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194 Cards in this Set

  • Front
  • Back
Does the cytoskeleton have a large or small surface area?
large
Which has a greater surface are, internal membranes or the plasma membrane and how much greater?
internal membranes, 10x
True or False. There is a strong correlation between size of genome and complexity of organism.
false, there is no correlation
Which 2 domains of life have the smallest genomes?
bacteria and archaea
How is genome size measured?
in nucleotide pairs of DNA per haploid genome
True or False. The fern has one of the largest genomes.
True
True or False. Mammals and reptiles have about the same range of genome size.
True
How many bps are in the human genome?
3 billion bp
How many times bigger is the human genome than a bacterial genome?
1000x
Which technique can be used to identify family members?
Sequence aligment/conservation
The conserved stretches shown in the sequence alignment/conservation example allowed for ____________________ to be searched for in databases.
SH2 domains
True or False. The Beta hemoglobin subunit is highly conserved.
True
T or F. Globins diverged recently in history.
False. They diverged early on and have been evolving and accumulating changes in parallel.
What is the end result of alternative splicing?
generates multiple transcripts of the same gene aka isoforms, increases diversity
Do males or females posses exon 3 of the sxl gene?
males
Sxl undergoes ____ regulation and transformer undergoes ____ regulation
auto; cross
Who coined the term 'gene?'
Wilhelm Johanssen
What did Morgan determine?
genes are on chromosomes
What did Beadle and Tatum propose?
one gene, one enzyme
What did Roberts and Sharp discover?
one gene can make several proteins
Name the 4 functions of proteins discussed in the intro lecture.
1 - cell division
2 - mechanical stability
3 - adhesion between cells
4 - cell death
Which dye allows for the visualization of dying cells between developing digits?
acridine orange (dying cells are more leaky)
TUNEL allows for the visualization of duing cells by labelling ______.
DNA
Name the 5 types of covalent modifications discussed in class.
1 -phosphorylation
2 - glycosylation
3 - acetylation
4 - ubiquitinylation
5 - sumoylation
True or False. Phosphate groups are neutral.
False. They are negatively charged.
Protein kinases _________ a phosphate group and protein phosphatases ________ a phosphate group.
add; remove
T or F. Phosphorylation can both activate and deactivate proteins.
True
Describe glycosylation. Which types of proteins are often glycosylated and why?
- proteins modified through addition of sugar chains
- cell surface proteins, secretory proteins
Name the 2 types of glycosylation.
1) N- linked
2) O-linked
How does acetylation affect DNA?
DNA more accesible upon acetylation
How many a.a.s long is ubiquitin?
76 aa
What is E1? (ubiquitination)
ubiquitin activating enzyme
What is E2? (ubiq)
ubiquitin-conjugating enzyme
What is E3 (ubiq) and what does it bind to?
ubiquitination ligase; E2
How does the ubiquitin E1E2E3 complex modify proteins?
puts a flag on proteins destined to die
What does SUMO stand for
Small Ubiquitin-like MOdifier
How many SUMO conjugating enzymes are there?
1 --> UBC9
Which type of filaments are sumoylated?
IFs
Which units are cells, organelles and molecules usually measured in?
um, nm, nm
Name the 4 types of light microscopy?
1 - bright field
2 - phase contrast
3 - differential interference contrast (DIC)
4 - dark field
How does DIC generate contrast? What happens to the ray of light? What are phase differences transformed into?
- by exploiting phase differences
- split in two beams
- amplitude differences
What takes longer to prepare, SEM or TEM?
TEM
How does the immunogold method of EM work?
antibody linked to colloidal gold particles, high density where proteins located
T or F. Resolution is proportional to wavelength.
False. Resolution is inversely proportional to wavelength.
T or F. Fluorescence microscopy can be used to visualize fixed specimens.
True. As well as live specimens
Which has better resolution, conventional or confocal fluorescence microscopy?
confocal
What's a problem with confocal fluorescence microscopy and how can it be improved?
light converges at a small point, use a computer to scan through each plane, store info and generate 3-D image
Is deconvolution imaging a type of microscopy?
