Biology - Molecules and Cells

 Terms and Concepts 

SECTION 1

CHAPTER 7 - Energy Processes in Living Things

Most of what a cell does involves endergonic reactions, requiring constant energy input;  these reactions are coupled to just a smaller number exergonic reactions which supply that energy.  

The key fuel source in cell reactions is Adenosine Triphosphate, or ATP.  The molecule is an amino acid linked to a ribose sugar, linked to a string of three phosphate groups (there are also ADP, Adenosine Diphosphate, and AMP, Adenosine Monophosphate).  With ATP, the breaking off of the last phosphate, often in a transfer to another molecule (a process called phosphorylation), can release or activate a fair amount of usable energy.  Having a phosphate group attached can destabilize a molecule or cause a critical change in an enzyme's active site. The energy available from a trade of phosphate groups is a type of group transfer potential.

ATP.

ADP.

AMP.

Importance of phosphorylation.

Energy and phosphorylation.

ATP is produced from ADP and phosphate by several exergonic reactions in cells, but the main sources of ATP are the major energy reactions:  photosynthesis and respiration.  In photosynthesis, captured light energy is transformed into the bonding energy between ADP and phosphate, and the glucose that is the ultimate product is assembled using mostly energy from ATP.  In respiration, the bonding energy holding glucose together is transferred to ATP.  Light and sugars may be the ultimate sources of energy in cells, but mobilizing those energies is too complex to do everywhere a cell needs it.  ATP is functional, easily put to use in many circumstances, whether it's pure chemistry, generation of cell movement, active transport, or any process requiring energy input.  A related molecule, guanosine triphosphate or GTP, is also used in several systems.  Sometimes, ADP can supply energy with its terminal phosphate, producing AMP, but it is more difficult to remove that closer-to-the-core phosphate.  AMP itself has several uses in cells that do not involve energy transfer - cyclic AMP will be discussed later in its role as a messenger molecule.

Photosynthesis and ATP (Slide).

 

Respiration and ATP (Image).
 

GTP and G proteins.
 

Cyclic AMP.

A couple of other molecules are important as electron-carrying molecules.  Nicotinamide Adenine Dinucleotide, or NAD, a coenzyme derived from the vitamin niacin, or B3, is important in reduction and oxidation (often called redox) reactions.  When an atom or molecule is oxidized, it loses electrons;  when one is reduced, it gains electrons (whose negative charges would reduce the charge of the recipient).  Remember, chemistry is pretty much all about electrons, and whenever electrons transfer there is oxidation and reduction going on.  What is less obvious is how hydrogen works as the actual means of shifting electrons.  In the case of NAD, it's NAD+ form picks up H₂ (by taking it from another source, it is an oxidizing agent) and briefly becomes NADH₂+, then quickly stabilizes by losing H+  and becoming NADH.  This molecule can return to NAD+ by losing a hydrogen and an electron (it is called a reducing agent in this role), allowing the electron to move elsewhere.  Then, with phosphorylation to NADPH, another important molecule, especially in the process of photosynthesis, is made.

NAD processing (image).

Information on vitamin B3.

NAD redox.

NADPH image.

Flavin-Adenine Dinucleotide, or FAD, another coenzyme, this one derived from riboflavin / B2, serves a similar function.  FAD can be reduced to FADH₂ and carry hydrogens / electrons between reactions.  The main sources of ATP in most cells are fueled by hydrogens carrying electrons.

FAD processing (image).

Information on vitamin B2.

