Transporters and Ion Channels

Transporters

• A uniport transporter moves only one type of solute across a membrane, following the concentration gradient
• An antiport transporter pumps inorganic ions and organic molecules in opposite directions
• Sodium is pumped into the cell down its gradient, while hydrogen is pumped out against its gradient
• Antiport helps in controlling pH levels
• One ion goes down its concentration gradient, providing the energy for the other to move against its gradient
• A symport transporter drives the import of solutes by coupling them
• Sodium moves down its gradient, dragging glucose along with it
• Both glucose and sodium must be present for the process to occur
• Symport transporters are actively importing coupled ions, like glucose

Ion Concentrations

• Sodium is more prominent extracellularly
• Potassium is more prominent intracellularly
• Calcium is more prominent extracellularly

Gated-Ion Channels

• Voltage-gated ion channels open upon depolarization
• Ligand-gated ion channels open when ligands bind to specific spots on the channel (can be extracellular or intracellular)
• Mechanically-gated ion channels are opened by a stimulus, such as cilia being pulled apart
• Light-gated ion channels open by reacting to light via channelrhodopsin

Action Potential

• Stimulation results in a shift to less negative membrane potential, known as depolarization
• Voltage-gated sodium channels mediate this, it opens transiently to further depolarize the membrane when the threshold potential is reached
• Sodium channels adopt an automatic inactivation conformation on a timer
• This leads to the channels closing and remaining inactive until the membrane potential is restored to its resting state, marking the refractory period
• Voltage-gated potassium channels open in response to depolarization but slower
• They stay open as long as the membrane is depolarized
• A rapid outflow of potassium helps bring the membrane potential back to its resting potential
• Sodium/potassium pumps restore the ion gradient

Electrical Signal to Chemical Signal

• Action potentials in the presynaptic neuron cause vesicles to fuse with the plasma membrane, releasing neurotransmitters into the synaptic cleft
• Action potentials trigger the opening of calcium channels
• Calcium triggers vesicle fusion
• Neurotransmitters stored in vesicles are released into the synaptic cleft
• Neurotransmitters received by the postsynaptic neuron bind to ligand-gated channels, opening them, therefore continuing or inhibiting nerve impulses

ΔG (Change in Free Energy)

• Free energy is the useful energy in a system
• A chemical reaction results in a change in molecular states
• Change in free energy: the difference in free energy of molecules that participate in reactions
• Chemical reactions only occur spontaneously if the ΔG value is negative
• ΔG = (C+D)products - (A+B)reactants

Coupled Reactions

• An energetically favorable reaction can drive an energetically unfavorable one
• Favorable reactions have a negative ΔG, while unfavorable reactions have a positive ΔG

Activated Carriers

• ATP carries phosphate
• NADH, NADPH, FADH2 carry electrons and hydrogens
• Acetyl CoA carries an acetyl group

NADH and NADPH

• NADH is an intermediate in catabolic reactions
• The NAD+/NADH ratio is kept high in the cell, indicating more NAD+
• NADPH is an intermediate in anabolic reactions
• The NADP+/NADPH ratio is kept low inside the cell, indicating more NADPH

FADH2

• A high-energy electron carrier intermediate generated in catabolic reactions
• Energy is stored in the redox potential of its flavin ring system
• Created in the Krebs Cycle
• FADH2 has electrons (reduced), while FAD is oxidized

Redox

• Oxidation is the loss of electrons, or more oxygen being added to carbon
• Whatever is oxidized is the reducing agent
• Reduction is the gain of electrons, or more hydrogen being added to carbon
• Whatever is reduced is the oxidizing agent

Three Stages of Metabolism (Aerobic)

• Mouth, gut, and lysosomes: Digestion of large macromolecules into simple monomers
• Cytosol: Gradual oxidation breakdown, where glycolysis converts one glucose into two pyruvates, producing ATP and NADH
• Mitochondria: Pyruvate is transported into the mitochondrial matrix and converted to acetyl CoA, then enters the Citric Acid Cycle
• A large amount of NADH and FADH2 is produced using e- from NADH, followed by oxidative phosphorylation which produces a large amount of ATP

