exam 2 Flashcards
What is the difference between a neuron cell and a liver cell
share the same genome, but have different morphology and function by expressing different sets of RNA and protein
In a isoelectric graph, what do the red and blue spots indicative of?
red: common proteins expressed in both tissues examined,
Blue: specific proteins for that tissue.
When can gene expression be regulated?
at many different steps from the conversion from DNA to RNA to Protein
- transcriptional control, translational control, and protein degradation control are notable/ effective regulation steps.
What percent of genes are for transcriptional regulators
about 10% of all protein-coding genes
What do Transcriptional regulators recognize
DNA cis-regulatory sequences and will make contact with the major grooves.
The protein will contact minor grooves, and the phosphates in the backbone, but not initially recognize them
how do transcriptional regulators increase their specificity for DNA
Dimerization of the transcriptional regulators
either a homodimer or heterodimer
What does the Eukaryotic gene control region consist of
A promoter, and many cis-regulatory sequences (general transcription factors)
what are co-activators
proteins that do not bind to DNA themselves, but assemble on other DNA-binding transcription regulators
The regulators and co-activators regulate the recruitment of RNA polymerase II by the general transcription factors to the promoter
What does DNA looping allow to happen
It allows transcription regulators bound at any position to interact with the general transcription factors
How can transcription repressors inhibit transcription
several ways:
-competitive DNA binding
-Masking the activation surface
-direct interaction with the transcription factors
-recruitment of chromatin remodeling complexes
-recruitment of histone deacetylases
-recruitment of histone methyl transferases
competitive DNA binding
activator and repressor both compete for the same binding site
Masking the activation surface
the activator is bound and working, but a repressor binds at a different site and inhibits it directly
direct interaction with the transcription factors
both the repressor and activator are bound, but the repressor will interact with general transcription factors before the activator can (like TFIID)
recruitment of chromatin remodeling complexes
A repressor will recruit a histone remodeling complex to inhibit transcription
(decreases accessibility of TATA box and to the general transcription factors and RNA polymerases)
recruitment of histone deacetylases
a repressor will recruit deacetylases to take of ac and inhibit transcription
(decreases accessibility of TATA box and to the general transcription factors and RNA polymerases)
recruitment of histone methyl transferases
A repressor will recruit a methyl transferase to methylate the genes and inactive them
(decreases accessibility of TATA box and to the general transcription factors and RNA polymerases)
What do insulator DNA sequences do
Prevent Eukaryotic transcription regulators from influencing distant genes
they directly block the action of enhancers over neighboring genes (by making a loop with proteins )
what do barrier sequneces do
prevent the spread of heterochromatin either by:
-tethering to a fixed site like a nuclear pore
-tightly binding to a nucleosome to prevent spreading
-Recruiting histone modifying enzymes that erase the marks that are required for heterochromatin to spread.
What can the Drosophila fly development tell us
genetic switches are built from smaller molecules
the even-skipped gene (eve) gets expressed in 7 strips shown in green the red/ giant gene gets both in the head and tail, and areas that they both express are in yellow
the reason these strips exist is due to several cis-regulatory sequences specific to one stripe
What is the EVE gene regulated by
Combinatorial controls (several sequences)– many cis-regularly sequences
At the half-way from the anterior to sprite 2, why is the gene-gene not expressed even if hunchback is very abundant (fig 7-32)
we don’t really know, but it is likely due to other transcription factors like the Kruppel repressor
What can combinatorial gene control do
create many different cell types (differentiated cells)
in experimentation, we are able to convert liver cells to neuronal cells by the artificial expression of three genes that are activated in neurons and repressed in liver cells, but a limitation is its hard to activate all the genes
How do you artifically express the eyeless gene in the leg precurseor cell
you need a transcriptional regulator after the insertion of the modified precursor cells
Can we convert specialized cell types to pluripotent stem cells?