The progress of food through a typical food chain starts with the producers, which have the unique ability to take materials from the environment and, using energy from the environment, produce compounds that store that energy in a usable molecular form.  The first producers probably had a simple form of chemosynthesis working, but the rise of photosynthesis eventually made plants the most widespread and successful producers.  In a food chain, successive levels of consumers (primary consumers eat mostly producers, secondary consumers eat mostly primary consumers, etc, etc...) depend ultimately on producers to provide the energy fuel of Life.  As fuel works its way up a food chain, it never is completely transferred from one level to the next, continually being lost to the environment in the randomness of heat (following the Second Law of Thermodynamics).  At the other end of the food chain are the decomposers, organisms that are critical to the recycling of the materials found in dead organisms and organic wastes.  The materials continually go round and round the system, but the energy is ultimately lost to unusable forms and requires constant input.  For the Earth, the main source of energy input for food chains comes from the Sun, which casts out mostly light to the surface of the planet.

Chemiosmosis, a step toward chemosynthesis.

The beginnings of such systems.

Image of the simple food chain.

Why life does not violate the 2nd Law.

Light is a form of electromagnetic radiation, energy that travels through space as waves.  These waves originate in the "dance" of charged atomic particles between different energy states - the vibratory frequency of the particles determines the wave frequency (how many wave peaks are emitted over a set period of time) and the wavelength (the distance between wave peaks).  High frequency / short wavelengths are associated with more powerful energy - gamma rays, X-Rays, and UltraViolet (in descending progression) are fairly strong types of energy.  Low Frequency is associated with less energy, as is found (in ascending progression) in radio, microwaves, and InfraRed / Heat.  Between InfraRed and UltraViolet is a range of frequencies that human eyes can pick up - visible light - which covers a large part of the Sun's emissions that actually reach the surface of the Earth.  In the range of visible light, red is at the low frequency end and purple at the high end.

The electromagnetic spectrum.

Wavelengths and frequencies.

Some well-known wave types.

What happens to the Sun's energy.

Wavelength energy (video).

Atoms, or really the electrons around atoms, can absorb and transform electromagnetic energy, often in very specific ways.  A particular atom won't absorb all types of radiation, and when it absorbs it, energizes, and then returns to a more stable form, it may release the energy at a new frequency or a few frequencies - this is called reradiation.  A simple example of this is the absorption of  most frequencies of visible light by a dark paved surface, reradiated as infrared / heat energy, or the absorption of electricity by gases in a fluorescent light tube, reradiated as ultraviolet, absorbed by the bulb coating and reradiated as many frequencies of light.

How wavelengths can be used to analyze interstellar materials.

Reradiation and plants.

In photosynthesis, pigments absorb various frequencies of light that actually liberate electrons completely from atoms, and the electrons are used to eventually supply the energy necessary to build molecules of glucose.  The primary pigment of photosynthesis, chlorophyll,  appears a strong green because those are the frequencies that reflect (are not absorbed) from the pigment.  It absorbs and uses energy in the red, blue, and purple ranges.  The other common pigments, from a group called the carotenoids, absorb in some of the green and blue frequencies and pass electrons to the photosynthetic process.  These pigments reflect yellows, oranges, and reds and are visible in autumn when the chlorophyll in leaves degrades and stops overwhelming their presence;  they are also common in coloring plant parts that need to stand out to pollinators (flowers) or seed-spreaders (ripened edible fruits).  As more research is done, it's also being found that this class of molecules may be doing a range of other things as well, from the logical - absorbing ultraviolet frequencies that might damage the plant - to the unexpected - acting as a part of the plant's reaction-to-pathogens pathways.

Discussion of biological pigments.
 

Chlorophyll absorption frequencies.
 

Other photosynthetic pigments.
 

Carotenoid absorption frequencies.

We are going to look at the most common form of photosynthesis, that done by chlorophyll a in multicelled plants and many single-celled ones as well.  In eukaryotes, the processes take place in chloroplasts.  Different parts of the process occur in different parts of these organelles.

Photosynthesis basics.

Chloroplasts.

Remember, the basic process of photosynthesis:

            6 CO₂  +   6 H₂O    ---with Light----->   C₆H₁₂O₆    +    6 O₂

But this is a simplified, overall representation of the reaction, which occurs in steps...

