BIO 106 - Metabolism to Animal Body: Chapter 5-8, 33,34

The Second Law of Thermodynamics -A living cell's primary tasks of _________________, __________________, using ____________________ to do work -In every energy transfer, some amount of energy is what in a form that is? Usually heat energy. High entropy means what? Living things are highly ordered and low? But the universe is constantly what due to loss of usable energy?

-*A living cell's primary tasks of obtaining, transforming, using energy to do work* may seem simple -However, the *second law of thermodynamics explains why these tasks are harder* than they appear. *None of the energy transfers* we've discussed, along with *all energy transfers and transformations in the universe*, is *completely efficient* -In every energy transfer, *some amount of energy is lost in a form that is unusable* -In most cases, *this form is heat energy* -Thermodynamically, *heat energy is defined as the energy transferred from one system to another that is not doing work* -Ex: when an airplane flies through the air, some of the energy of the flying plane is lost as heat energy due to friction with the surrounding air. This friction actually heats the air by temporarily increasing the speed of air molecules. Likewise, *some energy is lost as heat energy during cellular metabolic reactions* = this is *good for warm-blooded* creatures like us, because *heat energy helps to maintain our body temp* -Strictly speaking, *no energy transfer is completely efficient*, because *some energy is lost in an UNUSABLE form* -An important concept in physical systems is that of *order and disorder (also known as randomness)* = the *more energy that is lost by a system to its surroundings*, the *less ordered and more random the system is* -Scientists refer to the *measure of randomness or disorder within a system* = *ENTROPY* -*High entropy means high disorder/ energy* -To better understand entropy, think of a student's bedroom. If no energy or work were put into it, the room would quickly become messy. It would exist in a very disordered state, one of high entropy. *Energy must be put into the system*, in the form of the student doing work and putting everything away, in order *to bring the room back to a state of cleanliness and ORDER* -This state is one of low entropy. Similarly, a car or house must be constantly maintained with work in order to keep it in an ordered state. Left alone, the entropy of the house or car gradually increases through rust and degradation -*Molecules and chemical reactions have varying amounts of entropy as well* For example, as *chemical reactions reach a state of equilibrium* = *entropy increases* and *as molecules at a high concentration in one place diffuse and spread out* = *entropy also increases* -*All physical systems can be thought of in this way*: *Living things are highly ordered*, requiring *constant energy input to be maintained* in a state of low entropy. As *living systems take in energy-storing molecules and transform them through chemical reactions*, they *lose some amount of usable energy* in the process, because no reaction is completely efficient -They also *produce waste and by-products that ARE NOT USEFUL energy sources* = this process *INCR the entropy of the syLIstem's surroundings* -Since all *energy transfers result in the loss of some usable energy* + the second law of thermodynamics states that *every energy transfer or transformation incr the entropy of the universe* -Even though *living things are highly ordered/low entropy* the entropy of the *universe in total is constantly increasing due to the LOSS of usable energy* with each *energy transfer that occur*. Essentially, living things are in a continuous uphill battle against this constant increase in universal entropy.

Homeostasis: Thermoregulation

Been able to maintain equilibrium between inter-dependent elements. Allows organisms to keep its body temperature and it's normal temperature -*Body temp affects body activities* Generally, *as body temperature rises, enzyme activity rises as well* -For *every 10 degree centigrade rise in temp*, *enzyme activity doubles*, up to a point. *Body proteins, including enzymes, begin to denature and lose their function* with high heat (around 50oC for mammals) -*Enzyme activity will decr by 1/2 for every 10 degree centigrade drop* in temperature, to the point of freezing, with a few exceptions. *Some fish can withstand freezing solid and return to normal with thawing*

The Calvin Cycle

In plants, carbon dioxide (CO2) enters the leaves through stomata, where it diffuses over short distances through intercellular spaces until it reaches the mesophyll cells. Once in the mesophyll cells, CO2 diffuses into the stroma of the chloroplast—the site of light-independent reactions of photosynthesis. These reactions actually have several names associated with them. Another term, the Calvin cycle, is named for the man who discovered it, and because these reactions function as a cycle. Others call it the Calvin-Benson cycle to include the name of another scientist involved in its discovery. The most outdated name is dark reactions, because light is not directly required (Figure 8.17). However, the term dark reaction can be misleading because it implies incorrectly that the reaction only occurs at night or is independent of light, which is why most scientists and instructors no longer use it. Light reactions harness energy from the sun to produce chemical bonds, ATP, and NADPH. These energy- carrying molecules are made in the stroma where carbon fixation takes place. The light-independent reactions of the Calvin cycle can be organized into three basic stages: fixation, reduction, and regeneration. Stage 1: Fixation In the stroma, in addition to CO2, two other components are present to initiate the light-independent reactions: an enzyme called ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), and three molecules of ribulose bisphosphate (RuBP), as shown in Figure 8.18. RuBP has five atoms of carbon, flanked by two phosphates. RuBisCO catalyzes a reaction between CO2 and RuBP. For each CO2 molecule that reacts with one RuBP, two molecules of another compound (3-PGA) form. PGA has three carbons and one phosphate. Each turn of the cycle involves only one RuBP and one carbon dioxide and forms two molecules of 3-PGA. The number of carbon atoms remains the same, as the atoms move to form new bonds during the reactions (3 atoms from 3CO2 + 15 atoms from 3RuBP = 18 atoms in 3 atoms of 3-PGA). This process is called carbon fixation, because CO2 is "fixed" from an inorganic form into organic molecules. Stage 2: Reduction ATP and NADPH are used to convert the six molecules of 3-PGA into six molecules of a chemical called glyceraldehyde 3-phosphate (G3P). That is a reduction reaction because it involves the gain of electrons by 3-PGA. Recall that a reduction is the gain of an electron by an atom or molecule. Six molecules of both ATP and NADPH are used. For ATP, energy is released with the loss of the terminal phosphate atom, converting it into ADP; for NADPH, both energy and a hydrogen atom are lost, converting it into NADP+. Both of these molecules return to the nearby light-dependent reactions to be reused and reenergized. Stage 3: Regeneration Interestingly, at this point, only one of the G3P molecules leaves the Calvin cycle and is sent to the cytoplasm to contribute to the formation of other compounds needed by the plant. Because the G3P exported from the chloroplast has three carbon atoms, it takes three "turns" of the Calvin cycle to fix enough net carbon to export one G3P. But each turn makes two G3Ps, thus three turns make six G3Ps. One is exported while the remaining five G3P molecules remain in the cycle and are used to regenerate RuBP, which enables the system to prepare for more CO2 to be fixed. Three more molecules of ATP are used in these regeneration reactions.

Pathways of Photosynthesis and Cellular Metabolism

The processes of photosynthesis and cellular metabolism consist of several very complex pathways. It is generally thought that the first cells arose in an aqueous environment—a "soup" of nutrients—probably on the surface of some porous clays. If these cells reproduced successfully and their numbers climbed steadily, it follows that the cells would begin to deplete the nutrients from the medium in which they lived as they shifted the nutrients into the components of their own bodies. This hypothetical situation would have resulted in natural selection favoring those organisms that could exist by using the nutrients that remained in their environment and by manipulating these nutrients into materials upon which they could survive. Selection would favor those organisms that could extract maximal value from the nutrients to which they had access. An early form of photosynthesis developed that harnessed the sun's energy using water as a source of hydrogen atoms, but this pathway did not produce free oxygen (anoxygenic photosynthesis). (Early photosynthesis did not produce free oxygen because it did not use water as the source of hydrogen ions; instead, it used materials like hydrogen sulfide and consequently produced sulfur). It is thought that glycolysis developed at this time and could take advantage of the simple sugars being produced, but these reactions were unable to fully extract the energy stored in the carbohydrates. The development of glycolysis probably predated the evolution of photosynthesis, as it was well suited to extract energy from materials spontaneously accumulating in the "primeval soup." A later form of photosynthesis used water as a source of electrons and hydrogen, and generated free oxygen. Over time, the atmosphere became oxygenated, but not before the oxygen released oxidized metals in the ocean and created a "rust" layer in the sediment, permitting the dating of the rise of the first oxygenic photosynthesizers. Living things adapted to exploit this new atmosphere that allowed aerobic respiration as we know it to evolve. When the full process of oxygenic photosynthesis developed and the atmosphere became oxygenated, cells were finally able to use the oxygen expelled by photosynthesis to extract considerably more energy from the sugar molecules using the citric acid cycle and oxidative phosphorylation. •In *cellular respiration*, •*sugar is broken down to carbon dioxide and water* and •the *cell captures some of the released energy to make ATP* •*Cellular respiration takes place in the mitochondria of eukaryotic cells* •In these *energy conversions, some energy is lost as heat* Cellular respiration is the aerobic (oxygen-requiring) harvesting of energy from food molecules by cells •*Cellular respiration is an exergonic (energy- releasing)* process that *transfers energy from bonds in glucose to form ATP* •Cellular respiration •*can produce up to 32 ATP molecules* for each glucose molecule, •*uses about 34% of energy in glucose* and •*releases the other 66% as HEAT* •This *energy conversion efficiency is better than most energy conversion systems* •Only about *25% of the energy in gasoline produces the kinetic energy of movement* •A *kilocalorie (kcal)* = *quantity of heat required to raise temp of 1 kilogram (kg) of water by 1°C* •the same as a food Calorie, and •*used to measure the nutritional values indicated on food labels* •How do your *cells extract energy from glucose*? •The answer involves the *transfer of electrons during chemical reactions* •*electrons are transferred from glucose to oxygen* and •*energy is released* •*Oxygen attracts electrons very strongly* •An *electron loses potential energy* when it is *transferred to oxygen* •*Energy can be released* from *glucose by simply burning it* •This *electron "fall" happens very rapidly* •This *energy is dissipated as heat and light* and is *not available to living organisms* •Cellular respiration is a *more controlled descent of electrons* and like rolling *down an energy hill* •Energy is *released in small amounts + stored in the chemical bonds of ATP* •A *cellular respiration* equation is helpful to show the *changes in HYDROGEN atom distribution* •*Glucose loses hydrogen atoms* and becomes *oxidized to CO2* •*Oxygen gains hydrogen atoms* and becomes *reduced to H2O* •An important player in the process of *oxidizing glucose is a coenzyme called NAD+* which •*accepts electrons* and •*becomes reduced to NADH*

Negative and Positive Feedback

-Any *homeostatic process changes the direction of the stimulus is a negative feedback loop* -It *may either incr/decr the stimulus* but the *stimulus is not allowed to continue* as it did *before the receptor sensed it* -*If a level is too high*, the *body does something to bring it down*, and conversely, *if a level is too low*, the *body does something to make it go up -Hence the term *negative feedback* = An example is *animal maintenance of blood glucose levels* -When *an animal has eaten, blood glucose levels rise* -This is *sensed by the nervous system* *Specialized cells in the pancreas* sense this, and the *hormone insulin is released by the endocrine system* -*Insulin causes blood glucose levels to decr*, as would be expected in a *negative feedback system* -However, *if an animal has not eaten and blood glucose levels decr* this is sensed in another group of cells in the pancreas, and the *hormone glucagon is released causing glucose levels to incr* -This is still a *negative feedback loop, but not in the direction expected by the use of the term "negative."* Another example of an *increase as a result of the feedback loop is the control of blood calcium* If calcium levels decrease, specialized cells in the parathyroid gland sense this and release parathyroid hormone (PTH), causing an increased absorption of calcium through the intestines and kidneys and, possibly, the breakdown of bone in order to liberate calcium. The effects of PTH are to raise blood levels of the element. *Negative feedback loops are the predominant mechanism used in homeostasis* -A *positive feedback loop maintains the direction of the stimulus*, possibly *accelerating it*. Few examples of positive feedback loops *exist in animal bodies, but one is found in the cascade of chemical reactions* that result in *blood clotting, or coagulation* -As *one clotting factor is activated*, it *activates the next factor in sequence until a fibrin clot* is achieved. The *direction is maintained, not changed, so this is positive feedback* + another example of positive feedback is uterine contractions during childbirth -The hormone oxytocin, made by the endocrine system, stimulates the contraction of the uterus. This produces pain sensed by the nervous system. Instead of lowering the oxytocin and causing the pain to subside, more *oxytocin is produced until the contractions are powerful enough to produce childbirth* It is *possible to adjust a system's set point* + When this happens, the *feedback loop works to maintain the new setting* -An example of this is *blood pressure: over time*, the *normal or set point for blood pressure can incr as a result of continued incr in blood pressure* -The *body no longer recognizes the elevation* as *abnormal* and *no attempt is made to return to the lower set point* -The result is the maintenance of an *elevated blood pressure that can have harmful effects on the body* -Medication can *lower blood pressure and lower the set point* in the system to a more healthy level. This is called a *process of alteration of the set point in a feedback loop* -*Changes can be made in a group of body organ systems* in order to *maintain a set point* in another system. This is called *acclimatization*. This occurs, for instance, *when an animal migrates to a higher altitude than accustomed to*. -In order *to adjust to the lower oxygen levels at the new altitude*, the *body incr number of red blood cells* circulating in the blood to ensure *adequate oxygen delivery to the tissues*. Another example of *acclimatization is animals that have seasonal changes in their coats*: a heavier coat in the winter ensures adequate heat retention, and a light coat in summer assists in keeping body temperature from rising to harmful levels.

Oral Cavity: Trachea and Espohagus

Parts of the Digestive System: Oral Cavity, Esophagus, Stomach, Small Intestine, Large Intestine, Rectum & Anus, Accessory Organs -The *vertebrate digestive system* = *facilitates the transformation of food matter to nutrient components* that sustain organisms. Oral Cavity -The *oral cavity/mouth* is the *point of entry of food into the digestive system* -The *food is broken into smaller particles w/ mastication* (the chewing action of the teeth) -*All mammals have teeth* and *can chew* their food. -The extensive chemical process of *digestion begins in the mouth* -As *food is chewed* + *saliva* (by the salivary glands) *mixes w/ the food* -*Saliva* = *watery substance produced in the mouths* of many animals -*3 major glands that secrete saliva* = 1) the *parotid* 2) the *submandibular* 3) the *sublingual* -*Saliva contains mucus* that *moistens food/buffers the pH of the food* Saliva also contains immunoglobulins/lysozymes = *antibacterial action to reduce tooth decay by inhibiting growth of some bacteria* -*Saliva also contains an enzyme* called *salivary amylase* = *begins process of converting starches in the food into disaccharide-maltose* -Another enzyme called *lipase* = *produced by the cells in tongue* -*Lipases* are a class of *enzymes that break down triglycerides* -The *lingual lipase breaks down starches/fats in the food* -The *chewing/wetting action provided by teeth/saliva prepares food into a mass* = *bolus* (for swallowing) -The *tongue helps in swallowing*—*moving the bolus from the mouth to the pharynx* - The *pharynx opens to 2 passageways* = 1. *trachea* = leads *to the lungs* -The *trachea has an opening called the glottis*, which is *covered by a cartilaginous flap* = *epiglottis* -When *swallowing*, the *epiglottis closes the glottis* and *food passes into the esophagus NOT the trachea* -This arrangement *allows food to be kept out of the trachea* 2. *esophagus* = leads *to the stomach* -The esophagus is a *tubular organ connecting the mouth to the stomach* -The *chewed food passes through the esophagus after being swallowed* -The *smooth muscles* of the esophagus *undergo PERISTALSIS* = *a series of wave-like movements* that *push food toward the stomach* -The *peristalsis wave is unidirectional*—it *moves food from the mouth to the stomach*, and reverse movement is not possible. The *peristaltic movement of the esophagus is an involuntary reflex*; it takes place *in response to swallowing* -*SPHINCTER* = A *ring-like muscle forms valves in the digestive system* -The *gastro-esophageal sphincter is located at the STOMACH END of the esophagus* -*In response to swallowing/ pressure exerted by the bolus of food* = this *sphincter opens* + *bolus enters the stomach* -W/ *no swallowing action* = this *sphincter is shut/prevents contents of the stomach from traveling up the esophagus* -Many *animals have a true sphincter* -However, *in humans* = there is *no true sphincter*, but the *esophagus remains closed w/ no swallowing action* + *acid reflux/"heartburn"* occurs when the *acidic digestive juices escape into the esophagus*

Connections of Carbohydrate, Protein, and Lipid Metabolic Pathways

You have learned about the catabolism of glucose, which provides energy to living cells. But living things consume more than glucose for food. How does a turkey sandwich end up as ATP in your cells? This happens because all of the *catabolic pathways for carbohydrates*, *proteins, and lipids* eventually *connect into glycolysis + the citric acid cycle* pathways -*Metabolic pathways should be thought of as porous*—that is, *substances enter from other pathways*, and *intermediates leave for other pathways* -These *pathways ARE NOT closed systems* -*Many substrates, intermediates, and products in a particular pathway are reactants* in other pathways.

Essential Nutrients

-*ANIMALS MUST OBTAIN*= *1. organic building blocks for macromolecules* *2. chem energy* to *power cellular work* *3. essential nutrients* to *maintain health* *While the animal body can synthesize many of the molecules required for function from the organic precursors*, there are *some nutrients that need to be consumed from food* -These *nutrients are termed essential nutrients*, meaning *they must be eaten* body cannot produce them. -*The omega-3 alpha-linolenic acid* and the *omega-6 linoleic acid* = *essential fatty acids* needed *to make some membrane phospholipids* -*Vitamins* are *another class of essential organic molecules* that are *required in small quantities for enzymes to function* and, for this reason, are considered to be *COENZYMES* -Absence or low levels of vitamins can have a dramatic effect on health -*Fat-soluble/water-soluble vitamins* must be *obtained from food* -*Minerals = inorganic essential nutrients* that *must be obtained from food* -*Among their many functions* = *minerals help in structure + regulation* = *co-factors* -Certain *amino acids must be from food* + *cannot be synthesized by body* -These amino acids are the "essential" amino acids. *The human body can synthesize only 11/20 required amino acids*; the rest must be *obtained from food* -*4 classes* = 1. *Essential fatty acids*, such as linoleic acid, are •used to make phospholipids of cell membranes and •found in seeds, grains, and vegetables. 2. *Essential amino acids* are •used to make proteins and •found in meats, eggs, milk, and cheese. 3. *Essential vitamins and minerals* are •required in *minute amounts* + absolutely *essential to good health* 4. *Vitamins are organic nutrients* that may be *water-soluble* (vitamins B and C) or *fat-soluble* (vitamins A, D, E, K)

The Calvin Cycle

-*After energy from the sun is converted into chemical energy*, and *temporarily stored in ATP and NADPH molecules* the *cell has the fuel needed to build carbohydrate molecules for long-term energy storage* -The *products of the light-dependent reactions, ATP and NADPH,* have *lifespans in the range of millionths of seconds, whereas the products of the light- independent reactions* (carbohydrates and other forms of reduced carbon) *can survive for hundreds of millions of years* -The *carbohydrate molecules made will have a backbone of carbon atoms* Where does the carbon come from? It comes from *carbon dioxide, the gas that is a waste product of respiration in microbes, fungi, plants, and animals*

Introduction of Digestive Systems

-*All living organisms need nutrients to survive* -While *plants can obtain the molecules required for cellular function8 through the process of *PHOTOSYNTHESIS*, *most animals obtain their nutrients by the consumption of other organisms* -At the cellular level, the *biological molecules necessary for animal function are amino acids, lipid molecules, nucleotides, and simple sugars* -However, the *food consumed consists of protein, fat, complex carbohydrates* -*Animals must convert these macromolecules into the simple molecules* required for *maintaining cellular functions = new molecules, cells, tissues* -The *conversion of the food consumed to the nutrients* required is a *multi-step process involving digestion and absorption* -*During digestion, food particles are broken down to smaller components*, and later, *they are absorbed by the body* -One of the *challenges in human nutrition is maintaining a balance* *btwn food intake, storage, energy expenditure* -*Imbalances can have serious health consequences* -For example, eating too much food while *not expending much energy leads to obesity*, which in turn will *increase the risk of developing illnesses* such as type-2 diabetes and cardiovascular disease. The recent rise in obesity and related diseases makes understanding the role of diet and nutrition in maintaining good health all the more important -*Animals obtain their nutrition from the consumption of other organisms* -*Depending on their diet* = *animals can be classified as plant eaters (herbivores), meat eaters (carnivores)* and *those that eat both plants and animals (omnivores)* -The *nutrients and macromolecules present in food* are *not immediately accessible to the cells* -There are a *number of processes that modify food* within the animal body in order to *make the nutrients and organic molecules accessible for cellular function* -As *animals evolved in complexity of form and function* their *digestive systems have evolved to accommodate various dietary needs*

Other Types of Fermentation

-*ALL forms of fermentation*, *except lactic acid* fermentation, *produce gas* Other fermentation methods *occur in bacteria* -*Facultatively ANAEROBIC* = many *prokaryotes*, *need oxygen* -This means that they *can switch btwn AEROBIC respiration + FERMENTATION depending on availability of oxygen* -Certain prokaryotes, like *Clostridia, are obligate anaerobes* -*Obligative anaerobes* = *ANAEROBIC, live and grow* in the *absence of molecular oxygen* in stagnant *ponds/soils* -*Oxygen is a poison to these* + *kills them* on exposure -The *production of particular types of gas* is used as an *indicator of the fermentation of specific carbohydrates* which plays a role in the laboratory *identification of the bacteria* -Various methods of fermentation are *used to ensure enough of NAD+ for the 6th step in glycolysis* Without these pathways, that step would not occur and no ATP would be harvested from the breakdown of glucose.

Limits on Animal Size and Shape

-*Animals w/ BILATERAL SYMMETRY in WATER* = tend to *have a fusiform shape*: this is a *tubular shaped body* that is *tapered at both ends* -This *shape decr the drag on the body* as it moves through water and *allows the animal to swim* at high speeds - Certain types of *sharks can swim at 50km/hour* and some dolphins at 32 to 40 kilometers per hour -*Land animals frequently travel FASTER*, although the *tortoise and snail* are significantly *slower than cheetahs* -Another difference in the *adaptations of aquatic/land-dwelling organisms* is that *aquatic organisms are constrained in shape by the forces of drag in the water* since *water has higher viscosity than air* -On the other hand, *land-dwelling organisms are constrained mainly by gravity* and *drag is relatively unimportant* For example, most adaptations in birds are for gravity not for drag. -*Most animals have an exoskeleton*, including *insects, spiders, scorpions, horseshoe crabs, centipedes, crustaceans* -Scientists estimate that, of insects alone, there are over *30 million species on our planet -*The EXOSKELETON* = a *hard covering* or shell that *provides benefits to the animal, such as protection against damage from predators/water loss (for land animals)*; it also *provides for the attachments of muscles* -As the *tough and resistant outer cover of an arthropod*, the *exoskeleton may be constructed of a tough polymer such as CHITIN* and is often biomineralized with *materials such as CALCIUM CARBONATE* -This is *fused to the animal's epidermis* -*Ingrowths of the exoskeleton*, called *APODEMES* = function as *attachment sites for muscles*, similar to tendons in more advanced animals -In order *to grow*, the *animal must first synthesize a new exoskeleton underneath the old one* and then *shed or molt the original* covering -This *limits the animal's ability to grow continually* and may limit the individual's *ability to mature if molting does not occur* at the proper time -The *thickness of the exoskeleton must be incr* significantly to accommodate *any increase in weight* - It is estimated that a *doubling of body size* increases body *weight by a factor of 8* -The increasing thickness of the chitin necessary to support this weight *limits most animals w/ an exoskeleton to a relatively small size* -The *same principles apply to endoskeletons*, but they are more *efficient bc muscles are attached on the outside*, making it *easier to compensate for increased mass* -*An animal w/ an endoskeleton* has its *size determined by the amount of skeletal system* it needs in order to *support the other tissues/muscle* it needs for movement -As the *body size incr*, both *bone and muscle mass incr* -The *speed achievable by the animal is a balance between its overall size and the bone and muscle that provide support and movement*

Introduction of Energy in Living Systems Geothermal energy plant tranforms thermal energy into what? Electrical energy plant converts energy from_____________ to another. In photosynthesis, plants convert chemical energy into ____________

-This *geothermal energy plant transforms thermal energy* from deep in the ground *into electrical energy*, which can be easily used -The *electrical energy plant converts energy from 1 form to another* form that can be *more easily used* -This type of generating plant *starts w/ underground thermal energy (heat)* and *transforms it into electrical energy that will be transported to homes/factories* -Like a generating plant, *plants and animals also must take in energy from the environment* and *convert it into a form that their cells can use* -Energy enters an organism's body in *one form and is converted into another form* that can fuel the organism's life functions -In the process of *photosynthesis*, *plants/photosynthetic producers take in energy in the form of light (solar energy) and convert it into chemical energy* = *glucose* which *stores this energy in its chemical bonds* - Then, a *series of metabolic pathways, collectively* = *cellular respiration*, *extracts the energy from the bonds in glucose and converts it into a form that all living things can use*—both producers, such as plants, and consumers, such as animals.