Yes!
for fibroblasts, Genes encoding three transcription regulators an be introduced and expressed in the nucleus changing it to an IPS cell (induced pluripotent cell) which is similar to embryonic stem cells.
How are Stem cells and IPS cells simular
they can proliferate indefinitely in culture and are stimulated by appropriate signals to differentiate into almost any cell type
Stem cells
Undifferentiated cells that perpetuate themselves (make more stem cells)and give rise to other daughter cells capable of differentiating into specialized cells induced by transcriptional regulators
Why do we get gray hair
When we are stressed (triggering the sympathetic nervous system), we overproduce our melanocyte stem cells (located in the bulge of the hair follicle) which then causes the melanocytes to migrate out of the hair culture and go to the top
(the stem-melanocytes die and essentially we run out of them due to stress)
How can DNA methylation be inherited
when invertebrates divide, maintenance methylation transferases will recognize the one strand that is methylated after replication and methylate the other
(in general it happens during and after mitosis and histone modification and will repress gene expression)
What is the pattern of DNA methylation when vertebrate cells divide
a Transcription regulator brings a writer for histone modification which a code reader reads
reader relays the writer to keep condensing
sometimes the reader will bring in de novo DNA methylase
methylated cytosine lies in the major groove and interferes (assists) with the binding of proteins
more proteins bind to the methylated DNA adding insulation
What is genomic imprinting based on
DNA methylation
genomic impriting is
when the materially inherited gene is active, and the paternally inherited gene copy is silent or vise versa
due to DNA methylation in the inactive gene
This allowed for if one gene gets mutated it can have the other (protection)
review figs 7-51 and 7-52
What does alternative splicing produce
Different forms of a protein from the same gene
usually by RNA degradation or choosing to abort the RNA transcript as those occur at the end and start of transcription.
What percent of genes does alternative RNA splicing occur for
90% and is critically regulated
you can perform this analysis by looking at RNA sequencing via extracting RNA form the area of interest
What can change the C-term of a protein
A change in the site of RNA transcription cleavage, and poly-a addition
if CstF is low it skips the first polyadenylation signal and produces a loner transcript
in a weak site CstF level increases to cleave the weak site
What regulates mRNA translation and stability
MicroRNAs (miRNAs)
miRNAs form a complementary sequence with an RNA – calling RNA-induced silencing complex (RISC) over and gets held by Argonaute
if there is an extensive match (high base pairing) it will be degraded
if there is a less extensive match (at least 7 bp) it causes both inhibition and translation and mRNA degradation
siRNAs are formed when
RNA interference calls dicer to cut double-stranded RNA which create siRNAs with a 23nt Perfect match
what do siRNAs do
cause transcriptional silence if they interact with the RITS complex which forms heterochromatin
Or
trigger inhibition of translation and destruction of mRNAs similar to miRNAs with the use of RISC
both pathways need argonaute to help stabilize
What do long noncoding RNAs do (incRNA)
they have diverse function in the cell but do not code for proteins
most functions are unknown
however, they are used for scaffold as they carry proteins specific to RNA or DNA sequences via complementary base-pairing , can either be cis acting or diffuse and be trans acting
What are the main lipids in the cell membrane
Phosphoglycerides, sphingolipids, and sterols
What are the different types of phosphoglycerides derived from glycerols
Phosphatidylethanolamine, phosphatidylserine, phosphatidylcholine
they contain a fatty acid tail (hydrophobic) and a charge head (hydrophilic)
phosphatidylcholine most abundant
phosphatidylserine is net negatively charged
What are the different types of phosphoglycerides derived from sphigolipid
Sphingomyelin
sphingosine
Properties of cholesterol
polar head, rigid planer steroid ring structure, non poler carbon tail
plant membranes do not contain cholesterol and contain more unsaturated fatty acids
properties of the lipid bilayer
two-dimensional fluid
consists of fatty acid tails (hydrophobic)
polar heads (hydrophilic)
can laterally diffuse, flexion, and rotate easily
cant flip flop easily
Does the lipid bilayer have a high or low motility (movement)
high, this allows for it to accommodate for different environments, and cons: it can crack and break quickly since it needs to equalize
What is a raft domain
specialized domains or membrane regions involving protein-protein, protein-lipid, and lipid-lipid interactions. usually have increased membrane thickness.