No, its a ghetto version of confocal but its technically just a software program
What does FRET stand for?
Fluorescence Resonance Energy Transfer
Which type of microscopy for visualizing protein-protein interactions?
FRET
How is the FRET signal in budding yeast obtained?
by exciting CFP but recording fluorescence from YFP, get superimposed image
What does FRAP stand for?
Fluorescence Recovery After Photobleaching
How does AFM work?
fine tip moves up and down, scans object, looks at repulsion and attraction of atoms
Which type of indicators are used for FRET?
fluorescent protein-based Ca2+ indicators
Rank the cytoplasmic fibers/filaments in order of diameter.
MT > IF > AF
What are AFs assembled from?
actin monomers
What are MTs assembled from?
dimeric subunits of alpha and beta tubulin
What are IFs assembled from?
large diverse family of proteins including lamins and keratins
Are MTs, IFs or AFs responsible for stability?
IFs
Do MTs, IFs or AFs receive and transmit signals?
AFs
Do MTs, IFs or AFs interact with transport molecules, motor proteins and are involved in chromosome segregation?
MTs
Do MTs, IFs or AFs determine the shape of the cell's surface and are necessary for locomotion?
AFs
Do MTs, IFs or AFs determine the positions of organelles?
MTs
Are MTs, IFs or AFs polar?
MTs and AFs
Do MTs, IFs or AFs connect to desmosomes?
IFs
Do MTs, IFs or AFs include filopodia and lamellipodia?
AFs
Are MTs, IFs or AFs involved in cytokinesis?
AFs
Are MTs, IFs or AFs involved in the assembly of the mitotic spindle?
MTs
Do MTs, IFs or AFs form the nuclear envelope?
IFs
Are cilia and flagella composed of MTs, IFs or AFs ?
MTs
Are hairs and fingernails composed of MTs, IFs or AFs ?
IFs
What happens to platelets when an injury occurs?
large spread lamellipodium (AF), dramatic shape change due to myosin II mediated contraction, trying to sense environment to see where signal is coming from and migrate towards site of injury
Are MTs, IFs or AFs involved in the formation of a bud in yeast? Where is the concentration the highest?
AFs; where pinching is occurring
Are axons and dendrites filled with MTs, IFs or AFs ?
MTs
Is the cortex of the axon lined with MTs, IFs or AFs ?
AFs
Are neurofilaments a specialized form of MTs, IFs or AFs ?
IFs
Do developing growth cones in neurons utilize MTs, IFs or AFs for extensive branching?
AFs
True or False. Actin and tubulin are present in all eukaryotic cells.
True
About how many isoforms of actin are there invertebrates?
~3
About how many isoforms of alpha and beta tubulin are there in vertebrates?
~6
True or False. Yeast and human tubulin are very similar.
True
What is the function of accessory proteins?
catalyze nucleation of filaments, cross-link filaments, link filaments to other cell components, act as motor proteins
What is the diameter of AFs?
5-9 nm
What's another name for AFs?
microfilaments
Describe the shape of AFs.
two-stranded helical polymers of actin; bead-like structure
What is the MW of an actin monomer?
42 kD
How many actin genes to humans have?
6
What are the 3 isoforms of actin called?
alpha, beta, gamma
Where are AFs often nucleated?
at the plasma membrane
When was the crystal structure of AFs solved?
1990
How many subdomains does monomeric actin contain?
4
True or False. Actin can bind ATP but not hydrolyze it.
False. It can bind and hydrolyze ATP to ADP.
True or False. Before polymerization, each actin monomer is bound to ATP.
True.
How many protofilaments are in one MT and how are they arranged?
13; in a circular pattern
What is the diameter of MTs?
24 nm
True or False. Alpha and beta tubulin subunits can bind and hydrolyze GTP.
False. Both can bind to GTP but alpha is bound tightly and cannot be hydrolyze like beta.