Alcohol Fermentation

Another familiar fermentation process is *alcohol fermentation* that *produces ethanol = an alcohol* -The *first chemical reaction of alcohol fermentation* is the following (*CO2 doesn't participate in the 2nd reaction*): *Pyruvic acid → CO2 + acetaldehyde + NADH → ethanol + NAD+* -The *first reaction is catalyzed by pyruvate decarboxylase*( a cytoplasmic enzyme) *w/ a coenzyme of thiamine pyrophosphate* (TPP, derived from *vitamin B1 *and also called thiamine) -A *carboxyl group is removed from pyruvic acid*, *releasing CO2 as a gas* -The *loss of carbon dioxide REDUCES the size of the molecule by one carbon*, making =*acetaldehyde* -The *2nd reaction is catalyzed by alcohol dehydrogenase* to *oxidize NADH to NAD+* and *reduce acetaldehyde to ethanol* -The *fermentation of pyruvic acid by yeast* produces the *ethanol found in alcoholic beverages* -*Ethanol tolerance of yeast is variable* ranging from about *5-21%* depending on the *yeast strain and environmental conditions* •The *baking and winemaking industries* have used alcohol fermentation for thousands of years. •In this process, *yeast (single-celled fungi)*: •*oxidize NADH back to NAD+* and •*convert pyruvate to CO2 + ethanol*

Generating an Energy Carrier: ATP

As in the intermembrane space of the mitochondria during cellular respiration, the buildup of hydrogen ions inside the thylakoid lumen creates a concentration gradient. The passive diffusion of hydrogen ions from high concentration (in the thylakoid lumen) to low concentration (in the stroma) is harnessed to create ATP, just as in the electron transport chain of cellular respiration. The ions build up energy because of diffusion and because they all have the same electrical charge, repelling each other. To release this energy, hydrogen ions will rush through any opening, similar to water jetting through a hole in a dam. In the thylakoid, that opening is a passage through a specialized protein channel called the ATP synthase. The energy released by the hydrogen ion stream allows ATP synthase to attach a third phosphate group to ADP, which forms a molecule of ATP (Figure 8.16). The flow of hydrogen ions through ATP synthase is called chemiosmosis because the ions move from an area of high to an area of low concentration through a semi-permeable structure.

Four complexes of the ETC

Complex I -*2 electrons carried to first complex aboard NADH* -*This complex* labeled I is *composed of flavin mononucleotide (FMN)/iron-sulfur (Fe-S)*-*containing protein* -*FMN from vitamin B2* called *riboflavin*, is *1 of several prosthetic groups/co-factors in ETC* -*PROSTHETIC GROUP* is a *non-protein required for the activity of a protein* + *organic/inorganic*, *non-peptide molecules facilitate its function* include *co-enzymes* which are *prosthetic groups of enzymes* -The *enzyme in complex I is NADH dehydrogenase* and is a very *large protein of 45 amino acid chains* -Complex I can *pump 4 hydrogen ions across membrane* from the matrix into the intermembrane space* and it is in this way that the *hydrogen ion gradient is established* and *maintained btwn 2 compartments separated by the inner mitochondrial membrane* -*Complex II directly receives FADH2* which *DOES NOT pass through complex I -*UBIQUINONE (Q)* = The *compound connecting the 1/2 complexes to 3* -The *Q molecule is lipid soluble* and *freely moves thru hydrophobic core of the membrane* -*When reduced* = *(QH2), ubiquinone delivers its electrons to the next complex* in the *ETC* -*Q receives electrons from NADH from complex I* + *electrons from FADH2 from complex II* (succinate dehydrogenase) -This *enzyme + FADH2* form a *small complex that delivers electrons directly to ETC*, *bypassing the 1st complex* -Since *these electrons BYPASS + DON'T ENERGIZE the proton pump in 1st complex* = *fewer ATP molecules made from the FADH2 electrons* -The *number of ATP molecules ultimately obtained* is directly *proportional to the number of protons pumped across the inner mitochondrial membrane* -28 from ETC but *32 in total* -The *third complex = MADE OF CYTOCHROME B*, *another Fe-S protein* = *Rieske center (2Fe-2S center)* + *cytochrome c proteins* this *complex is also called CYTOCHROME OXIDOREDUCTASE* -*Cytochrome proteins* = *prosthetic group of heme* -The *heme molecule* is similar to the *heme in hemoglobin* but it *CARRIES ELECTRONS NOT OXYGEN* -*Iron ion at its core* is *reduced/oxidized* as it *passes electrons*, fluctuating *btwn diff oxidation states*: *Fe++ (reduced)* and *Fe+++ (oxidized)* -The *heme molecules in the cytochromes* have *slightly diff characteristics due to effects of diff proteins binding them* giving slightly *diff characteristics to each complex* -*Complex III pumps protons thru the membrane* + *passes electrons to cytochrome c for transport to 4th complex of proteins/enzymes* (*cytochrome c is the acceptor of electrons from Q* however, whereas *Q carries pairs of electrons, cytochrome c can accept only one at a time*). The *fourth complex = cytochrome proteins c, a, and a3* -This complex *contains 2 heme groups (one in each of the 2 cytochromes, a, and a3)* + *3 copper ions (a pair of CuA, one CuB in cytochrome a3)* -The *cytochromes hold an oxygen molecule very tightly btwn iron and copper ions until oxygen is completely reduced* -The *reduced oxygen then picks up 2 hydrogen ions from the surrounding medium to make water (H2O)* The *removal of the hydrogen ions from the system contributes to the ion gradient* used in the process of *chemiosmosis*

Photosynthesis fuels the biosphere + autotrophs

•*Photosynthesis* -*removes CO2 from atmosphere* and *stores it in plant matter* •The *burning of sugar in cellular respiration** of almost all organisms *releases CO2 back to the environment* •*Plants are autotrophs*, which •*sustain themselves*, •*don't consume organic molecules from other organisms*, and •*make their own food* through the process of *photosynthesis*, in which they *convert CO2 and H2O to sugars and other organic molecules* •*Photoautotrophs* = *feed* us, *clothe* us (think cotton), *house* us (think wood), *provide energy for warmth*, *light*, *transport*, and *manufacturing*

Neural Responses to Food

Neural Responses to Food In reaction to the smell, sight, or thought of food, like that shown in Figure 34.20, the first response is that of salivation. The salivary glands secrete more saliva in response to stimulation by the autonomic nervous system triggered by food in preparation for digestion. Simultaneously, the stomach begins to produce hydrochloric acid to digest the food. Recall that the peristaltic movements of the esophagus and other organs of the digestive tract are under the control of the brain. The brain prepares these muscles for movement as well. When the stomach is full, the part of the brain that detects satiety signals fullness. There are three overlapping phases of gastric control—the cephalic phase, the gastric phase, and the intestinal phase—each requires many enzymes and is under neural control as well. The response to food begins even before food enters the mouth. The first phase of ingestion, called the cephalic phase, is controlled by the neural response to the stimulus provided by food. All aspects—such as sight, sense, and smell—trigger the neural responses resulting in salivation and secretion of gastric juices. The gastric and salivary secretion in the cephalic phase can also take place due to the thought of food. Right now, if you think about a piece of chocolate or a crispy potato chip, the increase in salivation is a cephalic phase response to the thought. The central nervous system prepares the stomach to receive food. The gastric phase begins once the food arrives in the stomach. It builds on the stimulation provided during the cephalic phase. Gastric acids and enzymes process the ingested materials. The gastric phase is stimulated by (1) distension of the stomach, (2) a decrease in the pH of the gastric contents, and (3) the presence of undigested material. This phase consists of local, hormonal, and neural responses. These responses stimulate secretions and powerful contractions. The intestinal phase begins when chyme enters the small intestine triggering digestive secretions. This phase controls the rate of gastric emptying. In addition to gastrin emptying, when chyme enters the small intestine, it triggers other hormonal and neural events that coordinate the activities of the intestinal tract, pancreas, liver, and gallbladder.

Rectum and Anus + Accessory Organs

Rectum and Anus -The *rectum* = the *terminal end of large intestine* -The *primary role of the rectum* = to *store the feces until defecation* -Feces are propelled using peristaltic movements during elimination -The *anus* = an opening at the far-end of digestive tract* + the *exit point for waste* material -*Two sphincters btwn rectum + anus control elimination*: the *inner sphincter = involuntary* and the *outer sphincter = voluntary* Accessory Organs -*Accessory organs* are *organs that add secretions (enzymes) that catabolize food into nutrients* -*Accessory organs* = *salivary glands, liver, pancreas, gallbladder* are regulated *by hormones in response to the food consumed* -The *liver* = the *largest internal organ in humans* + *digests fats* + *detoxify blood* + *converts glucose to glycogen* -The *liver produces bile*, a digestive juice that is required for the *breakdown of fatty components* of the food in the duodenum The liver also *processes the vitamins/fats* + *synthesizes plasma proteins* -The *pancreas* =important *gland that secretes digestive juices* + *chyme produced from the stomach is HIGHLY ACIDIC* -The *pancreatic juices contain high levels of bicarbonate* = an *alkali that neutralizes acidic chyme* + contain a *large variety of enzymes for the digestion of protein/carbohydrates* -The *gallbladder* = a small *organ aids liver w/ storing bile/concentrating bile salts* When *chyme containing fatty acids enters the duodenum*, the *bile is secreted from the gallbladder into the duodenum*

Introduction of Glycolysis ALL energy used in cells comes in the bonds of ____________ Glycolysis is the first step in _____________ Is cellular respiration aerobic or anaerobic? Glucose enters _____________________ in 2 ways. What is a GLUT protein? Glycolysis is split into 2 phases: ______________ and _________________

- *All energy* used by living cells *comes in the bonds of the sugar* = *glucose* -*Glycolysis* is the *first step in the breakdown of glucose* to *extract energy for cellular metabolism* -Nearly *all living organisms carry out glycolysis as part of their metabolism* -The *process does not use oxygen* and is therefore *anaerobic* -*Cellular Respiration* = *aerobic + harvests energy from food molecules* + *exergonic (energy release)*from glucose to ATP -*Glycolysis takes place in the cytosol of both prokaryotic/eukaryotic cells* -*Glucose enters HETEROTROPHIC cells in 2 ways*. One method is through *secondary active transport = transport takes place against the glucose concentration gradient* + the other mechanism uses a *group of integral proteins = GLUT proteins* also known as *glucose transporter proteins* = *assist in the FACILITATED DIFFUSION of glucose* -*Glycolysis begins w/ 6-carbon ring-shaped structure* (C6H12O6) of a single glucose molecule and *ends w/ 2 molecules of a 3-carbon sugar called pyruvate* -*Glycolysis* = *2 distinct phases* -The first part (steps 1-4) of the glycolysis pathway *traps glucose molecule in the cell* + *uses energy to modify it* so that the *6-carbon sugar molecule can be split in HALF into two 3-carbon molecules* - *energy is consumed bc 2 ATP molecules are used to energize a glucose molecule* which is *then able to split into 2 small sugars* -The second part (steps 5-9) of *glycolysis extracts energy from the molecules* + *stores it in *2 molecules of NADH* (reduced by NAD+) + *2 molecules of ATP* -the energy payoff phase, two NADH molecules are produced for *each initial glucose molecule* and *4 ATP molecules are made but net gain of 2*

Anabolic and Catabolic Pathways Biosynthetic processes are critical to the what of the cell and take place constantly and demand what provided by NADH and NADPH? What is ATP? What kind of pathway is the breakdown of sugars or large proteins to amino acid building blocks? Molecular energy stored in the bonds of a complex molecule is ABSORBED/RELEASED in catabolic pathways and harvested to produce ATP?

-*Anabolic pathways* = *require an input of energy to synthesize complex molecules from simpler ones* -(Synthesizing sugar from CO2), (large proteins from amino acid building blocks), and the (synthesis of new DNA strands from nucleic acid building blocks) -These biosynthetic processes are *critical to the life of the cell* + *take place constantly* and demand *energy provided by ATP and other high-energy molecules like NADH* (nicotinamide adenine dinucleotide) and NADPH -*ATP* is an important molecule for *cells to have in sufficient supply at all times* -The *breakdown of sugars* illustrates how a *single molecule of glucose can store enough energy to make ATP, 36 to 38 molecules* = catabolic pathway -*Catabolic pathways* = involve the *degradation (or breakdown) of complex molecules into simpler ones* -*Molecular energy stored in the bonds of complex molecules* is *RELEASED in catabolic pathways* and harvested in such a *way that it can be used to produce ATP* -Other *energy-storing molecules, such as fats*, are also *broken down through similar catabolic reactions* to release energy and make ATP -It is important to know that the *chemical reactions of metabolic pathways DONT TAKE PLACE SPONTANEOUSLY*. Each reaction step is *facilitated, or catalyzed*, by a protein called an enzyme. *Enzymes are important for catalyzing all types of biological reactions*—those that require energy as well as those that release energy.

Body Plans

-*Animal body plans* follow *set patterns related to symmetry* -They are *asymmetrical, radial, bilateral in form* -*Asymmetrical animals* are *animals w/ no pattern/symmetry*; an example of an *asymmetrical animal is a sponge* -*Radial symmetry* describes when an *animal has an up-and-down orientation*: *any plane cut along its longitudinal axis* through the organism produces *equal halves* but not a definite right or left side -This *plan is found mostly in aquatic animals*, especially *organisms that attach themselves to a base (rock or a boat)* and *extract their food from the surrounding water* as it flows around the organism -*Bilateral symmetry* is *illustrated in the same figure by a goat* -The goat also has an *upper and lower component to it*, but a *plane cut from front to back separates the animal intodefinite right and left sides* -Additional terms used when describing positions in the body are *anterior (front)*, *posterior (rear)*, *dorsal (toward the back)*, and *ventral (toward the stomach)* -*Bilateral symmetry* is found in both *land-based and aquatic animals*; it *enables a high level of mobility*

Homeostasis

-*Animal organs and organ systems constantly adjust to internal and external changes*= *HOMEOSTASIS* ("steady state") -*These changes might be in the level of glucose or calcium in blood* or in external temperatures -*Homeostasis* means to maintain *dynamic equilibrium in the body*. It is *dynamic because it is constantly adjusting to the changes that the body's systems encounter*. It is equilibrium because *body functions are kept within specific ranges*. Even an animal that is apparently *inactive is maintaining this homeostatic equilibrium* -The *goal of homeostasis is the maintenance of equilibrium* around a point or value called a set point. While *there are normal fluctuations from the set point*, the body's systems will usually attempt to go back to this point. -*A change in the internal or external environment* = *stimulus and is detected by a receptor*; the response of the system is to *adjust the deviation parameter* toward the set point. For instance, *if the body becomes too warm, adjustments are made to cool the animal*. If the blood's glucose rises after a meal, adjustments are made to lower the blood glucose level by getting the nutrient into tissues that need it or to store it for later use. -*When a change occurs in an animal's environment*, an *adjustment* must be made. The *receptor senses the change in the environment, then sends a signal to the control center* (in most cases, the brain) which in turn generates a *response signaled to an effector* -The *effector is a muscle* (that contracts or relaxes) or a *gland that secretes*. Homeostasis is maintained by *negative feedback loops* + *Positive feedback loops actually push the organism further out of homeostasis* but may be necessary for life to occur. Homeostasis is *controlled by the nervous and endocrine system of mammals*

Endotherms and Ectotherms

-*Animals can be divided into 2 groups*: some *maintain a constant body temp in the face of differing environmental temps*, while others have a *body temp that is the same as their environment* and thus varies with the environment. -*Animals that do not control their body temperature* = *ectotherms* -This group has been called *cold-blooded*, but the term may not apply to an animal in the desert with a very warm body temperature -In contrast to ectotherms, which *rely on external temperatures to set their body temperatures*, *poikilotherms are animals with constantly varying internal temps* -An animal that *maintains a constant body temperature in the face of environmental changes* = *homeotherm* -*Endotherms are animals that rely on internal sources for body temp* but which can *exhibit extremes in temp* These animals are able to maintain a level of *activity at cooler temperature, which an ectotherm cannot due to differing enzyme levels of activity* -*Heat can be exchanged between an animal and its environment* through four mechanisms: *radiation, evaporation, convection, and conduction* -*Radiation is the emission of electromagnetic "heat" waves* Heat comes from the sun in this manner and radiates from dry skin the same way. *Heat can be removed with liquid from a surface during evaporation* This occurs when a mammal sweats. *Convection currents of air remove heat from the surface of dry skin as the air passes over it* Heat will be conducted from one surface to another during direct contact with the surfaces, such as an animal resting on a warm rock.

Heat Conservation and Dissipation

-*Animals conserve/dissipate heat* in a variety of ways -In certain climates, *endothermic animals have some form of insulation*, such as *fur, fat, feathers* -*Animals with thick fur or feathers create an insulating layer of air btwn their skin and internal organs* -Polar bears and seals live and swim in a subfreezing environment and yet maintain a constant, warm, body temperature -The arctic fox, for example, uses its fluffy tail as extra insulation when it curls up to sleep in cold weather -*Mammals have a residual effect from shivering and incr muscle activity: arrector pili muscles cause "goose bumps,"* causing small hairs to stand up when the individual is cold; this has the *intended effect of incr body temp* -*Mammals use layers of fat to achieve the same end* + *Loss of body fat will compromise this ability* to conserve heat. -*Endotherms use their circulatory systems to help maintain body temp* -*Vasodilation brings more blood and heat to the body surface**, facilitating *radiation and evaporative heat loss*, which *helps to cool the body* -*Vasoconstriction reduces blood flow in peripheral blood vessels*, forcing *blood toward the core and the vital organs found there*, and *conserving heat* -*Some animals* have adaptions to their circulatory system that *enable them to transfer heat from arteries to veins*, *warming blood returning to the heart* -This is called a *countercurrent heat exchange*; it *prevents the cold venous blood from cooling the heart and other internal organs* -This adaption *can be shut down in some animals to prevent overheating the internal organs* -The countercurrent adaption is *found in many animals, including dolphins, sharks, bony fish, bees, and hummingbirds* -In contrast, *similar adaptations can help cool endotherms when needed*, such as dolphin flukes and elephant ears. -*Some ectothermic animals use changes in their behavior to help regulate body temp* -For example, a desert ectothermic animal may simply seek cooler areas during the hottest part of the day in the desert to keep from getting too warm -The *same animals may climb onto rocks to capture heat during a cold desert night* Some animals seek water to aid evaporation in cooling them, as seen with reptiles. Other ectotherms use group activity such as the activity of bees to warm a hive to survive winter. -*Many animals, especially mammals, use metabolic waste heat as a heat source* -When *muscles are contracted, most of the energy from the ATP used in muscle actions is wasted energy* that translates into heat -*Severe cold elicits a shivering reflex that generates heat* for the body. Many *species also have a type of adipose tissue* called *brown fat* that *specializes in generating heat*

Invertebrate Digestive System

-*Animals have evolved diff types of digestive systems* to *aid in the digestion of the diff foods they consume* -The *simplest example is that of a gastrovascular cavity* and is *found in organisms w/ only 1 opening for digestion* -Platyhelminthes (flatworms), Ctenophora (comb jellies), and Cnidaria (coral, jelly fish, and sea anemones) use this type of digestion -*Gastrovascular cavities* = are typically a *blind tube/cavity w/ only 1 opening, the "mouth"*, which *also serves as an "anus"* -*Ingested material enters the mouth and passes through a hollow, tubular cavity* -*Cells in cavity secrete digestive enzymes* that *break down the food* -The *food particles are engulfed by cells lining the gastrovascular cavity* -*The alimentary canal* = *more advanced system*: it consists of *1 tube w/ a mouth at one end and an anus at the other* -Earthworms are an example of an animal with an alimentary canal. Once the *food is ingested thru the mouth + passes thru the esophagus* + *stored in an organ called the crop* then it passes into the gizzard where it is *churned and digested* From the gizzard, the food passes through the intestine, the nutrients are absorbed, and the *waste is eliminated as feces, called castings, through the anus*

Food Energy and ATP

-*Animals need food to obtain energy* + *maintain homeostasis* -*Homeostasis* = the *ability of a system to maintain a stable internal environment* in the face of external changes to the environment. Ex: the *norm body temp of humans is 37°C (98.6°F)* -*Humans maintain this temp even when external temp is hot/cold* -It *takes energy to maintain this body temp* + *animals obtain this energy from food* -The *primary source of energy for animals is carbs* (mainly glucose) -*Glucose* (body's fuel) -The *digestible carbohydrates in an animal's diet* = *converted to glucose molecules thru catabolic chem reactions* -*Adenosine triphosphate/ATP* = the *primary energy currency in cells*; *ATP stores energy in phosphate ester bonds* -*ATP releases energy when phosphodiester bonds* = *broken + ATP is converted to ADP* + *phosphate group* -*ATP is produced by the oxidative reactions in the cytoplasm* and mitochondrion of the cell, where carbohydrates, proteins, and fats undergo a series of metabolic reactions collectively called cellular respiration. For example, *glycolysis is a series of reactions in which glucose is converted to pyruvic acid* and some of its *chemical potential energy is transferred to NADH and ATP* -*ATP* = *required for all cellular functions* -It is *used to build the organic molecules required for cells/tissues* + it provides *energy for muscle contraction* + *transmission of electrical signals in nervous system* -When the *amount of ATP is available in excess of the body's requirements*, the *liver uses excess ATP* and *excess glucose to produce molecules* = *glycogen* -*Glycogen is a polymeric form of glucose* and is *stored in the liver/skeletal muscle cells* -*When blood sugar drops*, the *liver releases glucose from stores of glycogen* -*Skeletal muscle converts glycogen to glucose* during intense exercise -The process of *converting glucose/excess ATP to glycogen* and the storage of excess energy is an evolutionarily *important step in helping animals deal with mobility, food shortages, and famine*

Enzymes What is a catalyst? What are almost all enzymes known as and what monomers are they made of? What type of energy do they change and for what- to reach the _______________ energy? What type of energy do they NOT change?

