C. Proteins - (we will cover this in more detil during the lecture on protein synthesis)

        1. Structure:
                monomer - amino acid - amine (NH₂) group at one end and carboxyl group (COOH) at other
                        there are 20 different amino acids that are found in living systems.

                polymer - polypeptide - 100 to 300 amino acids long.  The AA's are linked by dehydration synthesis reactions into a long linear chain.  Because there are 20 Amino Acids ("letters") that can be used in their construction, proteins can have a limitless number of different combinations (like letters in different combinations make differnt "words").  This variety in form means variety in function.

**Higher levels of structure:

1. the primary structure of a polypeptide/protein is the linear sequence of amino acids

2. this linear sequence can take a helical or "pleated" sheet shape, depending on bond angles and soforth. These are secondary levels structure

3. some proteins then fold upon themselves, taking a globular shape. This globular shape is maintained by bonds between different functional groups of differnt amino acids. Enzymes and cell membrane proteins are common globular proteins.this is called tertiary structure.

4. Sometimes, single proteins are not functional on their own - they must be combined with other proteins to forma a protein with a quaternary structure. Hemoglobin, with 2 alpha and 2 beta globular polypeptides, is one example. collagen is another, composed of several helical polypeptides.

        2. Function:
                a. Energy Storage: (all biomolecules can be broken down for energy harvest.  Typically, since proteins are doing something else, too, they are broken down last so that the organism can maintain this function that the protein performs for as long as possible).
                b. Structural:
                        after water, animals are largely proteinaceous
                        collagen, elastin, muscle proteins, etc.
                c. Metabolic:
                        all biological reactions are catalyzed.  Most biological catalysts are proteinaceous ENZYMES
                d. transport:
                        cell membrane - there are proteins that assist transport across the membrane
                        organism - hemoglobin, for instance, transport oxygen
                e. Immunity:
                        antibodies are proteins.

D. Fats and Lipids:

        1. Structure:
            monomer - fatty acid - long carbon chain with a carboxyl group (COOH)
                 - can be saturated (with H - no double bonds between C's) or unsaturated (a double bond)

                 - animal fats are usually saturated, and are solid at room temp. Plant and fish fats are usually unsaturated, and are liquid at room temp and are called 'oils'. By saturating a plant fat, it can be made solid - hydrogenated fat or oil. (changing peanut oil into peanut butter, or vegetable oil into "crisco"). During this process, trans-fats are also created. These are unsaturated fats with a trans (not cis) conformation. Trans-fats have been associated with atherosclerosis
 
            polymer - fat (triglyceride)
                    - three fatty acids attached by dehydration synthesis to a glycerol molecule
 
                     - phospholipid:  glycerol with 2 fatty acids and a phosphate (PO₄) group.  The PO₄ is negatively charged (thus, polar), while the fatty acids are non-polar.  This accounts for how these molecules orient in aqueous solutions, forming membranes. A "choline" groups is typically attached to the phosphate.

        2. Function:
                a. Energy storage: saturated fats are very dense - the fatty acids fit together, in parallel, very snugly.  So, to store the most energy in the smallest space, fats are the preferred medium.

                b. Cell membranes - barrier to water soluble materials. The non-polar lipid "bilayer" is a barrier to water soluble materials (that are ionic or polar). So, ionic and polar compounds can't just flow into the cell; the cell can regulate how much of what gets in and out.

                c. Insulation
 
                d. Hormones - derived from fats, lipid soluble, slip right theough cell membranes into cells, so they can function at very low concentrations.

E. Nucleic Acids (DNA/RNA)

DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are nucleic acids - polymers consisting of a linear sequence of linked nucleotide monomers. We will describe the structure of the monomers first, and then describe how they are linked into linear polymers. Finally, we will describe the double-stranded structure of ds-DNA.

1. The monomers are "nucleotides"

three components:

- Pentose (5 carbon) sugar: either ribose (RNA) or deoxyribose (DNA). The carbons are numbered clockwise. The difference between the sugars is that ribose has an -OH group on the 2' carbon, whereas deoxyriboes has only 2 H groups and thus is "deoxygenated" relative to ribose. BOTH sugars have an -OH group on the 3' carbon, which will be involved in binding. The 5' carbon is a sidegroup off the ring.

