CELLS

Prof. Atsma © 2005

The following is a narrative summary of the topic. Click here for the Cells Part 1 "Classroom Notes" that you can print out and bring to class to save yourself a lot of note-taking. Click here for the Cells Part 2 "Classroom Notes." Click here for the Cells Part 3 "Classroom Notes."

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The basic units of life, separating disordered, random chemistry from the ordered biochemistry of living things, are the cells. Although many primitive cells such as bacteria do not have a large central nucleus, all cells have a plasma membrane to encase their special biochemistry. Within the plasma membrane are various cytoplasmic organelles responsible for particular life functions. The basic study of cells involves the study of each organelle and its functions.

THE PLASMA MEMBRANE

Although many scientists do not consider it an "organelle" the plasma membrane is the most essential component of a cell, as it separates the ordered chemistry that is life itself from the random "nonliving" chemistry outside. Its main component is a molecule called a phospholipid.

As you review your basic chemistry, you will see that phospholipids are similar to triglycerides, with a phosphate group attached to one of the carbons at the glycerol end. Why is this molecule so special? The fatty acid tails are non-polar, hydrophobic molecules that attempt to "hide" from water, while the glycerol/phosphate head is polar or hydrophilic. Thus, this molecule normally orients itself with the head facing water and its two fatty acid tails attempting to turn away from water. This tendency alone might not make for a good membrane for a cell, but membranes use a double layer of phospholipids, set up as mirror images. As you look at the figure below, you can appreciate how effective this strategy is. The water inside and outside the cell is facing a layer of phospholipid heads, while the intertwined fatty acid tails stick together in order to remain hidden from the water.

The Plasma Membrane - a phospholipid bilayer

Because most of the distance molecules would have to move across the membrane is Non-polar or hydrophobic, the plasma membrane's so-called phospholipid bilayer is a natural barrier to most molecules important to living things such as proteins, sugars, and sodium, potassium, calcium, and chloride ions. Thus, after a cell goes through the trouble of making a sugar or protein, it will not just dissolve out of the cell into the surrounding water and be lost.

Transport Proteins

For those situations where it is important to allow ions or other molecules to pass through the plasma membrane, transport proteins are used. These are three-dimensional proteins that either have channels which permit the desired ion or molecule to pass through, or have other modifications to allow it through.

The first and simplest variety of transport protein is called a channel protein. As the name implies, it simply creates a tunnel specific to the ion or molecule that it will let pass. Ions and smaller molecules often use channels.

Channel Protein

The other kind of transport protein is the carrier protein. The strategy here is the same as that of an "air lock" on a submarine. It simply has an opening on one side for the molecule to fit into, a "door-like" partition in the center to keep things from leaking out, and the ability to change shape when the molecule plugs in. Carrier proteins function by closing the "front door" behind the molecule once it plugs in, and then opening the center door to allow the molecule to pass through (like an air lock does with its two doors).

Carrier Transport Protein

When simply allowing molecules to pass from an area of high to low concentration (diffusion), the carrier molecule is said to be involved in passive transport. If the carrier has a site for ATP to bind so that it can force molecules against a concentration gradient, active transport is occurring (such carriers are nicknamed "pumps").

When substances are far too large to use channels or carriers, cells use processes involving invagination of the membrane or evagination of the membrane. Endocytosis is the process by which the membrane invaginates or puckers inward, and includes phagocytosis (large-scale "cell eating") and pinocytosis (smaller-scale "cell slurping"). When the cell expels a bubble of membrane, cellular products are released by exocytosis.

Membrane transport

Before discussing how molecules move through membranes, it is important to discuss why they move in the first place. Except for extremely low temperatures ("absolute zero" or -273o C), molecules absorb heat energy and translate it into energy of movement called kinetic energy. Since room temperature is blazing hot by comparison to absolute zero, the molecules we typically encounter are in rapid motion and constantly collide with each other and the walls of their container. This is true of gas molecules moving through air, solute (dissolved) molecules moving through water, and even limited movement of molecules trapped in the solid phase of matter.