also contain types of lipid-bound proteins
Which lipids are on the outer monolayer and inner monolayer of a lipid bilayer
Phosphatidylcholine, and sphingomyelin, and glycolipids are on the outer layer
ethanolamine with a terminal amino group and green serine is in the inner monolayer (negatively charged due to reducing cytosol environment)
*phosphatidylinositol is not very abundant but is located in either leaflet as some lipid kinases phosphorylate its head to make a binding site that recruits other proteins to the cell surface or cytosolic face.
What are the different membrane proteins
-transmembrane protein extends across the bilayer via a single alpha-helix but is cogently attached to a fatty acid chain on the cytosolic side
-multiple alpha helixes
-rolled up beta-sheet
-transmembrane anchors either a “face” (protein not part of the alpha helix) on the inside or outside
-anchored by a lipid chain
-accord by a GPI anchor
could associate with other peripheral proteins
what can trypsin reveal in regards to a protein
it can show which proteins are directly attached or which are on the surface (itll also cleaves some of the larger proteins)
what are the different types of linkages with proteins
amide linkage between terminal amino group and mystic acid, thioester linkage between cysteine and palmitic groups, thioether linkage between cysteine and prenyl group (usually in the cytosolic face)
what are the different types of anchors
myristoyl anchor (recruits Src Family tyrosine kinase in the cytosolic face)
palmitoyl anchor second anchor to recruit Src, and returns Src to cytosol when signal is off
farnesyl anchor tri-prenyl group as a 15-carbon unsaturated hydrocarbon chain
most transmembrane proteins the chain crosses the lipid bilayer in what type of conformation
alpha-helical conformation
hydrophobic amino acids with nonpolar side chains align with hydrophobic core
intra-molecular h-bonds between adjacent peptide bonds stabilize the alpha-helical structure
beta strands form what
channels that allow movement through the membrane
usually in the outer membrane of bacteria, mitochondria and chloroplasts.
what are the different types of beta barrels
8-stranded Ompa
12-stranded OMPLA
16-Stranded Proin
22-stranded FepA
ompA is a receptor of bacerial virus, and OMPLA is a lipase
Porin and FepA are transporters and the diameter of the channels are restricted by yellow strands
what are the two different features for inside and outside membrane protein domains
– most membrane proteins in animal cells are glycosylated on the cell surface or the oligosaccharide are found on the non-systolic surface (attachments)
- the intrachain or interchain disulfide bonds are only found on non-cytosolic surfaces. the sulfhydryl group is not forming disulfide bonds on the cytosolic side due to reducing environment
What are the three commonly used detergents to solubles and purify membrane proteins
Sodium dodecyl sulfate (SDS), Triton X-100, and Beta-octglucoside
what is triton x-100 made of
a mixture of composites in which the part of the hydrophilic part has several repeats (9-10 times), and the hydrophobic part starts with an aromatic ring
What can stabilize membrane proteins like the Na+-k+ pump
mild nonionic detergents, detergents initially purify the pump allowing for Na+-k+. to be incorporated into the phospholipid vesicles
– phospholipids are used in mixture with detergents
membrane proteins usually slowly diffuse across the plane of the membrane– how do they do this
they rotate and move laterally, they can separate from each other if they know something is off (mouse and human example)
How do cells confine proteins and lipid to specific domains within a membrane
tight junctions keep it sealed
the membrane itself has an apical plasma membrane facing outwards, a lateral plasma membrane in the middle (facing each other) and a basal plasma membrane attached (anchored) to the basal lamina
this helps with stability and making sure things stay in or stay out
what are the four ways of restricting the lateral mobility of specific plasma membrane proteins
- proteins can self-assemble into large aggregates (clumps)
-they can be tethered by interaction with assemblies of macromolecules outside the cell
–they can be tethered by interaction with assemblies of macromolecules inside the cell
– they can interact with protein on the surface of another cell
(think of other ways, for example, cell density for more interactions maybe?)
