Cell Bio Final Flashcards
1
Q
Gustavo Silva
A
Oxidative stress in cells and uses bakers yeast to study the mechanisms
Cellular oxidative stress is characterized by an imbalance between reactive oxygen species production and intracellular antioxidant defense, leading to potential damage
2
Q
Three major types of receptors
A
GPCR (G-protein-coupled receptors
Enzyme-Coupled Receptors
Ion-Channel- Coupled Receptors
3
Q
How is signaling managed?
A
Via protein phosphorylation/dephosphorylation (post translational modification) OR GTP nucleotide binding & hydrolysis
4
Q
Dephosphorylation
A
phosphatase: removing phosphate→ inactivates
5
Q
Phosphorylation
A
kinase: activates
6
Q
GEF
A
GDP to GTP to turn on
7
Q
GAP
A
removing phosphate to turn off
8
Q
Signal by protien phosphorylation
A
ATP to ADP using protien kinase to add phosphate and turn on
then uses protien phosphatase to remove phosphate turning off signal
9
Q
Signaling by GTP binding protien
A
GDP (off) to GTP (on) using GTP binding turning on signal
then using GTP hydrolysis removing the phosphate and turning off signal
10
Q
Endocrine
A
Hormones → bloodstream →body.
11
Q
Paracrine
A
signals →neighbors (cell A acts on cell B)
12
Q
Autocrine
A
cell signals itself “auto”
13
Q
Neuronal
A
electrical signals →nerve cell axon→nerve terminal→ neurotransmitter release→target cells
14
Q
Contact-dependent
A
cells must physically interact to signal
15
Q
Ligand/Receptor Interaction
A
Ligand (signal molecule)
- hormone/drug/ neurotransmitter
- Causes conformational change
Receptor: ligand binds
Activation of Heterotrimeric G-protein
- The alpha dissociates from the the Beta Gamma (Y)
- GTP binds to alpha (on signal)
Heterodimers can form due to sharing a common ligand
16
Q
Signal Transduction
A
when a cell responds to the ligand-receptor binding
17
Q
Signal Amplification
A
Amplifying signals using different enzymes
Also used second messengers, ex: calcium
18
Q
RTK (receptor tyrosine kinase)
A
type of cell surface receptors
Dephosphorylation/phosphatase: removing phosphate→ inactivates
Phosphorylation/kinase: activates
GPCR (G-protein coupled receptor) and RTK receptors
19
Q
Immediate Targets
A
Immediate: less than seconds to minutes
Fast
Signal binds to receptor→ intracellular IN CYTOPLASM altered protein function→altered cytoplasmic machinery→altered cell behavior
Peptide hormones (hydrophilic)
20
Q
Longer Targets
A
Longer: min to hours
Slow
Signal binds to receptor→ IN NUCLEUS (DNA + RNA) → altered protein synthesis→altered cytoplasmic machinery→altered cell behavior→control gene expression
Steroid hormones (hydrophobic)
Steroid hormone – can be initially cytosolic or nuclear but bind ligand (ligand passes through cell membranes) and makes receptor active in controlling gene expression
21
Q
GPCR – signaling through cAMP
A
cAMP is formed from ATP by adenylate cyclase
Inactivated by hydrolysis to AMP by PDE
22
Q
GPCR – signaling through PLC (phospholipase C) → IP3 & DAG second messengers
A
DAG attaches to plasma membrane and recruits protein kinase C (direct effect)
IP3 diffuses to the ER and is bound the IP3 receptor
The IP3 receptor serves as a calcium channel and releases calcium from the ER
- Calcium binds to protein kinase C and others and activates it
IP3 indirectly acts on PKC via Ca+2 ions
23
Q
RTK – signal to Ras and MAPK
A
Receptor tyrosine kinases respond to DIMERIC signals- these serve to dimerize & activate the receptor
RTK targets Ras protein & MAPK cascade
RTK type of cell surface receptors - dephosphorylation and phosphorylation - tyrosine residue
24
Q
Ras
A
Ras proteins is a cellular oncogene
GTP/GDP binding
Changes confirmation due to one or the other nucleotide being bound cause changes in target proteins it binds or controls
RAS activates the MAPK which transmits signals downstream resulting in transcription
25
MAPK
MAPK: mitogen activated protein (MAP) kinase→ transcription
Kinase cascade moves this signal
26
Tor
Tor is a kinase: a major regulator of metabolism and growth in all eukaryotes
Downstream target of RTKs
27
Notch-Delta signaling
Notch processing via protease cleavage
Upregulation and downregulation
Differentiation in the cell process, can delay the cells
Delta is ligand (signal)
Notch is receptor
The delta signal protein will bind to the delta receptor notch
When they bind, a cleaved notch tail migrates to the nucleus→ transcription of notch-responsive genes
28
Calmodulin
Alterations in Ca+2 are often “read” by calmodulin or calmodulin kinase
Calmodulin is a calcium binding protein that mediates calcium regulation
Activated by intracellular calcium
29
Mutant Ras
Mutant Ras that is always “on” can be useful
“Dominant active” or “gain of function”
30
Does gene X or gene Y act upstream of Ras?