-*CATALYST* = *A substance that helps a chemical reaction to occur* and *ENZYMES* = the *special molecules that catalyze biochemical reactions* -*Almost all enzymes are PROTEINS*, made up of chains of *amino acids*, and they perform the critical task of *lowering activation energies of chemical reactions* inside the cell -*Enzymes do this* by *binding to the reactant molecules*, and holding them in such a way as to make the chemical bond-*breaking and bond-forming processes take place more readily* -It is important to remember that *ENZYMES DO NOT CHANGE THE ∆G* of a reaction -They *don't change whether a reaction is exergonic (spontaneous) or endergonic (nonspontaneous)* - This is because they don't *change the free energy of the reactants or products* -They *ONLY reduce activation energy* required to *reach the TRANSITION STATE*

Regulation of Cellular Respiration

-*Cellular respiration* must be *regulated to provide balanced amounts of energy* in the form of *ATP* -The *cell must generate a number of intermediate compounds* that are used in the *anabolism and catabolism of macromolecules* -Without controls, *metabolic reactions would come to a stand still as the forward/backward reactions* reached a *state of equilibrium* -Resources would be used inappropriately. *A cell does not need the max amount of ATP that it can make all the time*: At times, the *cell needs to shunt some of the intermediates* to pathways *for amino acid, protein, glycogen, lipid, nucleic acid* production -In short, the *cell needs to control its metabolism*

Anaerobic Cellular Respiration

-*Certain prokaryotes*, including some *species of bacteria and Archaea*, USE ANAEROBIC CELL RESP* -Ex: the group of *Archaea-methanogens reduce CO2 to CH4 to oxidize NADH* -These *microorganisms are found in soil* and in the *digestive tracts of ruminants*/ cows and sheep -Similarly, *sulfate-reducing bacteria and Archaea*, most of which are anaerobic *reduce sulfate to hydrogen sulfide to regenerate NAD+ from NADH* •*Fermentation is a way of harvesting chemical energy that does not require oxygen* Fermentation •*uses glycolysis* •*produces 2 ATP* molecules per glucose, and •*reduces NAD+ to NADH* **•*Fermentation also provides an anaerobic path for RECYCLE NADH back to NAD+*

Free Energy When do chemical reactions release energy? What is a measurement of free energy used to quantitate? What is the second law of thermodynamics? What is Gibbs free energy? How do you calculate ∆G? What 3 conditions does standard free energy need?

-*Chemical reactions release energy when energy-storing bonds are BROKEN* an important next question is how is the energy associated with chemical reactions quantified and expressed? How can the energy released from one reaction be compared to that of another reaction? -*A measurement of free energy* is used to *quantitate these energy transfers* -*Free energy (Gibbs free energy)*(abbreviated with the letter G) after *Josiah Willard Gibbs* = the *scientist who developed the measurement* -Recall that according to the *second law of thermodynamics* = all *energy transfers involve the loss of some amount of energy in an unusable form such as heat* resulting in *entropy* -*Gibbs free energy* = the *energy associated w/ a chemical reaction available after entropy* is accounted for -*Gibbs free energy = usable energy/available to do work* -Every *chemical reaction involves a change in free energy*, called delta G (∆G) -The *change in free energy can be calculated for any system that undergoes such a change* such as a chemical reaction -*To calculate ∆G, subtract the amount of energy lost to entropy* (denoted as ∆S) from the *total energy change of the system* -This *total energy change in the system* = *enthalpy ∆H* -The formula for calculating ∆G is as follows, where the symbol *T refers to absolute temp in Kelvin* (degrees Celsius + 273): *ΔG = ΔH − TΔ* -The standard free energy change of a chemical reaction is expressed as an amount of *energy per mole of the reaction product* (either in kilojoules or kilocalories, kJ/mol or kcal/mol; *1 kJ = 0.239 kcal*) under *standard pH, temp, pressure conditions* Standard pH, temperature, and pressure conditions are generally *calculated at pH 7.0, 25 degrees Celsius, 100 kilopascals (1 atm pressure)* respectively. It is important to note that cellular conditions vary considerably from these standard conditions, and so standard calculated *∆G values will be diff inside the cell*

Understanding pigments

-*Diff kinds of pigments exist*, and each has evolved to *absorb only certain wavelengths (colors) of visible light* -*Pigments reflect/transmit the wavelengths they cannot absorb*, making them *appear in the corresponding color* -*Chlorophylls and carotenoids* are the two major classes of *photosynthetic pigments found in plants and algae*; each class has *multiple types of pigment molecules* -There are *five major chlorophylls: a, b, c and d and a* related molecule found in *prokaryotes called bacteriochlorophyll* -*Chlorophyll a* = form of *chlorophyll that absorbs VIOLET/BLUE and RED* and consequently has a *bluish-green color*; the only pigment molecule that *performs the photochemistry by getting excited and losing an electron to the ETC*, *HIGHER PLANT CHLOROPLAST* -*Chlorophyll b* = accessory pigment that *absorbs BLUE and RED/ORANGE light* and consequently has a *yellowish-green tintare found in *higher plant chloroplasts* -With *dozens of diff forms*, *carotenoids are a much larger group of pigments* -The *carotenoids found in fruit*—such as the red of tomato (lycopene), the yellow of corn seeds (zeaxanthin), or the orange of an orange peel (β-carotene)—are used as *advertisements to attract seed dispersers* -*In photosynthesis* = *carotenoids function as photosynthetic pigments* that are very *efficient molecules for the disposal of excess energy* -When a *leaf is exposed to full sun*, the *light-dependent reactions* are required to *process an enormous amount of energy*; if that energy is *not handled properly* = *does damage* -Therefore, *many carotenoids reside in the thylakoid membrane*, *absorb excess energy*, and *safely dissipate that energy as heat* -*Each type of pigment* can be *identified w/* the *specific pattern of wavelengths it absorbs from visible light* = *absorption spectrum* -The absorption spectra for chlorophyll a, chlorophyll b, and a type of *carotenoid pigment called β-carotene (which absorbs blue and green light)* + *each pigment has a distinct set of peaks/troughs*, revealing a highly specific pattern of absorption -*Chlorophyll a absorbs wavelengths from either end of the visible spectrum* (blue and red), but *not green* -Because *green is reflected or transmitted, chlorophyll* appears green. Carotenoids *absorb in the short-wavelength blue region*, and reflect the *longer yellow, red, and orange wavelengths* -*Not all photosynthetic organisms have full access to sunlight* b/c of the *comp/environment* -*When studying a photosynthetic organism*, *scientists can determine the types of pigments w/ absorption spectra* = *instrument that can differentiate which wavelengths of light a substance can absorb* -*Spectrophotometers* = *measure transmitted light* and *compute from* it the *absorption* -By *extracting pigments from leaves* and placing these samples into a *spectrophotometer*, scientists can *identify which wavelengths of light an organism can absorb* -Additional methods for the *identification of plant pigments include various types of chromatography that separate the pigments* by their relative affinities to *solid and mobile phases*

Digestion and Absorption

-*Digestion* = the mechanical and chemical break down of food into small organic fragments. It is important to break down macromolecules into smaller fragments that are of suitable size for absorption across the digestive epithelium. Large, complex molecules of proteins, polysaccharides, and lipids must be reduced to simpler particles such as simple sugar before they can be absorbed by the digestive epithelial cells. Different organs play specific roles in the digestive process. The

Energy in Living Systems What is a REDOX reaction? What is oxidation? What is reduction? What incr potential energy and decr potential energy? FAD+ is from what vitamin?

-*Energy production* within a cell involves many *coordinated chemical pathways* -Most of these *pathways are combinations of oxidation and reduction reactions* = *REDOX* = An *oxidation reaction strips an electron from an atom in a COMPOUND* and the *addition of this electron to another compound* is a reduction reaction. Because oxidation and reduction *usually occur together*, these pairs of reactions are called oxidation reduction reactions, or redox reactions -The *removal of an electron from a molecule* = *OXIDIZING IT* results in a *DECR POTENTIAL ENERGY IN THE OXIDIZED COMPOUND* -The electron (sometimes as part of a hydrogen atom), does not remain unbonded, however, in the cytoplasm of a cell -Rather, the *electron is shifted to a second compound, reducing the second compound* -The *shift of an electron from one compound to another removes some potential energy from the first compound (the oxidized compound) and INCREASES the potential energy of the second compound = (the REDUCED COMPOUND)* -The *transfer of electrons between molecules is important bc most of the energy stored in atoms and used to fuel cell functions is in the form of high-energy electrons* The transfer of energy in the form of electrons *allows the cell to transfer and use energy in an incremental fashion—in small packages (electrons)* rather than in a single, destructive burst. This chapter focuses on the extraction of energy from food; you will see that as you track the path of the transfers, you are tracking the path of electrons moving through metabolic pathways *Electron Carriers* -In living systems, a *small class of compounds functions as electron shuttles*: They *bind and carry HIGH-ENERGY ELECTRONS btwn compounds in pathways* -The *principal electron carriers* we will consider are derived from the *B vitamin group + derivatives of nucleotides* + compounds *can be easily reduced* (that is, they accept electrons) or oxidized (they lose electrons). -*Nicotinamide adenine dinucleotide* (NAD) is *derived from vitamin B3, niacin* -*NAD+* = the *oxidized form of the molecule*; *NADH* = the *reduced form of the molecule* after it has accepted *two electrons and a proton* (which together are the *equivalent of a hydrogen atom* with an extra electron). -*NAD+* can *accept electrons from an organic molecule* according to the general equation: Reducing agent *[RH]* + Oxidizing agent *[NAD+]* → *NADH Reduced* + *R* Oxidized -When *electrons are added to a compound* = *REDUCED* -A *compound reduces another* = *REDUCING AGENT* -*RH is a reducing agent*, and *NAD+ is reduced to NADH* -When *electrons are removed from compound* = *OXIDIZED* -A *compound oxidizes another* = *OXIDIZING AGENT* -*NAD+ is an oxidizing agent*, and *RH is oxidized to R* -Similarly, *flavin adenine dinucleotide (FAD+)* is derived from *vitamin B2, also called riboflavin* -Its reduced form is FADH2. -A *second variation of NAD, NADP* = *extra phosphate group* -Both *NAD+ and FAD+* are extensively *used in energy extraction from sugars*, and *NADP plays an important role in ANABOLIC* reactions and photosynthesis -The *oxidized form of the electron carrier (NAD+)* is shown on the left and the *reduced form (NADH)* is shown on the right. The *nitrogenous base in NADH has 1 more hydrogen ion* and *2 more electrons than in NAD+*

Potential and Kinetic Energy What is energy defined as? What is the energy type that is less tangible? What energy has bonds that hold the atoms of molecules together? What energy is not only associated with location but structure of matter as well? The fact that energy can be released implies what kind of energy do the bonds have when broken? Is cellular respiration exergonic or endergonic and anaerobic or aerobic? Is photosynthesis exergonic or endergonic? What is chemical energy?

-*Energy* = defined as the *ability to do work* -As you've learned, *energy exists in diff forms* -Ex: *electrical energy, light energy, and heat energy* are all *diff types of energy* -While these are all *familiar types of energy that one can see/feel, there is another type of energy that is much less tangible.* -This *energy is associated w/ an object held above the ground* -*When an object is in motion*, there is *energy associated* with that object -Ex: airplane in flight, - energy associated with the motion of the airplane bc moving objects are capable of enacting a change, or doing work. Think of a wrecking ball. Even a slow-moving wrecking ball can do a great deal of damage to other objects. However, a *wrecking ball that is not in motion = *incapable of performing work* -*Energy associated with objects in motion* is = *KINETIC ENERGY* -A speeding bullet, a walking person, the rapid movement of molecules in the air (which produces heat), and electromagnetic radiation like light all have kinetic energy. Now what if that same motionless wrecking ball is lifted two stories above a car with a crane? If the *suspended wrecking ball is unmoving*, is there *energy associated with it*? The answer is yes. The suspended wrecking ball has energy associated with it that is fundamentally different from the kinetic energy of objects in motion. This form of energy results from the fact that there is the* potential for the wrecking ball to do work* - If it is released, indeed it would do work -Because this type of *energy refers to the potential to do work* = POTENTIAL ENERGY -*Objects transfer their energy btwn kinetic and potential* in the following way: As the wrecking ball hangs *motionless, it has 0 kinetic and 100 percent potential energy*, when *released = ts kinetic energy begins to incr because it builds speed* due to gravity -At the same time, as it *nears the ground* = it *loses potential energy* -Somewhere mid-fall it has *50 percent kinetic and 50 percent potential energy* Just before it hits the ground, the ball has nearly lost its potential energy and has *near-maximal kinetic energy* Other examples of potential energy include the energy of water held behind a dam, or a person about to skydive out of an airplane. -*Potential energy is not only associated w/ location of matter* (such as a child sitting on a tree branch), but *also w/ structure of matter* A spring on the ground has *potential energy if it is compressed* = *rubber band that is pulled taut* -The very existence of living cells relies *heavily on structural potential energy* -On a chemical level, the *bonds that hold the atoms of molecules together have potential energy* -Remember that anabolic cellular pathways require energy to synthesize complex molecules from simpler ones, and catabolic pathways release energy when complex molecules are broken down. The fact that *energy can be released by the breakdown of certain chemical bonds implies that those bonds have potential energy* -In fact, there is *potential energy stored in bonds of all food molecules we eat*, which is eventually harnessed for use -This is because *these bonds can release energy when broken* -The type of *potential energy that exists within chemical bonds* and is *released when those bonds are broken* = *chemical energy* -*Chemical energy* is *responsible for providing living cells with energy from food* + the release of energy is brought about by breaking the molecular bonds within fuel molecules Ex: *Molecules in gasoline (octane, the chemical formula shown) contain chemical energy within the chemical bonds* + this *energy is transformed into kinetic energy* that allows a car to race on a racetrack -*CELL RESP* = *EXERGONIC* + *AEROBIC* -*PHOTOSYNTHESIS* = *ENDERGONIC*

Regulation of Enzymes by Molecules What's a competitive inhibitor and what does it have the same of from the substrate? What a noncompetitive inhibitor? Which type of inhibition is reversible and how? Which type of inhibition affects initial rate and which type affects maximal? What's an allosteric inhibitor?

-*Enzymes can be regulated* in ways that either *promote or reduce their activity* -There are many *different kinds of molecules that inhibit or promote enzyme function*, and various mechanisms exist for doing so -In some cases of *enzyme inhibition*, for example, *an inhibitor molecule is similar enough to a substrate that it can bind to the active site + block the substrate from binding* -When this happens, the *enzyme is inhibited thru competitive inhibition* = because an *inhibitor molecule competes w/ substrate for active site* binding w/ *SAME STRUCTURE* -On the other hand, in *noncompetitive inhibition* = an inhibitor molecule binds to the enzyme *in an allosteric site* + *blocks substrate* binding to the active site by *changing the shape of active site* -Competitive and noncompetitive inhibition *affect the rate of reaction differently* -*Competitive inhibitors affect initial rate* but *do not affect maximal rate* whereas *noncompetitive inhibitors affect maximal rate* -Some *inhibitor molecules bind to enzymes in a location where their binding induces a conformational change* that *reduces affinity of the enzyme for its substrate* = *ALLOSTERIC INHIBITION* -Most *allosterically regulated enzymes are made up of more than 1 polypeptide*, meaning that they have *more than 1 protein subunit* -When *allosteric inhibitor binds to an enzyme*, all *active sites on protein subunits are changed* slightly such that they bind their substrates with less efficiency -There are allosteric activators as well as inhibitors -*Allosteric activators* bind to locations on an enzyme away from the active site, *inducing a conformational change that increases the affinity of the enzyme's active site(s) for its substrate(s)* -*Allosteric inhibitors* *modify the active site of the enzyme so that substrate binding is reduced/prevented* -In contrast, allosteric activators *modify the active site of the enzyme so that the affinity for the substrate increases* -*The competitive inhibitor CAN BE REVERSED W/ incr the substrate* -*The noncompetitive inhibitor CAN'T bc it doesn't occur in active site* and they're not competing so reverse for what

Control of Catabolic Pathways

-*Enzymes, proteins, electron carriers, pumps* that play roles *in glycolysis, the citric acid cycle, electron transport chain* tend to *catalyze non-reversible reactions* -In other words, *if the initial reaction takes place, the pathway is committed to proceeding with the remaining reactions* -Whether a *particular enzyme activity is released depends upon the energy needs of the cell* (as *reflected by ATP, ADP, and AMP levels*) Glycolysis The *control of glycolysis begins w/ 1st enzyme* in the pathway, *hexokinase* -This *enzyme catalyzes phosphorylation of glucose*, which *helps to prepare the compound for cleavage in a later* -The *presence of negatively charged phosphate prevents the sugar from leaving* the cell -*When hexokinase is inhibited*, *glucose diffuses out of the cell* and *doesn't become a substrate for respiration in tissue* -The *product of hexokinase reaction* is *glucose-6-phosphate*, which *accumulates when a later enzyme, phosphofructokinase, is inhibited* -*Phosphofructokinase*= the *main enzyme controlled in glycolysis* -*High levels of ATP, citrate, lower, more acidic pH* *decrease the enzyme's activity* -An *increase in citrate concentration* can occur because of a *blockage in the citric acid cycle* -*Fermentation, w/ production of organic acids like lactic acid* frequently accounts for the *increased acidity in a cell* however, the *products of fermentation do not accumulate in cells* -The *last step in glycolysis is catalyzed by pyruvate kinase* -The *pyruvate produced can proceed to be catabolized/converted into amino acid alanine* -*If no more energy is needed* and *alanine is in adequate supply*, the *enzyme is inhibited* -The *enzyme's activity is incr* when *fructose-1,6-bisphosphate levels incr* (Recall that *fructose-1,6-bisphosphate is an intermediate in first half of glycolysis*) -The *regulation of pyruvate kinase involves phosphorylation by a kinase* (pyruvate kinase kinase), *resulting in a less-active enzyme* -*Dephosphorylation by a phosphatase reactivates it* -*Pyruvate kinase is also regulated by ATP (a negative allosteric effect)* -*If more energy is needed* = *more pyruvate will be converted TO acetyl CoA* *through pyruvate dehydrogenase* -*If either acetyl groups/NADH accumulate* = there is *less need for reaction* and the *rate decreases* -*Pyruvate dehydrogenase* is also *regulated by phosphorylation*: A *kinase phosphorylates to form an inactive enzyme*, and a *phosphatase reactivates it* -The *kinase and the phosphatase are also regulated* Citric Acid Cycle -The *citric acid cycle is controlled thru enzymes that catalyze the reactions* that *make the first 2 molecules of NADH* -These enzymes are *isocitrate dehydrogenase and α-ketoglutarate dehydrogenase* -When *adequate ATP and NADH levels are available*, the *rates of these reactions decr* -When *more ATP is needed, as reflected in rising ADP levels*, the *rate incr* -α-Ketoglutarate dehydrogenase will also be affected by the levels of succinyl CoA—a subsequent intermediate in the cycle—causing a decrease in activity. A decrease in the rate of operation of the pathway at this point is not necessarily negative, as the increased levels of the α-ketoglutarate not used by the citric acid cycle can be used by the cell for amino acid (glutamate) synthesis. Electron Transport Chain *Specific enzymes of the electron transport chain are unaffected by feedback inhibition*, but the *rate of electron transport through the pathway is affected by the levels of ADP and ATP* -*Greater ATP consumption by a cell* is *indicated by a buildup of ADP* -As *ATP usage decr*, the *concentration of ADP decr*, and now, *ATP begins to build up in the cell* -This *change is relative concentration of ADP to ATP* triggers the *cell to slow down the electron transport chain*

Activation Energy Even what type of reactions need some energy to proceed? What is this small energy called? What is the transition state? What does heat energy do? When do reactants reach the transition state? The higher the activation energy the what? This is why enzymes do what to the activation energy? Low activation energies are known as?

-*Even exergonic reactions require a small amount of energy* input to get going before they can proceed with their energy-releasing steps -These *reactions have a net release of energy, but still require some energy* in the beginning -This *small amount of energy* input *necessary for all chemical reactions to occur* = *ACTIVATION ENERGY* (or free energy of activation) and is abbreviated EA -Why would an energy-releasing, negative ∆G reaction actually require some energy to proceed? The reason lies in the steps that take place during a chemical reaction -During chemical reactions, *certain chemical bonds are broken and new ones are formed* -For example, when a glucose molecule is broken down, bonds between the carbon atoms of the molecule are broken. Since *these are energy-storing bonds* = they *release energy* when broken -However, to get them into a state that *allows the bonds to break, the molecule must be somewhat contorted* = *A small energy input is required to achieve this contorted state* This contorted state is called the = *TRANSITION STATE*, and it is a *high-energy, unstable state* -For this reason, *reactant molecules don't last long in their transition state*, but very quickly proceed to the next steps of the chemical reaction. Free energy diagrams illustrate the energy profiles for a given reaction. Whether the reaction is exergonic or endergonic determines whether the products in the diagram will exist at a lower or higher energy state than both the reactants and the products. However, regardless of this measure, the *transition state of the reaction exists at a higher energy state than the reactants, and EA is always positive* Where does the activation energy required by chemical reactants come from? -The *source of the activation energy needed to push reactions forward* = *HEAT energy* from the surroundings. -*Heat energy* (the *total bond energy of reactants/products* in a chemical reaction) *speeds up the motion of molecules*, *incr the freq/force w/ which they collide*; it also *moves atoms and bonds* within the molecule slightly, *helping them reach transition state* -For this reason, *heating up a system + *Increasing the pressure on a system has the same effect* = will cause *chemical reactants to react more frequently* -Once *reactants have absorbed enough heat energy from their surroundings to reach the transition state*, the reaction will proceed. The *activation energy* = of a particular reaction determines the *rate at which it will proceed* -The *higher the activation energy, the slower the chemical reaction will be* Ex: the burning of many fuels, which is strongly exergonic, will take place at a negligible rate unless their activation energy is overcome by sufficient heat from a spark. Once they begin to burn, however, the chemical reactions release enough heat to continue the burning process, supplying the activation energy for surrounding fuel molecules. Like these reactions outside of cells, the *activation energy for most cellular reactions is too high for heat energy to overcome* at efficient rates In other words, in order *for important cellular reactions to occur at appreciable rates* (number of reactions per unit time), their *activation energies must be lowered* = this is referred to as *CATALYSIS* This is a very good thing as far as living cells are concerned. Important macromolecules, such as *proteins, DNA, and RNA, store considerable energy, and their breakdown is EXERGONIC* -If cellular temperatures alone provided enough heat energy for these exergonic reactions to overcome their activation barriers, the essential components of a cell would disintegrate.

