Exam 3 Flashcards
What isotope indicates how old tissues are?
Carbon 14
What is Apoptosis
programmed cell death
Does apoptosis cause damage to tissue?
No
What cleans up cells which have undergone apoptosis?
Macrophages
True of False?
Intracellular constituents are released into extracellular milieu durring apoptosis.
False
What causes necrosis?
severe cell damage
What does necrosis lead to or present as?
Inflimation
What happens to the intracellular contents during necrosis?
The are released into the extracellulara milieu
How does apoptosis contribute to embryonic development?
Removes cells to sculpt the body
What causes a frog to loose its tail?
Induced apoptosis in the tail
What common disease is apoptosis important for protecting against?
uncontrolled cell division, cancer
What is the function of apoptosis generally?
serve as a safety system for removing cells which have lost normal comunication and control
What is the function of apoptosis in neuronal development?
it matches the number of developing nerve cells to the number of target cells
how do target cells match the correct number of nerve cells?
By releasing a limited amount of survival factor which prevents apoptosis of nerve cells
what morphology changes occur during apoptosis?
mild convolution
chromatin compaction and margination
condensation of cytoplasm
breakup of nuclear envelope
nuclear fragmentation
blebbing
cell fragmentation
True of False?
Asymmetric lypid distribution is maintained during apoptosis.
False
the negatively charged lipid phosphatidylserine (PS), which is usually only found on the inner side of the membrane, is exposed to the extracellular side of the membrane
what does phosphatidylserine (PS) do when exposed to the extracellular space?
signals macrophages to phagocytose the cell
what do restriction enzymes do?
they cut DNA at specific sites
How does agarose gel from gel electrophoresis seperate DNA?
size with the largest particles nearest to the well
What is the negative side of agarose gel in gel electrophoresis?
the well side
what is the DNA stain used at the end of agarose gel electrophoresis?
what is needed to visualize the stained DNA?
ethidium bromide
UV-light
What does necrosis do to DNA on agarose gel electrophoresis?
creates a DNA smear
What does apoptosis do with regards to DNA?
activates nucleases which cut the DNA between the nucleosomes
What executes apoptosis?
caspases
what are caspases?
proteases
what activates procaspases?
their prodomains are cleaved off
what do activated procaspases do?
dimerize to form on caspase molecule
what will one molecule of active initiatior caspase do?
activate many executioner caspase Y
What does executioner caspase y do?
cleave the nuclear lamin and activate many more executioner caspase Z
what does executioner caspase Z do?
cleaves cytosolic proteins
How does the initiator caspase get activated?
the aggregation of procaspases
what helps the procaspases agregate?
adaptor proteins
What do agregated procaspases do to each other and what is the result?
cleave each other resulting in the formation of active caspase
True of False?
The active initiator caspase can cleave and activate many executioner caspases
True
how many different caspases do human cells express?
15
what is released from the mitochondria that initiates the apoptic pathway?
cytochrome C
where is cytochrome C stored in the mitochondria?
intermembrane space
What does cytochrome C bind to and activate in the apoptic pathway?
What do those activated things subsequently bind to?
adaptor proteins
other adaptor proteins
What are cyclized adaptor proteins called?
apoptosome
How does p53 activate apoptosis
it acitvates the Bax transport protein which releases Cytochrome C into the cytoplasm
What cells contain the fas ligand?
killer lymphocytes
what doe the fas ligand bind to?
the fas receptor
What happens once the fas lignad binds the fas receptor?
A DISC is fromed which initiates apoptosis
What is a DISC?
the fas receptor bound to adaptor proteins which are bound on the other end to procaspase molecules
Describe how a virus infected cell gets delt with.
Virus infected cells present viral peptides at the cell surgace (antigen)
T Cell Receptors (TCR) recognize the antigen
this causes the fas ligand to bind the fas receptor and initiate apoptosis
How does the DISC initiate cell apoptosis?
By activating procaspases and helping them dimerize.
What are C. elegans?
Nematodes (round worms).
What are doomed cells?
cells that are genetically programmed to always undergoe apoptosis in the lifecylce of a multicellular organism
How many doomed cells were identified in C. elegans?
131
What are the CED-3 and CED-4 genes required for?
apoptosis
What is the function of CED-9?
suppress apoptosis
What is the vertebrate analog to C. elegans CED-9, CED-4, and CED-3?
Bcl-2, Apaf-1, and Casp9
Vertebrates require an aditional step to initate cell death when compared to C. elegans. What is it?
Casp9 needs to activate Casp3 in vertebrates
C. elegans undergo cell death after CED-3 (the Casp9 analog) is activated
What are the different stem cell types and how are the different?
Embryonic (pluripotent) stem cells
Adult (somatic) stem cells
somatic maintain a specific tissue while pluripotent differentiate into various tissue types
Where do pluripotent stem cells come from?
the blastocyst
True of False?