Dominant active rescues, so Ras should come after X, not before, otherwise loss of X block effect of dominant (always on) Ras
31
The opposite situation when the mutant gene Y functions downstream of Ras (you don’t know this before you do the experiment. What about the loss of Y?
Dominant active does not rescue loss of Ym so Ras should come before Y, not after, otherwise loss of Y would not block effect of dominant (alway on) Ras
32
Intracellular signals and second messengers
Levels of second messengers controlled during signaling enzymatic reactions or opening of ion channels to ensure that they are highly amplified
Second messengers are generated within the cells as a downstream step in signal transduction
33
Binding GTP to the G protein leads to
dissociation of the G-protein from the receptor
34
Activation of G protein
Steps A to D
A. Resting heterotrimer state of the G protein. GDP is bound to the alpha subunit in resting state and receptor is not associated with G protein.
B. Signal molecule (Ligand) binding to G protein receptor causes G protein to become physically associated with G protein receptor which then causes a conformational change that results in a reversal of the G proteins relative affinities for GDP/GTP.
C. GTP binding cause heterotrimer to disassociate into two activated subunits alpha and beta gamma.
D. beta gamma subunits opens the K+ (potassium) channel
35
Inactivation of G protein
Steps
Extracellular Space
Cytosol activated by beta gamma complex
Activated alpha subunit acts like GTPase - hydrolysis of GTP by the alpha inactivates and causes it to dissociate from the target protein
Inactive alpha reassembles with beta gamma complex to reform an inactive G protein
36
RTK can be down regulated by
RTK can be down regulated by protein tyrosine phosphatases dephosphorylates the RTKs or by endocytosis and lysosomal targeting of the receptor from the endosome the receptor many also recycle back to the plasma membrane
37
The axon of a neuron transmits an electrical signal from its cell body to its synapse where it releases a neurotransmitter agent onto its target cell. What of the following is used to describe the general process that changes the electrical signal to a chemical signal?
Transduction
38
Which of the following would explain the net inward movement of solute X into the cell?
Concentration of X higher outside than inside
An inward directed energy requiring a pump mechanism located in the plasmalemma
39
True or False: Membranes can be permeable to some small uncharged yet polar molecules?
True
40
For most animal cells the distribution of Na+ ions across the plasma membrane is such that
Na+ is higher outside the cell
Na (sodium)
41
Na+ ions are maintained at a higher level outside than inside the cell largely by the activity of what?
Na+/K+ ATPase pump
42
True or False: Channel proteins can perform active transport
False
43
True or False: The majority of channels operate to gate the movement of two or more similarly sized and charged cations (like Na+ and K+ or Ca2+ and Mg2+)
False
44
Selective permeability of membranes
Semi permeable to some small things like water and nonpolar stuff
45
What passes through the cell membrane?
Small molecules/uncharged molecules: water (osmosis), CO2 & oxygen
46
What can’t pass through the cell membrane?
Large molecules, glucose, H+ ions/protons, calcium, potassium, sodium
47
What keeps the sodium out and potassium in?
Na/K ATPase Pump→ against gradient
Keeps Na+ high outside the cell & K+ high inside
Potassium (K+) is higher on the INSIDE: KIN
48
What if the larger molecules, and things that can’t pass the cell membrane, want to pass?
Carriers: transport molecules down & against the concentration gradient
Channels: transport ions and molecules down their concentration gradient (no energy needed)
Ion channels are selective-they have specific ions to which they open
49
Active transport
requires energy for the movement of molecules and the molecules move against the concentration gradient
50
Passive transport
does not require energy for the movement of molecules and the molecules move along the concentration gradient
51
Symport
Movement of two molecules in the same direction
Ex moving glucose and sodium up its concentration gradient
52
Antiport
Movement of two molecules in the opposite direction
53
Electrochemical gradient
Ions carry net electrical charge
Cell membranes have an electrical potential difference between their interior & their exterior faces
So, the ions have TWO FORCES acting on them with regards to net movement across a biological membrane
- Concentration gradient + electrical gradient =electrochemical gradient
54
Roles of energy in pumps/carriers that perform active transport
During active transport, a protein pump uses energy, in the form of ATP, to move molecules from an area of low concentration to an area of high concentration.