The first step, the Light-Dependent Reaction, occurs in the small stacks of membrane inclusions of a chloroplast; the flattened sacs are thylakoids and the stacks are grana.  As the name implies, it works only when there is light available.  Light is picked up by a large collection of chlorophyll molecules (200 - 300) called an antenna complex, each wave peak photon exciting an electron, and relayed to a complex of proteins and cofactors around a pair of chlorophyll molecules, an area called the reaction center, where the actual reaction takes place.  Each chlorophyll molecule by itself does not pick up a lot of photons, but linked together in groups enough energy is captured to sustain a respectable process.  There are two types of reaction centers, attached to what is called Photosystem I and Photosystem II.  Each system has a different set of cofactors associated with the central chlorophylls, which are designated by different numbers according to the slightly different wavelengths of light they absorb (P700 for I, P680 for II).  In a complicated sequence, water molecules are reduced, freeing electrons and hydrogen atoms and releasing oxygen.  The electrons feed into a step called the electron transport chain, a cascade during which ATP is made from ADP and phosphate molecules, and NADPH is made at the very end.  This part of the basic process is similar to what happens in aerobic respiration, described below, and although some of the molecules involved are different, a group called the cytochromes are important to both.  Ferredoxin, a protein containing iron, is a critical participant in this process in photosynthesis.  If a plant were always exposed to light, the compounds made in this stage could be used as a regular fuel, but they are too unstable to last through a very long period of darkness - for that, a more stable energy-storage molecule is necessary, and the products of the light-dependent reaction are used to make them in...

Animation of process.

Chloroplast with parts labeled.

Image of the two systems.

Video explaining process.

Video on electron transport chain.

Studying cytochromes.

Studying ferredoxin.

The next step, the Light-Independent Reaction, is fueled by the ATP and NADPH from the light-dependent reaction (and sends ADP and NADP back for recharging).  As long as fuel remains, this step can go on, regardless of whether there is light or not.  The main piece of this process is called the Calvin Cycle, which processes 5-carbon molecules, 3 at a time, bringing in CO₂ to make 6-carbon molecules, breaking those into 3-carbon molecules, and either feeding those molecules into the next step or around the cycle to become 5-carbon molecules again.  In the next synthesis step, phosphorylated 3-carbon sugar-like molecules are combined, and the two phosphates lost, to produce the glucose that will serve as the primary stable fuel (and main structural constituent) of the plant.

Video on light-independent reaction.

Image of Calvin Cycle.
 

More on the process.

In modern plants, two slightly different approaches to photosynthesis occur.  The basic approach described here is used when CO₂ is readily available through opened pores (stomates) to the atmosphere.  However, in hot, dry conditions, stomates must be closed much of the time to prevent excessive water loss, and CO₂ levels inside leaves drop while oxygen levels rise.  C4 photosynthesis works better under these circumstances, using a 4-carbon intermediate to better hold CO₂ in the process (the regular process is C3 photosynthesis).  There is also CAM photosynthesis ( for crassulacean acid metabolism), an even more specialized approach found in a few desert plants.

C4 and crop plants.
 

Overview of photosynthesis types.

A fuel is made to be consumed, and glucose has become the basic fuel of Life.  Plants use it when photosynthesis isn't active, and plants are the basis for the food chain because they are the main source of the fuel that all consumers need to support their chemistries.  The processes by which molecules are taken apart and the energy is put to use probably date back to the first molecular systems, but organisms in today's world depend mostly upon sugars to supply them, through a process that breaks the sugars down and relays the energy into ATP.  The various ways to do this are collectively called cellular respiration.

The most efficient respiration processes use the best electron acceptors to get the most energy out of their fuel - nitrates, or sulfates, or carbonates can be used, but electrons are not mobilized enough to pull a lot of energy from the fuel.  This is best done with oxygen as the terminal electron acceptor.  Oxygen-using respiration is called aerobic respiration, while less efficient processes that do not use oxygen are called anaerobic respiration.