What happens when a GTP cap is present on a MT?
growth is favored (dissociation less likely)
Compare the dissociation rates of GTP and GDP tubulin dimers.
GTP tubulin dimers have 4 times slower dissociation rate
At which end of the MT is tubulin with bound GTP located?
+ end
Which end of AFs and MTs is the fast-growing end?
+ end
Is the + or - end also known as the barbed end?
+
What must occur in order for the + end to accept another subunit?
back end must change conformation (become barbed)
What must ocurr in order for the - end to accept another subunit?
subunit must change conformation (become barbed)
Does Kon or Koff depend on concentration of the monomer?
Kon
True or False. AF and MT subunits leave at a constant rate.
True
What are association and dissociation of AFs and MTs measured in?
association - per mole per second
dissociation - per second
What is the critical concentration? (Cc)
when rate of subunit addition equals rate of subunit loss
T or F. K is inversely proportional to Cc.
True
What happens when C > Cc ?
Kon will be high, polymerization will continue until C = Cc
What happens when C < Cc?
Kon will be low, dissociation will occur
T or F. Cc = Kt/Kd
False. Cc = Kd/Kt = Koff/Kon
What is the Cc of the + end?
0.1 um
What is the Cc of the - end?
0.6 um
At which end is there a lower threshold?
+ end
What happens when the concentration of free monomers is intermediate between the Cc values for the - and + ends?
The filament grows at the plus end wherease shrinks at the minus end --> treadmilling
What is steady-state treadmilling?
polymer maintains a constant length
When does dynamic instability occur?
When concentration of T subunits is low
What is catastrophe?
rapid shrinkage due to accidental loss of GTP cap
What is rescue?
rapid growth due to regain of GTP cap
Is treadmilling preferentially observed in AFs or MTs?
AFs
Is dynamic instability preferentially observed in AFs or MTs?
MTs
What is the Cc of actin in a test tube?
< 1 um
What is the concentration of actin in the cell?
50-200 um
What prevents soluble actin monomers from polymerizing into filaments inside the cell?
sequestering proteins
What is the protein called that binds and sequesters actin monomers so they are not available for polymerization?
Thymosin beta4
What is the name of the protein that promotes filament assembly by binding acting monomer and making them available at the + end?
profilin
True or False. Profilin is one of the few actin-binding proteins that allows exchange of ADP for ATP.
False. It is the only one
What is the rate limiting step for AF polymerization?
nucleation
Where are AFs nucleate in eukaryotic cells?
at the plasma membrane in the cell cortex
What are the 3 classes of nucleator proteins?
Arp2/3 complex, formins, spire
T or F. Polymerization of AFs occurs more slowly in the presence of oligomers.
False. More quickly.
T or F. Arp2 and 3 proteins are very similar to actin.
True
How do Arp2 and 3 serve as a template for monomer addition?
mimic barbed end of growing actin filament
Where does nucleation of the AF occur?
at the - end, allowing elongation at the + end
What happens when the ARP complex binds to the side of a preexisting AF?
filament branching
AF branching occurs at what angle?
70 deg
How does the absence of nuclei affect AF elongation?
delays elongation
How many proteins is the Arp2/3 complex composed of?
7
T or F. Arp2 and 3 must be bound to ATP in order to initiate branching.
True.
What is a VCA domain and what is its role?
- composed of an actin-bining, connecting and acidic region
- promotes nucleation and branching
Is the VCA domain necessary or sufficient for activation of Arp2/3?
both
The VCA domain containing protein is a member of which family?
WASP family
The 3 proposed model of how debranching occurs in the Arp2/3 complex consist of which 3 steps, but in different orders?
- nucleation and elongation
- ATP hydrolysis of Arp2 (possibly Arp3 also)
- VCA dissociation
Which domains of formins bind actin?
FH2 domains
Describe the structure of formins.
form dimer that has hoop-shaped structure
Which domains of spire bind to actin?