What molecules can pass through the lipid bilayer
most able to:
-hydrophobic molecules
-small uncharged polar molecules
-larger uncharge polar molecules
least able too: IONS
what are the two main classes of membrane transport proteins
Transporters: bind to specific solutes and undergo a series of conformational changes (slow but specific)
Channels: form a pore across the bilayer through solutes can diffuse (fast but not specific)
whats the difference between passive and active transport
passive does not use energy and goes with the gradient (channels and transporters)
active uses energy and goes against the gradient has to be a transporter
depolarization is usually due to channels and hyperpolarization is caused by channels
What are coupled transporters
use energy stored in concentration gradients of couple the downhill transport of one solute to the uphill transport of another
could be atp-driven or light-driven or two molecules (ions)
what are the three types of ion-concentration gradients
uniport, one molecule goes one way
symport: coupled both molecules go the same way
antiport: two molecules coupled in different directions
glucose transport for example is fueled by Na+ gradient as symport in a cooperative manner (alternative between inward open and outward open)
The asymmetric distribution of transporters in ethical cells underlies the …
transcellular transport of solutes
-Na+ linked symporters are in the apical domains
-glucose transporters are in the basal or lateral domains (passively allows glucose in
how is the Na+ gradient maintained
by a Na+-K+ pump in the basolateral domain, keeping the Na+ concentration low (internal)
we need the pumps to maintain a gradient
What are the three types of ATP-driven pumps
-P-type pump: phosphorylate themselves and maintain gradients of the four ions – takes one atp
-ABC transporter (ATP binding cassette) primarily pumps small molecules across cell membranes, but can also do large if needed (uses 2 ATP)
– V-type proton pumps pump H+ into organelles to acidify them (v-type) takes one atp
(ions out create ATP due to going with gradient, done by F-type Atp synthase– makes one atp )
How does the Na+-K+ pump work
sense 3 Na+ go out, it allows 2K+ in, so it can get past its steep electrochemical gradient by coupling
Where are importers and exporters found
importers (using 2 atp to pump small solute molecules in via ATPase) and exporters are found in bacteria
exporters (using ATPase domains to pump small solute molecules out with 2 ATP ) are only found in eukaryotes
for example, antimalarial drug chloroquine is pumped out of the cell by a acquired ABC transporter of the protist
what is the largest family of membrane transport proteins
ABC transporters
what are the different ion channels
- voltage-gated
-ligand-gated (extracellular ligand)
-ligand-gated (intra-cellular)
-mechanically gated
ions can diffuse at a fast rate and fluctuate from open and closed states (selectivity is due to pore size)
How do neurons function
their function depends on the elongated structure
dendrites branch from the cell body and receive signals from the axons of other neurons
axons send singles and without attenuation via a action potential/ nerve impulse 100 Meters/Sec
What happens when a action potential is fired
Na+ channels open allowing sodium in (increasing membrane potential), and then K+ channels open (membrane potential goes down) allowing potassium to flow out to restore potential
why does the action potential continue to propagate (go in) the same direction
the sodium channel deactivation (the opening of the potassium channels –repolarization) keeps it going in one direction
Are neurotransmitters destroyed or recycled once they are done firing and why
recycled as it is more energy-efficient — they are structurally hard to make
They get taken up into atrocities and then vesicularized and passed that way
how do transmitter-gated ion channels convert chemical signals into electrical ones at chemical synapses
-once the action potential arrives at a pre-synaptic cell it, releases voltage-gated Ca2+ channels
-this releases neurotransmitters stored in synaptic vesicles through exocytosis
-neurotransmitters bind and open channels in the post-synaptic cell membrane. -> ion flows alter the membrane potential and transmit a signal