How different acceptors affect other factors.

Image of different processes.

Anaerobic respiration would have been a primary metabolic process back before the evolution of photosynthesis, which changed the oxygen availability in the world.  Today's remaining anaerobic organisms tend to occupy niches that have little to no oxygen available, on the fringes of modern ecosystems.  They still have roles to play, however - symbiotic bacteria and protozoans live in animal digestive systems and aid in the breakdown of plant fiber;  occasionally anaerobic bacteria make us sick with their toxic chemical byproducts, as in the diseases botulism or tetanus;  many commercial products depend upon such anaerobe respiratory products as ethyl alcohol (wines, liquors, and beer), carbon dioxide (rising of dough), propionic acid (some cheeses), and lactic acid (butter, yogurt).  It also remains as the first step of aerobic respiration, done in the cytoplasm before the mitochondria take over.

Anaerobes in humans - good and bad.

Introduction to symbiont usefulness.

THE PROCESS OF AEROBIC RESPIRATION -

The basic process of aerobic respiration, simplified to its basic substrates and products, is very much the reverse of photosynthesis -

            C₆H₁₂O₆    +    6 O₂    ---------------->   6 CO₂  +   6 H₂O
                                                         \-------  Energy to ATP

of course, it's much more complex than that...

Step one:  Glycolysis.  Glucose is broken into 2 3-carbon molecules in this multi-step pathway.  The main steps go this way -

• Glucose is phosphorylated.  Glucose has 5 carbons in its ring, and a side-chain carbon.  ATP transfers a phosphate to that carbon (that's an investment of one ATP so far), destabilizing the molecule and facilitating its conversion into -

• Glucose is symmetrically rearranged.  The molecule becomes a 4-carbon ring, with another side-chain carbon on the other side of the oxygen bridge.  This is now fructose, a close-to symmetrical molecule.

• The new side-chain carbon is phosphorylated.  This makes the molecule more symmetrical and less stable.  ATP investment in the process is now 2.

• Fructose splits into 2 3-carbon phosphorylated molecules.  This molecule shifts between two configurations, but while in one form...

• A second phosphate is attached to each molecule.  This does not require ATP, though, just phosphate and the oxidation potential of NAD+.  NADH is made, to be used later.

• ATP is made using the new phosphates.  This makes 2 ATPs to balance the 2-ATP investment earlier.  

• ATP is made from the phosphates added in the first step.  This produces a net gain of 2 ATPs.  Another step removes H₂O and rearranges the molecules, producing pyruvic acid or pyruvate.  The various products of the different types of anaerobic respiration are produced from this intermediate product.  In vertebrates, the intermediate lactic acid or lactate may be produced;  this will be discussed later in terms of oxygen debt.

• Carbon dioxide breaks off the molecules, replaced by Acetyl Coenzyme A (acetyl CoA).  This is the molecule that is passed on to the next step.

Glycolysis animations.
 

Image of molecular changes.
 

Visual outline of process.
 

Glycolysis...rap?? (Video)
 

Glycolysis video.
 

Longish lecture on glycolysis. (Video)
 

Ancient origins of Coenzyme A.

Step Two:  Krebs Cycle or Citric Acid Cycle.  This occurs in the mitochondria, on the cristae.  The 2-carbon molecule attached to CoA is linked to a 4-carbon molecule, oxaloacetate, inside the cycle, producing an unstable 6-carbon molecule that, through a succession of steps, is rearranged, dehydrates, loses 2 carbons as carbon dioxide, transfers electrons via hydrogens to 3 NADH molecules, 3 H+ ions, and a FADH₂, and energy to produce an ATP.  Eventually, the molecule in the cycle is back to oxaloacetate and ready to pick up another Acetyl CoA from glycolysis.

Process animation.

More on the Krebs Cycle.

Mitochondrion animation.