Glycolysis

• Glycolysis occurs in the cytosol
• Glucose is used with 2 ATP to create pyruvate
• Produces 4 ATP and 2 NADH from one glucose
• Net production of 2 ATP
• Produces two pyruvate molecules

Two Mechanisms of Transporting Electrons from Cytosolic NADH

• Malate-Aspartate Shuttle (MAS) results in NADH = 2.5 ATP
• NADH in the cytosol needs to get to the mitochondria and enters through photosystems 1, 3, and 4
• Glycerol-Phosphate Shuttle (GPS) results in NADH = 1.5 ATP (less)
• NADH never gets into the mitochondria, enters photosystems 3 and 4

The Link Reaction

• Pyruvate is transported from the cytosol into the mitochondrion's matrix
• Pyruvate dehydrogenase complex converts each pyruvate molecule into CO2 and acetyl CoA
• Results in one NADH per pyruvate (two per one molecule of glucose)

The Citric Acid Cycle

• For every pyruvate, 3 NADH is sent to complexes 1, 3, and 4, 1 FADH2, and 1 GTP
• For every glucose, 6 NADH, 2 FADH2, and 1 GTP
• 1 NADH = 2.5 ATP, 1 FADH2 = 1 ATP, 1 GTP = 1 ATP, which results in 19 ATP per 1 glucose in the Citric Acid Cycle
• The total ATP production from 1 glucose molecule is 31 ATP

Oxidative Phosphorylation

• NADH donates electrons to complex 1, which goes to 3 and 4
• FADH2 donates electrons to complex 2
• Turns on ATP synthase to create ATP
• Oxygen is the final acceptor of electrons

Anaerobic Production of Energy

• Glycolysis remains the same, with all energy coming from the net product of 2 ATP
• NADH is converted to NAD+ to continue glycolysis
• Pyruvate is converted to lactate in mammals, or to CO2 and ethanol in fungus

Two Stages of Oxidative Phosphorylation

• Electron Transport Chain: Energy released by electron transport is used to pump protons across the membrane
• ATP Synthesis: Energy stored in the proton gradient is harnessed by ATP synthase to make ATP

Transport of Electrons from NADH

• Ubiquinone is aka coenzyme q

Redox Potentials

• There is an increase along the electron transport chain
• Oxygen has the highest electron affinity and is energetically favorable
• Coenzyme q < cytochrome c and is energetically favorable

ATP Synthase

• ATP synthase can work in both directions
• Converts ADP to ATP using the F0 rotor and H+ from the intermembrane space into the matrix
• ATP hydrolysis converts ATP to ADP using F1 ATPase and releasing H+ from the matrix into the intermembrane space

Comparison of Cyanobacteria and Chloroplasts

• Both contain an outer and inner membrane, nucleoid, thylakoids, lipid droplets, and ribosomes
• Chloroplasts only contain an intermembrane space and granum
• Cyanobacteria only contain a carboxysome, peptidoglycan wall, mucoid sheath, capsule, and slime coat

Photosynthesis

• Light reactions occur in the thylakoid membrane using a photosynthetic electron transport chain to create NADPH and ATP
• Carbon fixation reactions are light independent and occur in the chloroplast stroma, where NADPH and ATP are used

Photosystem II

• There is ATP synthesis
• Light is absorbed and electrons are passed to plastoquinone using a mobile carrier from the stroma
• The plastoquinone then goes to the cytochrome b6-f complex

Photosystem I

• Receives electrons from photosystem II
• Creates NADPH
• Plastocyanin transports electrons to photosystem I, where electrons are re-energized
• Ferredoxin brings electrons to ferredoxin-NAD+ reductase, which creates NADPH

The Calvin Cycle

• For every 3 CO2
• One molecule of glyceraldehyde 3-phosphate can leave the cycle though 6 are produced
• 9 ATP is used
• 6 NADPH is used
• ATP and NADPH cannot leave the chloroplast.

