BIOB10 - Second Half

Lipid structure

Polar head group, non-polar hydrocarbon tail

Polar covalent bonds

Oxygen has a higher EN than hydrogen so oxygen pulls electrons towards it.

Self healing

(lipids provide ideal membrane structure) Small tear in plasma membrane will be okay because the phospholipids react with water and help membrane do sealing.

Fluidity

(lipids provide ideal membrane structure) Phospholipid molecules can easily switch within a monolayer (leaflet), not as easily with one across from it in the other layer of the bilayer. Flip flop, flexion, rotation, or later diffusion.

Flip flop

when lipid molecules move across bilayer to other side, more rare.

Flexion

A lipid molecule’s tails switch position

Rotation

The whole lipid molecule spins around in bilayer

Lateral diffusion

A lipid molecule moves between the other molecules and proteins on same layer.

Cholesterol

Modulates bilayer. Steroid rings interact with hydrocarbon chain. Decreases mobility and permeability.

Transmembrane proteins

Stuck in membrane proteins. Single pass, multi pass, barrel pore.

Peripheral protein

Aren’t physically stuck in the membrane, but are associated with transmembrane proteins.

Multi-pass transmembrane proteins

They may originally be separated but to make and specialize into a specific transmembrane protein they will move their passes laterally to get together.

Protein-free lipid bilayer

Hydrophobic right through

Small uncharge polar partially through

Large uncharge polar barely through

Ion cannot get through

Transporter

Transfer solutes across membrane, May have solute-binding site to undergo shape change (makes it accessible). Can be active or passive.

Ion-coupled transport

Also called secondary active transport. Coupling movement uphill with downhill movement to drive the uphill movement.

Uniporter

When one thing goes across a transporter (as opposed to coupled transporter)

Symporters

(ion-couple transporter) Both move in same direction but their gradients are in opposite direction so one is going uphill and one is going downhill.

Antiporters

(ion-couple transporter) Moving in opposite directions and their gradients are in same direction so one is going uphill and one is going downhill.

ATP-driven transport

Also called primary active transport. ATP is hydrolyzed to bring something against the chemical gradient

P-type pump

(ATP-driven transport) hydrolyzes ATP, pumps ions across.

ABC transport

(ATP-driven transport) Hydrolyzes ATP and pumps small molecules across.

V-type pump

(ATP-driven transport) Hydrolyzes ATP and pumps protons into organelles like lysosomes that need high acidity.

F-type ATP synthase

(ATP-driven transport) Works in reverse, uses proton gradient to drive ATP synthesis

Channels

When open, lets continuous flow through, passive transport. Forms pores across membranes.

Ion channels

Gated and when open, completely open. Selectivity filters to allow ions with intimate sizes to pass through. Shed water molecule to pass.

Voltage-gated channel

Depends on voltage and charge distribution in order to open

Ligand-gated channel

(intracellular or extracellular) Ligand changes shape to open up the gate. Binding causes gated channel to open and allow passing through.

Mechanically gated channels

Mechanical disruption or mechanical triggering allows it to stay open or closed (like a neuron reacting to a bump)

Potassium leak channels

Permeable mainly to K+, allows potassium to flow along potassium gradient. Helps maintain the membrane potential across the membrane.

Passive transport

The difference in the concentration on the two sides on the two sides of the membrane drives the transport and determines its directions. Channel or transport mediated.

Simple diffusion

Goes right through plasma membrane, most likely a hydrophobic molecule. Diffuses down concentration gradient.

Electric gradient

(membrane potential) A difference in charge across a membrane. It has an active potential because inside is negative and positive on outside. Trying to balance by bringing in positively charged solutes inside or opposite.

Electrochemical gradient

Electric gradient and concentration gradient. Concentration with a membrane potential.

Cellular respiration

ATP is produced by energy converting organelles like mitochondria. Mainly oxidative phosphorylation (Cristae where ETC and ATP synthesis occurs)

Oxidative phosphorylation

Starts with fatty acids and pyruvate turns into Acetyl CoA by enzymes (in mitochondrial matrix via citric acid cycle). NADH+ is going to donate electrons to ETC. End with carbon dioxide and water molecules

Electron Transport Chain

Respiratory chain. Electrons passed to protein complexes, generate energy required to pump protons out. NADH passes its electron to first complex and is passed along this in cristae’s inner membrane.