Step Three:  Electron Transport Chain.  The mitochondrial membrane contains a sequence of molecules that will pass the Hydrogen ions from the Krebs Cycle, including those carried in NADH and FADH₂, producing electrical gradients in the membrane that will fuel ATP Synthase.  Energy supplied by setting up a gradient of charges comes from what's called an electrical potential.  By latest estimates, each NADH (6 from each glucose fed into the Krebs Cycle) contributes to the production of 2.5 ATPs, and each FADH₂ (2 from Krebs) contributes to 1.5 ATPs.  This is where most of aerobic metabolism's ATP yield comes from.  Eventually, the hydrogens used in this chain must be picked up by oxygen in the form of water molecules - if there is no oxygen available, hydrogens build up and the entire reaction grinds to a halt.

Video on electron transport chain.

Image of electron transport chain.

More on ATP synthase.

Other complex molecules can be used in respiratory pathways, especially the fatty acids of lipids. The long carbon chains of the fatty acids are broken down to 2-carbon subunits, attached to coenzyme A, and fed into the Krebs cycle, which explains why fats contain a lot of metabolic energy / Calories.  Proteins and nucleic acids can be broken down and used the same way, but the nitrogen components comes out as waste - nitrogenous wastes, commonly ammonia or another simple but less-toxic compound.  Many organisms with limited access to carbohydrates (like predators - not a lot of sugars and starches in animal prey) may get most of their energy this way, and may even be able to use those molecules in pathways to build carbohydrates that they need but don't get in their diets.

Lipids and respiration image.

Protein breakdown and amino acid use.

Nitrogenous wastes.

Some cells, most notably muscle cells, will continue glycolysis for ATP production even when oxygen isn't available in enough quantity to complete aerobic respiration.  The glycolysis product lactic acid or lactate builds up, to be processed later (if the muscle's owner survives whatever is making it work so hard).  This process is known as building up and repaying an oxygen debt.

Image of 2 pathways.

Information about the lactic acid conversion.

Terms and Concepts

In the order they were covered.

Adenosine Triphosphate (ATP) 
Adenosine Diphosphate (ADP) 
Adenosine Monophosphate (AMP) 
Phosphorylation  
Group Transfer Potential  
ATP Production  
Guanosine Triphosphate (GTP)  
Nicotinamide Adenine Dinucleotide (NAD)  
Niacin  
Reduction  
Oxidation  
Redox  
Hydrogen as Electron Carrier  
Oxidizing Agent  
Reducing Agent  
Flavin-Adenine Dinucleotide (FAD)  
Riboflavin  
Food Chains  
Producers  
Consumers  
Primary, Secondary, etc., Consumers  
Energy in Food Chains  
Materials in Food Chains  
Heat as Energy Loss  
Decomposers  
Recycling in Food Chains  
Light  
Electromagnetic Radiation  
Frequency, Radiation  
Wavelength, Radiation  
Gamma Rays  
X-Rays  
UltraViolet  
InfraRed  
Light, Visible  
 Radiation Absorption  
Reradiation  
Pigments  
Chlorophyll  
Carotenoids  
Photosynthesis  
Chlorophyll a  
Light-Dependent Reaction  
Thylakoids  
Grana  
Antenna Complex  
Reaction Center  
Photosystems  
Electron Transport Chain (Photosynthesis)  
Ferredoxin  
Light-Independent Reaction  
Calvin Cycle  
C4 (and C3) Photosynthesis  
Cellular Respiration  
Respiration - Electron Acceptors  
Anaerobic Respirators  
Botulism  
Ethyl Alcohol  
Propionic Acid  
Aerobic Respiration  
Glycolysis  
Pyruvic Acid / Pyruvate  
Acetyl Coenzyme A  
Krebs Cycle  
Cristae  
Oxaloacetate  
Electron Transport Chain - Aerobic  
ATP Synthase  
Electrical Potential  
Respiration using Other Molecules  
Nitrogenous Wastes  
Oxygen Debt  
Lactic Acid / Lactate