- Nitrogenous Base: each nucleotide has a single nitrogenous base attached to the 1' carbon of the sugar. This nitrogenous base may be a double-ringed structure (purine) or a single ringed (pyrimidine) structure. The purines are adenine (A) and guanine (G). The pyrimidines are thymine (T), cytosine (C), and uracil (U). DNA nucleotides may carry A, G, C, or T. RNA nucleotides carry either A, G, C, or U.

- The third component of a nucleotide is a phosphate group, which is attached to the 5' carbon of the sugar. When a nucleotide is incorporated into a chain, it has a single phosphate group. However, nucleotides can occur that have two or three phosphate groups (dinucleotides and trinucleotides). ADP and ATP are important examples of these types of molecules. In fact, the precursors of incorporated nucleotides are trinucleotides. When two phosphates are cleaved, energy is released that can be used to add the remaining monophosphate nucleotide to the nucleic acid chain.

2. Polymerization is by 'dehydration synthesis'

As with all other classes of biologically important polymers, monomers are linked into polymers by dehydration synthesis. In nucleic acid formation, this involves binding the phosphate group of one nucleotide to the -OH group on the 3' carbon of the existing chain. For the purposes of seeing how this reaction works, we can envision an H+ on one of the negatively charged oxygens of the phosphate group. Then, a molceule of water can be removed from these two -OH groups, leaving an oxygen binding the sugar of one nucleotide to the phosphate of the next.

This creates a 'dinucleotide'. It has a polarity/directionality; it is different at its ends. At one end, the reactive group is the phosophate on the 5' carbon. This is called the 5' end of the chain. At the other end, the reactive group is the free -OH on the 3' carbon; this is the 3' end of the chain. So, a nucleic acid strand has a 5' - 3' polarity.

3. Most DNA exists as a 'double helix' (ds-DNA) containing two linear nucleic acid chains.

a. the nitrogenous bases on the two strands are 'complementary' to each other, and form weak hydrogen bonds between them. A always pairs with T, and C always pairs with G. As such, there is always a double-ringed purine pairing with a single-ringed pyrimidine, and the width of the double-helix is constant over its entire length.

b. the two strands (helices) are anti-parallel: they are arranged with opposite polarity. One strands points 5' - 3', while the other points 3' - 5'. The direction of the pentose sugars and the type of reactive group at the ends of the chains show this relationship.

4. RNA performs a wide variety of functions in living cells:

a. m-RNA (for "messenger") is the copy of a gene. It is the sequence of nitrogenous bases in m-RNA that is actually read by the ribosome to determine the structure of a protein.

b. r-RNA (for "ribosomal") is made the same way, as a copy of DNA. However, it is not carrying the recipe for a protein; rather, it is functional as RNA. It is placed IN the Ribosome, and it helps to ‘read’ the m-RNA.

c. t-RNA (for "transfer") is also made as a copy of DNA, but it is also functional as an RNA molecule. Its function is to bind to a specific amino acid and incorporate it into the amino acid sequence as instructed by the m-RNA and ribosome.

d. mi-RNA (micro-RNA) and si-RNA (small interfering RNA) bind to m-RNA and splice it; inhibiting the synthesis of its protein. This is a regulatory function.

e. sn-RNA (small nuclear RNA) are short sequences that process initial m-RNA products, and also regulate the production of r-RNA, maintain telomeres, and regulate the action of transcription factors. Regulatory functions.