ATP synthase

Protons pumped uphill via ETC, and so the protons move the this protein complex and generate power to synthesize ATP from ADP and Pi.

pH imbalance

High pH of around 8 in the matrix, and thus proteins move across matrix. Protons are kicked out, the protons are positively charged and they wanna balance it out. Electric charge difference.

Proton motive force

pH gradient + voltage gradient = electrochemical gradient =

Chloroplasts

Energy from sunlight is used to transfer protons against the electrochemical gradient. Similar to mitochondria by thylakoid membrane is the system for ATP production.

Phosphosynthetic electron transfer reactions/light reactions

Reaction centre 1 and 2.

A photo knocks an electron out of chlorphyll in first reaction centre into second reaction centre. Harnesses energy and creates NADPH.

H+ is pumped against gradient and will move back down to produce ATP. ATO and NADPH used by the next reactions.

Carbon fixation reactions/dark reactions

NADPH and ATP are fed into the cycle (calvin). Converts carbon dioxide into sugar, amino acids, or fatty acids. Indirect depends on sunlight. NADPH and ATP are converted into stuff that can be transported out and used to make food for the plant.

Cytoskeleton

System in the cell of filaments, that help with moving the cell. Actin filament border cells, microtubules are like a highway. Filament system is dynamic and adaptable.

Microtubules

Cell highway system. Extended cell periphery, quickly rearrange themselves to form mitotic spindles during cell division. Serves as tracks. Tubulin subunits (13 protofilaments/straight line of them = microtubules)

Alpha-tubulin

minus end, bottom end. Its GTP is not hydrolyzed.

Beta-tubulin

Plus end, top end is the plus end. Removal happens at the plus end. GTP is hydrolyzed, key to how microtubules function.

Critical concentration \[Cc\]

Kon = Koff

rate of addition = rate of removal of subunits.

TIP

T form is growing, D form is shrink → dynamic instability

Catastrophe: growth → shrinkage

Rescue: shrinkage → growth

Tubulin subunit

Once T form is added, D form is taken off by hydrolysis. Accumulation of T form is a GTP cap.

Dynamic instability

When they’re been hydrolyzed to D form, the GTP → GDP and subunits want to fall off. This is because they’re not as straight, curved so they come right off, when they’re coming off they’re depolymerizing. Confirmation changes so it struggles staying linear and straight.

Nucleation

gamma-tubulin is involved in this phase of microtubule growth. Happens from microtubule-organizing centre. Depends of gamma-tubulin small complex. 13 of them is gamma-TuSC. Gamma-tubulin is like the foundation for this step.

Centrosome

MTOC for animal cells. Centrioles are embedded inside. All are nucleating sites, plus end extending outward where all the action is happening.

Kinesins

It walks toward the plue end of the microtubules, coiled coil form.

Kinesin step

Step 1: ATP is hydrolyzed (lagging strand)

Step 2: Pi from step one leaves along with leading strand ADP. ATP binds to leading head. Neck linker changes confirmation to allow ADP bound head forward.

Step 3: New ADP bound head comes over. New leading strand with neck linker and lagging strand with ATP bound head.

Dyneins

Walks towards the minus end of microtubules. Golgi → ER.

Actin

Underlies plasma membrane, gives it strength and provides movement. Muscle contraction. The cytoskeleton is made up of the subunit G-*blank*. Put all together to get coiled coil structure with ATP in middle and plus and minus end. F-*blank* is the group of the subunits.

Treadmilling

Actin process. You have a lot of addition happening at plus end and subunit depolymerization at minus end. When the rate is equal, the length of actin is going to stay the same, but it is moving in that end. Addition is winning at one end so hydrolysis has to catch up at the other end.

Myosin

Motor proteins that work with actin, similar to a slide. Collectively a bunch of it is called the thick filament. ATP hydrolysis to do conformational change.

Sarcomere

Thick and thin filaments stacked. Contracting when thick moves out and thin moves in. Myosin heads to right move right. They receive messages arriving at plasma membrane thanks to T-tubules and sarcoplasmic reticulum.