Connections of Other *Sugars to Glucose Metabolism* Connections of *Proteins to Glucose Metabolism* Connections of *Lipid and Glucose Metabolisms*

-*Glycogen* (polymer of glucose) is an *energy storage molecule in animals* -When *there is adequate ATP present* = *excess glucose is shunted into glycogen for storage* -*Glycogen* = *made and stored in both liver* and *muscle* - The *glycogen will be hydrolyzed into glucose monomers (G-1-P)8 if BLOOD SUGAR DROPS* -The presence of *glycogen as a source of glucose allows ATP* to *be produced for a longer period of time during exercise* -*Glycogen is broken down into G-1-P* and *converted into G-6-P in muscle/liver cells* and this product enters the *glycolytic pathway* -*Sucrose is a disaccharide w/ a molecule of glucose/fructose together w/ glycosidic linkage* -Fructose is one of the three dietary monosaccharides, along with glucose and galactose (which is part of the milk sugar, the disaccharide lactose), which are *absorbed directly into the bloodstream during digestion* -The *catabolism of fructose/galactose produces the same number ATP* molecules as glucose -*Proteins are hydrolyzed by enzymes* in cells -Most of the time, the *amino acids are recycled into new proteins* -*If there are excess amino acids* = however, or if the *body is starved* = some *amino acids will be shunted into the pathways of glucose catabolism* -*Each amino acid must have its amino group* removed *prior to entry* into these pathways -The *amino group is converted into ammonia* -*In mammals/liver synthesizes urea from 2 ammonia molecules* and *a carbon dioxide molecule* -Thus, *UREA = principal waste product in mammals* produced *from nitrogen originating in amino acids* and it *leaves the body in urine* The *lipids that are connected to the glucose pathways* = *cholesterol and triglycerides* -*Cholesterol = lipid that contributes to cell membrane flexibility/temp* and is a *precursor of steroid hormones* -The *synthesis of cholesterol starts w/ acetyl groups* and *proceeds in only 1 direction* -The *process cannot be reversed* -*Triglycerides* are a form of *long-term energy storage in animals* -*Triglycerides* = *glycerol and 3 fatty acids* -Animals can make most of the fatty acids they need -*Triglycerides can be made/broken down via glucose catabolism pathways* -*Glycerol can be phosphorylated to glycerol-3-phosphate* which *continues through glycolysis* -*Fatty acids are catabolized* in a process called *beta-oxidation that takes place in the matrix of the mitochondria* and *converts their fatty acid chains into 2 carbon units of acetyl groups* -The *acetyl groups are picked up by CoA* to form *acetyl CoA* that *proceeds citric acid cycle* -*Glycogen from liver/muscles*, *hydrolyzed into glucose-1-phosphate, w/ fats and proteins*, can feed into the catabolic pathways for carbohydrates.

Outcomes of Glycolysis

-*Glycolysis starts w/ glucose (C6H12O6)* and *ends w/ 2 pyruvate molecules*, *2 ATP molecules* and *2 NADH* -*2 ATP molecules were used in first half* of the pathway to *prepare the 6-carbon ring for cleavage*, so the *cell has a net gain of 2 ATP*/*2 NADH* molecules for its use -If the *cell cannot catabolize the pyruvate further* = it *will harvest only 2 ATP molecules from 1 glucose -*Mature mammalian red blood cells are not capable of aerobic respiration*—the process in which organisms convert energy in the presence of oxygen—and glycolysis is their sole source of ATP. If *glycolysis is interrupted* = these *cells lose their ability to maintain their sodium-potassium pumps*, and eventually, they *die* -The last step in glycolysis *will not occur if pyruvate kinase*, the enzyme that catalyzes the formation of pyruvate, *is not available in sufficient quantities*. In this situation, the entire glycolysis pathway will proceed, but only two ATP molecules will be made in the second half. Thus, *pyruvate kinase is a rate-limiting enzyme for glycolysis*

Herbivores, Omnivores, and Carnivores

-*Herbivores are animals whose primary food source* = *PLANT-BASED* -Ex: "deer, koalas, bird species* as well as *Invertebrates such as crickets and caterpillars* -These *animals have evolved digestive systems capable of handling large amounts of plant material* -*Herbivores can be further classified into: *frugivores (fruit-eaters)* *granivores (seed eaters)* *nectivores (nectar feeders)* *folivores (leaf eaters)* -*Carnivores* are *animals that eat other animals* = *"meat eater"* -Ex: *Wild cats* = lions, tigers* of vertebrate carnivores, snakes, sharks, while *invertebrate carnivores include sea stars, spiders, ladybugs* -*Obligate carnivores* = those that *rely ONLY on animal flesh to obtain their nutrients* -Ex: obligate carnivores are *members of the cat family* = lions and cheetahs -*Facultative carnivores* = those that also *eat non-animal food in addition to animal food* -*Facultative carnivores = Omnivores*; *dogs would be considered facultative carnivores* -*Omnivores are animals that eat both plant- and animal*-derived food. In Latin, omnivore means to eat everything -Ex: *Humans, bears, chickens = vertebrate* omnivores *cockroaches, crayfish = invertebrate* omnivores

Energy from ATP + Phosphorylation What is hydrolysis? In hydrolysis, water is __________ and the resulting ________ and _______ are added to the LARGER MOLECULE ATP is continuously broken down into ADP and ADP is continuously generated into ___ Enzymes may bind to several substrates that react with each other, what do you call an enzyme and substrate that are bound together? What is it called when ATP transfers its third phosphate group to the substrate?

-*Hydrolysis* = the *process of breaking complex macromolecules apart* -During *hydrolysis*= *water is split, or lysed* and *the resulting hydrogen atom (H+) and a hydroxyl group (OH-) are added to the LARGER molecule* -The *hydrolysis of ATP produces ADP* together *w/ an inorganic phosphate ion (Pi)* and the *release of free energy* -To carry out life processes, *ATP is continuously broken down into ADP* and like a rechargeable battery, *ADP is continuously regenerated into ATP* by the *reattachment of a third phosphate group* -*Water* which was *broken down into its hydrogen atom + hydroxyl group* during *ATP hydrolysis* is *regenerated when a third phosphate is added to the ADP molecule* = *ATP* -Obviously, *energy must be infused into the system* to *regenerate ATP* Where does this energy come from? In nearly every living thing on earth, the *energy comes from the metabolism of glucose* -*ATP = direct link btwn the limited set of exergonic pathways of glucose catabolism* + *endergonic pathways that power living cells* -In some chemical reactions, *enzymes may bind to several substrates that react w/ each other on the enzyme* = forming an *INTERMEDIATE COMPLEX* -An *intermediate complex* is a *temp structure* + *allows one of the substrates* (such as ATP) and *reactants to more readily react* with each other; in reactions involving ATP, *ATP = one of the substrates* and *ADP = a product* -During an *endergonic chem reaction* = *ATP forms an intermediate complex* w/ *substrate and enzyme* in the reaction -This intermediate complex *allows the ATP to transfer its third phosphate group* with its energy, *to the substrate* a process =*PHOSPHORYLATION* = *addition of the phosphate (~P)* -This is illustrated by the following generic reaction: *A + enzyme + ATP → [A − enzyme − ∼ P] → B + enzyme + ADP + phosphate ion* -When the *intermediate complex breaks apart* = the *energy is used to modify the substrate* and *convert it to a product of the reaction* -The *ADP molecule + free phosphate* ion are *released into the medium and are available for recycling* through cell metabolism -*ATP is generated through 2 mechanisms during glucose breakdown* -A *few ATP molecules are generated* (regenerated from ADP) as a *direct result of chemical reactions in catabolic pathways* -A *phosphate group is removed from an intermediate reactant* in the pathway + *free energy of the reaction is used to add the third phosphate to an available ADP* molecule, *producing ATP* = direct method of phosphorylation is called *substrate-level phosphorylation* -Most *ATP generated during glucose catabolism*= *much more complex* process = *chemiosmosis* which takes place in *mitochondria* within a *eukaryotic cell/plasma membrane of a prokaryotic cell* -*Chemiosmosis* = *process of ATP production in cellular metabolism* is used to *generate 90% of the ATP made during glucose catabolism* + *method used in LIGHT REACTIONS of photosynthesis* to harness the energy of sunlight. The production of *ATP using the process of chemiosmosis* = *OXIDATIVE PHOSPHORYLATION* because of the *involvement of oxygen* in the process ATP synthase enzymes and the ETC are embedded in the inner membrane

Endergonic Reactions and Exergonic Reactions If the energy is ____________ + ∆G is negative, what does that mean? If the energy is ____________+ ∆G is positive, what does that mean? At equilibrium/cell metabolism, the reaction can be __________________. When is equilibrium at its lowest possible free energy and a state of maximal entropy? What will push reactants/products away from equilibrium? If it were a closed system, there would be insufficient what left to perform the work needed to maintain life? When are chemical reactions constantly moving towards equilibrium but never reaching it?

-*If energy is released* = *∆G < 0* - negative ∆G also *means that the products have less free energy than the reactants*, because they *gave off some free energy* during the reaction -*Reactions w/ negative ∆G* + *release free energy* = *EXERGONIC REACTIONS* -Think: exergonic means energy is exiting the system. These reactions are also referred to as *SPONTANEOUS reactions*, because they can *occur w/o addition of energy* into the system -Understanding which chemical reactions are spontaneous and release free energy is extremely useful for biologists, because these *reactions can be harnessed to perform work inside the cell* -An important distinction must be drawn between the term spontaneous and the idea of a chemical reaction that occurs immediately. Contrary to the everyday use of the term, a spontaneous reaction is not one that suddenly or quickly occurs. The rusting of iron is an example of a spontaneous reaction that occurs slowly, little by little, over time. -*If a chemical reaction requires an input of energy* rather than releasing energy, then the *∆G will be a positive value* = the *products have more free energy than the reactants* + Thus, the *products of these reactions* are *energy-storing molecules* = *ENDERGONIC REACTIONS* and they are *non- spontaneous* -An endergonic reaction will not take place on its own without the addition of free energy. Let's revisit the example of the synthesis and breakdown of the food molecule, glucose. Remember that the building of complex molecules, such as *sugars, from simpler ones is an anabolic process and requires energy* Therefore, the chemical reactions involved in *ANABOLIC = endergonic reactions* -On the other hand, the *CATABOLIC = exergonic reactions* Like the example of rust above, the breakdown of sugar involves spontaneous reactions, but these reactions don't occur instantaneously -An important concept in the study of metabolism and *energy is that of chemical equilibrium* -*Most chemical reactions are REVERSIBLE* + *releasing energy into their environment in one direction*, and *absorbing it from the other direction* -The *same is true for the chemical reactions in cell metabolism*, such as the *breaking down/building up of proteins* into and from individual amino acids, respectively -*Reactants within a CLOSED SYSTEM will undergo chemical reactions* in *both directions until a state of equilibrium is reached* -This state of *equilibrium is one of the LOWEST possible free energy and a state of maximal entropy* -*Energy must be put into the system* to *push reactants/products away from a state of equilibrium* -*Either reactants/products must be added, removed, or changed* -If a cell were a closed system, its *chemical reactions would reach equilibrium + would die b/c there would be insufficient free energy left to perform the work needed to maintain life* -In a *living cell, chemical reactions are constantly moving towards equilibrium, but never reach it* This is because a *living cell is an OPEN SYSTEM* -*Materials pass in and out* the cell recycles the products of certain chemical reactions into other reactions, and chemical *equilibrium is never reached* -In this way, living organisms are in a *constant energy-requiring, uphill battle against equilibrium and entropy* -This constant supply of energy ultimately *comes from sunlight, which is used to produce nutrients in the process of photosynthesis*

Metabolism with Oxygen

-*In aerobic respiration* = the *final electron acceptor* = an *oxygen molecule, O2* -*If aerobic respiration occurs, then ATP WILL BE PRODUCED* via the *energy of high-energy electrons from NADH or FADH2* to the electron transport chain -If *aerobic respiration does not occur* = *NADH must be reoxidized to NAD+* for *reuse as an electron carrier* for the glycolytic pathway to continue. How is this done? Some *living systems use an organic molecule as the final electron acceptor* -*FERMENTATION* = *Processes that use an organic molecule to regenerate NAD+ from NADH* -*Some living systems use an inorganic molecule as a final electron acceptor.* -*Both methods are called *ANAEROBIC cellular respiration* = in which *organisms convert energy for their use in the absence of oxygen*

Absorption of Light

-*Light energy* initiates the *process of photosynthesis when pigments absorb the light* -*Organic pigments* whether in the *human retina/the chloroplast thylakoid*, have a *narrow range of energy levels that they can absorb* -*Energy levels lower than those represented by red light* are *insufficient to raise an orbital electron to a populatable, excited (quantum) state* -*Energy levels higher than those in blue light* will physically *tear the molecules apart*, = *bleaching* -So *retinal pigments can only "see" (absorb) 700- 400nm light* which is therefore called *visible light* -For the same reasons, *plants pigment molecules absorb only light in the wavelength range of 700 nm to 400 nm* -plant physiologists refer to this *range for plants as photosynthetically active radiation* -The *visible light seen by humans as white light actually exists in a rainbow of colors* -Certain objects, such as a *prism or a drop of water*, disperse white light to *reveal the colors to the human eye* -The visible light portion of the electromagnetic spectrum shows the *rainbow of colors*, with *violet/blue having SHORTER wavelengths* and therefore *HIGHER energy* -At the other end of the *spectrum toward red* the *wavelengths are LONGER and have LOWER ENERGY*

Citric Acid Cycle Almost all enzymes of the citric acid cycle are _________________ How many turns does the citric acid cycle do? What are the products of the cycle? Is the citric cycle aerobic or anaerobic?

-*Like the conversion of pyruvate to acetyl CoA*, the *citric acid cycle takes place in the matrix of mitochondria* -*Almost all enzymes of citric acid cycle are SOLUBLE*, with the single exception of the enzyme succinate dehydrogenase in inner membrane of the mitochondrion *Unlike glycolysis, the citric acid cycle is a closed loop* -The *last part of the pathway regenerates the compound used in the first step = *2-Carbon Acetyl CoA is joined to a 4Carbon compound to make CITRATE* = back to 4 Carbon* = irreversible bc it is highly exergonic. The rate of this reaction is controlled by negative feedback/ATP available. If ATP levels incr, the rate of this reaction decr. If ATP is in short supply, the rate incr. -The eight steps of the cycle are a series of *redox, dehydration, hydration, decarboxylation* reactions that *produce 2 CO2* (combines w/ carbon), *1 ATP(substrate phosphorylation) *,* 3 NADH* and *1 FADH2* *TWO CYCLES for every glucose* = *4 CO2*, *2 ATP*, *6 NADH*, *2 FADH2* -*AEROBIC pathway bc NADH/FADH2 must transfer their electrons to the next pathway* in the system, *which will use oxygen* -If this transfer does not occur, the oxidation steps of the citric acid cycle also do not occur. Note that the *citric acid cycle produces very little ATP directly and does not directly consume oxygen* Because the *final product of the citric acid cycle is also the first reactant*, the cycle runs *continuously* in the presence of sufficient reactants. -*GTP* = uses *anabolic pathways in the tissues/liver*, *equivalent but more restricted*, *protein synthesis uses GTP*

Cofactors and Coenzymes What does binding to helper molecules do for the enzymes? What are cofactors? What are coenzymes?

-*Many enzymes don't work optimally*, or even at all, *unless bound to specific non-protein helper molecules through ionic/hydrogen bonds/stronger covalent bonds* -Two types of *helper molecules* = *cofactors and coenzymes* -*Binding to these molecules promotes optimal conformation/function* for their respective enzymes -*Cofactors* = *INORGANIC IONS such as iron (Fe++)/magnesium (Mg++)* -One example of an *enzyme that requires a metal ion as a cofactor* is the *enzyme that builds DNA molecules* = *DNA POLYMERASE* which requires bound zinc ion (Zn++) to function -*Coenzymes* = *organic helper molecules*, with a basic *atomic structure made up of carbon and hydrogen*, which are required for enzyme action -The most common *sources of coenzymes are dietary vitamins* -Some *vitamins are precursors to coenzymes and act as coenzymes* *Vitamin C* is a coenzyme for multiple enzymes that take part in building the important *connective tissue component, collagen* -An important step in the *breakdown of glucose to yield energy is catalysis* by a *multi-enzyme complex called pyruvate dehydrogenase* -*Pyruvate dehydrogenase is a complex of several enzymes that actually requires 1 cofactor (a magnesium ion)* + *5 diff organic enzymes* to *catalyze its specific chemical reaction* -Therefore, *enzyme function is, in part, regulated by an abundance of various cofactors and coenzymes*, which are supplied primarily by the *diets of most organisms*. *Vitamins are important coenzymes or precursors of coenzymes*, and are required for enzymes to function properly. Multivitamin capsules usually contain mixtures of all the vitamins at different percentages.

Evolution of Metabolic Pathways What is the name of the primary pathway in which photosynthetic organisms harvested the sun's energy and converted it to carbs? What are the by-products of photosynthesis? What is the name of the process where some eukaryotes perform catabolic processes without oxygen? If all branches of life share some of the same metabolic pathways, then all organisms evolved from what same ancestor? Pathways diverged and added what to allow organisms to better adapt and what principle remains?

-*Metabolic complexity varies from organism to organism* -*Photosynthesis* is the *primary pathway in which photosynthetic organisms (plants)* (the majority of global synthesis is done by *planktonic algae*) *harvest the sun's energy/convert it into carbs* -The *by-product of photosynthesis* is *oxygen*, required by *some cells to carry out cellular respiration* -During *cellular respiration* = *oxygen aids in the catabolic breakdown of carbon compounds*, like carbohydrates -Among the *products of this catabolism are CO2/ATP* -In addition, *some eukaryotes perform catabolic processes w/o oxygen (fermentation)* that is, they *perform or use anaerobic metabolism* -Organisms probably evolved *anaerobic metabolism to survive (living organisms came into existence about 3.8 billion years ago, when the atmosphere lacked oxygen)* -Despite the differences between organisms and the complexity of metabolism, researchers have found that *all branches of life share some of the same metabolic pathways* suggesting that all *organisms evolved from the same ancient common PROKARYOTE ancestor* -Evidence indicates that over time, the *pathways diverged, adding specialized enzymes to allow organisms to better adapt* to their environment, thus increasing their chance to survive. However, the underlying principle remains that all *organisms must harvest energy from their environment* and *convert it to ATP to carry out cellular functions*

Nervous Tissues

-*Nervous tissues are made of cells specialized to receive/transmit electrical impulses* from *specific areas of the body* and to *send them to specific locations* in the body -The *main cell of the nervous system* is the *neuron* -The *large structure w/ a central nucleus* is the *cell body of the neuron* -*Projections from the cell body* are either *dendrites specialized in receiving input or a single axon specialized in transmitting impulses* -*Some glial cells are also shown*. *Astrocytes regulate the chemical environment* of the *nerve cell*, and *oligodendrocytes insulate the axon* so the *electrical nerve impulse is transferred* more efficiently Other glial cells that are not shown *support the nutritional and waste requirements of the neuron*. Some of the glial cells are phagocytic and remove debris or damaged cells from the tissue. *A nerve consists of neurons and glial cells* neuron has projections called dendrites that receive signals and projections called axons that send signals. Also shown are two types of glial cells: astrocytes regulate the chemical environment of the nerve cell, and oligodendrocytes insulate the axon so the electrical nerve impulse is transferred more efficiently.

Obesity

-*Obesity* = major *health concern in US* + there is a *growing focus on reducing obesity* and the *diseases it may lead to = diabetes, cancers of the colon/breast, cardiovascular disease* -How does the food consumed contribute to obesity? -*Fatty foods = calorie-dense*, they have *more calories per unit mass than carbs/proteins* -*1g carbohydrates* = *4 calories* + *1g of protein* = *4 calories* + *1g of fat* = *9 calories* -*Animals* tend to *seek lipid-rich food for higher energy content* -The *signals of hunger* ("time to eat") + *satiety* ("time to stop eating") = *controlled in the hypothalamus region* of the brain. Foods that are rich in *fatty acids tend to promote satiety* more *than foods rich only in carbohydrates* -*Excess carbohydrate/ATP* = *used by liver to synthesize glycogen* -The pyruvate produced during glycolysis is used to synthesize fatty acids. When there is more glucose in the body than required, the resulting excess pyruvate is converted into molecules that eventually result in the synthesis of fatty acids within the body. These fatty acids are stored in adipose cells—the fat cells in the mammalian body whose primary role is to store fat for later use. It is important to note that some animals benefit from obesity. Polar bears and seals need body fat for insulation and to keep them from losing body heat during Arctic winters. When food is scarce, stored body fat provides energy for maintaining homeostasis. Fats prevent famine in mammals, allowing them to access energy when food is not available on a daily basis; fats are stored when a large kill is made or lots of food is available.

The Two Parts of Photosynthesis

-*Photosynthesis takes place in 2 sequential stages*: 1) the *light-dependent reactions* and 2) the *light independent-reactions* -In the *light-dependent reactions* = *energy from sunlight is absorbed* by *CHLOROPHYLL* and *that energy is converted into STORED chemical energy* = *energy carriers* -*ENERGY CARRIERS* = *move light from light dependent reactions* to *light independent* = *full* bc they're rich in *energy*, after they're *"empty"*, they *go back to light dependent for more energy* -In the *light-independent reactions*, the *chem energy harvested during light-dependent reactions takes place in CHLOROPLASTS (outer/inner)* + *drive the assembly of sugar from carbon dioxide* + *do not use light as a REACTANT* -Several *enzymes of light independent reactions are ACTIVATED by light* -*Stacks of thylakoids called grana* form a *third membrane layer* -On a *hot, dry day*, *plants close their stomata to conserve water*. What impact will this have on photosynthesis? -Photosynthesis takes place in two stages: light dependent reactions and the Calvin cycle -*Light-dependent reactions*, which take place in the *thylakoid membrane*, use *light energy/H2O to make ATP (from ADP+Phosphate), NADPH ("reducing power"), O2* -The *Calvin cycle* which takes place in the *stroma*, uses *energy from ATP, NADPH, CO2 to make GA3P (from CO2), ADP, Pi, NADP+* •During the Calvin cycle, *CO2 is incorporated into organic compounds* in a process called *carbon fixation* •After carbon fixation, the *carbon compounds are reduced to sugars* •*Photosynthesis* = *redox (oxidation-reduction) process* •*CO2 becomes reduced by sugar as electrons*, along *with hydrogen ions (H+) from water*, are added to it. •*Water molecules are oxidized by oxygen* when they lose electrons along with hydrogen ions -*The electrons lose potential* as they *travel down the electron transport chain to O2* -the *food-producing redox reactions of photosynthesis require energy*

Main Structures and Summary of Photosynthesis

-*Photosynthesis* is a *multi-step process requiring sunlight, CO2* (which is *low energy*), and (H2O as substrates* -After the process is complete, *it releases O2* and *produces glyceraldehyde-3-phosphate (GA3P)*, *carbohydrate molecules* (which are *high in energy*) that can *subsequently be converted into glucose, sucrose, any dozens of sugar molecules* -These *sugar molecules contain energy* and the *energized carbon that all living things need to survive* -*Photosynthesis uses solar energy*, *CO2*, *H2O* to *produce energy-storing carbs* -*Oxygen* = generated as a *waste product of photosynthesis* The basic equation for photosynthesis is deceptively simple. In reality, the *process takes place in many steps* involving *intermediate reactants and products.* Glucose, the *primary energy source in cells*, is *made from two three-carbon GA3Ps* -IN *plants* = *photosynthesis takes place in leaves*, which *consist of several layers of cells* -*Photosynthesis occurs in middle layer* = *Mesophyll* -The *gas exchange of CO2 enter + O2 exits* in *small, regulated openings/pores* = *stomata* (singular: stoma) = *regulation of gas exchange/water balance* -The stomata are *typically located on the underside of the leaf*, which helps to *MINIMIZE WATER LOSS* + *flanked by guard cells that regulate the opening and closing* of the stomata by swelling or shrinking *in response to osmotic changes* -*IN autotrophic eukaryotes* = *photosynthesis takes place inside an organelle* = *chloroplast* -For plants, *chloroplast- containing cells exist in the mesophyll* -*Chloroplasts* = green tissue in the interior of a leaf *double membrane envelope* (outer membrane/inner membrane) -*Within the chloroplast* = *stacked, disc-shaped structures* = *thylakoids* -*Embedded in the thylakoid membrane* = *chlorophyll, a pigment* (molecule that *ABSORBS LIGHT*) responsible for *GREEN PIGMENT*, *solar to chem energy* and numerous proteins that make up the electron transport chain -The *thylakoid membrane* = encloses an *internal space called the thylakoid space/lumen house for chem energy from light*/*functions similar to intermembrane space of mitochondria in generating ATP* -*Granum*= *a stack of thylakoids* and the *Stroma* = *liquid-filled space surrounding the granum* •Photosynthetic bacteria have infolded regions of the plasma membrane containing clusters of pigments and enzymes. *Leaf>Mesophyl>Mesophyll Cell>Chloroplasts>Stroma>Inner and outer membranes>granum>thylakoid>thylakoid space>chlorophyll*

Enzyme Active Site and Substrate Specificity What are substrates? What is the active site? Enzymes are proteins with a unique what? Incr. temp will do what to the reaction? And to the enzyme?

