Sunday, November 23, 2014

2.B.1-2.B.3: Cell Membranes and How They Work

AP Biology: 2.B.1 – 2.B.3 Cell Membranes

All cells have a cell membrane. These membranes are all semipermeable, which means only certain particles can pass through. A cell needs to be able to move things in and out of the membrane so that it can survive, as all living things need energy and nutrients. They serve the purpose of separating the inside of the cell from the outside as well.

These cell membranes are made of two layers of what is known as a phospholipid. These phospholipids are amphipathic because they contain a hydrophilic head, which likes water due to its polarity, and a fatty acid “tail” that’s nonpolar and detests water. The heads line both the outer facing part of the membrane and the inner facing membrane, with the tails facing one another.


Phospholipids also move around. Once a month the outer phospholipids switch places with the inner facing ones and are almost constantly moving around with other phospholipids around them laterally.

In order to move larger and polar substances into and out of the cell, protein channels are needed.

There are three types of protein channels: Integral membrane, trans-membrane and peripheral proteins.

Integral membrane proteins are proteins that are only in one half of the phospholipid bilayer.

Trans-membrane proteins go all the way through and are key to the transport of large substances from one side to the other. A good example of this is the sodium potassium pump.

Peripheral proteins are bound to the surface of the bilayer.

Membrane proteins, oddly enough, have hydrophilic and hydrophobic like phospholipids. Likely to stay in the membrane and perform their tasks to the best of their abilities. They function to transport things, produce and contain enzymatic activity, signal transduction, cell-to-cell identification, intercellular joining and forming attachments to the cytoskeleton & cellular matrix.

In addition to proteins, there are also other things attached to the phospholipid bilayer, such as membrane carbohydrates, glycolipids (which send and receive signals from other cells) and glycoproteins (also are important with interacting with other cells. They are very diverse).

Cholesterol, contrary to “common belief” are absolutely necessary to the functioning of cells (and bodily processes). These special molecules are integrated in the membrane and prevent it from becoming overly fluid or overly firm.

Transport proteins, which are often trans-membrane, serve the purpose of transporting substances in and out of the cell. They have a hydrophilic channel that goes through it vertically and connects the extracellular fluid and the cytoplasm. Certain molecules like sugars can use this.


Although all cells have a plasma membrane, not all have what is known as a cell wall. Only plants, fungi and bacteria have this rigid structure that in addition to providing protection, prevents the cell from absorbing too much water and bursting. Cell walls are made up of a substance called cellulose. In fact, one of a few ways scientists have discovered how to kill harmful bacteria is by destroying the cell.


Prokaryotes have a cell wall made up of a substance called peptidoglycan and fungi have cell walls made of chitin, which is also the substance that makes the exoskeleton of arthropods.

Osmosis is the process of water moving across a semipermeable membrane. As water is a polar molecule, it can’t freely pass through the phospholipid bilayer without assistance. A special protein called an aquaporin forms a protein channel in the membrane that allows water to diffuse (move from a point of high concentration to low concentration) into and out of the cell.  This is an example of facilitated diffusion, which occurs when a protein is required to move a certain substance across a membrane.

When water inside a cell has a higher concentration of water inside it than outside, the cell is hypotonic. When that scenario is reversed, then it is hypertonic. When dynamic equilibrium is achieved and the concentration inside and out is equal to the point of there being no significant travel inside or outside by water, both the internal and external cell are isotonic. 


There are two ways molecules move: through passive transport which requires no energy and active transport, which requires energy (ATP) to move molecules from areas of low concentration to high concentration. It is used whenever molecules need to be transported against their concentration gradient.

Sometimes groups of ions move through the plasma membrane through endocytosis and exocytosis in what is called bulk transport. In exocytosis it is often seen in organelles called vesicles that fuse with the lipid bilayer to remove wastes from the cell. Phagocytosis is when the vesicles take in large substances from outside the cell. Pinocytosis is when water and dissolved particles are taken in.


Like earlier stated, water prefers to move from areas of higher water potential to low lower water potential. Water potential is defined by the sum of the solute concentration and water pressure.


To understand this equation, one must first know the basics:
Yp = the pressure on the water. In an open container, it is 0. In a turgid plant cell, it is greater than zero.