Cell Biology

I. Overview

Cell biology is another great thread of biology. Evolution explains life's diversity, genetics and heredity explain how life reproduces itself, and cell biology explains the fundamental structure of living systems. The birth of cell biology can be traced to the observations of Robert Hooke in 1655, who observed thin sections of cork through a microscope. The box-like compartments reminded him of cells in a monastery, and he coined the term. Of course, he was not observing true living cells - only the cell walls in dead plant tissue. The first observation of live cells was made by Antony van Leeuwenhoek in 1674 who observed protists, algal cells, and bacteria. In 1838-9, Schleiden and Schwann independently proposed that all plants and animals (respectively) were composed of cells - the 'cell theory' of life. They also supported the notion that cells propogated 'spontaneously' like crystals; but this would premise would be rejected by Virchow who, in 1858, famously wrote "omnis cellula e cellula" - 'all cells from cells'. Several cellular structures were observed during this period, as well: Brown described the nucleus in 1833, Kolliker described mitochondria in 1857, and Flemming described the movement of chromosomes and the stages of mitosis in 1879. Robert Koch isolated the bacteria that caused anthrax (1876), TB (1882), and cholera (1883). Pasteur developed vaccines and treatments for killing bacteria and fungi with heat (pasteurization). The contributions of Koch and Pasteur firmly established the 'germ theory' of disease and finally laid the idea of spontaneous generation - even by microbes - to rest. Following Van Beneden's description of the movement of chromosomes during meiosis in 1883, August Weismann proposed that the 'germ cells' of egg and sperm, although produced by 'somatic' body cells, were separated from them and were uninfluenced by them (1893); eliminating the possibility of the inheritance of characteristics acquired by the body. After the 'rediscovery' of Mendel's work in 1900 by Tschermak, DeVries, and Correns, Walter Sutton (1902) unified heredity and cell biology by recognizing the correlation between the movement of chromosomes during meiosis and Mendel's principles of heredity. He proposed that chromosomes carry the hereditary material - the 'chromosomal theory of heredity'.

All living things are composed of cells, so understanding how a cell works is fundamental to understanding all living systems (reductionism, remember?). Before we examine the patterns of heredity and the structure and function of DNA (topics directly relevant to our discussion of evolution), we will quickly review the cellular context in which DNA functions. At the most simplistic level, cells must absorb matter/energy, convert this matter/energy into a useable form, and then use this energy and matter to make the things they need, respond to the environment, and reproduce. To understand the material that follows, you must know the basics of atom structure, types of chemical bonds, the structure and properties of water, and the basic structure of biologically important molecules. This is basic science stuff covered in every high school chemistry and biology class, so it is assume knowledge here. If you want an overview of what you are responsible for, see this link: review of atoms, bonds, and molecules.

A. Membrane Structure

All living cells are bounded by a membrane composed of a phosopholipid bilayer. Proteins are present on and within each layer, and some also cross all the way through the membrane.

1. Phospholipid Bilayer:
        - phospholipids have hydrophobic fatty acid tails and hydrophilic phosphate group "heads" (charged). In an aqueous solution, phospholipids will form micelles (single layer spheres) and bilayers (two layer spheres and films) as a function of the hydrophobic and hydrophilic nature of these molecules. These spatial orientations surround the hydrophobic fatty acid 'tails' with the hydrophilic phosphate 'heads' that interact with the polar water molecules in the solution. When arranged as a bilayer, they separate the internal aqueous solution of the cell from the external aqueous environment. Because the principle boundary is the hydrophobic, non-polar layers of fatty acids, the bilayer is permeable to lipid-soluble materials but not water soluble (polar and ionic) materials unless they are very small. These bilayers are also very dynamic or "fluid"... the phospholipids are moving laterally all the time, like the lipids in a soap bubble.
2. Proteins arepresent on both inner and outer surfaces, and also extending through the lipid bilayer.
3. Carbohydrates on the surface; usually attached to proteins and forming a "glycoprotein"

2. Transport: matter does cross the membrane. However, unless it is a small or non-polar molecule, it cannot cross the lipid bilayer "on its own". Rather, crossing the membrane must be assisted by a protein. These proteins may be rather unselective "tubes", or they may be specific for the transport of a particular class of molecules. By using proteins as 'gates' the cell gains control over the composition of its cytoplasm. There are three ways that material can cross a membrane:

a. Diffusion: As a consequence of the random movement of molecules, molecules will disperse from areas of high concentration and move to areas of lower concentration. So, when you uncork a bottle of perfume, the molecules diffuse through the room from high concnetration at the bottle to low concentration in the rest of the room. Molecules may cross membranes as they move in this manner, moving from areas of high concentration on one side of the membrane to areas of lower concentration on the other. With respect to the lipid bilayer in living membranes, non-polar molecules and some small molecules can diffuse directly through the lipid bilayer. The movement of CO₂ and O₂ across the membrane happens by diffusion. Every molecule moves by diffusion in response to its own concentration gradient.