-*SUBSTRATES* = *The chemical reactants to which an enzyme binds* -There *may be more than 1 substrate* depending on the *particular chemical reaction* -In some reactions, a *single-reactant substrate is broken down into multiple products* but in others, *two substrates may come together to create one larger molecule* -*Two reactants might also enter a reaction, both become modified*, and leave the reaction as two products -*ACTIVE SITE* = The *location within the enzyme where the substrate binds*. The active site is where the *"action" happens*, so to speak -Since *enzymes are proteins*, there is a unique *combination of amino acid residues (R groups) within the active site* -*Each residue is characterized by diff properties/large or small/weakly acidic or basic/hydrophilic or hydrophobic/positively or negatively charged/neutral* -The unique combination of *amino acid residues*, their *positions*, *sequences*, *structures*, and properties create a very *specific chemical environment within the active site* -This specific environment is *suited to bind to a specific chemical substrate(s)* -Due to this jigsaw puzzle-like match between an enzyme and its substrates (which adapts to find the best fit between the transition state and the active site), *enzymes are known for their specificity* -The *"best fit" results from the shape/amino acid functional group's attraction* to the substrate -There is a specifically matched enzyme for each substrate and, thus, for each chemical reaction; however, *there is flexibility as well* -The fact that active sites are so perfectly suited to provide specific environmental conditions also means that they are subject to influences by the local environment -It is true that *incr the environmental temp generally incr reaction rates* enzyme-catalyzed or otherwise -However, *increasing or decreasing the temperature outside of an optimal range* can *affect chemical bonds* within the active site in such a way that they are less well suited to bind substrates -High temperatures will eventually cause enzymes, like other biological molecules, to *denature* = a process that *changes the natural properties* By the end of this section, you will be able to: Describe the role of enzymes in metabolic pathways Explain how enzymes function as molecular catalysts Discuss enzyme regulation by various factors of a substance. Likewise, the *pH* of the local environment can also affect enzyme function -*Active site amino acid residues have their own acidic or basic properties* that are *optimal for catalysis* -These residues are *sensitive to changes* in pH that can impair the way substrate molecules bind. Enzymes are suited to function best within a certain pH range, and, as with temperature, extreme pH values (acidic or basic) of the environment can cause enzymes to denature.

ATP (adenosine triphosphate) energy-supplying molecule called? What is the molecule made of? Bonds that link the phosphates are equally ________ ________? How is ATP hydrolyzed into ADP? Is this reaction reversible? Is ATP stable/unstable? How does energy coupling work?

-Even exergonic, energy-releasing reactions require a small amount of activation energy in order to proceed -However, consider *endergonic reactions, which require much more energy input*, because *their products have MORE free energy than reactants* Within the cell, where does energy to power such reactions come from? The answer lies with an *energy- supplying molecule called adenosine triphosphate, or ATP* -*ATP* = a *small, relatively simple molecule*, but within *some of its bonds, it contains the potential for a quick burst of energy that can be harnessed to perform cellular work* This molecule can be thought of as the *primary energy currency* of cells in much the same way that money is the currency that people exchange for things they need -ATP is *used to power the majority of energy-requiring cellular reactions* As its name suggests, adenosine triphosphate is *comprised of adenosine bound to three phosphate groups* -*Adenosine is a nucleoside consisting of the nitrogenous base adenine and a five-carbon sugar, ribose* -The three phosphate groups, in order of *closest to furthest* from the *ribose sugar, are labeled alpha, beta, and gamma* -Together, these *chemical groups constitute an energy powerhouse* However, *not all bonds within this molecule exist in a particularly high-energy state* -Both *bonds that link the phosphates are equally high-energy bonds (phosphoanhydride bonds)* that, *when broken, release sufficient energy to power a variety of cellular reactions and processes* -These *high-energy bonds are the bonds between the second and third (or beta and gamma) phosphate groups and between the first and second phosphate groups* The reason that these bonds are considered *"high-energy" is because the products of such bond breaking—adenosine diphosphate (ADP) and one inorganic phosphate group (Pi)—have considerably lower free energy than the reactants* ATP and a water molecule. Because this reaction takes place with the use of a water molecule, it is considered a *hydrolysis reaction. In other words, ATP is hydrolyzed into ADP* in the following reaction: *ATP + H2 O → ADP + Pi + free energy* -Like most chemical reactions, the *hydrolysis of ATP to ADP is REVERSIBLE* The reverse reaction regenerates *ATP from ADP + Pi* -Indeed, *cells rely on the regeneration of ATP* just as people rely on the regeneration of spent money through some sort of income -Since *ATP hydrolysis releases energy, ATP regeneration must require an input of free energy* -The formation of ATP is expressed in this equation: *ADP + Pi + free energy → ATP + H2O* -Two prominent questions remain with regard to the use of ATP as an energy source. Exactly *how much free energy is released with the hydrolysis of ATP*, and how is that free energy used to do cellular work? The calculated *∆G for the hydrolysis of one mole of ATP into ADP and Pi is −7.3 kcal/mole (−30.5 kJ/mol)* -Since this *calculation is true under standard conditions*, it *would be expected that a different value exists under cellular conditions* -In fact, the *∆G for the hydrolysis of one mole of ATP in a living cell is almost double the value at standard conditions: 14 kcal/mol (−57 kJ/mol)* -*ATP* is a *highly UNSTABLE molecule* -Unless quickly used to perform work, *ATP spontaneously dissociates into ADP + Pi* and the *free energy released during this process is lost as heat* The second question posed above, that is, *how the energy released by ATP hydrolysis is used to perform work inside the cell* depends on a strategy = *energy coupling* -*Cells couple the exergonic reaction of ATP hydrolysis with endergonic reactions*, allowing them to proceed. One example of *energy coupling using ATP involves a transmembrane ion pump* that is extremely important for cellular function -This *sodium-potassium pump (Na+/K+ pump) drives sodium out of the cell and potassium into the cell* -A large percentage of a *cell's ATP is spent powering this pump*, because cellular processes bring a *great deal of sodium into the cell and potassium out of the cell* -The pump *works constantly to stabilize cellular concentrations of sodium and potassium* -In order for the pump to turn one cycle (*exporting three Na+ ions and importing two K+ ions*), *one molecule of ATP must be hydrolyzed* -*When ATP is hydrolyzed, its gamma phosphate doesn't simply float away*, but is *actually transferred onto the pump protein* - This process of a *phosphate group binding to a molecule is called phosphorylation*. As with most cases of *ATP hydrolysis, a phosphate from ATP is transferred onto another molecule* -In a phosphorylated state, *the Na+/K+ pump has more free energy and is triggered to undergo a conformational change* -This change allows it to *release Na+ to the outside of the cell* It then *binds extracellular K+* which, through another conformational change, *causes the phosphate to detach from the pump*. This release of phosphate triggers the K+ to be released to the inside of the cell. Essentially, the *energy released from the hydrolysis of ATP is coupled w/ the energy required to power the pump* and transport Na+ and K+ ions. ATP performs *cellular work using this basic form of energy coupling* through *phosphorylation*

Energy Requirements Related to Body Size Energy Requirements Related to Levels of Activity Energy Requirements Related to Environment

-*Smaller endothermic animals* have a *GREATER SURFACE AREA* than larger ones -Therefore, *smaller animals lose heat at a faster rate than larger animals* and require *more energy to maintain a constant internal temp* -This results in a *smaller endothermic animal* having a *higher BMR, per body weight*, than a larger endothermic animal Ex: The mouse has a much higher metabolic rate than the elephant -The *more active an animal is*, the *more energy is needed to maintain that activity*, and the *higher its BMR/SMR* -The *average daily rate of energy consumption* is about *2-4x an animal's BMR or SMR* -*Humans are more sedentary* than most animals and have an *average daily rate of only 1.5x the BMR* -The *diet of an endothermic animal is determined by its BMR* -Ex: the type of *grasses, leaves, or shrubs that an herbivore eats affects the number of calories that it takes in* -The relative caloric content of herbivore foods, in descending order, is tall grasses > legumes > short grasses > forbs (any broad-leaved plant, not a grass) > subshrubs > annuals/biennials -*Animals adapt to extremes of temp/food availability through torpor* -*Torpor* = a process that *leads to a decr in activity/metabolism and allows animals to survive adverse conditions* -Torpor *can be used by animals for long periods*, such as entering a state of *hibernation during the winter* months, in which case it *enables them to maintain reduced body temp* -During hibernation, *ground squirrels can achieve an abdominal temperature of 0° C (32° F)* while a *bear's internal temperature is maintained higher at about 37° C (99° F)* -If *torpor occurs during the summer months* with *high temp/little water* = *ESTIVATION* -Some *desert animals use this to survive the harshest months* of the year. Torpor can occur on a *daily basis*; this is seen in bats and hummingbirds -While *endothermy is limited in smaller animals by surface to volume ratio*, some *organisms can be smaller and still be endotherms* because they *employ daily torpor during the part of the day that is coldest* -This allows them to *conserve energy during the colder parts* of the day, when they *consume more energy to maintain their body temperature*

Neural Control of Thermoregulation

-*The nervous system is important to thermoregulation* -The *processes of homeostasis and temperature control are centered in the hypothalamus of the advanced animal brain* -The *hypothalamus maintains the set point for body temp through reflexes that cause vasodilation* and sweating when the body is too warm, or vasoconstriction and shivering when the body is too cold -It *responds to chemicals from the body.* When a *bacterium is destroyed by phagocytic leukocytes, chemicals endogenous pyrogens are released* into the blood -These *pyrogens circulate to the hypothalamus and reset the thermostat* -This *allows the body's temp to incr* in what is commonly called a *fever* -An *incr in body temp causes iron to be conserved*, which *reduces a nutrient needed by bacteria* -An *incr in body heat also incr the activity of the animal's enzymes and protective cells while inhibiting the enzymes* and activity of the invading microorganisms. Finally, *heat itself may also kill the pathogen* -A *fever* that was once thought to be a complication of an infection is now understood to be a *normal defense mechanism* -The *body is able to regulate temp in response to signals from the nervous system* When *bacteria are destroyed by leuckocytes*, *pyrogens are released into the blood* -*Pyrogens reset the body's thermostat to a higher temp*, resulting in fever. How might pyrogens cause the body temperature to rise?

The Laws of Thermodynamics What is thermodynamics? The matter /environment of energy transfer refers to? Everything outside of the system? What is an open system and what is a closed? Biological organisms are what type of system?

-*Thermodynamics* = refers to the *study of energy and energy transfer involving physical matter* -The *matter/environment of energy transfer* = *SYSTEM* and *everything outside of that system* = *SURROUNDINGS* -For instance, when heating a pot of water on the stove, the system includes the stove, the pot, and the water. *Energy is transferred within the system* (between the stove, pot, and water). There are *two types of systems: open and closed* -An *open system is one in which energy can be transferred between the system and its surroundings* The stovetop system is open because heat can be lost into the air -A *closed system is one that cannot transfer energy to its surroundings* -*Biological organisms are open systems* + *energy is exchanged and their surroundings* as they *consume energy- storing molecules and release energy* to the environment by doing work -Like all things in the physical world, *energy is subject to the laws of physics* The laws of thermodynamics *govern the transfer of energy in and among all systems in the universe*

Vertebrate Digestive Systems

-*Vertebrates evolved more complex digestive systems to adapt to their dietary needs* -Some animals have a *single stomach + some have multi-chambered stomachs* -*Birds have developed a digestive system* adapted to *eating unmasticated food* -*Monogastric: Single-chambered Stomach* + *humans and many animals have a monogastric digestive system*. The process of *digestion begins w/ the mouth + intake of food* -The *teeth play an important role in masticating (chewing)* or physically *breaking down food into smaller particles* -The *enzymes present in saliva begin to chemically break down food* -The *esophagus is a long tube that connects the mouth to the stomach* -Using *peristalsis/wave-like smooth muscle contractions* = the *muscles of the esophagus push the food towards the stomach* -In order to *speed up the actions of enzymes in the stomach* the stomach is an *extremely acidic environment* w/ a *pH of 1.5 and 2.5* -The *gastric juices include enzymes in the stomach*, act on the *food particles + continue digestion* -Further *breakdown of food takes place in the small intestine* where *enzymes produced by the liver, small intestine*, *pancreas continue the process of digestion* -The *nutrients are absorbed into the bloodstream across epithelial cells* lining the walls of the small intestines The *waste material travels to the large intestine* where *water is absorbed* and the *drier waste material is compacted into feces*; it is stored until it is excreted through the rectum. Avian -*Birds have special challenges when obtaining nutrition from food* -They *DON'T have teeth* and so their *digestive system must be able to process un-masticated food* -Birds have *evolved a variety of beak types that reflect the vast variety in their diet* ranging *from seeds, insects, fruits, nuts* -Bc most birds fly, they *have HIGH metabolic rates to efficiently process food + keep body weight low* -The *stomach of birds has 2 chambers*: the *proventriculus = gastric juices are produced to digest food before entering stomach* + *gizzard = where the food is stored, soaked, mechanically ground*' -The *undigested material forms food pellets* = *regurgitated* -Most of the *chemical DIGESTION/ABSORPTION happens in the intestine *and the *waste is excreted through the cloaca* Ruminants -*Ruminants are HERBIVORES* (cows, sheep, goats) whose *entire diet consists of eating roughage/fiber* -They have *evolved digestive systems* that help them *digest vast amounts of cellulose* -Ruminants' mouth is that they *don't have upper incisor teeth* + instead *use their lower teeth, tongue, lips to chew* their food -From the mouth, the food travels to the esophagus and on to the stomach. To help digest lots of plant material, the *stomach of the ruminants is a MULTI-CHAMBERED ORGAN* w/ 4 compartments of the stomach = the *rumen, reticulum, omasum, abomasum* -These *chambers contain many microbes that break down cellulose + ferment ingested food* -The *abomasum* = *"true" stomach* and is the *equivalent of the monogastric stomach chamber* where *gastric juices are secreted* -The *4-compartment gastric chamber* DOESN'T HAVE ENZYMES TO DIGEST CELLULOSE but has *larger space* + *bacteria/protists to help digest* -The *fermentation process produces large amounts of gas* in the stomach chamber, which must be eliminated. As in other animals, the *small intestine does nutrient absorption* + *large intestine helps rid waste* Pseudo-ruminants -Some *animals* (camels, alpacas) *are pseudo-ruminants* -They *eat a lot of plant material/roughage* -*Digesting plant material* is *not easy bc plant cell walls have cellulose* + the digestive enzymes of these animals cannot break down cellulose, but *microorganisms present in the digestive system can* -Therefore, the *digestive system must be able to handle roughage + break down the cellulose* -*Pseudo-ruminants* have a *3- chamber stomach in the digestive system* However, their *cecum—a pouched organ at the beginning of the large intestine* containing many microorganisms that are necessary for the digestion of plant materials—is large and is *the site where the roughage is fermented/digested* -These animals *DON'T have a rumen but have an omasum, abomasum, reticulum*

Introduction of Energy/Metabolism How does a bird obtain its energy from? Every task performed by living organisms need what? Humans use energy when doing what (2) Nutrients are ________________, __________________, _______________ What molecules are transported btwn cells What molecules are broken down/ingested? Cells need to do what to move _________/_________

-A *hummingbird needs energy to maintain prolonged periods of flight* -The *bird obtains its energy from taking in food* and *transforming the nutrients into energy* through a series of biochemical reactions. The flight muscles in birds are extremely efficient in energy production. -Virtually *every task performed by living organisms requires energy* -*Energy is needed to perform heavy labor/exercise*, but *humans also use a great deal of energy while thinking*, and even during *sleep* -*Living cells of every organism constantly use energy* -*Nutrients/other molecules* are *imported, metabolized* (broken down), *synthesized into new molecules*, modified if needed, transported around the cell, and *may be distributed to the entire organism* -Ex: *large proteins make up muscles* are actively built from smaller molecules. Complex *carbohydrates are broken down into simple sugars* that the *cell uses for energy*. Just as energy is required to both build and demolish a building, *energy is required for synthesis/breakdown of molecules* Additionally, *signaling molecules* such as *hormones/neurotransmitters* are transported *btwn cells* -*Pathogenic bacteria/viruses* are ingested and *broken down by cells* -*Cells* must also *export waste* and toxins to *stay healthy*, and many cells must swim/*move surrounding materials* via the beating motion of *cellular appendages of cilia/flagella* -The cellular processes listed above *require a steady supply of energy* From where, and in what form, does this energy come? How do living cells obtain energy, and how do they use it? This chapter will discuss different forms of energy and the physical laws that govern energy transfer. This chapter will also describe how cells use energy and replenish it, and how chemical reactions in the cell are performed with great efficiency.

Stomach: Small and Large Intestine

-A *large part of digestion* occurs *in STOMACH* -The *stomach* = a *saclike organ secreting gastric digestive juices* w/ *pH of 1.5-2.5* -*Acidic environment is required for breakdown of food* + *extraction of nutrients* -When *empty* = the *stomach becomes a small organ* but *expands to 20x the resting size when filled w/ food* -Useful for animals that need to eat when food is available. The *stomach* = the *major site for protein digestion in animals besides ruminants* -*Protein digestion* is *mediated by an enzyme* = *PEPSIN* (stomach chamber) that's *secreted by chief cells in stomach* in an *inactive form* = *PEPSINOGEN* -*Pepsin breaks peptide bonds* + *cleaves proteins to smaller polypeptides*; it also helps *activate more pepsinogen that generates more pepsin* = *POSITIVE FEEDBACK* -*Parietal cells* = *secrete H+* (hydrogen) and *Cl-*(chloride) ions *into lumen to form hydrochloric acid*(primary acidic component of the stomach juices) -*HCl (Hydrochloric acid) helps to convert the inactive pepsinogen to pepsin* -The highly *acidic environment kills many microorganisms in food w/ action of enzyme pepsin*, results in the *hydrolysis of protein* in the food -Chemical digestion is facilitated by the churning action of the stomach -*Contraction/relaxation of smooth muscles* = *mixes the stomach contents to form CHYME* every 20 mins -passes *from the stomach to small intestine* -Further protein digestion takes place in the small intestine. *Gastric emptying occurs within 2-6 hours after a meal* Only a small amount of chyme is released into the small intestine at a time -The *movement of chyme from the stomach to small intestine is regulated by the pyloric sphincter* -When *digesting protein/some fats* = the *stomach lining must be protected from digestion by pepsin* -*Enzyme pepsin synthesized in the inactive form protects chief cells bc pepsinogen doesn't have the same enzyme functionality of pepsin* -*Stomach has a thick mucus lining protecting the underlying tissue* from the digestive juices -*When mucus lining is ruptured* = *ulcers can form in the stomach* (open wounds in/on an organ by bacteria) -*Chyme moves from stomach to small intestine* = *organ for digestion of protein, fats, carbs* -The *small intestine* = 6m, site of chemical digestion/absorption, *long tube-like organ w/ highly folded surface containing finger-like projections = VILLI* -*Microvilli line epithelial cells on the luminal side and allow nutrient absorption* + *absorbed into blood stream* on the other side -The *villi/microvilli w/ their many folds incr surface area of the intestine* + *absorption efficiency* of the nutrients carried into the hepatic portal vein to the liver which regulates the distribution of nutrients to the rest of the body and removes toxic substances -*3 parts*: 1. *duodenum* = *"C-shaped," fixed part* of the small intestine + *separated from stomach by the pyloric sphincter which allows chyme to mix w/ pancreatic juices* + acts as a *buffer* 2. *jejunum* = *hydrolysis of nutrients + carbohydrates/amino acids digestion and absorption via intestinal lining* 3. *ileum* = *last part of small intestine where salts/vitamins are absorbed* into blood + *ileum ends/large intestine begins at ileocecal valve* -*BILE* = *produced in the liver and stored and concentrated in the gallbladder* -Bile contains bile salts which emulsify lipids while the pancreas produces enzymes that catabolize starches, disaccharides, proteins, and fats. These digestive juices break down the food particles in the chyme into glucose, triglycerides, and amino acids in the duodenum too. -The *large intestine* = *reabsorbs water from the undigested food material* + *processes waste material* -The *human large intestine is MUCH SMALLER* in length *compared to small intestine* but *LARGER in diameter* -3 parts: 1) the *cecum* = joins the ileum to the colon and is the *receiving pouch for the waste matter*+ *bears the appendix* 2) the *colon*= *home to many bacteria/"intestinal flora"* that *aid in the digestion* + can be *divided into 4 regions* = the *ascending colon, transverse colon, descending colon, sigmoid colon* -*extracts the water/mineral salts from undigested food* + *stores waste material* Carnivorous mammals have a shorter large intestine compared to herbivorous mammals due to their diet. 3) the *rectum* = helps form *firm feces stored until elimination*

Induced Fit and Enzyme Function What does induced fit and lock and key method mean? What 3 chemical properties contribute to the enzyme's shape? How does an enzyme contort the substrate to its transition state?

