)
- active transport along cytoskeleton
How does everyone start off?
bi-potential, has mullerian duct and wolfien duct
What are barr bodies?
- in all females
- second x is silenced
How many chromosomes do all people have?
44 chromosomes + 2 sex chromosomes
What are mesonephros?
- middle kidney of embryos . source of hematopoeitic stem cells and male sex organs
What is the genital ridge?
- thickening of mesoderm on medial edge of mesonephros
What is a bipotential gonad?
- ruminant tissue from genital ridge
- derives ovaries and testes
What happens at 8 weeks development?
- xx wolfien disappears
- xy mullerien disappears
What happens at 20 weeks?
- egg cells are covered by somatic cells called nurse cells
- sperm cells are covered by netowrk forming tubes
What do males need?
-SRY
- SOX 9
- FGF9
What do females need?
- WNT and RSPO4
What are cell autonomous mutations?
- affects cell harboring mutation
- transcription factors
What are cell non-autonomous mutations?
- affect cells around mutated cell
- secretions