C. elegans have somatic stem cell lines for most of their tissue types?
False
the only somatic stem cell lines in C. elegans are the germ line stem cells (GSCs)
What are the vili?
specialized epithelial areas of the gut that absorb nutrients
True of False?
The vili have a high turnover rate and must constantly be replaced.
True
Where do find vili?
Mammalian intestines
What is the tip of the vili called?
Villus
What is the basal cavity of a vili called?
the crypt
What is the function of goblet cells in the vili?
mucus secretion
Where are new cells made for the vili?
at the bottom of the crypt
where are old cells recycled in the vili?
at the villus
How long does it take a new cell in the crypt to navigate to the villus?
3 to 6 days
How is the crypt structured?
The very bottom are dividing stem cells
middle half is dividing precursor cells (non-differentiated)
top portion is non-dividing, differentiated cells
What are the cells types at the very bottom of the crypt in villi?
dividing stem cells
non-dividing terminally differentiated Paneth cells
True of False?
Cells continue to divide in the villus?
false
What are the two cell types of the villus?
secratory cells
absorbative cells
Where are skin cells born?
The bottom of the epidermis
What happens to newly replicated skin cells?
They differentiate into keratin containing cells, die, and finally shed
What is the major layer below the epidermis?
The dermis
What sepperates the dermis from the epidermis?
The Basal Lamina
Define Tissues.
Tissues are groups of cells that act together to perform a specific function
What are groups of cells that perform specific functions called?
Tissues
What are gap junctions?
Transmembrane proteins that link the cytoplasm of neighboring cells
What is allowed to flow through gap junctions?
ions and small molecules.
Describe the morphology of gap junctions.
Six subunits cyclize to form a nm channel.
These macrounits are called connexons
Two connexons from different cells connect to form a gap junction.
The space between cells with gap junctions is 2-4 nm.
What are desmosomes?
Protein complexes that form strong physical connections between cells.
Describe the morphology of desmosomes.
Keratin filaments bind to cytoplasmic plaque.
Cytoplasmic plaque binds to transmembrane cadherin proteins.
Cadherin proteins of differnet cells interact to bind the cells together.
What is the cytoplasmic plaque made of?
intracellular linker proteins
In reference to the Extra Cellular Matrix (ECM) what facilitates a strong network between cells?
Secreted proteins and polysaccharides.
True or False?
Integrin links the cell to the collagen of the ECM?
True
Where is integrin found?
The plasma membrane
What is vitamin C deficiency commonly known as and what does it do?
Scurvy
It weakens connective tissues (loss of ECM)
What is proline?
An amino acid.
What is hydroxylation?
The addition of an alcohol (hydroxyl) group
What hydroxylizes proline?
What does this enzyme require as a co-factor?
procollagen-proline dioxygenase
vitamin C (ascorbate)
What is the Ascorbate also known as?
Vitamin C
What is vitamin C also known as?
Ascorbate
Describe the morphology of collagen fibers.
Amino acid chains containing proline fold into a-helical chains.
Three a-helical cahins form a collagen molecule.
Many collagne molecule form a collagen fibril (like rope).
Many fibrils form a collagen fiber (like a bigger rope).
True or False?
There are many distinct epithelial systems disconnected from one another.
False
There are many epithelial systems but they are all connected.
Describe the various functions of epithelial cells.
protection, secretion, absorption, excretion, filtration, diffusion, and sensory reception.
Describe where epithelial cells can be found.
All body surfaces, lining of cavities and hollow organs, and glands.
What is the major cell type found in glands?
epithelial
What is the general category of disease caused by aging?
Name three specific examples.
damage-based diseases
cancer, diabetes, and alxheimer’s
How does aging affect telomeres?
Aging reduces telomere length.
How does aging affect dividing cells?
Aging causes a loss of dividng cells (stem cells).
About how many times can stem cells divide?
Aproximately 50
What things accumulate with aging?
damaged cells and molecules as well as mutations in nuclear and mitochondrial DNA.
True or False?
Researchers originally thought yeast were immortal.
True
How many times can yeast divide before going into senescence?
about 25 to 30 times
What is senescence?
G zero phase of the cell cycle
What is the replicative lifespan of yeast?
The time when yeast are actively replicating
What is the chronological lifespan of yeast?
Aproximately how long is the chronological lifespan in yeast?
The survival of non-replicative yeast.
weeks to months
True or False?
90% (aprox.) of a cells DNA and proteins are dedicated to regulation.
True, maybe
Babst made up the number
True or False?
There is a corilation between complexity of organism and genes dedicated to regulation.
True
more complex = more regulation genes
Name some cellular programs.
cell differentiation, cell cycle initiation, celly cycle exiting, apoptosis
True or False?
Each step from brith to death of a protein can be regulated
True
and it usually is regulated
What does each type of regulation require?