DIFFUSION: Because of this random movement/collision, there is net movement of molecules (or atoms or ions) from an area of high concentration to low concentration. The reason behind this process, called diffusion, is a matter of simple common sense - molecules in an area of high concentration are likely to collide with each other and bounce outward. Once a collision bounces a molecule out toward an area of low concentration, there is nothing to stop it (until it reaches the wall of the container). This is why someone may open a bottle of perfume several feet away, and you can smell it within a few seconds. The molecules in the bottle collide with each other, and many bounce out of the bottle. Once out of the bottle, there is very little to stop them until they reach your nose. The size of the molecule is an important factor in the speed of diffusion as smaller molecules diffuse more rapidly than larger ones.

Semi-permeable membranes

Understanding diffusion, it is obvious that only the wall of a solid container stops most molecules once they bounce off toward the area of low concentration. But what if a porous wall or semi-permeable membrane were placed in the way of these molecules? Would they pass through or bounce off? Common sense suggests that passing through will depend entirely upon the size (which is proportional to the weight) of the molecule vs. the size of the pores in the membrane. If you have made spaghetti, you understand this principle. Water passes through the holes in the strainer/colander, but the larger spaghetti is trapped on one side. There are several concepts involving the way in which molecules may (or may not) move through a membrane. Since the human body and its cells are mostly water, this movement typically involves solutes dissolved in water.

DIALYSIS: Perhaps easiest to understand of all of these concepts, dialysis is simply the movement of some solute molecules across a semi-permeable membrane while larger ones may be trapped on one side. Always remember that it is concentration that drives dialysis as the molecules are simply diffusing across a membrane from an area of high to low concentration. The reason behind why there is net movement from the high to the low concentration side of the membrane is also common sense - more molecules equals more random collisions with the membrane, and more chances to push through.

OSMOSIS : This is a tricky concept, since you must think backwards to imagine the way in which the presence of a solute might effect the movement of water across a semi-permeable membrane. Water molecules must obey the same physical laws governing diffusion as all other molecules, that is, they move from an area of high water molecule concentration to low water molecule concentration. Therefore, anything that effects the amount of (free) water molecules on one side of a membrane can cause movement of water. Although it is a concept, not a definition, osmosis can be summarized as the diffusion of water from an area of high free water molecules to an area of low free water molecules (keeping in mind that it is the solute that effects the number of free water molecules).

You may recall from earlier discussions that water is a polar molecule (has slight negative and positive charges), and that there is some attraction between opposite charges. Imagine adding a solute to one side of the membrane. Assume the solute molecules are too large to fit through the membrane, so they stay trapped on one side. Since any substance that is water soluble must either be an ion or polar molecule, charge attraction will cause the solute molecule or ion to stick to several water molecules at any given time. Since these "stuck" water molecules are not free to diffuse, the solute has effected the number of free water molecules. Thus, the side of the membrane with less solute has more free water molecules. A second reason why solutes reduce the number of water molecules free to diffuse is that solutes takes up some space, leaving less room for water molecules.

Understanding all of the above, it is clearly the amount of solute, referred to as the "tonicity" of a solution, that drives osmotic pressure. Hypertonic solutions have comparatively more solute (and therefore less free water), hypotonic solutions have less solute (and therefore more free water), and isotonic solutions have equal solute concentrations on either side of the membrane. Thus net diffusion of water (osmosis) is always from the hypotonic to the hypertonic side of the membrane.

FILTRATION: Filtration may seem just like dialysis at first, since it is movement of molecules across a membrane depending on molecular size. The critical difference is that it is hydrostatic pressure, not concentration or diffusion that provides the impetus for net movement. Thus, if the pressure is high enough, and enough time is given, all molecules small enough to fit through the membrane may pass, regardless of the concentration gradient.

THE CELL CYCLE AND MITOSIS

INTRODUCTION: The "traditional" way to present mitosis had been to refer to Interphase as the "resting" phase of the cell, and then to describe the stages of mitosis. This can be misleading since Interphase is a very active stage in which the cell is doing its job! It is more accurate to describe the life of a cell as cyclical - alternating between Interphase and the mitotic phase of its life.