Ys = - iCRT
i = ionization constant (for sucrose this is 1.0, for NaCl this is 2.0)
C = molar concentration
        Molarity: Moles Solute/Volume of Solution. M = Moles/L
R = pressure constant (R = .0832 liter bars/mole K)
T = temperature in Kelvin (273 + degrees Celsius)
Also, in order for eukaryotic cells to function at best despite their large sizes, they have evolved to contain many internal membranes (called organelles) that carry out specific cell processes. They compartmentalize to efficiently carry out cellular processes that need different environments to work. The digestion that occurs in lysosomes requires an acidic environment, for example.

Internal membranes also increase the surface area, which allows more reactions to occur because there are more membrane bound organelles. The larger the surface area to volume ratio a cell has, the easier it is to transport things in and out, and to the organelles inside.

There are several membrane-bound organelles:

The Rough Endoplasmic Reticulum modifies secretory proteins that are then synthesized by ribosomes and moved to the lumen of the Rough E.R.

The smooth endoplasmic reticulum synthesizes lipids, phospholipids and steroids in addition to carrying out cell metabolism and detoxifying drugs like alcohol.

The Golgi Apparatus, which is known as the post office of the cell, packages and sorts proteins for secretion. These packaged proteins are then sent to the cisface and are modified as they move through the organelle’s cisternae (the inside of the Golgi’s main body). They are then sent in vesicles to the cell’s membrane.

The nuclear membrane is a bilayer with the same lumen as the E.R. It has many ribosomes imbedded into it and houses the nucleus, nucleolus and DNA of the cell.

The vacuoles in plant cells contain large amounts of water in addition to storing things. The vacuoles of animal cells contain food particles and can merge with lysosomes to digest it.

In Bacteria and Archaea lack inner membranes because they’re usually too small for that, but their cell processes and enzymes are confined to different parts of the cell.










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Monday, November 10, 2014

The Utilization of Free Energy in Biological Sysytems

2.A.1- 2.A.3

All living systems require a constant input of free energy as well as matter to grow, reproduce and maintain order.

The concept of thermodynamics that represents the amount of free energy available is Delta G.

Thermodynamics is the law that says energy is transferred from the sun to something that converts it into energy available to be transferred to more energy users.

The First Law of Thermodynamics states that energy can neither be created nor destroyed, but it can be transferred and transformed.

 The Second Law of Thermodynamics states that spontaneous changes that do not require outside energy increase the entropy, or disorder, of the universe. This law is represented by Delta S. Living organisms can not violate this law, as entropy always increases over time.

Biological processes or entropy increase order. An example is photosynthesis.

Metabolism is the totality of the organisms’ chemical reactions (cellular respiration, photosynthesis etc.)

A metabolic pathway is started by a specific molecule, each step thereafter being catalyzed by a specific enzyme.

Catabolic pathways break down complex molecules into simpler compounds (polysaccharide, for example, into a monosaccharide). They are spontaneous and release energy. Delta G < 0 represents catabolic reactions, which are exergonic.

Anabolic pathways are the opposite of catabolic in which they build more complex compounds from simple ones and energy. There are endergonic, and therefore NOT spontaneous. This type of reaction is represented by Delta G > 0.

As order is maintained by a constant supply of free energy, when that energy supply is cut off, the organism dies, as it can no longer maintain cell processes that keep it “alive.”

The energy that an organism takes in must also exceed what is let out, as energy is lost as heat in cellular processes such as metabolism, any movement and homeostasis (which is the maintaining of inner and external boundaries.) But when an organism obtains excess free energy then it is either stored s far or used in growth. Insufficient energy causes the loss of mass and if prolonged, the death of the organism. Endergonic and exergonic reactions must go hand-in-hand to maintain entropy, which keeps organism alive.





The chloroplasts absorb most light waves, reflecting primarily green light waves, making the photosynthetic areas of autotrophs appear to be what we perceive as “green,” depending on the kind of chlorophyll contained within the leaf.

Photosynthesis is the process that occurs in the chloroplasts of a plant. It uses sunlight, water (6H2O) and carbon dioxide (CO2) to make glucose (C6H12O6) and oxygen (6O2). It is a two-step process of the Light Reaction and then the Calvin Cycle.