-For many years, *scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion* -This model *asserted that the enzyme and substrate fit together perfectly in one instantaneous step* -However, *current research supports* a more refined view called *INDUCED FIT* = *expands upon the lock-and-key model* by describing a *more dynamic interaction btwn enzyme/substrate* -As the *enzyme and substrate come together*, their *interaction causes a mild shift in the enzyme's structure* that confirms an ideal *binding arrangement btwn the enzyme and transition state of the substrate* -This *ideal binding maximizes the enzyme's ability to catalyze* its reaction. -*When an enzyme binds its substrate*, an *enzyme-substrate complex is formed* -This *complex lowers the activation energy* of the reaction and *promotes its rapid progression* in one of many ways -On a basic level, enzymes promote chemical reactions that involve more than one substrate by *bringing the substrates together in an optimal orientation* -The appropriate region (atoms and bonds) of one molecule is *juxtaposed to the appropriate region of the other molecule with which it must react* -Another way in which enzymes promote the reaction of their substrates is by *creating an optimal environment* within the active site for the reaction to occur. Certain chemical reactions might proceed best in a slightly acidic or non-polar environment -*The chemical properties that emerge from the particular arrangement of amino acid residues* within an active site *create the perfect environment for an enzyme's specific substrates* to react. You've learned that the activation energy required for many reactions includes the *energy involved in manipulating/contorting chemical bonds so that they can easily break* and allow others to reform -Enzymatic action can aid this process. The enzyme-substrate complex can *lower the activation energy by contorting substrate molecules in such a way as to facilitate bond-breaking*, helping to reach the *transition state* -Finally, *enzymes can also lower activation energies* by *taking part in the chemical reaction itself* The amino acid residues can provide certain ions or chemical groups that actually form covalent bonds with substrate molecules as a necessary step of the reaction process. In these cases, it is important to remember that the *enzyme will always return to its original state at the completion* of the reaction. One of the hallmark properties of enzymes is that they *remain ultimately unchanged by the reactions they catalyze* After an enzyme is done catalyzing a reaction, *it releases its product(s)* -According to the induced-fit model, *both enzyme and substrate undergo dynamic conformational changes upon binding* -The *enzyme contorts the substrate into its transition state* thereby *incr the rate of the reaction*

ATP in Living Systems A living cell cannot store significant amounts of free energy bc excess free energy would result in: Adding a phosphate group to a molecule requires____________ Phosphate groups are ______________-charged and repel one another when arranged in a series

-A *living cell cannot store significant amounts of free energy* -*Excess free energy* would result in an = *increase of heat* in the cell, which would result in *excessive thermal motion that could damage/destroy the cell* -Rather, a *cell must be able to handle that energy in a way that enables the cell to store energy safely* and *release it for use only as needed* -*Living cells accomplish this by using the compound adenosine triphosphate (ATP)* -ATP is often called the *"energy currency" of the cell* and, like currency, this versatile compound *can be used to fill any energy need of the cell* How? It functions similarly to a rechargeable battery. -*When ATP is broken down* = usually by the *removal of its terminal phosphate group*, *energy is released* -The *energy is used to do work by the cell* usually *by the released phosphate binding to another molecule* = *activating it* -Ex: the *mechanical work of muscle contraction*, *ATP supplies the energy* to *move contractile muscle proteins* -Recall the *active transport work of the sodium-potassium pump in cell membranes* -*ATP alters the structure of the integral protein* that functions as the pump, *changing its affinity for sodium and potassium* -In this way, the cell performs work, *pumping ions AGAINST their electrochemical gradients* ATP Structure and Function -At the heart of *ATP* is a molecule of *adenosine monophosphate* (AMP), which is *composed of an adenine molecule* bonded to a *ribose molecule* and to a *single phosphate group* -*Ribose is a five-carbon sugar* found in *RNA*, and *AMP is one of the nucleotides* in RNA -The *addition of a second phosphate group to this core* molecule *results in* the formation of *adenosine diphosphate (ADP)*; the *addition of a third phosphate group* forms *adenosine triphosphate (ATP)* -*ATP (adenosine triphosphate)* has *3 phosphate groups* that can be *removed by hydrolysis* to *form ADP (adenosine diphosphate)* or *AMP (adenosine monophosphate)* -The *negative charges on the phosphate group* naturally *repel each other*, *requiring energy to bond them together* and *releasing energy when bonds are broken* -The *addition of a phosphate group* to a molecule *requires energy* -*Phosphate groups are negatively charged* and thus *repel one another when arranged in series*, as they are in ADP and ATP. This *repulsion makes the ADP and ATP molecules* inherently *UNSTABLE* The release of one or two phosphate groups from ATP, a process called *dephosphorylation, releases energy*

Animal Body Planes and Cavities

-A *standing vertebrate animal* can be *divided by several planes* -A *SAGGITAL PLANE* = divides the body into *right and left portions* -A *MIDSAGGITAL PLANE* divides the body *exactly in the middle*, making two *equal right and left halves.* -A *FRONTAL PLANE* (also called a coronal plane) *separates the front from the back* -A *TRANSVERSE PLANE* (or, horizontal plane) divides the animal into *upper and lower portions* -This is sometimes called a *cross section*, and, if the *transverse cut is at an angle* = *oblique plane* -Shown are the planes of a quadruped goat and a bipedal human. The midsagittal plane divides the body exactly in half, into right and left portions. The frontal plane divides the front and back, and the transverse plane divides the body into upper and lower portions. -*Vertebrate animals* have a number of defined *body cavities* -*Two of these are major cavities that contain smaller cavities* within them. The *DORSAL CAVITY* contains the *cranial and the vertebral (or spinal) cavities* -The *VENTRAL CAVITY* contains the *thoracic cavity*, which in turn contains the *pleural cavity around the lungs and the pericardial cavity* which surrounds the heart -The *ventral cavity also contains the abdominopelvic cavity*, which can be separated into the *abdominal and the pelvic cavities*

Regulatory Mechanisms

-A variety of *mechanisms is used to control cellular respiration* -*Some type of control exists* at *each stage of glucose metabolism* -*Access of glucose* to the cell can be *regulated using the GLUT proteins* that *transport glucose* -*Diff forms of GLUT protein control passage of glucose into the cells* of specific tissues. -*GLUT4 is a glucose transporter* that is *stored in vesicles*. A cascade of events that *occurs upon insulin binding to a receptor* in the plasma membrane causes *GLUT4-containing vesicles to fuse w/ plasma membrane so that glucose may be transported in* the cell. -Some reactions are controlled by having *two different enzymes—one each for the two directions of a reversible reaction* -*Reactions that are catalyzed by 1 enzyme can go to equilibrium*, stalling the reaction -In contrast, *if 2 diff enzymes (each specific for a given direction) are necessary for a reversible reaction*, the *opportunity to control the rate of the reaction incr*, and *equilibrium is not reached* -A number of *enzymes involved in each of the pathways*—in particular, the *enzyme catalyzing the first committed reaction* of the pathway—are *controlled by attachment of a molecule to an allosteric site* on the protein -The molecules most commonly used in this capacity are the nucleotides *ATP, ADP, AMP, NAD+, NADH* -These *regulators, allosteric effectors, may incr/decr enzyme activity* depending on the prevailing conditions -The *allosteric effector alters the steric structure of the enzyme* usually *affecting the configuration of the active site* -This *alteration of the protein's (the enzyme's) structure either inc/decr its affinity for its substrate*, with the effect of increasing or decreasing the rate of the reaction. The *attachment signals to the enzyme*. This *binding can incr/decr the enzyme's activity* = *providing feedback* -This feedback type of *control is effective as long as the chemical affecting it is attached to the enzyme* Once the *overall concentration of the chemical decr* = it will *diffuse away from the protein*, and the *control is relaxed*

Animal Bioenergetics

-All *animals must obtain their energy from food INGESTED/ABSORBED* -These *nutrients are converted to adenosine triphosphate (ATP)* for short-term *storage and use by all cells* -Some *animals store energy for slightly longer times as glycogen* and others *store energy for much longer times in the form of triglycerides* housed in *specialized adipose tissues* -*No energy system* is one hundred percent *efficient*, and an *animal's metabolism produces waste energy in the HEAT* -*If an animal can conserve that heat* and maintain a relatively *constant body temp* = *warm-blooded animal + endotherm* -The *insulation* used to conserve the body heat comes in the forms of *fur, fat, or feathers* -The *absence of insulation in ectothermic animals incr their dependence on the environment for body heat* -The *amount of energy expended by an animal over a specific time* = *METABOLIC RATE* -The *rate is measured variously in joules, calories, kilocalories (1000 calories)* -*Carbohydrates and proteins* contain about *4.5 to 5 kcal/g*, and *fat* contains about *9 kcal/g* -*Metabolic rate is estimated as the basal metabolic rate (BMR)* = *endothermic animals at rest* and as the *standard metabolic rate (SMR)* = *ectotherms* -Human males have a BMR of 1600 to 1800 kcal/day, and human females have a BMR of 1300 to 1500 kcal/day. Even *w/ insulation* = *endothermal animals require extensive amounts of energy to maintain a constant body temperature* -An ectotherm such as an *alligator* has an SMR of 60 kcal/day.

Introduction of Animal Form and Function

-An arctic fox is a complex animal, well adapted to its environment. It changes coat color with the seasons, and has longer fur in winter to trap heat. The *arctic fox is an example of a complex animal* that *has adapted to its environment* and *illustrates the relationships btwn an animal's form/function* -The *structures of animals consist of primary tissues that make up more complex organs and organ systems* -*Homeostasis* = allows an *animal to maintain a balance btwn its internal/external environments* *Animals vary in form and function* From a sponge to a worm to a goat, an *organism has a distinct body* plan that *limits its size and shape* -*Animals' bodies are also designed to interact w/ their environments* whether in the deep sea, a rainforest canopy, or the desert -Therefore, a *large amount of information about the structure of an organism's body* (anatomy) and the *function of its cells, tissues and organs (physiology)* can be learned by studying that organism's environment.

Food Requirements

-Given the *diversity of animal life on our planet*, it is *not surprising that the animal diet would also vary substantially* -The *animal diet* = the *source of materials needed for building DNA* + *other complex molecules needed for growth, maintenance, reproduction*; collectively these processes = *biosynthesis* -The *diet is also the source of materials* = *ATP prod in the cells* -The *diet must be balanced to provide minerals/vitamins* that are required for *cellular function* What are the fundamental requirements of the animal diet? The animal diet should be well balanced and provide nutrients required for bodily function and the minerals and vitamins required for maintaining structure and regulation necessary for good health and reproductive capability.

Pyruvate Oxidation What three steps occur? What are the outcomes?

-If *oxygen is available, aerobic respiration will go forward* -In eukaryotic cells, the *pyruvate produced at end of glycolysis are transported into mitochondria* which are the sites of cellular respiration -*Pyruvate* is transformed into *an acetyl group* that will be picked up and *activated by a carrier coenzyme A (CoA)* = resulting compound is *acetyl CoA* -*CoA = from vitamin B5* pantothenic acid -*Acetyl CoA can be used in a variety of ways by the cell*, but its major function is *to oxidize acetyl group from pyruvate* to the *next* •The *pyruvate formed in glycolysis is transported from the CYTOSOL into a MITOCHONDRION* where the *citric acid cycle/oxidative phosphorylation will occur* •*2 molecules of pyruvate are produced* for each molecule of glucose that enters glycolysis •*Pyruvate DOESN'T enter the citric acid cycle* but undergoes chemical grooming in which 1) a *carboxyl group is removed* and *releases CO2* This *step proceeds 2x* (remember: there are two pyruvate molecules produced at the end of glycolsis) for every molecule of glucose metabolized; two of six carbons will have been removed at the end of both steps 2)*2C compound remaining is oxidized* (3 carbons to 2) while *NAD+ reduced to NADH* 3) *coenzyme A joins 2-carbon group to form acetyl coenzyme A* (acetyl CoA) •Then *2 acetyl CoAs enter citric acid cycle* + in the presence of oxygen, *acetyl CoA delivers acetyl group to 4C molecule, oxaloacetate, to form citrate* a six-carbon molecule with three carboxyl groups; this pathway will harvest the remainder of the extractable energy from what began as a glucose molecule.

Control of Metabolism Through Enzyme Regulation Which type of cell works much harder to process/break down nutrients? The rates of biochemical reactions are controlled by ______________energy?

-It would seem ideal to have a scenario in which all of the enzymes encoded in an organism's genome existed in abundant supply and functioned optimally under all cellular conditions, in all cells, at all times. In reality, this is far from the case -A variety of mechanisms ensure that this does not happen. Cellular needs and conditions vary from cell to cell, and change within individual cells over time -The *required enzymes and energetic demands of stomach cells* are *diff from those of fat storage cells, skin cells, blood cells, and nerve cells* -Furthermore, a *digestive cell works much harder to process/break down nutrients* during the time that closely follows a meal compared with many hours after a meal -As these *cellular demands and conditions vary*, *so do the amounts and functionality of diff enzymes* -Since the *rates of biochemical reactions are controlled by* = *ACTIVATION ENERGY* and *enzymes lower and determine activation energies for chemical reactions* the relative *amounts/functioning of the enzymes within a cell ultimately determine which reactions will proceed and at which rates* -This determination is *tightly controlled* -In *certain cellular environments*, *enzyme activity is partly controlled by environmental factors, like pH and temp* -There are *other mechanisms* through which *cells control the activity of enzymes and determine the rates at which various biochemical reactions* will occur.

Introduction of the Circulatory System

-Just as highway systems transport people and goods through a complex network, *the circulatory system transports nutrients, gases, wastes throughout the animal body* -Most *animals* = complex *multicellular organisms* that require a *mechanism for transporting nutrients throughout their bodies/removing waste prods* -The *circulatory system* has *evolved from simple diffusion thru cells in early evolution of animals* to a *complex network of blood vessels that reach all of the human body* -This extensive network *supplies cells, tissues, organs w/ O2 + nutrients*, and *removes CO2 + waste* which are byproducts of respiration -At the *core of circulatory system* = *heart* -The *human heart is protected beneath rib cage* -Made of *specialized/unique cardiac muscle* it pumps blood throughout the body and to the heart itself -*Heart contractions* are *driven by intrinsic electrical impulses* that the *brain/endocrine hormones help to regulate*. Understanding the heart's basic anatomy and function is important to understanding the body's circulatory and respiratory systems -*Gas exchange* = *essential* to the *circulatory system* -A *circulatory system* is *not needed in organisms w/o specialized respiratory organs* bc *O2 + CO2 diffuse btwn body tissues + external environment* but *for lungs/gills, O2 must transport to organs* to the body tissues via a circulatory system. Therefore, circulatory systems have had to evolve to accommodate the great diversity of body sizes and body types present among animals -In *all animals* = *circulatory system is used to transport nutrients and gases* through the body. Simple *diffusion* allows some water, nutrient, waste, and gas exchange into primitive animals that are *only a few cell layers thick*; however, *bulk flow* = only method by which the entire body of *larger more complex organisms is accessed* -

Energy and Metabolism What is bioenergetics? What is oxidized and what is reduced in cellular respiration? Cellular processes use the _________/____________ of complex molecules Some are spontaneous and ___________ energy and some need ___________ to proceed Most life forms on earth get their ____________ from the _____________ (plants) *Herbivores* = ____________-eaters *Carnivores* = _____________-eaters *Decomposers* = digest ___________/___________ matter

-Scientists use the term *bioenergetics* = *energy flow thru living systems*, such as *cells (CELL RESPIRATION = DOWNHILL ENERGY)* •*Glucose* loses its hydrogen atoms and *becomes oxidized to CO2* •*Oxygen* gains hydrogen atoms and becomes *reduced to H2O* -*Cellular processes* such as the *building/breaking down of complex molecules* occur through stepwise chemical reactions -Some of these chemical reactions *are spontaneous/release energy* whereas others require *energy to proceed* -Just as living things must *continually consume food to replenish* what has been used, *cells must continually produce more energy* to replenish that used by the many energy-requiring chemical reactions that constantly take place -All chemical reactions *use energy/release energy*, are the *cell's metabolism* -Most life forms on earth *get their energy from the sun* -*Plants* use *photosynthesis* to capture sunlight* -*Herbivores eat those plants* to obtain energy -*Carnivores eat the herbivores* -*Decomposers digest plant and animal matter*

Second Half of Glycolysis (Energy-Releasing Steps)

-So far, *glycolysis has cost the cell 2 ATP and produced two small, 3-carbon sugar molecules* -*Both will proceed thru the second half of the pathway* + *sufficient energy will be extracted to pay back the 2 ATP molecules* used as an *initial investment* produce a *profit* for the cell of two additional ATP molecules and *2 even higher-energy NADH* 6) *Oxidation of the sugar (glyceraldehyde-3-phosphate)* + *extracting high-energy electrons* which are *picked up by electron carrier NAD+* = producing *NADH* -The *sugar is then phosphorylated by a second phosphate group* producing *1,3-bisphosphoglycerate*Note that the *second phosphate group doesn't require another ATP* molecule -*The second half of glycolysis involves phosphorylation without ATP investment (step 6) and produces 2 NADH and 4 ATP molecules* -*Potential limiting factor* = *continuation of the reaction DEPENDS upon the AVAILABILITY OF THE OXIDIZED NAD+* -*NADH must be continuously oxidized back into NAD+ to keep this step going THROUGH FERMENTATION* -If *NAD+ is not available* = the *2nd half of glycolysis SLOWS DOWN* + *if oxygen is available = NADH will be oxidized readily* though indirectly, and the *high-energy electrons from hydrogen released in this process will be used to produce ATP* -In an *environment w/o oxygen* an alternate pathway (*fermentation*) can *provide the oxidation of NADH to NAD+* 7) In the seventh step, *catalyzed by phosphoglycerate kinase* (an enzyme named for the reverse reaction), *1,3-bisphosphoglycerate donates a high-energy phosphate to ADP* = *forming ATP* (This is an example of *substrate-level phosphorylation*) *A carbonyl group on the 1,3-bisphosphoglycerate is OXIDIZED to a carboxyl group* = forms*3-phosphoglycerate* 8) In the eighth step, the *remaining phosphate group in 3-phosphoglycerate moves from the 3rd to 2nd carbon* = *producing 2-phosphoglycerate (an isomer of 3-phosphoglycerate)* The *enzyme catalyzing* this step is a *MUTASE* (isomerase). 9) *ENOLASE catalyzes* + *causes 2-phosphoglycerate to lose water from its structure* = *dehydration reaction* resulting in the *formation of a DOUBLE bond that INCR the PE in the remaining phosphate bond* = *PHOSPHOENOLPYRUVATE (PEP)* 10) The last step in *glycolysis is catalyzed by the enzyme pyruvate KINASE* (the enzyme is named for the reverse reaction of pyruvate's conversion into PEP) and *results in the prod of a 2nd ATP molecule by SUBSTRATE LEVEL CONCENTRATION* + *pyruvic acid* (or its salt form, pyruvate) -Many *enzymes in enzymatic pathways* are named for the *REVERSE REACTIONS* = the *enzyme can catalyze both forward/reverse reactions* (these may have been described initially by the reverse reaction that *takes place in vitro* under non-physiological conditions).

Electron Transport Chain

-The *electron transport chain* is the *LAST step* + glucose metabolism *uses atmospheric oxygen* -*Oxygen CONTINUOUSLY DIFFUSES into PLANTS* but *in ANIMALS enters thru RESPIRATORY SYSTEM* -*Electron transport *is a series of *REDOX REACTIONS* that resemble a relay race or bucket brigade in that *electrons are passed rapidly from 1 to the next* to the endpoint of the chain *where electrons reduce oxygen produce water* -There are *4 complexes composed of proteins* and the aggregation of these 4 complexes *together w/ associated mobile, accessory electron carriers* is called the = *electron transport chain* The electron transport chain is *present in multiple copies in the inner mitochondrial membrane* of *eukaryotes* and the *plasma membrane of prokaryotes* -The *electron transport chain = series of electron transporters* embedded in the *inner mitochondrial membrane that shuttles electrons from NADH/FADH2* to *molecular oxygen* -*W/O NADH/FADH* = you *cannot get energy/synthesize ATP* -In the process, *protons are pumped from the mitochondrial matrix to the intermembrane space*, and *oxygen is reduced to water* •The *NADH* produced in glycolysis passes its electrons *across the mitochondrial membrane* to either *NAD+/FAD* -*Bc FADH2 adds its electrons farther along the ETC* it *contributes less to the H+ gradient* and thus *generates less ATP* •Some of the *energy of the H+ gradient* may be *used for work other than ATP prod*, such as the *active transport of pyruvate into the mitochondrion* O2: •*accepts 2 electrons*, *picks up 2 H+*, and •becomes reduced to water -*MAKES 28 ATP* but there will overall be *32* -*THIS STAGE* = *DEPENDENT ON STAGES 1-2*

Limiting Effects of Diffusion on Size and Development

-The *exchange of nutrients and wastes btwn a cell and its watery environment* occurs through the process of *DIFFUSION* -*All living cells are bathed in liquid*, whether they are in a *single-celled organism* or a *multicellular one* -*Diffusion* = *effective over a specific distance* and *limits the size* that an individual *cell can attain* -If a *cell is a single-celled microorganism* such as an *amoeba* it can *satisfy all of its nutrient/waste needs through diffusion* -If the *cell is too large*, then *diffusion is ineffective and the center of the cell does not receive adequate nutrients/dispel its waste* -An important concept in understanding *how efficient diffusion is as a means of transport is the surface to volume ratio* -Recall that any three-dimensional object has a surface area and volume; the ratio of these two quantities is the surface-to-volume ratio. Consider a cell shaped like a perfect sphere: it has a surface area of 4πr2, and a volume of (4/3)πr3. The surface-to-volume ratio of a sphere is 3/r; *as the cell gets bigger, its surface to volume ratio decreases* making *diffusion LESS EFFICIENT* -The *larger the size of the sphere*, or animal, the *less surface area* for diffusion it possesses -The *solution to producing larger organisms is for them to become multicellular* -*Specialization occurs in complex organisms*, allowing *cells to become more efficient* at doing *fewer tasks* -Ex: *circulatory systems bring nutrients and remove waste*, while respiratory systems provide oxygen for the cells and remove carbon dioxide from them. -Other *organ systems have developed further specialization of cells and tissues* and efficiently *control body functions* -Moreover, *surface-to- volume ratio applies to other areas of animal development*, such as the relationship between *muscle mass and cross-sectional surface area* in supporting skeletons, and in the *relationship btwn muscle mass + generation of dissipation of heat*

Lactic Acid Fermentation

-The *fermentation method BY ANIMALS/BACTERIA* (like those in yogurt) is *lactic acid fermentation* -This *type of fermentation is used ROUTINELY* in *mammalian red blood cells& and in *skeletal muscle* that has an *insufficient oxygen supply to allow aerobic respiration to continue* (that is, in muscles used to the point of fatigue) -In muscles, *lactic acid accumulation must be removed by blood circulation* and the *lactate brought to the liver for further metabolism* -The chemical reactions of lactic acid fermentation are the following: *Pyruvic acid + NADH ↔ lactic acid + NAD+* -The *enzyme used in this reaction* = *lactate dehydrogenase (LDH)* -The *reaction can proceed in either direction*, but the *reaction from left to right is INHIBITED by acidic conditions* -Such *lactic acid accumulation was once believed to cause muscle stiffness, fatigue, soreness* = *more recent research disputes this hypothesis* Once the *lactic acid has been removed from the muscle and circulated to the liver* = it *can be reconverted into pyruvic acid* and further *catabolized for energy* •*Lactate is carried by the blood to the liver*, where it is *converted back to pyruvate* and *oxidized in the mitochondria of liver cells* •Your *muscle cells and certain bacteria can regenerate NAD+* through lactic acid fermentation, in which •*NADH is oxidized back to NAD+* and •*pyruvate is reduced to lactate*

Metabolism of Carbohydrates The metabolism of sugar breakdowns molecules + exemplifies cellular processes that ___________/__________ energy Living things consume sugar as a ________ _____________ ___________ bc sugar molecules hold energy stored in _________ -Breakdown of glucose equation (cellular respiration): -During photosynthesis, plants use _________ ________ to convert _______ __________ into *sugar molecules = glucose (C6H12O6)* -This process involves synthesizing a larger, energy-storing molecule + _______________ _____________ to proceed -The *sugar (glucose) = stored as _____________ In photosynthesis, light energy is transformed into _________ _________

-The *metabolism of sugar* - breakdown molecules + perform reactions (a simple carbohydrate) is a classic example of the *many cellular processes that use and produce energy* -*Living things consume sugar* as a *MAJOR ENERGY SOURCE* bc *sugar molecules hold energy stored in bonds* -The breakdown of glucose, a simple sugar, is described by the equation: *C6H12O6* + *6O2* = *6CO2* + *6H2O* + *energy* -*Carbohydrates consumed* have their *origins in photosynthesizing plants* -During photosynthesis, *plants use energy of sunlight* to *convert carbon dioxide gas (CO2)* into *sugar molecules = glucose (C6H12O6)* -Because this process involves *synthesizing a larger, energy-storing molecule*, it *REQUIRES ENERGY* to proceed/NOT SPONTANEOUS -The *synthesis of glucose* is described by this equation (notice that it is the reverse of the previous equation): *6CO2* + *6H2O* + *energy* = *C6H12O6* + *6O2* -During the chemical reactions of photosynthesis, *energy is provided in high-energy molecule = ATP*, or adenosine triphosphate, which is the *primary energy currency of all cells* -*Cells use molecules of ATP* as energy currency *to perform immediate work* - The *sugar (glucose) = stored as starch/glycogen* -*Energy-storing polymers* like these are *broken down into glucose to supply molecules of ATP* -*Solar energy* is required to *synthesize a molecule of glucose* during the reactions of photosynthesis -In photosynthesis, *light energy from the sun is initially transformed into chemical energy* that is *temporally stored in energy carrier molecules ATP/NADPH*(nicotinamide adenine dinucleotide phosphate) -The *stored energy in ATP/NADPH* is then *used later in photosynthesis to build 1 molecule of glucose from 6 molecules of CO2* -Under ideal conditions, *energy from 18 molecules of ATP* is required to synthesize *1 molecule of glucose* during the reactions of photosynthesis -Glucose molecules can also be *combined with/converted into other types of sugars* -When sugars are consumed, molecules of *glucose eventually make their way into each living cell* of the organism -Inside the cell, each *sugar molecule is broken down through a complex series of chemical reactions* The goal of these reactions is to *harvest the energy stored inside the sugar molecules* -The harvested energy is *used to make high-energy ATP molecules*, which can be used to perform work, powering many chemical reactions in the cell The amount of energy needed to make *1 molecule of glucose from 6 molecules of CO2 is 18 molecules of ATP/12 molecules of NADPH* (each one of which is energetically equivalent to three molecules of ATP), or a total of *54 molecule equivalents required for the synthesis of one molecule of glucose* This process is a fundamental and efficient way for cells to generate the molecular energy that they require.