Intermediate filaments

Provides strength and line the inner face of nuclear envelope. Protective cage. Allow the formation of tough appendages.

8 tetramers (32 monomers) make up structure. N-terminus and C-terminus. Plectin.

Plectin

A family of proteins that link the intermediate filaments to bind to other cytoskeletal components (microtubules are one).

Epithelial tissue

Cytoskeleton filaments in one cell are connected to those of another cell. Cell-cell junction, and all together forms this, which connects to the basal lamina.

Connective tissue

Cells aren’t right next to each other + extracellular matrix is exposed. Cells don’t perform usual governing, matrix is in charge of mechanical stresses. Cell-matrix junction.

Adherens junction

Connects actin filament bundle in one cell with next cell

Desmosome

Connects intermediate filaments in one cell with next cell

Actin-linked cell-matrix junction

Anchors actin filament in a cell to extracellular matrix

Hemidesmosome

Anchors intermediate filaments in a cell to extracellular matrix

Tight junction

Sealing gap between epithelial cells. Adherens junction and desmosome.

Transmembrane adhesion proteins

Proteins that allow for binding. Intracellular adaptor proteins mediate it.

Cadherin superfamily

Mediates cell to cell binding. Adherens junction and desmosomes.

Homophilic, N-terminal binding, EC domain binding, hinges need calcium to bind.

Integrin superfamily

Mediates cell to matrix binding. Actin-linked cell-matrix junction or hemidesmosomes.

Protein made in cell, EC proteins need to be let out.

Matrix receptors

Tie the matrix outside the cell its cytoskeleton inside it

Integrins

Principal receptor for cell-matrix interactions.

Has an alpha and beta end, heterophilic, can be inactive or active for binding, strong ligand bind, not directly bound to actin, for hemidesmosomes it binds to basal lamina.

Matrix components

Fibrous proteins, proteoglycans, glycoproteins, basal lamina

Collagen

Major protein in EC matrix, most abundant (25%) of mass of proteins in mammals, triple stranded alpha chains, skin and bones.

Type 1, 9, and 12.

Type 1 collagen

Fibrillar collagen → collagen fibrils → collagen fibers. + fibril forming collagen.

Fibrillar collagen made by cell and secreted into matrix. Helps resist tensile fore, different patterns based on where they are.

Collagen type 9/12

Fibril-associated collagens, help organize collagen fibrils, help by binding onto collagen 1, they will help with formation.

Elastin

Helps with elasticity, allows for temporary give

Elastic fiber

Random coil conformation, they’re still connected, this conformation allows it to do what it does. Cross links.

Proteoglycans

Perlecan

Glycoproteins

Nidogen, lamina

Basal lamina

Helps connect epithelium and connective tissues. Each cell on either side gives structure to it.

Major components: laminin, and type 4 collagen.

Laminin

Made up of three chains, hetero-trimer. Has areas devoted to interacting with different areas.

Type 4 collagen

Heterotrimer, makes up basal lamina, parallel to plasma membrane.

Isolating cells

Disrupt extracellular matrix- and cell-cell junctions that hold the cells. Mess with the calcium binding agents in cadherins so they unbind.

Purifying proteins

To isolate a protein. Subcellular fractionation, chromatography, epitope tagging, SDS-PGE, Purified Cell-Free System.

Subcellular fractionation

Ultracentrifuge and velocity sedimentation.

Spinning at high speeds + sucrose solution to separate parts of the cell.

Chromatography

A mixture of proteins in a solution is passed through a column containing porous solid matrix

Charge, hydrophobia, size, affinity for molecules

Tandem affinity purification

Purification using affinity column 1 (cleave), protease, purification using affinity column 2 (cleave)

Epitope tagging

Altering Gene A by adding a tag to find corresponding protein. Using chromatography to narrow it down.

Purified cell-free system

Isolating the process to discover what is important and applying it to the bigger picture.

SDS polyacrylamide-gel electrophoresis

Step 1: Proteins given negative charge (SDS)

Step 2: An electric field is applied

Small proteins will move faster

Chemical inhibitors

Stopping one process in order to see if it is necessary in a process. Cochicine inhibits microtubules.