In the light reaction phase, light enters the chloroplast and travels to the thylakoid where it hits Photoreceptor II, exciting electrons within it that are then sent along the Electron Transport Chain. Water is split up into hydrogen and oxygen ions (a by-product that leaves the cell) by the moving electrons. The H+ ions go into the thylakoid’s lumen.. As more water is split, the accumulated H+ protons form a proton gradient. New electrons then replace electrons lost to the electron transport chain.


The protons diffuse through ATP synthase, which uses the energy of the proton gradient to phosphorylate ADP back into ATP.  This is known as photophosphorylation.

Another photon of light hits Photoreceptor I, exciting another electron. This electron reduces NADP+ to form NADPH, which is the final electron receptor in photosynthesis, where it leaves the thylakoid membrane.

The second step of photosynthesis is known as the Calvin cycle, which occurs in the stroma of the chloroplast. This cycle uses the energy produces in the Light Reaction to power the synthesis of carbohydrates. Rubisco is the prime enzyme for this process. It takes carbon dioxide out of the air and combines it with the products of the light process, making it useable to organisms. In order to work, it must go through the Calvin cycle twice. This step is called carbon fixation and creates CH2O.





All organisms stay alive by metabolizing energy through cellular respiration. Photoautotrophs consist of plants, algae, bacteria and some protist & prokaryotes, break down and use the energy/glucose they create through a process called photosynthesis. 
Heterotrophs metabolize the energy they take from plants and other heterotrophs through cellular respiration.



Photoautotrophs are the only organisms that capture, use and store free energy from the sun.

Other, non photosynthetic autotrophs use chemosynthesis to capture free energy from their environment.



Cellular respiration is how organisms use the free energy available in glucose to phosphorylate and create ATP. It is a catabolic reaction pathway that yields energy by oxidizing organic fuels. Exergonic reactions break down the sugars and release energy needed for cellular respiration.

Cellular respiration has several steps. The first step is Glycolysis, which occurs in the cytoplasm of the cell, outside the mitochondria. Glycolysis breaks down glucose to create 2 pyruvate molecules. It is an anabolic process that does not require oxygen.

Then is the transition reaction where the pyruvate enters the mitochondrion where it releases CO2, picks up Coenzyme A and turns into AcetylcoA.



The next step is known as the Kreb's cycle. The Kreb's cycle occurs in the inner matrix of the Mitochondria. It turns AcetylcoA into 2CO2 + 6NADPH + 2FADH2 + 4 CO2

After the Kreb's cycle is the Electron Transport Chain. It occurs in the inner cell membrane of mitochondria. In order to convert the stuff right, it must go through it twice. 

Then the remaining products go through Oxidative phosphorylation and through that energy and CO2 are released. 

Environmental changes cause cells to develop in certain ways to survive. 

Nutrient cycling is the cycling of matter through reservoirs. There are several cycles: The Carbon cycle, the nitrogen cycle, the water cycle and the phosphorous cycle. 


In order for an ecosystem to survive, nutrients have to circle through it in just the right proportions, or else the ecosystem will die. 

Sometimes a cell must increase its volume to surface area ratio. A larger surface area allows the cell to absorb more nutrients and also expel them.



<Citations>
http://upload.wikimedia.org/wikipedia/commons/thumb/1/11/Chloroplast-new.jpg/400px-Chloroplast-new.jpghttp://upload.wikimedia.org/wikipedia/commons/1/18/Thylakoid_membrane.png 
http://s3.amazonaws.com/rapgenius/1376071616_photosynthesis-overview.gif 
http://longpointbiosphere.com/Publications/Grasses/Pics/figure2.1pg11.jpg
http://berryberryeasy.com/wp-content/uploads/2011/06/Photoautotrophs.jpg
http://www.phschool.com/science/biology_place/biocoach/images/cellresp/Overview.gif
http://www.dvice.com/sites/dvice/files/styles/blog_post_media/public/krebs1.png?itok=Uy1_lCGZ
http://www.mhhe.com/biosci/esp/2001_gbio/folder_structure/ce/m2/s1/assets/images/cem2s1_1.jpg