INTERPHASE: As mentioned above, Interphase is not a resting phase, but one in which most cells are actively doing their jobs. Interphase is divided into three sections. The G1-phase follows mitosis and initially is a period of rapid growth. This phase is highly variable in length, lasting perhaps a day or two for growing tissues, or almost indefinitely for mature tissues. A "signal" of some kind triggers the S-phase where the cell begins preparing for cell division by duplicating ("Synthesizing") its DNA. The short S-phase is followed by the G2-phase in which the cell may continue to do its job while making final preparations for division.

PROPHASE: This is the stage where the cell largely shuts down operations related to its particular job and begins serious preparations for division. Most of these cellular changes are those important to the job of pulling one copy of the duplicated DNA toward opposite sides of the cell. The DNA (loosely coiled for storage as chromatin) coils up into chromosomes. In animal cells, structures called centrioles migrate to opposite sides ("poles") of the cell and seem to be the origination point for spindle fibers to radiate out toward the chromosomes.* The nuclear membrane disintegrates, as does the cytoskeleton (an internal network of protein fibers that gives a cell its shape). By late Prophase, the spindle fibers have attached to the central "organelle"* on the chromosome called the centromere. Shortening of these protein fibers pulls the chromosomes closer and closer to the center of the cell.

METAPHASE: The pulling of chromosomes by each part of the spindle apparatus eventually begins a "tug-of-war" with the duplicated chromosome stuck in the middle. Metaphase is the short phase in which the chromosomes are lined up along the "equator" of the cell.

ANAPHASE: Imagine a "tug-of-war" between two equally matched opponents. Tension would build until the rope broke. Similarly, the duplicated chromosome is split, and each half (a single chromosome) is yanked toward each pole. Anaphase describes this "reeling-in" of the split chromosomes.

TELOPHASE: Contrary to popular belief, it is incorrect to describe this phase as the stage in which the cell splits. Most cells do split during telophase, but that is a different process. Telophase is simply the reverse of Prophase. Recall that prophase is where the cell stops doing its job in order to get serious about dividing. Well, in order to go back to doing its job, it must undo everything that occurred in Prophase. The chromosomes must uncoil, the nuclear membrane must reform, etc.

CYTOKINESIS: The actual splitting of the cell (for most cells) begins during late Anaphase, and continues on through Telophase. A protein fiber laces through the cell membrane around the equator, and begins to tighten like the closing of draw-string purse. When pulled tight enough, this splits the cell in two.

*Note: some aspects of the cell cycle have been simplified due to the limited time available for coverage. For more information check your textbook for the exact make-up of the centrosome and centromere.

PROTEIN SYNTHESIS

There are two distinct parts to protein synthesis - Transcription (which takes place in the nucleus), and Translation (which takes place in the cytoplasm). Transcription involves copying the original code found on a DNA strand over to a strand of RNA. Translation is the actual manufacture of the protein using the RNA code. The steps of transcription and translation are outlined below.

Transcription

1. An unzipping enzyme breaks the hydrogen bonds between the two opposing strands of DNA. Other proteins may play some role in keeping the strands from reattaching until the next step.

2. RNA Polymerase attaches to this newly opened area. As it rolls along the strand of DNA, it fits in matching RNA nucleotides (including "uracil" instead of thymine).

3. As RNA Polymerase rolls onward, the slightly mismatched hydrogen bonds between DNA and RNA nucleotides automatically begin to separate. Almost as quickly as it is formed, the new RNA strand unzips from its DNA "template."

4. Three different forms of RNA are formed this way: mRNA (messenger) is the long, thread-like kind of RNA that actually carries the code for the protein to be made; rRNA (ribosomal) which merges with certain proteins to form the worksites for protein synthesis; tRNA (transfer) who brings amino acids to the right place at the right time.