ATP Yield

-The *number of ATP molecules generated from glucose catabolism varies* -Ex: the *number of hydrogen ions the ETC complexes can pump thru membrane varies btwn species* -*Another source of variance* = stems *from the shuttle of electrons across mitochondria membranes*(The *NADH generated from glycolysis cannot easily enter mitochondria*) -Thus, *electrons are picked up on the inside of mitochondria by either NAD+ or FAD+* -As you have learned earlier, these *FAD+ molecules can transport FEWER ions*; consequently, *fewer ATP molecules are generated* when FAD+ acts as a carrier. *NAD+ is used as the electron transporter in the liver and FAD+ acts in the brain* -Another factor that affects the *yield of ATP molecules generated from glucose* = *intermediate compounds in these pathways are used for other purposes* -*Glucose catabolism connects w/ pathways that build/break down biochemical compounds in cells* and the result is somewhat messier than the ideal situations described thus far -Ex: *sugars other than glucose are fed into the glycolytic pathway for energy extraction* -Moreover, the *five-carbon sugars that form nucleic acids* are made from *intermediates in glycolysis* -Certain *nonessential amino acids can be made from intermediates of glycolysis/citric acid cycle* -*Lipids*, such as cholesterol and triglycerides, are also *made from intermediates in these pathways*, and both *amino acids and triglycerides are broken down for energy through these pathways. Overall, in living systems, these pathways of glucose catabolism extract about 34 percent of the energy contained in glucose.

Organic Precursors

-The *organic molecules required for building cellular material/tissues must come from food* = *Carbohydrates or sugars* are the primary sources in the animal body -During *digestion* = *digestible carbs are ultimately broken down into glucose* + *used to provide energy thru metabolic pathways* = *complex carbs including polysaccharides* can be *broken down into glucose thru biochem modification* -*Humans DON'T prod the enzyme cellulase* + *lack the ability to derive glucose from the polysaccharide cellulose* -In humans, *these molecules provide the fiber required for moving waste thru large intestine* + *healthy colon* -The *intestinal flora* in the *human gut* are able to *extract some nutrition* from these *plant fibers* -The *excess sugars are converted into glycogen* and *stored in the liver/muscles for later* -*Glycogen stores fuel prolonged exertions*, (long-distance running) and to *provide energy during food shortage* -*Excess glycogen can be converted to fats*, which are *stored in lower layer of skin* of mammals *for insulation + energy storage* -*Excess digestible carbs* are *stored by mammals* to *survive famine/aid in mobility* -Another important requirement is that of nitrogen. *Protein catabolism provides a source of organic nitrogen*. Amino acids are the building blocks of proteins and *protein breakdown provides amino acids that are used for cellular function* -The *carbon + nitrogen from these become the building block for nucleotides, nucleic acids, proteins, cells, tissues* -*Excess nitrogen* must be *excreted as it is toxic* -*Fats* add flavor to food and *promote satiety* -*Fatty foods* = *significant sources of energy* bc *1g of fat contains 9 calories* *Fats are required* in the diet *to aid absorption of fat-soluble vitamins* and the *production of fat-soluble hormones*

How Light-Dependent Reactions Work

-The *overall function of light-dependent reactions is to convert solar energy into chemical energy in the form of NADPH and ATP* -This *chemical energy supports the light-independent reactions* and fuels the *assembly of sugar molecules* -*Protein complexes + pigment molecules* = work together to *produce NADPH and ATP* -A *photosystem consists of a light-harvesting complex* and a *reaction center* -*Pigments in the light-harvesting complex pass light energy* to *2 chlorophyll a molecules* in the reaction center -The *light excites an electron from chlorophyll a pair*, which *passes to electron acceptor* -The *excited electron must then be replaced* -In (a) *photosystem II,* the *electron comes from splitting of water*, *which releases oxygen as a waste product* -In (b) *photosystem I*, the *electron comes from the chloroplast electron transport chain* -The *actual step that converts light energy to chemical energy* = takes place *in a multiprotein complex* called a *photosystem* = *2 types found embedded in the thylakoid membrane*, *photosystem II (PSII)* and *photosystem I (PSI)* -The *two complexes differ on the basis of what they oxidize* (that is, the source of the low-energy electron supply) and *what they reduce* (the place to which they deliver their energized electrons). -*Both photosystems have the same basic structure*; a number of *antenna proteins to which the chlorophyll molecules are bound surround the reaction center* where the (*photochemistry takes place*) -*Each photosystem* is *serviced by the light-harvesting complex*, which *passes energy from sunlight to the reaction center*; it *consists of multiple antenna proteins w/ mixture of 300-400 chlorophyll a and b + pigments like carotenoids* -The *absorption of a single photon* or distinct quantity or "packet" of light *by any of the chlorophylls pushes that molecule into an excited state* -*Light energy has now been captured by biological molecules* but is *not stored in any useful form* yet -The *energy is transferred from chlorophyll to chlorophyll until delivered to the reaction center* -Up to this point, *only energy has been transferred btwn molecules, not electrons* -*In the photosystem II (PSII) reaction center*, *energy from sunlight extracts electrons from water* -The *electrons travel through the chloroplast electron transport chain to photosystem I (PSI)*, which *reduces NADP+ to NADPH* -*The electron transport chain moves protons across the thylakoid membrane* in*to the lumen* -At the same time, *splitting of water adds protons to the lumen*, and *reduction of NADPH removes protons from the stroma* -The net result is a *low pH in the thylakoid lumen*, and a *high pH in the stroma* -*ATP synthase uses this electrochemical gradient to make ATP* The reaction center contains a pair of chlorophyll a molecules with a special property. Those two chlorophylls can undergo oxidation upon excitation; they can actually give up an electron in a process called a photoact. It is at this step in the reaction center, this step in photosynthesis, that light energy is converted into an excited electron. All of the subsequent steps involve getting that electron onto the energy carrier NADPH for delivery to the Calvin cycle where the electron is deposited onto carbon for long-term storage in the form of a carbohydrate.PSII and PSI are two major components of the photosynthetic electron transport chain, which also includes the cytochrome complex. The cytochrome complex, an enzyme composed of two protein complexes, transfers the electrons from the carrier molecule plastoquinone (Pq) to the protein plastocyanin (Pc), thus enabling both the transfer of protons across the thylakoid membrane and the transfer of electrons from PSII to PSI. The reaction center of PSII (called P680) delivers its high-energy electrons, one at the time, to the primary electron acceptor, and through the electron transport chain (Pq to cytochrome complex to plastocyanine) to PSI. P680's missing electron is replaced by extracting a low-energy electron from water; thus, water is split and PSII is re-reduced after every photoact. Splitting one H2O molecule releases two electrons, two hydrogen atoms, and one atom of oxygen. Splitting two molecules is required to form one molecule of diatomic O2 gas. About 10 percent of the oxygen is used by mitochondria in the leaf to support oxidative phosphorylation. The remainder escapes to the atmosphere where it is used by aerobic organisms to support respiration. As electrons move through the proteins that reside between PSII and PSI, they lose energy. That energy is used to move hydrogen atoms from the stromal side of the membrane to the thylakoid lumen. Those hydrogen atoms, plus the ones produced by splitting water, accumulate in the thylakoid lumen and will be used synthesize ATP in a later step. Because the electrons have lost energy prior to their arrival at PSI, they must be re-energized by PSI, hence, another photon is absorbed by the PSI antenna. That energy is relayed to the PSI reaction center (called P700). P700 is oxidized and sends a high- energy electron to NADP+ to form NADPH. Thus, PSII captures the energy to create proton gradients to make ATP, and PSI captures the energy to reduce NADP+ into NADPH. The two photosystems work in concert, in part, to guarantee that the production of NADPH will roughly equal the production of ATP. Other mechanisms exist to fine tune that ratio to exactly match the chloroplast's constantly changing energy needs.

Animal Primary Tissues

-The *tissues of multicellular, complex animals* are *four primary types*: 1. *epithelial* 2. *connective* 3. *muscle* 4. *nervous* -Recall that *tissues are groups of similar cells group* of *similar cells carrying out related functions* -These *tissues combine to form organs*—like the *skin or kidney*—that have *specific, specialized functions within the body* -*Organs* are organized into organ systems to *perform functions*; examples include the *circulatory system*, which consists of the heart and blood vessels, and the *digestive system*, consisting of several organs, including the stomach, intestines, liver, and pancreas -*Organ systems* come together to *create an entire organism* 1. *Epithelial tissues* = *cover the outside of organs and structures* in the body and *line the lumens of organs* in a single layer or multiple layers of cells -The types of epithelia are *classified by the shapes of cells* present and the *number of layers of cells.* -Epithelia *composed of a single layer of cells is called simple epithelia* epithelial tissue *composed of multiple layers = STRATIFIED EPITHELIA* -could be squamous, cuboidal, columnar, transitional 2. *Squamous epithelial cells* are generally *round, flat, small, centrally located nucleus* -The *cell outline* is slightly *irregular, and cells fit together to form a covering or lining* -When the *cells are arranged in a single layer (simple epithelia)*, they *facilitate diffusion in tissues*, such as the areas of *gas exchange in the lungs + exchange of nutrients and waste at blood capillaries -Squamous cells with their membranes joined together to *form an epithelium* Squamous epithelial cells arranged in stratified layers, where protection is needed on the body from outside abrasion and damage. This is called a stratified squamous epithelium and occurs in the skin and in tissues lining the mouth and vagina. 3. *Cuboidal epithelial cells*, shown in *cube-shaped w/ a single, central nucleus -They are most commonly found in a *single layer representing a simple epithelia in glandular tissues* throughout the body where they *prepare and secrete glandular material* + *walls of tubules* and in the ducts of the *kidney and liver* Simple cuboidal epithelial cells line tubules in the mammalian kidney, where they are involved in filtering the blood. 4. *Columnar epithelial cells* are *taller* than they are wide: they resemble a *stack of columns in an epithelial layer*, and are most commonly *found in a single-layer arrangement* -The *nuclei of columnar epithelial cells in the digestive tract* appear to be lined up at the *base of the cells*. These cells *absorb material from the lumen of the digestive tract* and prepare it for *entry into the body through the circulatory and lymphatic systems* -*Columnar epithelial cells lining the respiratory tract* appear to be *STRATIFIED* -However, each *cell is attached to the base membrane of the tissue* and, therefore, they are *simple tissues* -The *nuclei are arranged at diff levels in the layer of cells*, making it *appear as though there is more than one layer* = *pseudostratified, columnar epithelia* -This cellular covering has *cilia at the apical, or free, surface of the cells.* -The cilia enhance the movement of mucous and trapped particles out of the respiratory tract, *helping to protect the system from invasive microorganisms* and harmful material that has been breathed into the body. Goblet cells are interspersed in some tissues (such as the lining of the trachea). The goblet cells contain mucous that traps irritants, which in the case of the trachea keep these irritants from getting into the lungs 5. *Transitional or uroepithelial cells* appear only in the *urinary system, primarily in the bladder and ureter*. These cells are *arranged in a stratified layer*, but they have the *capability of appearing to pile up* on top of each other in a relaxed, empty bladder. As the *urinary bladder fills, the epithelial layer unfolds and expands to hold the volume of urine* introduced into it. As the *bladder fills, it expands and the lining becomes thinner* In other words, the tissue transitions from *thick to thin tissue* 6. *Connective tissues* are made up of a *matrix consisting of living cells and a non-living substance*/*ground substance* -The *ground substance is made of an organic substance (usually a protein)* and an *inorganic substance* (usually a mineral or water) -The *principal cell of connective tissues* is the *fibroblast* -This cell *makes the fibers found in connective tissues* -*Fibroblasts are motile*, able to *carry out mitosis, and can *synthesize whichever connective tissue* is needed. -*Macrophages, lymphocytes, leukocytes* can be found in some of the tissues. Some tissues have *specialized cells not in others* -The matrix in *connective tissues gives the tissue its density* + When a *connective tissue has a high concentration of cells* or fibers, it has proportionally a *LESS DENSE MATRIX* -The *organic portion or protein fibers * = *collagen, elastic, or reticular fibers* -Collagen fibers provide *strength to the tissue, preventing it from being torn or separated* from the surrounding tissues. Elastic fibers are made of the *protein elastin; this fiber can stretch to one and one half of its length* and return to its original size and shape. Elastic fibers *provide flexibility to the tissues* + *Reticular fibers* are *thin strands of collagen that form a network of fibers* to *support the tissue and other organs* to which it is connected. The various types of connective tissues, the types of cells and fibers they are made of, and sample locations of the tissues 7. *Loose connective tissue/areolar* = sampling of *all of the components of a connective tissue* + *Loose connective tissue has some fibroblasts/macrophages* are present as well -*Collagen fibers = wide and stain a light pink*, while *elastic fibers = thin and stain dark blue to black* The space between the formed elements of the tissue is filled with the *matrix.* -The material in the connective tissue gives it a *loose consistency similar* to a cotton ball that has been pulled apart. Loose connective tissue is found around *every blood vessel and helps to keep the vessel in place* The tissue is also found around and *between most body organs* In summary, areolar tissue is *tough, yet flexible, and comprises membranes* 8. *Fibrous connective tissues* contain *large amounts of collagen fibers* and *few cells or matrix* material. The fibers can be *arranged irregularly or regularly* with the strands lined up in parallel. *Irregularly arranged* fibrous connective tissues are found *in areas of the body where stress occurs from all directions*, such as the dermis of the skin. *Regular fibrous* connective tissue, is found in *tendons (which connect muscles to bones) and ligaments* (which connect bones to bones) 8. *Cartilage* is a *connective tissue w/ large amount of the matrix/variable amounts of fibers* -The cells, called *chondrocytes, make the matrix and fibers* of the tissue. Chondrocytes are found in spaces within the tissue called *lacunae*. A *cartilage w/ collagen and elastic fibers is hyaline cartilage* + the *lacunae are randomly scattered* throughout the tissue and the matrix takes on a milky or scrubbed appearance with routine histological stains -*Sharks have cartilaginous skeletons*, as does nearly the entire human skeleton during a *specific pre-birth developmental stage* -A *remnant of this cartilage* persists in the *outer portion of the human nose* -*Hyaline cartilage* is also found at the ends of *long bones, reducing friction* and cushioning the articulations of these bones. -*Elastic cartilage has a large amount of elastic fibers*, giving it tremendous flexibility -The *ears of most vertebrate animals contain this cartilage* as do portions of the larynx, or voice box -*Fibrocartilage contains a large amount of collagen fibers*, giving the tissue tremendous *strength* Fibrocartilage comprises the intervertebral discs in vertebrate animals. -*Hyaline cartilage found in movable joints* such as the knee and shoulder becomes damaged as a result of age or trauma. Damaged hyaline cartilage is *replaced by fibrocartilage and results in the joints* becoming "stiff." 9. *Bone/osseous tissue* = a *connective tissue that has 2 diff types of matrix material* The *organic matrix* is similar to the matrix material found in other *connective tissues* + amount of *collagen and elastic fibers* -This gives *strength and flexibility* to the tissue. The *inorganic matrix consists of mineral salts*—mostly calcium salts—that give the *tissue hardness*. Without adequate organic material in the matrix, the tissue breaks; *without adequate inorganic material* in the matrix, the *tissue bends* There are three types of cells in bone: *osteoblasts, osteocytes, and osteoclasts* + *Osteoblasts are active in making bone for growth* and remodeling. *Osteoblasts deposit bone material* into the matrix and, after the matrix surrounds them, they continue to live, but in a reduced metabolic state as osteocytes. *Osteocytes are found in lacunae of the bone*. *Osteoclasts are active in breaking down bone for bone remodeling*, and they provide access to calcium stored in tissues. Osteoclasts are usually found on the surface of the tissue. *Bone can be divided into two types*: *compact and spongy*. Compact bone is found in the shaft (or diaphysis) of a long bone and the surface of the flat bones, while spongy bone is found in the end (or epiphysis) of a long bone. *Compact bone is organized into subunits called osteons* -A blood vessel and a nerve are found in the center of the structure within the *Haversian canal, with radiating circles of lacunae* around it known as *lamellae*. The *wavy lines seen btwn the lacunae* are microchannels called *canaliculi*; they *connect the lacunae to aid diffusion btwn cells* + *Spongy bone is made of tiny plates* called trabeculae these plates *serve as struts to give the spongy bone strength* Over time, these plates can break causing the bone to become less resilient. Bone tissue forms the internal skeleton of vertebrate animals, providing structure to the animal and points of attachment for tendons 10. *Adipose tissue/fat tissue*, is considered a *connective tissue even though it does not have fibroblasts* or a *no real matrix + few fibers*. Adipose tissue is *made up of cells called adipocytes* that *collect and store fat in triglycerides*, for energy metabolism. Adipose tissues additionally serve as *insulation to help maintain body temp*, allowing animals to be *endothermic*, and they function as cushioning against damage to body organs. Under a microscope, adipose tissue cells appear *empty due to the extraction of fat* during the processing of the material for viewing. The thin lines in the image are the cell membranes, and the nuclei are the small, black dots at the edges of the cells. 11. *Blood is considered a connective tissue* because it *has a matrix*. The living cell types are *red blood cells (RBC)/ erythrocytes*, and *white blood cells (WBC)/ leukocytes* -The *fluid portion of whole blood, its matrix*, is commonly called *plasma* + *cell found in greatest abundance* in the blood is the *erythrocyte* = in millions in a blood sample: the average number of red blood cells in primates is 4.7 to 5.5 million cells per microliter. Erythrocytes are *consistently the same size in a species, but vary in size between species*. For example, the average diameter of a primate red blood cell is 7.5 μl, a dog is close at 7.0 μl, but a cat's RBC diameter is 5.9 μl. Sheep erythrocytes are even smaller at 4.6 μl. Mammalian erythrocytes *lose their nuclei and mitochondria* when they are released from the bone marrow where they are made. Fish, amphibian, and avian red blood cells maintain their nuclei and mitochondria throughout the cell's life. The principal job of an erythrocyte is to carry and deliver oxygen to the tissues. -*Leukocytes are the predominant white blood cells found in the peripheral blood*. Leukocytes are counted in the thousands in the blood with measurements expressed as ranges: primate counts range from 4,800 to 10,800 cells per μl, dogs from 5,600 to 19,200 cells per μl, cats from 8,000 to 25,000 cells per μl, cattle from 4,000 to 12,000 cells per μl, and pigs from 11,000 to 22,000 cells per μl. -*Lymphocytes function primarily in the immune response to foreign antigens* or material. Different types of lymphocytes make *antibodies tailored to the foreign antigens* and control the *prod of those antibodies* -*Neutrophils are phagocytic cells* and they participate in one of the *early lines of defense against microbial invaders*, *aiding in the removal of bacteria that has entered the body* Another leukocyte that is found in the peripheral blood is the *monocyte = phagocytic macrophages that clean up dead and damaged cells in the body* whether they are foreign or from the host animal. Two additional leukocytes in the blood are *eosinophils and basophils—both help to facilitate the inflammatory response* The slightly granular material among the cells is a cytoplasmic fragment of a cell in the bone marrow. This is called a platelet or thrombocyte. *Platelets participate in the stages leading up to coagulation of the blood to stop bleeding through damaged blood vessels*. Blood has a number of functions, but primarily it transports material through the body to bring nutrients to cells and remove waste material from them.

Metabolic Pathways The processes of making/breaking down sugar are examples of two what? What is a metabolic pathway? What is an anabolic pathway? Catabolic? And metabolism is composed of ______________ and _______________ pathways

-The processes of *MAKING/BREAKING DOWN SUGAR* = *2 types of metabolic pathways* -A *metabolic pathway* = a series of *interconnected biochem reactions that convert a substrate molecule* or molecules, step-by-step, *through a series of metabolic intermediates* eventually *yielding a final product* or products -In the case of *sugar metabolism*, the first metabolic pathway *synthesized sugar from smaller molecules*, and the other pathway *broke sugar down into smaller molecules* -These *2 opp processes*—the first *requiring energy* and the second *producing energy*—are referred to as *anabolic (building) and catabolic (breaking down)* pathways, respectively -Consequently, *metabolism is composed of building (anabolism) and degradation (catabolism)*

Introduction of Photosynthesis

-This *world map shows Earth's distribution of photosynthesis* as seen *via chlorophyll a concentrations* -On land, *this is evident via terrestrial plants*, and in oceanic zones, via phytoplankton.= -*Photosynthesis* = *essential to all life on earth*; both *plants and animals depend on it* -It is the *only biological process* that *can capture energy* that *originates in outer space (sunlight)* and *convert it into chemical compounds (carbohydrates)* that *every organism uses to power its metabolism* -In brief, the *energy of sunlight is captured/used to energize electrons*, which are then *stored in the covalent bonds of sugar molecules* -How long lasting and stable are those covalent bonds? The *energy extracted today by the burning of coal and petroleum products* represents *sunlight energy captured and stored by photosynthesis almost 200 million years ago* -*Plants, algae, cyanobacteria* are the *only organisms capable of performing photosynthesis*, *producers* -Because they *use light to manufacture their own food*, = *photoautotrophs* (literally, *"self-feeders using light"*) -Other organisms, such as *animals, fungi, other bacteria* are termed *heterotrophs* (*"other feeders"*) bc they must *rely on sugars produced by photosynthetic organisms* for their *energy needs* -A *third very interesting group of bacteria* (prokaryotes) *synthesize sugars*, *NOT BY sunlight's energy*, but by *extracting energy from INORGANIC chemical compounds* = *chemoautotrophs* -Photosynthesis is *not just that it can capture sunlight's energy* -A *lizard sunning itself on a cold day* can *use the sun's energy to warm up* -*Photosynthesis* is *vital bc it evolved as a way to store energy in solar radiation* (the "photo-" part) as *high-energy electrons in the carbon-carbon bonds of carbohydrate molecules* (the "-synthesis" part) -Those *carbohydrates are the energy source of heterotrophs for synthesis of ATP* via respiration -Therefore, *photosynthesis powers 99% of Earth's ecosystems* -When a *top predator* (wolf) *preys on a deer*, the *wolf is at the end of an energy path* that went *from nuclear reactions on sun*, to *light* to *photosynthesis* to *vegetation*, to *deer*, and finally to *wolf*

First Half of Glycolysis (Energy-Requiring Steps)

1) The first step in glycolysis is *catalyzed by hexokinase* = *enzyme w/ broad specificity* that *catalyzes the phosphorylation of 6-carbon sugars* -*Hexokinase phosphorylates glucose using ATP* as the source of the phosphate, *producing glucose-6-phosphate* (reactive form of glucose) -This reaction *prevents interaction of phosphorylated glucose w/ GLUT proteins* and can't longer leave the cell *bc the negatively charged phosphate will not allow it to cross the hydrophobic interior* of the plasma membrane 2) An *isomerase converts glucose-6-phosphate into one of its isomers* = *fructose-6-phosphate* -An *ISOMERASE* = *an enzyme that catalyzes the conversion of a molecule into one of its isomers* (This change from *phosphoGLUCOSE to phosphoFRUCTOSE* allows the *eventual split of sugar into two 3-carbon molecules* 3) The third step is the *phosphorylation of fructose-6-phosphate, catalyzed by the enzyme phosphoFRUCTOKINASE* -A *second ATP molecule donates a high-energy* phosphate to fructose-6-phosphate, *producing fructose-1,6-bisphosphate* In this pathway, *phosphofructokinase* = *rate-limiting enzyme* -It is *ACTIVE* = when *high ADP concentration*; it is *LESS ACTIVE* = when *low ADP* and the *high ATP concentration* -Thus, *if there is "sufficient" ATP in the system* = the *pathway slows down* -This is a *type of end product inhibition* since *ATP is the end product of glucose catabolism* 4) The newly added *high-energy phosphates further destabilize fructose-1,6-bisphosphate* The fourth step in glycolysis *employs an enzyme* = *ALDODASE* to cleave 1,6-bisphosphate into *two 3-carbon isomers*: *dihydroxyacetone-phosphate* + *glyceraldehyde-3-phosphate* 5) *An isomerase transforms dihydroxyacetone-phosphate into its isomer* = *glyceraldehyde-3-phosphate* -*pathway will continue with 2 molecules of a single isomer* At this point in the pathway, there is a *net investment of energy from 2 ATP molecules in the breakdown of one glucose* molecule. -*The first half of glycolysis uses two ATP molecules in the phosphorylation of glucose, which is then split into two three-carbon molecules*

Chemiosmosis What is it? Many ions cannot diffuse thru the nonpolar regions of phospholipid membranes without _____________ What is ATP synthase?