A certain time to respond to a signal
What types of things are controlled via regulatory processes?
transcription, enzyme activity, protein stability, protein localization, cellular programs, RNA processing, mRNA transport and localization, mRNA degredation, translation, etc.
Why does regulation inhibit enzymes from creating their product?
an overaccumulation of product makes product synthesis inefficient.
Where is product inhibition (enzyme regulation) used commonly?
Metabolic pathways
is feedback regulation (enzyme regulation) inhibitory or activating?
inhibitory
What is feedback regulation (enzyme regulation) mainly used for?
regulating non-reversible reactions
regulating key steps in metabolic pathways
describe feedback regulation (enzyme regulation).
A chemical affects the quantity or activity of an enzyme such that the chemicals synthesis is blocked. I.e. a chemical blocks a reaction upstream in the pathway that led to its synthesis.
True or False?
Chemicals can only block one step/reaction in a cellular pathway (feedback regulation).
False
What is aspartate transcarbamoylase?
What does it do?
An enzyme involved in the synthesis of the nucleotides CTP,UTP, and TTP
How does aspartate transcarbamoylase (asp-t) get regulated?
What kind of regulation is this?
A downstream product of asp-t, CTP, binds the regulatory site of asp-t and inactivates.
feedback regulation
What does CTP bind and inactivate?
aspertate transcarbamoylase
When CTP bind aspertate transcarbamoylase what is CTP functioning as?
a regulatory ligand
What do kinases do?
phosphorylate things
What is phosphorylation?
The addition of a phosphate group to something via covalent bond
Describe how covalent modifications can regulate proteins.
The presence of a phosphate group covalently bound to a protein can activate or inactivate the protein.
What do phosphotases do?
remove phosphate groups from proteins
What does acetylation do to lysine?
removes the posative charge by adding an acetyl group to the amine
R-NH3+ to R-NH-Acetyl
True or False?
Ubiquitination is a form of protein regulation.
True
it is a form of regulation via covalent modification
True or False?
p53 has a relatively simple regulation system.
False
it hase many phosphorylation, acetylation, and ubiquitination sites
True or False?
p53 acts as a coincidence detector.
True
How does localization regulate proteins?
The presence of certain bound molecule affects the functionality of a protein.
Think when GTP is bound protein equals ON
When GDP is bound protein equals OFF
Describe how Sar1 is an example of protein regualtion via localization.
When Sar1 is bound to GDP it is inactivated and soluable
When the GDP is swapped for GTP by an exchange factor (GEF ) a hydrophobic tail is esposed on Sar1 allowing it to bind to a membrane
What does active, anchored Sar1 do?
initiates vesicle formation
What is an alternative name for protein regulation via assembly?
protein complex formation
What does the assembly of coat proteins and cargo receptors do?
drives vesicle formation
What are Sec23 and Sec24?
coat proteins
What form of regulation controls Actin and why?
assembly/disassembly and localization
the presence of ATP vs ADP changes what actin subunits can do. the synthesis or degredation of AF is what drives the functionality of AF
What are the different types of protein regulation via proteins synthesis?
Regulation of transcription
Regulation of mRNA processing
Regulation of mRNA nuclear export
Regulation of mRNA stability
Regulation of translation
What are transcription factors?
DNA binding proteins that regualte transcription initiation
What are the two domains of transcription factors?
DNA binding domains and transcription regualtory domains
True or False?
Most transcription factors are monomers but some are dimers.
False
most are dimers
What do homeodomains do?
form hydrogen bonds with nucleobases
Where do homeodomains locate themselves when binding to nucleobases?
Mostly the major groove of DNA
True or False?
Homeodomain-DNA interactions are specific for certain DNA sequences.
True
What are homeodomains important for?
development in multicellular organisms
What are homeodomains?
The parts of transcription factors which bind to the DNA
What do homeodomain transcription factors do to increase specificity?
function together with other transcription factors
How do leucine zipper transcription factors interact?
They form dimers
Describe the leucine zipper transcription factor complex structure when bound to DNA.
Two a-helix cross and from an x shape reffered to as the leucine zipper. one groove of the x stratles DNA and the two legs bind the DNA on opposite sides
True or False?
Yeast are an example of simple eukaryotes.
True
what is the promoter region of a gene?
the region upstream of a transcription start site where transcription factors bind the DNA
What is an enhancer region of a gene?
a binding site for transcriptional activator proteins
Where are enhancer regions of genes located?
They can be upstream or downstream of the transcriptional start site
In what type of eukaryote can transcriptional acitvators act far away from the transcription start site?
higher eukaryotes (more complex)
True or False?
Many transcription factors act together to regulate transcription.
True
How specific are transcription factor binding sites?
not that specific
What is the mediator complex?
a protein complex that interacts with several transcription factors to regulate transcription initiation
How do transcription repressors do their job?
Physically compteing with activating transcription factors for DNA binding sites or suppressing transcription via the mediator complex
What is a transcription factor?
DNA binding protein that affects transcription initiation