An example of active transport is the sodium-potassium pump, which moves 3 sodium ions to the outside of the cell and 2 potassium ions to the inside of the cell.
55
Ligands or gating of channels – signals that open channels
Ligand-gated ion channels open when a chemical ligand such as a neurotransmitter binds to the protein.
Voltage channels open and close in response to changes in membrane potential.
Mechanically-gated channels open in response to physical deformation of the receptor, as in sensory receptors of touch and pressure.
56
How action potentials are initiated and propagated – major channels involved.
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Are mediated by voltage-gated cation channels
The neuron, like most cells, in resting state is usually electronegative inside (-60mV)
An action potential is caused by either threshold or suprathreshold stimuli upon a neuron.
- Threshold: how likely that the voltage gated Na+ channel will open
It consists of three phases: depolarization (Na+ goes in cell, Na+ goes down their concentration gradient & electrochemical gradient), overshoot (once threshold is reached, the action potential spikes up), and repolarization (K+ leaves cell) .
An action potential propagates along the cell membrane of an axon until it reaches the terminal button.
57
How is resting potential reset?
How does the membrane potential reset inside the cells?
K+ channels → undershoots to equilibrium potential of K+ & the inactivation of Na+ is removed→ Na+ closes.
58
Open/inactive/closed state of voltage gated Na+ channel
Open: Na+ goes in the cell once threshold is reach to depolarize the cell→upstroke to start the action potential
Inactive: temporarily inactivates Na+ channels at the peak
Closed: prevents action potential initiation and conduction and therefore prevents sensory communication
59
Nature of membrane voltage differences
Differences in concentration of ions on opposite sides of a cellular membrane produce a voltage difference called the membrane potential.
60
Resting potential of cell membrane for most cells and neurons
In most neurons the resting potential has a value of approximately −70 mV. The resting potential is mostly determined by the concentrations of the ions in the fluids on both sides of the cell membrane and the ion transport proteins that are in the cell membrane.
61
Neurotransmitters can be excitatory or inhibitory “stack the deck” by changing the probability for an action potential to happen
Excitatory=entry of cations to further depolarize
Inhibitory= entry of anions to further polarize
62
Role of voltage gated Ca2+ channels in synaptic vesicle docking/regulated exocytosis at neuron:neuron and neuromuscular cell-cell junctions.
Steps 1-8
1. Threshold reached
2. Depolarization
3. Repolarization
4. Hyperpolarization
5. Activated nerve-terminal with action potential arriving at the axon terminals (electrical signal)
6. Open voltage gated Ca+ in presynaptic nerve terminal
7. Ca+ enters the cell and allows vesicles to exocytose the neurotransmitter to be released (chemical signal)
** note: the VGCC (in presynaptic terminal) in nerve terminal convert an electrical signal into a chemical signal
** the synapse is rich in regulated secretory vesicles containing neurotransmitters & specific Ca+2 channels
8. That neurotransmitter act on postsynaptic cell (binding of these neurotransmitters to the postsynaptic cell creates an effect of propagation of signal or muscle contraction)
**note: the transmitter-gated ion channels on the postsynaptic membrane convert the chemical signal back into the electrical signal
63
Meaning of term chemiosmotic coupling
ATP generation by a mitochondria or chloroplast occurs largely through a 2-step process known as chemiosmotic coupling→ linking chemical bond formation to solute transport
Step 1: active H+ transport causes an electrochemical gradient for protons to develop across the mitochindiral inner membrane (or the thylakoid membrane of chloroplasts)
Step 2: The energy in this H+ electrochemical gradient powers the synthesis of ATP using a membrane-localized enzyme, ATP synthase2.
This is another example of coupling the movement of an ion down its electrochemical gradient to power another process
In this case, the movement of an ion (H+) “downhill” is coupled to the synthesis of ATP
64
H+ gradient – where does it come from, what different functions of the mitochondrion does it enable?