The movement of water across a membrane, in response to its water potential, is called osmosis (video). Although water is polar, it is also a small molecule. So, it can cross the lipid bilayer directly, or through specialized protein channels called 'aquaporins'. Water potential is a bit more complicated than just 'concentration', although it includes this idea. The higher the concentration of dissolved solutes, the lower the 'concentration' of water and the lower the water potential. These solutes may be one or many things, so water potential is a function of total solute concentration. So, water will osmose across a membrane from an area of low solute concentration (high water potential) to an area of high solute concentration (low water potential), or in other words, from a dilute solution to a concentrated solution. Another component of water potential is water pressure: water will also cross a membrane due to pressure exerted by an outside force or the force of its own mass responding to gravity. So water can be pushed across a membrane.

Consider the figure, below. The purple circles are dissolved solutes. SO! In the first figure at left, total solute concentration is HIGH on the right side of the u-tube, so water potential is LOW . Water will move across the membrane from the dilute solution on the left (high water potential) to the concentrated solution on the right (low water potential), and the water level will rise (figure on the right). Eventually, in this rigid vertical system, the tendancy of the water to move left to right in response to solute concentration is balanced by the tendancy of water to move right to left - "leaking" back across the membrane - in response to the greater water pressure. An equilibrium is reached where there is no NET flow. In a rigid plant cell (with a cell wall), the influx of water creates "hydrostatic pressure" and makes the cell rigid or 'turgid'. The loss of water (from evapotranspiration or osmosis out of the cells to a saltier environment) reduces this turgidity - or 'turgor pressure' - and the plant tissue wilts (gets 'floppy'). In an animal cell bounded only by a thin membrane, the influx of water can create a pressure large enough to rupture the cell. We will deal with these concepts more in lab.

b. Faciliated Diffusion: Large polar molecules cannot diffuse across the lipid bilayer. However, they can cross the membrane 'passively' from high to low concentration, through integrated proteins channels. Some of these channels are rather unspecialized 'tubes', while other channels are rather specific and will only permit the transport of certain classes of molecules. In any case, this is the way that large polar molecules cross the membrane in response to their concentration gradient (high to low). video.

c. Active Transport: If material only crossed the membrane by some form of diffusion, then the cell's cytoplasm would come to be very similar to the surrounding environment. They cell would be unable to raise or lower the concentration of material above the concentration in the environment. In order for cells to be differnt from the environment (in the concetration of some stuff), another mechanism is needed. This is 'active transport'. In active transport, a cell uses energy to 'pump' material across the membrane - against the concentration gradient (from low to high). So, although sugars might be in higher concetration within the cell than outside it, and although sugars may be "leaking" from the cell by diffusion, the cell can pump sugar against the concentration gradient and accumulate it in the cell. Likewise, a cell can pump toxins or waste OUT of the cell, even if the concentration outside of the cell is already high. THIS TAKES ENERGY - LIKE ROLLING A BALL UPHILL, AGAINST THE 'GRADIENT' OR SLOPE. An important active transport mechanism is the "sodium-potassium" pump. In this process, both ions are pumped against their concentration gradient, using energy (breaking ATP) to change the conformation of the transport protein. video

7. Attachment of the cytoskeleton: a cell is not a "baggie" with organelles floating around in the cytoplasm. Most organelles (like mitochondria and chromosomes) are bound to cytoskeletal fibers that hold them in position. The cytoskeleton is also responsible for changin the cells' shape.

III. Energy Harvest: Cellular Respiration and Photosynthesis

Overview of Respiration:

All living cells - eubacteria, archaea, protists, fungi, plants, and animals - can harvest the energy contained in the chemical bonds of complex organic molecules. By breaking the covalent bonds between carbon atoms in these molecules, energy is released. The energy released by these catabolic reactions is used to bind ADP + P --> ATP in coupled, anabolic reactions. As such, some of the energy in the covalent bonds of the initial organic molecules is transformed into chemical energy in bonds of ATP. Energy in this form is now available to all of the enzymes in the cell, for catalyzing their own reactions (chemical energy) or doing work like muscular contraction (mechanical energy) or pumping ions across a membrane against their concentration gradient (active transport).