Four Classes of Intermediate Filaments

• Cytoplasmic: Keratin filaments found in skin (epithelial cells), Vimentin is found in connective-tissue cells, and Neurofilaments are found in nerve cells
• Nuclear: Nuclear lamins are found in all animal cells
• These are a mesh that surrounds the inside of the nuclear envelope
• These use SUN/KASH proteins to link the nuclear and cytosolic skeleton, including cytosolic components, actin, microtubulin, chromatin, and other filaments
• KASH = cytosol, SUN = nucleus

Microtubule Organizing Centers

• Centrosomes have 2 centrioles
• Gamma-tubulin is a nucleation site, where all growth of microtubules starts
• Grows from the minus end out into to the plus end

Motor Proteins

• Motor proteins are ATPases
• ATP hydrolysis loosens the attachment of head 1 to the microtubule
• ADP release and ATP binding change the conformation of head 2, which pulls head 1 forward

Directions of Different Motor Proteins

• Kinesins move from the minus end to the plus end
• Dyeins move from the plus end to the minus end and cause microtubule bending in flagellum (microtubule sliding)

Actin Filament Polymerization

• The minus end is not anchored to centrioles
• The plus end is bound with ATP, while the minus end is bound with ADP
• Treadmilling occurs where the actin filament moves towards the plus end, but the length does not change

Rho-Family GTPases Control Actin Polymerization

• Contractile unbranched filaments have Rho Activation to contract
• Lamellipodia have Rac Activation for being lame
• Filopodia have Cdc42 Activation for filaments at the CDC

Cell Crawling

• Actin Polymerization at the plus end protrudes lamellipodia
• Myosin motor proteins slide along actin filaments, contracting back towards the front

Mechanism of Muscle Contraction

• An inactive T-tubule membrane (voltage-gated) is activated by depolarization, increasing Ca levels
• Increased Ca levels activate the adjacent Ca2+ release channel in the lumen sarcoplasmic reticulum
• Ca2+ binds to the troponin complex, causing tropomyosin to block the myosin-binding site and dissociate
• Myosin binds to actin, causing muscle contraction

The Cell Control System

• Late G1 (start) allows the cell to enter the cell cycle and proceed to S phase if the environment is favorable
• G2/M allows the cell to enter mitosis if all DNA has been replicated and all DNA damage has been repaired
• Mid-way M allows the cell to pull the duplicated chromosomes apart if all chromosomes are properly attached to the mitotic spindle

Cell Cycle

• Interphase G1, S, and G2
• Mitosis is the division of chromosomes
• Cytokinesis is the division of cytosol

Go vs. G1 vs. Terminally Differentiated

• Go cells are still capable of entering the cell cycle
• G1 cells are heading towards division
• Terminally Differentiated cells are never capable of cell division

Cdks and Cyclins

• Kinases phosphorylate using Cyclin-dependent kinases, which are Cdks
• Cyclins are proteins without enzymatic functions that bind and activate Cdks
• Concentrations vary and are needed by Cdks
• Together they create cyclin-dependent protein kinases
• Phosphatases dephosphorylate

Cyclin-Cdk Complexes Regulated by Phosphorylation

• Inhibitory kinase (Weel) places inhibitory phosphates on an M-Cdk
• Activating phosphatase (Cdc25) dephosphorylates activated M-Cdk

Regulation of Cyclin Concentrations

• Synthesis is a Gradual increase via transcriptional regulation
• Degradation is a Rapid increase via Ubiquitylation and proteasomal degradation
• An active cyclin-Cdk complex is degraded by the APC/C complex

S Phase Initiation

• G1 phase occurs
• Cdc6 dissociates from the Origin recognition complex when DNA helicase binds
• S phase occurs
• S-Cdk activates the DNA helicase, and the replication machine is recruited
• Each component is phosphorylated exactly once, so only one round of DNA replication takes place
• Completion of DNA replication occurs