WH2 domains
How to amoebas move?
Move along cAMP concentration gradient (chemotaxis), exten filopodia
What types of proteins are gelsolin and cofilin?
AF severing proteins
What do CapZ and tropomodulin do?
stabilize AFs by capping ends
What do CH-domains do?
organize AFs into bundles and filaments
Which are denser, filopodia or lamellipodia?
filopodia
What is the MW of gelsolin?
87 kD
What is the MW of cofilin?
15 kD
Which are arranged in parallel, bundles or networks of AFs?
bundles
True or False. Fimbrin is very flexible.
False. Filamin is
Crosslinking is facilitated by proteins that are members of which superfamily?
C-H domain
Name the 3 bundling proteins.
- fimbrin
- alpha-actinin
- villin
Name the 2 gel-forming proteins.
- spectrin
- filamin
Which protein helps maintain the shape of RBCs?
spectrin
Which proteins are found in microvilli?
villin & fimbrin
Filamins clamp together 2 AFs at what angle?
90 deg
What does filamin facilitate?
cell movement
What happens when filamin is restored in malignant melanoma cells?
form normal lamellipodia allowing them to crawl and metastasize
Which end does CapZ bind to? Which end does tropomodulin bind to?
+ end; - end
The nucleation of AFs is catalyzed by _______ and _______. Binding of ARP complex to AF leads to ________________. Thymosin beta4 and profilin regulate ____________.
Arp2; Arp3; branching; actin polymerization
What does stathmin do?
binds to MT subunits and makes them unavailable for polymerization
Which type of tubulin is involved in nucleation of MTs?
gamma
T or F. Gamma tubulin is needed in much greater amounts than alpha and beta tubulin.
False
At which end does gamma tubulin bind?
- end
What is a common MTOC?
centrosome
What type of complexes cover centrosome?
gamma-tubulin ring complexes
Which end of the MT interacts with the MTOC?
- end
What helps position the centrosome at its centre?
MTs
T or F. Cell division cannot occur in the absence of centrosomes.
False. Other cellular structures can be used as the MTOC (such as pericentriolar material, or PCM)
T or F. Organelles can act as MTOCs.
True. Ex. Golgi Complex
Which type of proteins control assembly and dissasembly of MTs?
MAPs
Which proteins stabilize MTs?
MAP1, MAP2, MAP4, Tau, gamma-TuRC, EB1
Which are more spaced out, Tau or MAP2 bundles?
MAP2 (due to longer arms)
Where in neurons is MAP2 primarily found?
dendrite
T or F. Map4 is not found in neurons.
False. IT is found in both neuronal and non-neuronal cells
Where in the neuron is tau found?
axons and dendrites
T or F. Other MAPS can compensate the loss of Tau.
True
What happens when Tau is hyperphosphorylated?
tau misfolds, poor MT binding, low MT assembly activity, tangles/PHFs and NFTs accumulate, MTs less stable, reduced axonal transport along MTs, amount of normal tau reduced
T or F. Misfolding of tau is due to hyperphosphorylation and not mutation.
True
Which event is believed to lead to aggregation of tau?
misfolding of a-beta species
How do kinases and phosphatases play a role in hyperphosphorylation of tau?
can be caused by increased kinase activity or decreased phosphatase activity
Which proteins does hyperphosphorylated Tau sequester?
normal tau, MAP1, MAP2
Which proteins destabilize MTs?
katenin (or stathmin), catastrophins
What are +TIPS?
+end tracking proteins, bind to + end of MTs, prevent premature catastrophes, promote MT growth, interact with CLIPS and CLASPS
T or F. EB1 has a tip-tracking function.
True
Where on the MT does EB1 bind?
the seam (the weakest point of the MT)
Which proteins can bring TIPs to the + end?
motor proteins
How many subunits is the Dam1 complex composed of?
10
How does the Dam1 complex help stabilize MTs?
form rings that surround MTs and slide, can bring in other MTs and form parallel bundles