All four classes of biological molecules (carbo's, fats, proteins, and nucleic acids) are broken down for energy harvest.  The process of carbohydrate metabolism, however, is the central process.  Fats, proteins, and nucleic acids are broken into their monomers, these are modified, and then these products can be shunted into the carbohydrate digestion process. So, although we will focus on carbohydrate metabolism - and glucose metabolism in particular - you should appreciate that all other polymers can be broken down for energy harvest. And respiration not only harvests energy - respiration also provides the monomers needed by the cell to build its own biomolecules. So, when you digest protein, energy is harvested and the separated amino acids can be used by your cells to make your DNA-specified proteins. This is why a balanced diet is important - digestion of varied complex organic molecules provides the different monomers and other essential vitamins and minerals (often used as cofactors in reactions) that your cells require.

The metabolism of glucose can accur in the presence of absence of oxygen. The first step is glycolysis, in which the six-carbon sugar is split into 2 C₃ molecules of pyruvate. The breaking of this bond releases a small amount of energy. In the absence of oxygen, fermentation occurs. The primary function of this "anaerobic" respiration is to recyclce some chemicals needed to keep glycolysis going. So, anaerobic respiration, including glycolysis and fermentation, breaks only a couple bonds and produces only a small amount of energy. In the presence of oxygen, the pyruvates can be completely oxidized. The C₃ molecules are completely broken down into 3 one-carbon molecules of carbon dioxide. The complete breakdown of the the pyruvates releases much more energy. This is probably why aerobic organisms have come to dominate the planet - they harvest more energy from the food they consume, and can use this energy to survive and reproduce more effectively.

1. Glycolysis

a. the process:

The "splitting of glucose" (glyco-lysis) is probably an ancient metabolic reaction; it is performed in the cytoplasm of ALL living cells from prokaryotes to eukaryotes, and cells can perform this reaction in the presence OR absence of oxygen gas. So, it seems likely that this was an important energy harvesting reaction for ancient cells that lived before ~2 bya - before oxygen became abundant in the oceans and atmosphere. As you can see in the flowchart, glycolysis is not ONE reaction - it is a series of reactions catalyzed by a variety of enzymes. For our purposes here, we will consider the primary "inputs" and "outputs" of the entire reaction, rather than concerning ourselves with each step.

Through this series of reactions, the six-carbon glucose is modified and split into 2 C₃ molecules of pyruvate. Glycolysis requires an input of energy to "get the reaction going". This activation energy is provided by 2 ATP. A phosphate is transferred from each ATP to the terminal carbons on the glucose. These phosphates destabilize the glucose, and also give it a charge - it will not diffuse back across the lipid bilayer. The splitting of the molecule releases energy and high energy electrons. Some of the energy is used to phosphorylate 4 ADP--> 4 ATP. Thus, although 2 ATP were used to start the reaction, there is a net gain of 2 ATP. The high energy electrons are accepted by an important molecule called NAD (nicotinamide adenine dinucleotide). With the acceptance of an electron, each NAD becomes negative charged (NAD-) and reacts with a H+ ion in solution - making NADH. So, NAD is a low energy form of the molecule, and NADH is a high energy form of the molecule.

So, for our purposes here, we can summarize glycolysis as:

glucose (C₆) + 2 ATP + 2NAD ----> 2 pyruvate (C₃) + 4 ATP + 2NADH

video

2. Aerobic Respiration

Oxygen is a very reactive gas - it oxidizes things - stripping electrons from other molecules and breaking bonds. Combustion is an oxidative process, and it can occur spontaneously, without an ignition source. So, if combustible material heats up above its ignition temperature, and if a strong oxidative agent like oxygen is present, it will ignite. Gasoline is a long hydrocarbon polymer. When raised above it's ignition point, it will combust. The gasoline will be oxidized to CO₂ and H₂O - and the breaking of the carbon-carbon bonds that occurs during this process will release energy. A gallon of gasoline contains ALOT of bonds and ALOT of energy; and if it is released all at once, the energy is difficult to control or use - you get an uncontrolled explosion. In a car's internal combustion engine, very small amounts of gasoline are ignited in sequence, by spark plugs, causing a little explosion in each cylinder that pushes the piston that turns the crankshaft that turns the wheels of the car. In a diesel engine, there are no spark plugs and no spark; the fuel ignites when the temperature exceeds its ignition point when placed under high pressure when the piston rises. By controling the reaction, by oxidizing just a little at a time, the energy released can be used to do work.