the neurotransmitter then gets destroyed or recycled
What is the function of acetylcholine receptors
at the junction in a neuron, they act as excitatory transmitter-gated cation channels
they have 5 total subunits 2 identical, three unidentical
when the acetylcholine bind the two identical subunits (alpha) a conformational change happens opening the channel for Na+ and K+ with some Ca+
What are the five activations of ion channels (in order) to trigger neuromuscular transmission (11-41)
1) a voltage-gated Ca2+ channel Ca2+ go in with where the nerve impulse
2) acetylcholine gated cation channel lets 1 Na+ go into the receiving muscle
3)a voltage-gated Na+ channel lets 1 more Na+ go in to receiving muscle
4) a voltage-gated ca2+ channel and a ca2+ release channel lets 1 calcium 2+ goes in to the receiving muscle
What do rough Ers do
package proteins and lipids, and then send them to the Golgi apparatus
what does the Golgi apparatus do
modify the proteins and lipids and dispatch them to various destinations
what do lysosomes do
they contain digestive enzymes that allow them to degrade intracellular organelles and macromolecules and particles from outside through endocytosis
on the way to lysosomes, the materials must pass endosomes
what do peroxisomes do
they are small vesicular compartments that contain enzymes used in various oxidative reactions
what can explain the topological relationships of organelles
evolutionary origins
where does the nuclear membrane originate
an invasion of the plasma membrane and pinch off with a double membrane
how do nucleus and cytosol communicate
the nuclear pore complexes and are topologically continuous
what is the luman of the ER topologically equivalent to
extracellular equivalent
it is continuous with the space between the inner and outer nuclear membranes
what are the organelles in the secretory and endocytic pathways topologically equivalent to on the inside and outside of them
the exterior of the cell including the ER, Golgi, endosomes, lysosomes, and peroxisomes
What are the different ways a protein can move between compartments
-protein translation via translocators
-gated transport via nuclear pore complexes
-vesicular transport via vesicles loaded with cargo that bud off and fuse to a second topologically equivalent structure
-engulfment, moving proteins from the cytosol into the lysosome in autophagy or enclosing chromosomes inside the nucleus during nuclear envelope re-formation after mitosis
order of sorting singles that direct proteins to the correct cell address
-import into nucleus :positively charged amino acids
-export from nucleus: hydrophobic amino acids
-import into mitochondria: alternating hydrophobic and positively charged
-import into plastid: uncharged polar or hydroxylated amino acids
-import into peroxisomes: uncharged polar/positively charged/hydrophobic at C terminus
-import into ER: hydrophobic amino acids
-return to ER: negative changed amino acids
What kind of translation is signal- recognition particle (SRP)
co-translational meaning translation continues and translocation begins
the sequence gets brought to the translocator then binds ribosomes, inserts the polypeptide chain into the membrane, and transfers it across the lipid bilayer to the lumen
what part of transmembrane proteins allow them to be recognized like signal sequences
the hydrophobic segments, the n terminal part first anchored by the sec61 translocator
the next one signals the peptidase (the original sequences get left behind–cleaved)
this alternation will then be repeated and sec 61 will interpret their orientation (back and forth from the cytosol with the N term and will eventually end in the ER lumen with the N-term)
How to proteins that get synthesized in the rough ER get glycosylated
by the addition of a common N-linked oligosaccharide
we attach an N-Acetylglucosamine, many mannose, and glucose
we then use ASN to anchor the precursor in the ER membrane
How do peroxisomes form
the original vesicle buds from the ER and then proximal precurses proteins attach to the vesicle turning it into a peroxisome, then binaryfission it makes more
Where does the Ser-lys-leu single on the C-terminus end of a get synthesized