In both organelles, the “power” comes in the form of a proton gradient produced across a membrane
Electron transport creates a proton & pH gradient across the mitochondrial INNER membrane (NOT THE OUTER)
- These protons then drive the ATP synthase
The H+ (proton) gradient is established by ELECTRON TRANSPORT process resulting in the movement of H+ against its electrochemical gradient
- These protein complexes (electron transport chain) are embedded in the membrane to function as a PROTON PUMP
65
Why does proton pumping take place across a membrane in the mitochondria or chloroplast?
to permit the development of a gradient
66
Chloroplasts and Photosynthesis
Photosynthesis: series of light-driven reactions that create ORGANIC molecules from atmospheric CO2 (carbon fixation)
Light transfer reactions (“light reactions”)
- Develop the H+ gradient
- Synthesizes ATP & NADPH
Carbon fixation reactions (“dark reactions”)
- ATP NADPH+CO2→sugars & amino acids (“carbon fixation”)
Inputs – light energy, carbon dioxide, water
Outputs – glucose, oxygen
67
What would happen to the ATP synthase
reaction if we add a drug that collapses the
electrical potential across the inner membrane?
ATP synthesis would be reduced due to overall
reduction of the electromotive
68
ATP synthase
The ATP synthase is a mitochondrial enzyme localized in the inner membrane,
Synthesis of ATP from ADP and phosphate, driven by a flux of protons across a gradient generated by electron transfer
69
Structures/membranes in mitochondria and chloroplasts - similarities and differences; permeabilities
Both mitochondria & chloroplasts serve as energy producers.
Both develop transmembrane proton gradients using electron
transport systems embedded in their membrane.
Both use the proton gradients to “power” the synthesis of ATP.
ATP made by mitochondria is made available directly to the rest
of the cell (ATP can cross the inner membrane by a special carrier
and the outer membrane through the porin channels).
ATP cannot cross the inner membrane of the chloroplast
Instead, ATP made by chloroplasts is used to make sugars, fatty acids and amino acids which cross the inner & outer chloroplast membranes to the cytoplasm.
The sugars & fatty acids are metabolized and then oxidized by the mitochondria via oxidative phosphorylation to make ATP available to the rest of the plant cells.
70
How do you suppose this micro-anatomical
arrangement affects the ability of chloroplasts to
develop a pH gradient compared to mitochondria?
Chloroplasts can develop a much
larger gradient because they pump H+
into the thylakoid space which is not
only small but is also bounded by a
membrane impermeable to H+.
71
What other aspects of mitochondria are interesting
to cell biologists?
Distribution in cells, morphology
Evolution of mitochondria – the diversity of
mitochondria in various eucaryotes.
Key integrating role in Apoptosis
72
Which of the following would you predict would happen to the PH of the cytoplasm (PHc) and the PH of the interior (matrix or stroma) of the mitochondrion/chloroplast (PHm/c) as a result of normal proton pumping?
Increase of PHm/c and decrease of PHc
73
4 phases
G1, S (DNA replication), G2, M (mitosis and cytokinesis)
Prophase, Prometaphase, Metaphase, Anaphase, Telophase, Cytokinesis
74
Prophase
Prophase → sister chromatids condense
Spindle assembly
Kinetochores interact with kinetochore microtubules that are parallel to interpolar microtubules in the spindle
Microtubules interacting protein complexes build at centromeres
ASTER (unattached) microtubules position the spindle in many cells
75
Prometaphase
NE breakdown, chromosomes associate with spindle
76
Metaphase
Congression of chromosomes
Forces from motors & microtubule dynamics balance chromosomes (kinetochores) on the plate (center of areas of spindles)
77
Anaphase
Dissolution of sister chromatid cohesion, migration to poles
Forces from motor & microtubules pull chromosomes (kinetochores) to respective poles
78
Telophase
NE reassembly, migration of nuclei
Nuclear envelope assembly: dephosphorylation of lamins
Decondensation of chromosomes
Division of the cytoplasm beings with the assembly of the contractile ring
79
Cytokinesis
Cytoplasm division by a contractile ring of ACTIN & MYOSIN FILAMENTS
80
Cyclin dependent kinase (CDK): needs cyclin
Activate form of CDK complex is CDK paired with cyclin
S and M phase versions
Unique about cyclin it does activates cycle through the cell cycle but itself has to be correct when bound to the right cyclin
Moving from one phase of the cycle to the other cyclin becomes ubiquetled and is turned over
Cyclin cycle whereas CDK is stay at flat levels
Cyclin regulated by ubiquitin
CDK regulated by phosphorylation and dephosphorylation
81
What if there is a problem in the cell cycle?
They ask for extension for quality control called checkpoints monitored by DNA repair
82
Regulates entry into the cell cycle
Mitogens are signals that cause cell division
Extracellular signals like ligands that activate receptor RTK
RAS - MAPKKK, MAPKK, MAPK, cell cycle - positive regulation
Negative regulation is RB that acts as a break with phosphorylation
Tumor suppressor are RB act normally to block cell repression
Oncogene are RAS and stimulate the formation of cancers
Some mutations in RAS
When RB dephosphorylated re-establishes the break
Switch regulation on and off by RB
Cell proliferation would happen all the time without RB
83
Stem Cells
special human cells that are able to develop into many different cell types. This can range from muscle cells to brain cells. In some cases, they can also fix damaged tissues.