Types of Microtubules

• Astral Microtubules bind the spindle for cortex and anchor it to the spindle
• Kinetochore Microtubules bind to kinetochores
• Non-kinetochore microtubules (interpolar) make up most of the spindle, interconnect with motor proteins, and project towards each other to form gel-like substance

Interphase

• Chromosome condensation occurs
• Mitotic Spindle Assembly occurs with the duplicated centrosome
• M-Cdk is activated, so entry into M phase can occur

Prophase

• Has Mitotic spindle forming, moving it towards opposite poles
• A nuclear envelope exists
• Kinetochores bound to chromosomes, so chromosomes are visibly separated
• There are lots of condensins when the chromosomes are duplicated

Prometaphase

• Fragmentation of nuclear envelope (phosphorylation) occurs
• Chromosome motion is caused by polymerization and depolymerization of microtubules
• Kinetochore microtubules exist
• Adds to the end of the microtubule and binds to the chromosome

Metaphase

• All chromosomes are arranged at the equator of the spindle (metaphase plate)
• Kinetochores of all chromosomes are aligned in a plane midway between the two spindle poles, which causes the M checkpoint and leads to stop signals being sent by the kinetochores

Anaphase

• Cohesion rings break apart, and sister chromatids are pulled towards opposite ends
• Structures are kept under tension
• Anaphase A chromosomes pulled polewards by kinetochore microtubules
• Anaphase B poles pushed/pulled apart by non-kinetochore microtubules

Telophase

• Final phase of mitosis
• A set of chromosomes occurs at each spindle pole
• A contractile ring is visible
• A nuclear envelope reassembles around the chromosomes
• Cdks get phosphorylated, which causes the nuclear envelope to collapse

Cytokinesis

• A completed nuclear envelope surrounds decondensing chromosomes
• A contractile ring creates a cleavage furrow
• Created by actin
• Re-formation of interphase array of microtubules nucleated by the centrosome
• Non-kinetochore microtubules remain inside signal where the contractile ring should start forming (contractile cortex)

Apoptosis vs. Necrosis

• Apoptosis is Programmed Cell Death that causes inflammation
• It causes membrane blebbing
• The cell breaks apart into several apoptotic bodies, which are then phagocytosed
• There is no inflammation
• Necrosis is Uncontrolled Cell Death
• It causes cell swelling and plasma membrane rupture, causing cellular and nuclear lysis

Apoptotic Stimulus

• Apoptotic stimulus that activates adaptor proteins and therefore activates initiator caspase
• Active initiator caspase activates executioner caspase
• Executioner caspase causes cleavage of multiple substrates, leading to apoptosis

Bcl2 Family

• Bcl2 Family of proteins regulate apoptosis
• Bax and Bak promote apoptosis
• Activate cytochrome c, which activates adaptor protein
• Bcl2 inhibits apoptosis, inhibiting Bax and Bak

Survival Factors

• Survival factor activates the receptor
• Signals from receptor activate transcription regulator
• Transcription regulator activates Bcl2 gene, which transcribes RNA that translates to Bcl2 gene
• Bcl2 gene blocks apoptosis, inhibiting Bak and Bax

Junction to Junction Connections

• Tight junctions seal neighboring cells together in an epithelial sheet to prevent leakage of extracellular molecules between them and helps polarize cells
• Adherens junctions join an actin bundle in one cell to a similar bundle in a neighboring cell
• Desmosomes join the intermediate filaments in one cell to those in a neighbor
• Gap junctions form channels that allow small, intracellular, water-soluble molecules, including inorganic ions and metabolites, to pass from the cell to cell
• Hemidesmosomes anchor intermediate filaments in a cell to the basal lamina

Paths to Oncogenic Mutations

• Mutation in the coding sequence leads to a hyperactive protein made in normal amounts that is too active and causes a tumor
• Gene Amplification leads to a normal protein overproduced
• There ate Multiple copies and too many proteins are created because of over-replication of the cell which causes a tumor
• Chromosome Rearrangement leads to a nearby regulatory DNA sequence causing normal protein to be overproduced
• Fusion to actively transcribed gene produces hyperactive fusion protein