5. These different forms of RNA leave the nucleus and enter the cytoplasm of the cell. The tRNA molecules bond to certain specific amino acids with the help of and enzyme and ATP.

Translation

1. Initiation: All three forms of RNA, including the large and small ribosomal subunits, come together at the start codon (sequence of three nucleotides on mRNA). Note that the there are two places in the ribosome for tRNA molecules to plug in (A-site & P-site). Initiation starts with a tRNA carrying the amino acid methionine plugging into the A-site.

2. Elongation: A second tRNA with an anticodon matching the codon in the P-site inserts. This tRNA is already bonded to its own particular amino acid. There are now two amino acids in close proximity to eachother, and within range of a ribosomal enzyme (peptidyl transferase).

The enzyme transfers the amino acid's covalent bond from the first tRNA to the amino acid in the P-site. Since the tRNA in the A-site no longer has an amino acid, it changes shape and pops out of the A-site.

3. Translocation: The A-site is not permitted to remain empty for any significant amount of time. The solution is simple - the ribosome pivots on its P-site so that the ribosome appears to have moved one codon down the mRNA strand. As long as there are more codons, this process can alternate between steps 2 & 3 many times.

4. Termination: When a codon is encountered in the P-site with not matching tRNA, the site stays empty long enough for a terminator protein to enter. When this occurs, the ribosomal enzyme is signaled to cut the amino acid string and terminate protein synthesis.

In case it is still not clear how this process directs the production of all of the tremendous varieties of proteins in cells, reference the table titled "The Genetic Code." It illustrates that each amino acid is carried only by tRNA molecules with certain anticodons. For example the amino acid tryptophan can only be carried by a tRNA that matches up with the codon UGG. The tRNA that fits into the codon GGU can only carry the amino acid glycine. This specificity ensures that a sequence of codons on mRNA can only translate into a very specific amino acid sequence in the finished protein.

Also note that there are specific start and termination codons used by mRNA to mark the beginning and end of protein synthesis.

A TOUR OF THE CELL

Membranous organelles, as the name implies, are cellular structures made of phospholipid bilayers. A summary appears below.

Nucleus - Usually spherical membrane shell that houses DNA and makes RNA for use in directing protein synthesis. By controlling what proteins are made, the nucleus controls most cellular functions.

Endoplasmic reticulum (ER) - "Maze-like" network of membrane often spanning out from the nucleus. The rough ER is dotted with ribosomes and is often an industrial complex for protein production. The smooth ER, a site where some of the proteins produced do their job, is where detoxification, materials processing and lipid synthesis occur.

Golgi apparatus (also Golgi complex/body) - Packaging and special processing of molecules (mainly proteins) for export out of the cell.

Mitochondria - Nicknamed "the powerhouse of the cell," they are membranous energy transducers that convert molecular energy from one molecule to another (usually from sugars, lipids, and amino acids to ATP).

Chloroplasts (in plant cells) - A collection of membranous structures that convert sunlight and low-energy molecules into carbohydrates.

Vacuole - Typically a large bubble of membrane used for storage inside a cell.

Vesicle - Small storage bubble of membrane.

Lysosome - Vesicle or small vacuole containing digestive enzymes.

The protein-based organelles are very different, but no less important in their support roles in the cell.

Cytoskeleton - Network of protein fibers and tubes that support and move the cell.

Flagella & cilia - contractile proteins important for moving the cell (i.e. sperm) or moving other substances in a multicellular organism (i.e. ciliated epithelium of the human respiratory tract).

Finally, there are miscellaneous organelles who's structure is less well defined, or otherwise do not fall into the preceding categories.

Ribosomes - Debated by some as to whether it is an organelle or a just a simple (even if elegant) mixture of rRNA and proteins; worksites for protein synthesis.

Centrosome - Area (containing the centrioles in animal cells) responsible for directing many aspects of cell division.

Nucleolus - Area within the nucleus most closely associated with RNA production.

Microvilli - Folds in the plasma membrane to increase surface area (for absorption, transport, etc.).

Cell wall - "Polysaccharide container" associated with plant cells (and fungi).

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