84
Potencies
pluripotent stem cells may give rise to all types of cells in an organism
Most induced pluripotent stem (iPS) cells are generated by retroviral or lentiviral transduction of reprogramming factors. Multiple viral integrations into the genome may cause insertional mutagenesis and may increase the risk of tumor formation.
85
ES Cells
Embryonic stem cells are obtained from early-stage embryos — a group of cells that forms when eggs are fertilized with sperm at an in vitro fertilization clinic.
86
Tight Junctions
that form between adjacent cells and also separate applicable and basal
87
Adherens Junctions
initiate cell-cell contacts, and mediate the maturation and maintenance of the contact. Adherens junctions consist of the transmembrane protein E-cadherin, and intracellular components, p120-catenin, β-catenin and α-catenin.
88
Gap Junctions
connect cell together
89
Nature of Cadherins and their interactions, requirements for activity
Structures called hemidesmosomes interact with the outside world through integrations
Desmosomes places where there are proteins on instead of the cell and then transmembrane proteins that interact with watch and these are calcium dependent and then on the inside of cell are connected to proteins that interact with intermediate cytoskeleton - Cadherins there job is to provide integrity
Intermediate filaments between cells that come from desmosomes that connect to each other and provide a net work so that when you have the whole set of cells resist in the epithelium when rubbing arm unless you have mutagens affecting these things - bruise more easily
90
Cellulose and Collagen
Cellulose is composed of β-glucose residues
- the main substance found in plant cell walls and helps the plant to remain stiff and strong
Collagen is composed of glycine, proline and hydroxyproline
- becomes organized extracellulary into multistranded fibrils
- phosphoryaltion
- componet of connective tissues in animals and funcutions in part to provide mechinacl/tensile strength
91
Plasmodesmata
The plasmodesmata is a channel through the cell wall that allows molecules and substances to move back and forth as needed.
The function of the plasmodesmata is to provide communication between cells or a pathway for the intercellular transfer of molecules.
92
The source of most different types of cancers is?
Environmental factors
93
True or False –
Both copies of the cell proliferation/division “brake”
gene Rb, encoding the Retinoblastoma protein, are
frequently inactivated by mutations in cancers – this fits
a definition of Rb as an oncogene
False
94
True or False –
A gene in flies promotes initiation of the cell cycle. A human version is found and it is seen that a single mutant copy is present in many cancers. Upon cloning the mutant version you see it removes a lysine from its sequence where the protein is normally ubiquitylated to degrade it in the proteasome. The mutant protein
is stable and accumulates, further promoting cell division. The normal version of this gene fits the definition of a proto-oncogene.
True
95
p53/p21
p53/p21 DNA damage
checkpoint preventing
replication of DNA with
breaks or extensive
mutations (note that more
mutations = more
chances cells will carry
inactivating mutations in
tumor suppressors or
activating hits in different
oncogenes). Also more
chances to impair
repair functions, further
elevating mutation rates
96
The chemotherapeutic/anti-cancer drug
Gleevec acts by
Blocking access of the binding
site for ATP of the kinases
mutated in CML and some other
cancers
97
True or False –
Channels as opposed to carrier proteins in ion
transport are the same as gap junctions in that they
are non-selective and when open allow many,
many ions to pass at once?
False
98
True or False –
A stem cell gives rise to only one type of
differentiated cell type or another stem cell
False
99
True or False –
Glycosoaminoglycans (GAGs) are sugars
which are hydrophilic and part of the ECM
True
100
True or False -
Plant cells orient their cellulose synthesis relative to stomata found in the cell cortex
False
101
Which cell-cell connections provide seals between
adjacent epithelial cells?
Tight junctions
102
Plant cells have connections between cells of
their tissues that are similar to gap junctions.
These are called
Plasmodesmata
103
Oncogene
Oncogene are RAS and stimulate the formation of cancers
Some mutations in RAS
gain of function
104
Tumor suppressor
Tumor suppressor are RB act normally to block cell repression
When RB dephosphorylated re establishes the break
Switch regulation on and off by RB
Cell proliferation would happen all the time without RB
105
Mendel
Mendel's Postulates was independent assortment which is genes tends to assort independently of each other because they are far apart with lost of recombination with crossover events
he never said anything about linkage when two genes are close together with little recombination
