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

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2
Q

Three major types of receptors

A

GPCR (G-protein-coupled receptors
Enzyme-Coupled Receptors
Ion-Channel- Coupled Receptors

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3
Q

How is signaling managed?

A

Via protein phosphorylation/dephosphorylation (post translational modification) OR GTP nucleotide binding & hydrolysis

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4
Q

Dephosphorylation

A

phosphatase: removing phosphate→ inactivates

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5
Q

Phosphorylation

A

kinase: activates

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6
Q

GEF

A

GDP to GTP to turn on

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7
Q

GAP

A

removing phosphate to turn off

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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

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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

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10
Q

Endocrine

A

Hormones → bloodstream →body.

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11
Q

Paracrine

A

signals →neighbors (cell A acts on cell B)

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12
Q

Autocrine

A

cell signals itself “auto”

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13
Q

Neuronal

A

electrical signals →nerve cell axon→nerve terminal→ neurotransmitter release→target cells

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14
Q

Contact-dependent

A

cells must physically interact to signal

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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

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16
Q

Signal Transduction

A

when a cell responds to the ligand-receptor binding

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17
Q

Signal Amplification

A

Amplifying signals using different enzymes

Also used second messengers, ex: calcium

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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

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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)

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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

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21
Q

GPCR – signaling through cAMP

A

cAMP is formed from ATP by adenylate cyclase

Inactivated by hydrolysis to AMP by PDE

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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

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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

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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

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25
Q

MAPK

A

MAPK: mitogen activated protein (MAP) kinase→ transcription

Kinase cascade moves this signal

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26
Q

Tor

A

Tor is a kinase: a major regulator of metabolism and growth in all eukaryotes

Downstream target of RTKs

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27
Q

Notch-Delta signaling

A

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

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28
Q

Calmodulin

A

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

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29
Q

Mutant Ras

A

Mutant Ras that is always “on” can be useful
“Dominant active” or “gain of function”

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30
Q

Does gene X or gene Y act upstream of Ras?

A

Dominant active rescues, so Ras should come after X, not before, otherwise loss of X block effect of dominant (always on) Ras

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31
Q

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?

A

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

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32
Q

Intracellular signals and second messengers

A

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

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33
Q

Binding GTP to the G protein leads to

A

dissociation of the G-protein from the receptor

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34
Q

Activation of G protein
Steps A to D

A

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

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35
Q

Inactivation of G protein
Steps

A

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

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36
Q

RTK can be down regulated by

A

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

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37
Q

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?

A

Transduction

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38
Q

Which of the following would explain the net inward movement of solute X into the cell?

A

Concentration of X higher outside than inside

An inward directed energy requiring a pump mechanism located in the plasmalemma

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39
Q

True or False: Membranes can be permeable to some small uncharged yet polar molecules?

A

True

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40
Q

For most animal cells the distribution of Na+ ions across the plasma membrane is such that

A

Na+ is higher outside the cell

Na (sodium)

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41
Q

Na+ ions are maintained at a higher level outside than inside the cell largely by the activity of what?

A

Na+/K+ ATPase pump

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42
Q

True or False: Channel proteins can perform active transport

A

False

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43
Q

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+)

A

False

44
Q

Selective permeability of membranes

A

Semi permeable to some small things like water and nonpolar stuff

45
Q

What passes through the cell membrane?

A

Small molecules/uncharged molecules: water (osmosis), CO2 & oxygen

46
Q

What can’t pass through the cell membrane?

A

Large molecules, glucose, H+ ions/protons, calcium, potassium, sodium

47
Q

What keeps the sodium out and potassium in?

A

Na/K ATPase Pump→ against gradient
Keeps Na+ high outside the cell & K+ high inside

Potassium (K+) is higher on the INSIDE: KIN

48
Q

What if the larger molecules, and things that can’t pass the cell membrane, want to pass?

A

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
Q

Active transport

A

requires energy for the movement of molecules and the molecules move against the concentration gradient

50
Q

Passive transport

A

does not require energy for the movement of molecules and the molecules move along the concentration gradient

51
Q

Symport

A

Movement of two molecules in the same direction

Ex moving glucose and sodium up its concentration gradient

52
Q

Antiport

A

Movement of two molecules in the opposite direction

53
Q

Electrochemical gradient

A

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
Q

Roles of energy in pumps/carriers that perform active transport

A

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
Q

Ligands or gating of channels – signals that open channels

A

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
Q

How action potentials are initiated and propagated – major channels involved.

jhbjbcfvgbhnjm

A

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
Q

How is resting potential reset?
How does the membrane potential reset inside the cells?