the cytosolic ribosomes, this process needs ATP hydrolysis
This sequence is needed for the import receptors to be recognized
Parts of a mitohondrion
The outer membrane, crista space, inner membrane, intermembrane space, matrix space
parts of a chloroplast
outer membrane, inner membrane, intermembrane space, stroma (matrix space), thylakoid (not connected to the inner membrane) , thylakoid space
The transport of mitochondrial membrane requires which two protein complexes
Tom complex: recognises protein and binds to the peptide (outer membrane)
Tim23 complex: binds to a peptide on the inner membrane
How can transport into the inner mitochondrial membrane occur
several ways
- a hydrophobic transmembrane segment binds to TIM23
-protein chaperones guide TIM22 complex which inserts the multipass inner membrane proteins
-protein is first made in matric space, then a signal directs it to the OXA complex which sticks it in (the inner membrane)
-nuclear-encoded proteins translocated into the matrix space via TOM and Tim23 complexes, cleavage unmasks the hydrophobic signal sequence N-term, and then it is inserted via the OXA complex
what does the SAM complex do
inserts and maintains a protein to the outer membrane
How can proteins get into the chloroplast membrane
via two signal sequences
- the entrance through the stroma called the TOC which binds both the outer membrane and the protein
- TIC complex is on the inner membrane and binds the peptide
- together they unmake the thylakoid signal the initiates that translocation
How can translocation to the thylakoid space or membrane happen
-they use a homolog of Sec that mediates protein translocation across the bacterial plasma membrane
-homolog of OXA pathway
-a TAT (twin-arginine translocation) pathway (two arginines are critical in the single sequences that direct proteins to the thylakoid
topologically equivalent refers to
two cellular compartments or spaces that are considered the same in terms of connectivity, meaning molecules can move between them without crossing a membrane, essentially treating them as if they are part of the same continuous space
Toc and tic are connected by what
Tic 236 in the intermembrane space (toc on outer and tic on inner)
What do nuclear pore complexes do to the nuclear envelope
perforate them
What is the nuclear lamina
a fibrous protein meshwork underlying the inner membrane but links to the cytoskeleton
each nuclear pore complex is made of what
-30 nucleoporin, symmetric on both sides,
-ring proteins anchor the pore complex to the nuclear membrane
-scaffold nucleoporin form layered ring structures
- channel nucleoporins that line a central pore, and restrict larger molecule passage
What do nuclear localization signals do
direct nuclear proteins to the nucleus
for example the SV40 Virus T-antigen to its site of action in the nucleus by switching a Lys to a Thr a signal is triggered
What do nuclear import recpetors bind to
both nuclear localization signals and NPC proteins
this receptor will the directly bind to cargo, but may need an adaptor to bind to their nuclear import receptor
they then bind to Phenylalanine-glycine (FG) repeats in the unstructured domains of the channel nucleoporins
What is Ran ATPase
it imposes directionality on transport through NPCs
what do GTPase activating protein (gap) and Guanine exchange factor (GEF) do
it produces Ran-GDP in the cytosol and Ran-GTP in the nucleus respectivly
Order of transport from cytosol to neuclous
-Protein bind to the receptor and takes it through the pore
-Ran-GTP binds to the receptor
-protein gets delivered to the nucleus, the rest of the complex leaves back into the cytosol
-GTP is hydrolyzed, Ran-GDP dissociates from the receptor
-repeat (reverse way for export)
What does ran-GTP binding do for nuclear import vs export
import: causes the receptor to release the cargo on the nuclear side (critical from the directionality of nuclear transport)
export: promotes the loading of cargo (gap in the cytosol triggers GTP hydrolysis and its dissociation from the receptor
What happens to the nuclear envelope during mitosis
it disassembles – the NPCs (nuclear pore complexes) and lamina disassemble the nuclear envelope fragments