All organic molecules - sugars, nucleic acids, proteins, and fats - can be oxidized in the presence of a strong oxidative agent like oxygen gas. In fact, after oxygenic photosynthesis evolved and after iron precipitated out of suspension, when oxygen began to accumulate in the oceans and atmosphere, it was probably toxic to life. As described above, most of the most ancient forms of life - like archaeans - are obligate anaerobes and are still poisoned by oxygen to this day. Some life forms evolved specific enzymes and 'anti-oxidants' to protect themselves from the oxidative effects of oxygen gas, and they tolerated this new environment. Some of their descendants evolved a mechanism to use the oxidative effects of oxygen gas in a productive way - in a way that released the energy in organic molecules in controlled reactions where the energy could be harvested effectively and used to do chemical work. These aerobic organisms came to dominate the planet, probably in part because they could harvest more energy from the food they consumed; energy they could use to grow, survive, and reproduce. Aerobic respiration probably evolved about 2.0 billion years ago, in response to the increase in oxygen concentrations. Shortly thereafter, aerobically respiring bacteria were engulfed by other cells but not consumed; rather, the host cells used the ATP produced by these energetically efficient 'bacteria'. These host cells were the first eukaryotes, that evolved about 900 million years ago. Their energetic endosymbionts evolved into the mitochondria present in living eukaryotic cells. Like chloroplasts, mitochondria have their own bacteria-like chromosome and a bacteria-like double membrane system. In eukaryotes, the process of aerobic respiration occurs within these organelles. From these ancestral eukaryotes, some absorbed photosynthetic endosymbionts, too; these because the photosynthetic algae and their descendants, the plants. SO - PLEASE KNOW THIS: all eukaryotes (except a couple wierd protists like Giardia), HAVE MITOCHONDRIA - that includes protists, fungi, animals, and PLANTS. Photosynthetic eukaryotoes, the agae and plants, ALSO HAVE chloroplasts.

- 34 to 36 ATP are made from the energy tranferred from NADH and FADH₂ molecules produced in the Krebs Cycle.

4. Summary of Glucose Metabolism

5. Metabolizing other Biomolecules

a. Fats:
- Glycerol broken from fatty acids; glycerol (3C) fed into glycolysis and are modified into pyruvates (C₃). - the Fatty Acids are broken down into C₂ groups that are modified to react with CoA - they are shuinted to the Krebs Cycle - these reacts are reversible, so if there is a surplus of C₂-CoA, it can react to form fatty acids ---> energy consumed in carbo's can be stored as bonds in fat.

b. Proteins:
- Broken into Amino Acids which, depending on their structure, can be shunted into glycolysis, modified into pyruvate, or broken into acetate (C₂). - In all cases, the amine groups are cleaved, producing ammonia (NH₃) as a toxic waste. In mammals, this is converted into urea which must be diluted in water for removal from the body (urine). Reptiles and birds convert it to uric acid, which is expelled as a paste that does not require as much water for dilution.

c. Nucleic Acids: - ribose can be metabolized after coversion to glucose.
 

Study Questions:

1) What is the structure of a fatty acid? A triglyceride?

2) What is the monomeric unit of proteins? Draw one, without specifying the variable group.

3) Show how two amino acids are linked together. What is the name of the reaction?

4) Diagram the parts of an RNA nucleotide.

5)  Show how two nucleotides are linked together by dehydration synthesis reactions.

6) Why does the purine - pyrimidine structure relate to the complementary nature of double-stranded DNA?

7)  Draw a DNA double helix, showing three base pairs and the antiparallel nature of the helices.

8) Describe the higher levels of eukaryotic chromosome structure, including the terms nucleosome and solenoid.

9) List three differences between prokaryotic and eukaryotic cells.

10) Why is the lipid bilayer a barrier to water soluble molecules?

11) Describe diffusion, facilitated diffusion, and active transport.

12) Describe glycolysis.

13)  What happens in the gateway step?

14)  What happens in the krebs cycle?

15) What happens in the elEctron transport chain?  Explain chemiosmosis.

16) How is oxygen involved in the process of aerobic respiration?