A process for synthesizing ATP using the energy of an electrochemical gradient/ATP synthase enzyme. Process by which a Hydrogen pump pumps protons into the thylakoid membrane. H+ passively flows through the ATP synthase which leads to the creation of ATP. -*chemiosmosis* = the *free energy from series of redox reactions* just *described is used to pump hydrogen ions (protons) across the membrane* -The *uneven distribution of H+ ions across membrane establishes concentration/electrical gradients* (thus, an *electrochemical gradient*), *owing to hydrogen ions' positive charge* and their *aggregation on one side of the membrane* If the membrane were open to diffusion by the hydrogen ions, *the ions would tend to diffuse back across into the matrix driven by electrochemical gradient* -Recall that *many ions cannot diffuse thru nonpolar regions of phospholipid membranes* without the *aid of ion channels* -Similarly, *hydrogen ions in the matrix space can only pass* through the inner mitochondrial membrane through an *integral membrane protein called ATP synthase*= This *complex protein acts as a tiny generator* turned by the *force of hydrogen ions diffusing through it down their electrochemical gradient* -The *turning of parts of this molecular machine facilitates the addition of a phosphate to ADP*, forming *ATP, using the potential energy of hydrogen ion gradient* -*ATP synthase* is a *complex, molecular machine uses a proton (H+) gradient* to *form ATP from ADP* and *inorganic phosphate (Pi)* -*used to generate 90% of ATP during aerobic glucose catabolism* + *also the method in LIGHT REACTIONS* of photosynthesis to *harness energy of sunlight in the process of photophosphorylation* -Recall that the *production of ATP using process of chemiosmosis* in *mitochondria is called oxidative phosphorylation* -The *overall result of these reactions is the production of ATP from energy of the electrons removed from hydrogen atoms* -These *atoms were originally part of a glucose molecule* -At the *end of the pathway, the electrons reduce an oxygen molecule to oxygen ions* -The *extra electrons on the oxygen attract hydrogen ions (protons)* from the *surrounding medium, and water is formed*

The Light-Dependent Reactions of Photosynthesis What is Light Energy?

How can light be used to make food? When a person turns on a lamp, electrical energy becomes light energy -*Like all other forms of kinetic energy*, *light can travel*, *change form*, and *be harnessed to do work* -In the case of photosynthesis, *light energy is converted into chemical energy*, which *photoautotrophs use to build carbohydrates* -However, *autotrophs only use a few specific components of sunlight* -The *sun emits an enormous amount of electromagnetic radiation (solar energy)* -*Humans can see only* a *fraction of this energy*, which portion is therefore referred to as *"visible light"* -The manner in which *solar energy travels in waves*+ *can determine the amount of energy of a wave w/ its wavelength*, the *distance btwn consecutive points of a wave* -A *single wave is measured from 2 consecutive points*, such as from *crest to crest* or from *trough to trough* -*Visible light constitutes* only *1 of many types of electromagnetic radiation from the sun/stars* -*Scientists differentiate the various types of radiant energy* from the sun *within the electromagnetic spectrum* -*The electromagnetic spectrum* = the *range of all possible frequencies of radiation* -The *difference btwn wavelengths relates to the amount of energy carried by them* -The *sun emits energy in the form of electromagnetic radiation* -This *radiation exists at diff wavelengths*, each of which *has its own characteristic energy* -*All electromagnetic radiation*, including visible light, is *characterized by its wavelength* -*Each type of electromagnetic radiation travels at a particular wavelength* -The *longer the wavelength* (or the more stretched out it appears in the diagram), the *less energy is carried* -*Short, tight waves carry the most energy* -The *electromagnetic spectrum shows several types of electromagnetic radiation* originating from the sun, *including X-rays and ultraviolet (UV) rays* -The *higher-energy waves can penetrate tissues/damage cells/DNA* explaining *why both X-rays/UV rays can be harmful* to living organisms.

Enzyme Compartmentalization + Feedback Inhibition in Metabolic Pathways In eukaryotic cells, enzymes are usually what? ______________ are involved in the digestion of cellular debris and foreign materials What is feedback inhibition? ATP is an _______________ molecule that can spontaneoulsy dissociate into ADP. ___ serves as a positive allosteric reguator

In *eukaryotic cells* = *molecules (enzymes) are *usually compartmentalized into diff organelles* -This *allows for yet another level of regulation* of enzyme activity -*Enzymes required only for certain cellular processes can be housed separately* along with their substrates, allowing *for more efficient chemical reactions* -Examples of this sort of *enzyme regulation based on location and proximity include the enzymes involved in the latter stages of cellular respiration*, which take place exclusively *in the mitochondria*, and the *enzymes* involved in the *digestion of cellular debris and foreign materials, located within lysosomes* -*Molecules can regulate enzyme function in many ways*. A major question remains, however: What are these molecules and where do they come from? Some are *cofactors and coenzymes, ions, and organic molecules*, as you've learned. What other molecules in the cell provide enzymatic regulation, such as allosteric modulation, and competitive and noncompetitive inhibition? The answer is that a wide *variety of molecules can perform these roles*. Some of these molecules include *pharmaceutical and non-pharmaceutical drugs, toxins, and poisons* from the environment -Perhaps the *most relevant sources of enzyme regulatory molecules*, with *respect to cellular metabolism* = *products of the cellular metabolic reactions* themselves -In a most efficient and elegant way, *cells have evolved to use products of their own reactions for feedback inhibition* of enzyme activity -*Feedback inhibition* = involves the *use of a reaction product to regulate its own further production* -The *cell responds to the abundance of specific products by slowing down prod during anabolic/catabolic reactions* -Such reaction products *may inhibit the enzymes that catalyzed their production through the mechanisms* described above -*Metabolic pathways are a series of reactions catalyzed by multiple enzymes.* -*Feedback inhibition* = where the *end product of the pathway inhibits an upstream step*, is an important *regulatory mechanism in cells*. The production of both *amino acids and nucleotides is controlled through feedback inhibition* Additionally, *ATP is an allosteric regulator of some of the enzymes involved in the catabolic breakdown* of sugar, the process that produces ATP -In this way, when *ATP is abundant, the cell can prevent its further production* Remember that *ATP is an UNSTABLE molecule that can SPONTANEOUSLY dissociate into ADP* -If *too much ATP* were present in a cell, much of it would *go to waste* -On the other hand, *ADP serves as a positive allosteric regulator (an allosteric activator)* for some of the same enzymes that are inhibited by ATP. Thus, when *relative levels of ADP are high compared to ATP*, the *cell is triggered to produce more ATP through the catabolism of sugar*

Lipids

Lipids Lipid digestion begins in the stomach with the aid of lingual lipase and gastric lipase. However, the bulk of lipid digestion occurs in the small intestine due to pancreatic lipase. When chyme enters the duodenum, the hormonal responses trigger the release of bile, which is produced in the liver and stored in the gallbladder. Bile aids in the digestion of lipids, primarily triglycerides by emulsification. Emulsification is a process in which large lipid globules are broken down into several small lipid globules. These small globules are more widely distributed in the chyme rather than forming large aggregates. Lipids are hydrophobic substances: in the presence of water, they will aggregate to form globules to minimize exposure to water. Bile contains bile salts, which are amphipathic, meaning they contain hydrophobic and hydrophilic parts. Thus, the bile salts hydrophilic side can interface with water on one side and the hydrophobic side interfaces with lipids on the other. By doing so, bile salts emulsify large lipid globules into small lipid globules. Why is emulsification important for digestion of lipids? Pancreatic juices contain enzymes called lipases (enzymes that break down lipids). If the lipid in the chyme aggregates into large globules, very little surface area of the lipids is available for the lipases to act on, leaving lipid digestion incomplete. By forming an emulsion, bile salts increase the available surface area of the lipids many fold. The pancreatic lipases can then act on the lipids more efficiently and digest them, as detailed in Figure 34.18. Lipases break down the lipids into fatty acids and glycerides. These molecules can pass through the plasma membrane of the cell and enter the epithelial cells of the intestinal lining. The bile salts surround long-chain fatty acids and monoglycerides forming tiny spheres called micelles. The micelles move into the brush border of the small intestine absorptive cells where the long-chain fatty acids and monoglycerides diffuse out of the micelles into the absorptive cells leaving the micelles behind in the chyme. The long-chain fatty acids and monoglycerides recombine in the absorptive cells to form triglycerides, which aggregate into globules and become coated with proteins. These large spheres are called chylomicrons. Chylomicrons contain triglycerides, cholesterol, and other lipids and have proteins on their surface. The surface is also composed of the hydrophilic phosphate "heads" of phospholipids. Together, they enable the chylomicron to move in an aqueous environment without exposing the lipids to water. Chylomicrons leave the absorptive cells via exocytosis. Chylomicrons enter the lymphatic vessels, and then enter the blood in the subclavian vein.

Ingestion

Obtaining nutrition and energy from food is a multi-step process. For true animals, the first step is ingestion, the act of taking in food. This is followed by digestion, absorption, and elimination. In the following sections, each of these steps will be discussed in detail. The large molecules found in intact food cannot pass through the cell membranes. Food needs to be broken into smaller particles so that animals can harness the nutrients and organic molecules. The first step in this process is ingestion. Ingestion is the process of taking in food through the mouth. In vertebrates, the teeth, saliva, and tongue play important roles in mastication (preparing the food into bolus). While the food is being mechanically broken down, the enzymes in saliva begin to chemically process the food as well. The combined action of these processes modifies the food from large particles to a soft mass that can be swallowed and can travel the length of the esophagus.

Protein

Protein Disaccharides (maltose), oligosaccharides Disaccharides (maltose), monosaccharides Monosaccharides (e.g., glucose, fructose, galactose) A large part of protein digestion takes place in the stomach. The enzyme pepsin plays an important role in the digestion of proteins by breaking down the intact protein to peptides, which are short chains of four to nine amino acids. In the duodenum, other enzymes— trypsin, elastase, and chymotrypsin—act on the peptides reducing them to smaller peptides. Trypsin elastase, carboxypeptidase, and chymotrypsin are produced by the pancreas and released into the duodenum where they act on the chyme. Further breakdown of peptides to single amino acids is aided by enzymes called peptidases (those that break down peptides). Specifically, carboxypeptidase, dipeptidase, and aminopeptidase play important roles in reducing the peptides to free amino acids. The amino acids are absorbed into the bloodstream through the small intestines.

Brown fat

Source of heat unique to neonates that is capable of greater thermogenic activity than ordinary fat; deposits are found around the adrenals, kidneys, and neck; between the scapulae; and behind the sternum for several weeks after birth •*Oxygen is a reactant in cellular respiration*, the process that *breaks down sugar/food molecules* and *generates ATP*, the energy currency in cells, and heat. •Brown fat has a *"short circuit" in its cellular respiration, which generates only heat, not ATP* •Brown fat is *important for heat production in small mammals, including humans* •*Mitochondria in brown fat can burn fuel and produce heat without making ATP* •Ion channels spanning the inner mitochondrial membrane •allow *H + to flow freely across the membrane* and •*dissipate the H+ gradient that the electron transport chain produced*, which does *not allow ATP synthase to make ATP* •*Scientific studies of humans* indicate that *•brown fat may be present in most people* and *babies* •when *activated by cold environments, the brown fat of lean individuals is more active*

The First Law of Thermodynamics The first law of thermodynamics deals with the what in the universe? It states that the _______________ is constant. Energy may be transferred but cannot be __________________ or _____________________ Energy in ATP is needed for what kinds of activities

The *first law of thermodynamics* deals with the *total amount of energy in the universe* -It states that this *total amount of energy is constant* -In other words, there has always been, and always will be, exactly the *same amount of energy in the universe* -*Energy exists in many different forms* According to the first law of thermodynamics, *energy may be transferred from place to place or transformed into different forms, but it CANNOT BE CREATED OR DESTROYED* -The transfers and transformations of energy *take place around us all the time* -Light bulbs transform electrical energy into light energy. Gas stoves transform chemical energy from natural gas into heat energy. Plants perform one of the most biologically useful energy transformations on earth: that of *converting the energy of sunlight into the chemical energy stored within organic molecules* -The *challenge for all living organisms is to obtain energy from their surroundings in forms that they can transfer or transform into usable energy* to do work. Living cells have evolved to meet this challenge very well. *Chemical energy stored within organic molecules such as sugars and fats is transformed through a series of cellular chemical reactions into energy within molecules of ATP* -Energy in ATP molecules is easily accessible to do work. Examples of the types of work that cells need to do include building *complex molecules, transporting materials, powering the beating motion of cilia or flagella, contracting muscle fibers to create movement, and reproduction*

Carbohydrates

The digestion of carbohydrates begins in the mouth. The salivary enzyme amylase begins the breakdown of food starches into maltose, a disaccharide. As the bolus of food travels through the esophagus to the stomach, no significant digestion of carbohydrates takes place. The esophagus produces no digestive enzymes but does produce mucous for lubrication. The acidic environment in the stomach stops the action of the amylase enzyme. The next step of carbohydrate digestion takes place in the duodenum. Recall that the chyme from the stomach enters the duodenum and mixes with the digestive secretion from the pancreas, liver, and gallbladder. Pancreatic juices also contain amylase, which continues the breakdown of starch and glycogen into maltose, a disaccharide. The disaccharides are broken down into monosaccharides by enzymes called maltases, sucrases, and lactases, which are also present in the brush border of the small intestinal wall. Maltase breaks down maltose into glucose. Other disaccharides, such as sucrose and lactose are broken down by sucrase and lactase, respectively. Sucrase breaks down sucrose (or "table sugar") into glucose and fructose, and lactase breaks down lactose (or "milk sugar") into glucose and galactose. The monosaccharides (glucose) thus produced are absorbed and then can be used in metabolic pathways to harness energy. The monosaccharides are transported across the intestinal epithelium into the bloodstream to be transported to the different cells in the body.

Hormonal Responses to Food

The endocrine system controls the response of the various glands in the body and the release of hormones at the appropriate times. One of the important factors under hormonal control is the stomach acid environment. During the gastric phase, the hormone gastrin is secreted by G cells in the stomach in response to the presence of proteins. Gastrin stimulates the release of stomach acid, or hydrochloric acid (HCl) which aids in the digestion of the proteins. However, when the stomach is emptied, the acidic environment need not be maintained and a hormone called somatostatin stops the release of hydrochloric acid. This is controlled by a negative feedback mechanism. In the duodenum, digestive secretions from the liver, pancreas, and gallbladder play an important role in digesting chyme during the intestinal phase. In order to neutralize the acidic chyme, a hormone called secretin stimulates the pancreas to produce alkaline bicarbonate solution and deliver it to the duodenum. Secretin acts in tandem with another hormone called cholecystokinin (CCK). Not only does CCK stimulate the pancreas to produce the requisite pancreatic juices, it also stimulates the gallbladder to release bile into the duodenum. Another level of hormonal control occurs in response to the composition of food. Foods high in lipids take a long time to digest. A hormone called gastric inhibitory peptide is secreted by the small intestine to slow down the peristaltic movements of the intestine to allow fatty foods more time to be digested and absorbed. Understanding the hormonal control of the digestive system is an important area of ongoing research. Scientists are exploring the role of each hormone in the digestive process and developing ways to target these hormones. Advances could lead to knowledge that may help to battle the obesity epidemic.

elimination

The final step in digestion is the elimination of undigested food content and waste products. The undigested food material enters the colon, where most of the water is reabsorbed. Recall that the colon is also home to the microflora called "intestinal flora" that aid in the digestion process. The semi-solid waste is moved through the colon by peristaltic movements of the muscle and is stored in the rectum. As the rectum expands in response to storage of fecal matter, it triggers the neural signals required to set up the urge to eliminate. The solid waste is eliminated through the anus using peristaltic movements of the rectum. Common Problems with Elimination Diarrhea and constipation are some of the most common health concerns that affect digestion. Constipation is a condition where the feces are hardened because of excess water removal in the colon. In contrast, if enough water is not removed from the feces, it results in diarrhea. Many bacteria, including the ones that cause cholera, affect the proteins involved in water reabsorption in the colon and result in excessive diarrhea. Emesis Emesis, or vomiting, is elimination of food by forceful expulsion through the mouth. It is often in response to an irritant that affects the digestive tract, including but not limited to viruses, bacteria, emotions, sights, and food poisoning. This forceful expulsion of the food is due to the strong contractions produced by the stomach muscles. The process of emesis is regulated by the medulla.

Muscle Tissues

There are *three types of muscle in animal bodies: smooth, skeletal, and cardiac* -They *differ by the presence or absence of striations or bands*, the *number and location of nuclei*, whether they are voluntarily or involuntarily *controlled, and their location within the body* 1. *Smooth muscle does not have striations in its cells*. It has a *single, centrally located nucleus*. Constriction of smooth muscle occurs under *involuntary, autonomic nervous control* and in response to local conditions in the tissues. Smooth muscle tissue is also called non-striated as it *lacks the banded appearance of skeletal and cardiac muscle*. The walls of blood vessels, the tubes of the *digestive system, and the tubes of the reproductive systems* are composed of mostly smooth muscle 2. *Skeletal muscle has striations across its cells* caused by the arrangement of the *contractile proteins actin and myosin*. These muscle cells are *relatively long and have multiple nuclei* along the edge of the cell. Skeletal muscle is *under voluntary, somatic nervous system control* and is found in the muscles that move bones. 3. *Cardiac muscle*, shown in Figure 33.18, is *found only in the heart*. Like skeletal muscle, it has *cross striations in its cells*, but cardiac muscle has a *single, centrally located nucleus* Cardiac muscle is *not under voluntary control but can be influenced* by the autonomic nervous system to speed up or slow down. An added feature to cardiac muscle cells is a line than extends along the end of the cell as it abuts the next cardiac cell in the row. This *line is called an intercalated disc: it assists in passing electrical impulse efficiently from one cell to the next* and maintains the strong connection between neighboring cardiac cells.

The Energy Cycle

Whether the organism is a bacterium, plant, or animal, all living things access energy by breaking down carbohydrate molecules. But if plants make carbohydrate molecules, why would they need to break them down, especially when it has been shown that the gas organisms release as a "waste product" (CO2) acts as a substrate for the formation of more food in photosynthesis? Remember, living things need energy to perform life functions. In addition, an organism can either make its own food or eat another organism—either way, the food still needs to be broken down. Finally, in the process of breaking down food, called cellular respiration, heterotrophs release needed energy and produce "waste" in the form of CO2 gas. In nature, there is no such thing as waste. Every single atom of matter and energy is conserved, recycling over and over infinitely. Substances change form or move from one type of molecule to another, but their constituent atoms never disappear (Figure 8.20). CO2 is no more a form of waste than oxygen is wasteful to photosynthesis. Both are byproducts of reactions that move on to other reactions. Photosynthesis absorbs light energy to build carbohydrates in chloroplasts, and aerobic cellular respiration releases energy by using oxygen to metabolize carbohydrates in the cytoplasm and mitochondria. Both processes use electron transport chains to capture the energy necessary to drive other reactions. These two powerhouse processes, photosynthesis and cellular respiration, function in biological, cyclical harmony to allow organisms to access life-sustaining energy that originates millions of miles away in a burning star humans call the sun. Figure 8.20 Photosynthesis consumes carbon dioxide and produces oxygen. Aerobic respiration consumes oxygen and produces carbon dioxide. These two processes play an important role in the carbon cycle. (credit: modification of work by Stuart Bassil)

Oxidative Phosphorylation What two functions does this step involve? When hydrogen ions accumulate within the matrix space = what is created? Through what do they diffuse out? What is the electron acceptor and who are the donors?

You have just read about *2 pathways in glucose catabolism*—*glycolysis and the citric acid cycle*—that generate AT -*Most of the ATP generated during the aerobic catabolism* of glucose, however, is *not generated directly from these pathways*= Rather, it is *derived from a process that begins w/ moving electrons through electron transporters that undergo REDOX reactions* -This *causes hydrogen ions to accumulate within the matrix space* = *creates a HYDROGEN gradient* helpful *in ATP synthesis* -Therefore, a concentration gradient *forms in which hydrogen ions DIFFUSE OUT of the matrix space via ATP SYNTHASE* -The *current of hydrogen ions POWERS the catalytic action of ATP synthase*, which *phosphorylates ADP, producing ATP* •The *final stage of cellular respiration is oxidative phosphorylation* which •*involves electron transport + chemiosmosis (Hydrogen high energy to low energy/ outside to inside the mitochondrial membrane* use the *energy coming in to synthesize ATP*) •*requires an adequate supply of oxygen* •The *arrangement of electron carriers* built into a membrane *makes it possible to* •*create an H+ concentration gradient across the membrane* and then •*use the energy of that gradient to drive ATP synthesis* -*Without oxygen*: *accept electrons*, *create a H+ gradient*, you can't *use your organic molecules*, 28 ATPS •*Electrons from NADH and FADH2 travel down* the *ETC to O2*, the final *electron acceptor* •*Oxygen picks up H+, which forms water* in ETC after Cytochrome C •*Energy released by redox reactions* is used to *pump H+ from mitochondrial matrix to intermembrane space* •In *chemiosmosis* = the *H+ leaves w/ protein complex* of electron carriers *diffuses back w/ inner membrane* through ATP synthase complexes* forming *ATP*