A

K+ channels → undershoots to equilibrium potential of K+ & the inactivation of Na+ is removed→ Na+ closes.

58
Q

Open/inactive/closed state of voltage gated Na+ channel

A

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
Q

Nature of membrane voltage differences

A

Differences in concentration of ions on opposite sides of a cellular membrane produce a voltage difference called the membrane potential.

60
Q

Resting potential of cell membrane for most cells and neurons

A

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
Q

Neurotransmitters can be excitatory or inhibitory “stack the deck” by changing the probability for an action potential to happen

A

Excitatory=entry of cations to further depolarize

Inhibitory= entry of anions to further polarize

62
Q

Role of voltage gated Ca2+ channels in synaptic vesicle docking/regulated exocytosis at neuron:neuron and neuromuscular cell-cell junctions.

Steps 1-8

A
  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

  1. 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
Q

Meaning of term chemiosmotic coupling

A

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
Q

H+ gradient – where does it come from, what different functions of the mitochondrion does it enable?

A

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
Q

Why does proton pumping take place across a membrane in the mitochondria or chloroplast?

A

to permit the development of a gradient

66
Q

Chloroplasts and Photosynthesis

A

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
Q

What would happen to the ATP synthase
reaction if we add a drug that collapses the
electrical potential across the inner membrane?

A

ATP synthesis would be reduced due to overall
reduction of the electromotive

68
Q

ATP synthase

A

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
Q

Structures/membranes in mitochondria and chloroplasts - similarities and differences; permeabilities

A

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
Q

How do you suppose this micro-anatomical
arrangement affects the ability of chloroplasts to
develop a pH gradient compared to mitochondria?

A

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
Q

What other aspects of mitochondria are interesting
to cell biologists?

A

Distribution in cells, morphology

Evolution of mitochondria – the diversity of
mitochondria in various eucaryotes.

Key integrating role in Apoptosis

72
Q

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?

A

Increase of PHm/c and decrease of PHc

73
Q

4 phases

A

G1, S (DNA replication), G2, M (mitosis and cytokinesis)

Prophase, Prometaphase, Metaphase, Anaphase, Telophase, Cytokinesis

74
Q

Prophase

A

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
Q

Prometaphase

A

NE breakdown, chromosomes associate with spindle

76
Q

Metaphase

A

Congression of chromosomes

Forces from motors & microtubule dynamics balance chromosomes (kinetochores) on the plate (center of areas of spindles)

77
Q

Anaphase

A

Dissolution of sister chromatid cohesion, migration to poles

Forces from motor & microtubules pull chromosomes (kinetochores) to respective poles

78
Q

Telophase

A

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
Q

Cytokinesis

A

Cytoplasm division by a contractile ring of ACTIN & MYOSIN FILAMENTS

80
Q

Cyclin dependent kinase (CDK): needs cyclin

A

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
Q

What if there is a problem in the cell cycle?

A

They ask for extension for quality control called checkpoints monitored by DNA repair

82
Q

Regulates entry into the cell cycle

A

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
Q

Stem Cells

A

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
Q

Potencies

A

​​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
Q

ES Cells

A

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
Q

Tight Junctions

A

that form between adjacent cells and also separate applicable and basal

87
Q

Adherens Junctions

A

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
Q

Gap Junctions

A

connect cell together

89
Q

Nature of Cadherins and their interactions, requirements for activity

A

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
Q

Cellulose and Collagen

A

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
Q

Plasmodesmata

A

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
Q

The source of most different types of cancers is?

A

Environmental factors

93
Q

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

A

False

94
Q

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.

A

True

95
Q

p53/p21

A

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
Q

The chemotherapeutic/anti-cancer drug
Gleevec acts by

A

Blocking access of the binding
site for ATP of the kinases
mutated in CML and some other
cancers

97
Q

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?

A

False

98
Q

True or False –
A stem cell gives rise to only one type of
differentiated cell type or another stem cell

A

False

99
Q

True or False –
Glycosoaminoglycans (GAGs) are sugars
which are hydrophilic and part of the ECM

A

True

100
Q

True or False -
Plant cells orient their cellulose synthesis relative to stomata found in the cell cortex

A

False

101
Q

Which cell-cell connections provide seals between
adjacent epithelial cells?

A

Tight junctions

102
Q

Plant cells have connections between cells of
their tissues that are similar to gap junctions.
These are called

A

Plasmodesmata

103
Q

Oncogene

A

Oncogene are RAS and stimulate the formation of cancers
Some mutations in RAS

gain of function

104
Q

Tumor suppressor

A

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
Q

Mendel

A

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