Energy

Catabolism: break a substance down, producing energy Anabolism: build a substance up, consuming energy

Adenosine triphosphate

Energy - ability to do work implies potential?

Thermal energy is kinetic energy -- energy from movement What does this mean?

Cells

Parts:

Since the phospholipid bilayer in the cellular membrane is polar, this allows non-polar molecules to pass through (like lipids), but prevents polar molecules from flowing through (like water). Other molecules in the membrane, like proteins, are need to get polar molecules through the membrane.

The endoplasmic reticulum is attached to the nucleus and has ribosomes attached to its surface. DNA is transcribed into mRNA which is carried to ribosomes on the endoplasmic reticulum, where protein gets created.

Proteins detach from the endoplasmic reticulum in vesicles, which are pieces or bulbs of the endoplasmic reticulum that detach and float away. These bulbs are called vesicles

These vesicles can then attach to the the golgi apparatus. The golgi apparatus secretes proteins in vesicles to be used by other parts of the cell.

Rough endoplasmic reticulums are so-called because they have ribosome bumps attached to them.

The golgi apparatus does some kind of sorting and tagging or labeling of vesicles to say where they need to go in the cell.

The lysosome is an organelle that digests substances. For example, a pathogen may enter one side when the membrane "invaginates" (folds inward) and surrounds the pathogen in a coating. This coated pathogen is called a phagosome

Plants do not have lysosomes, and instead have vacuoles. It has similar functionality to lysosomes and have extra storage capabilities.

Peroxisomes also have metabolic function, breaking down fatty and amino acids. It is so-called because it produces hydrogen peroxide (H2O2) as a metabolic by-product. It can also be detoxifying

Mitochondria are ATP factories and are descended from independent, bacteria-like organisms. Mitochondria have two membrane layers -- both are phospholipid bi-layers. The inner-most area is called the "matrix".

Mitochondria have their own DNA! They are in the "matrix" in loops, similar to prokaryotes. Your mitochondrial DNA comes originall from the egg cell at your conception, so it is inherited only from your mother.

There is a supportive structure outside and between cells called the extracellular matrix. In animals, this is primarily made of collagen.

Integrin anchor the cell to the extracellular matrix

Plants have no collagen, and instead have cell walls made of cellulose

Chloroplasts are the energy factories for plants, instead of mitochondria. They capture light energy to make sugars.

Eukaryotic cells have a cytoskeleton with three types of protien fibers: microfilaments can "pinch off" a cell when forming new cells can assemble and dissassemble quickly and aids cell movement vesicles and organelles can "walk" across these intermediate filaments second thickest filament often made of keratin (hair, nails, skin) more permanent and structural microtubules largest diameter * during cell division, they assemble into a "spindle", pulling chromosomes apart

The extracellular matrix has components that inform cells when to grow and divide or even to produce other molecules.

ATP

ATP converts to ADP

ATPase catalyzes the reaction to convert ATP to ADP

ATP + H2O <-> ADP + P_i + energy

This is a reaction catalyzed by water -- aka hydrolysis

Endergonic -- a reaction that requires and absorbs energy Exergonic -- a reaction that releases energy

Enzymes

Enzymes are biological catalysts.

They often need cofactors, which are other connected molecules required for a reaction to occur.

An example cofactor is the magnesium ion, which is requires by the enzyme that builds DNA. Often these cofactors are inorganic, such as iron or magnesium. Coenzymes are organic cofactors, such as vitamins (eg. vitamin C)

Substrates are the molecules that enzymes are catalyzing a reaction for.

If two substrates are simultaneously "trying" to bind with an enzyme, then one will "block" the other, either spatially, because they both want to bind at the same site and one has arrived first, or chemically, where they are binding at different sites but both cannot react at once.

An allosteric site is any point on the enzyme where a substrate has been bound, but there is already another substrate bound to the enzyme.

In competitive inhibition, one substrate binds to the enzyme first and catalyzes, while the other is blocked. In non-competitive inhibition, then both bind, but both chemically block each other, so neither get to catalyze at all.

When the substrate concentration (in a cell?) is low, then reaction time for enzymes is slow. As the substrates get more dense, the reactions gets faster, almost exponentially. Reactions will slow down less for non-competitive inhibitors because (TODO why?)

The drug tipranivir is an HIV treatment. It is an enzyme inhibitor, meaning it blocks binding sites and blocks the enzyme from catalyzing. In this case, the enzyme helps the HIV virus.

Feedback inhibition is when a metabolic product rebinds to the same enzyme to block other products of the same type from getting produced. This is a way to regulate production of that product over time, when you don't want to over-produce it. So clever.

For example, ATP inhibits more ATP from being made. When there is ADP instead, then it acts as an activator to make more ATP.

Cellular membranes and transport

Transporting substances into and out of the cell is an essential mechanism of the system.

The simplest and lowest-energy transport is when you have molecules that are able to pass through the membrane, because they are uncharged and very small (eg oxygen or carbon dioxide). They are small enough to sneak through the biphosphate layer. They don't get stuck on charged phosphate heads in the membrane, as they have neutral charge.

This type of transport is simple diffusion, where molecules naturally spread their concentration to equilibrium.

Molecules that are charged need channels to pass through the membrane because the hydrophobic tails of the membrane block them. Channel proteins provide a hydrophilic passage for specific molecules to be able to diffuse through the cell. They have the ability to open or close based on cell signals of some sort.

Carrier proteins are another way to facilitate diffusion through the membrane -- they have a different, slower mechanism that acts like a gate.

Sometimes molecules need to move against their concentration gradient. In this case, we use active transport mechanisms that require ATP energy from the cell (this is the primary usage for cell energy).

TODO how exactly does ATP allow molecules to move against their concentration gradient? ATP breaks down into ADP, releasing heat, or that heat is used up in another reaction, somehow connected to the transport mechanism.

Primary active transport requires ATP, while secondary active transport uses a different energy pathway (see below).

The sodium-potassium pump moves Na+ into cells and K+ out of cells, and requires ATP. The pump can open either inwardly or outwardly. When it opens inwardly, it sucks up Na+. Then, ATP binds and somehow causes the pump to open outwardly and release the Na+, while sucking up K+

Bulk transport

Absorption of large resources by enclosing them in a membrane/vesicle

endocytosis -- moving resources into a cell phagocytosis -- a form of endocytosis where a large particles are absorbed -- eg white blood cells absorbing pathogens pinocytosis -- a much smaller absorption, where only smaller bits are taken in. An example is egg cells taking in nutrients from the outside fluid.

Phagocytosis is how eukaryotic amoebas "eat" other cells.

The lysosome will process and break down an eaten cell inside a vesicle during phagocytosis

Exocytosis Send multiple resources out of the cell

A macrophage white blood cell will consume pathogens, re-using some of their parts as resources. They will also "display" parts of the pathogen on the macrophage's outer body, serving as a warning signal to other cells. Wow.

Exocytosis could be done for signaling, releasing waste,

Cellular respiration

Converting Glucose and Oxygen into Carbon Dioxide, Water, some heat, and 38 ATPs (ideally, often less).

C6H1206 + 6O2 -> 6CO2 + 6H20 + energy (heat + 38ATP)

Glycolysis breaks up glucose by breaking the carbon chain into two carbon chains. - Requires 2 ATPs - Generates 4 ATPs - Net is 2 ATPs - Does not need oxygen - anaerobic

Kreb's cycle happens after glycolysis and generates another 2xATP - aerobic - requires oxygen - produces 2 ATPs

The electron transport chain produces 34 ATPs -- aerobic

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