Biodiversity and Life II - Textbook Notes

Paragraph 1

• Carbohydrates = type of molecule that can be small and singular or much larger 

• Monosaccharide = monomer of carbohydrates, a single unit of sugar/carb

Carbohydrates exist in many forms, ranging from syrups and sugars to complex starches and fibers. The monomers of carbohydrates are called monosaccharides (glucose, fructose, galactose, etc) which can then bond through dehydration synthesis to form longer, more complex polysaccharides. Honey is a mixture of glucose and fructose monosaccharides. 

Paragraph 2

• Glucose = common monosaccharide that has multiple hydroxyl groups and one carbonyl group

The molecular formulas of carbohydrates are all usually some form of CH₂O, multiplied to various scales. For example the molecular formula of glucose is C₆H₁₂O₆, where it can be seen to have both hydroxyl and carbonyl groups. 

Paragraph 3

• Fructose = another common monosaccharide with hydroxyl (3) and carbonyl groups (1) as well

As an isomer to glucose, fructose also has the molecular formula of C₆H₁₂O₆, however its carbonyl group is placed differently, which gives it different reactive properties (also tastes sweeter). All monosaccharides have between 3-7 carbons (glucose and fructose have 6), and the five-carbon sugars called pentoses and six-carbon sugars called hexoses are the most common forms of monosaccharides. (most sugars end with -ose, most enzymes end with -ase)

Paragraph 4:

Although the sugars exist in linear form, when in aqueous solutions, they take on a circular structure. To do this, carbon 1 bonds to the oxygen of carbon 5, forming a circular shape and leaving carbon 6 to exist above the main circular structure. With carbons at each corner of the resulting shape, the structural formula can be abbreviated by implying the carbons at these bends. The different thickness in the lines show that the ring is mostly 2D → flat surface, and it also shows that atoms are also below or above it. Further simplification turns a glucose molecule into a ring with a simple O in its top right corner. 

Paragraph 5:

Carbohydrates act at the primary fuel source for all cellular activity. When glucose is broken down by the cell in an aqueous solution, it releases energy, which can be exploited to help repair tissue (especially for sick people through a water and glucose solution called dextrose that is injected). Additionally, after breaking down carbohydrates, the carbon skeletons left behind can be used to create amino acids or fatty acids. Sugar is both an energy and construction resource. 

Paragraph 6: 

• Disaccharide = two bonded monosaccharides

To form a disaccharide such as maltose, dehydration synthesis is used to form the glycosidic bonds between two glucose monosaccharides. First, one of the hydroxyl of one monomer must be removed. Then the hydrogen of the hydroxyl group of another monomer is removed as well. This forms the byproduct of H₂O, and also allows the remaining O of that monomer to bond to the C of the other, creating the disaccharide. Although maltose is used to make beer, candy, and whiskey, sucrose is he most common disaccharide, as it is the sugar transported through a plant’s veins to provide energy and other materials. Humans get table sugar from the sucrose in cane sugars. 

Paragraph 7

There is clear overconsumption of sugar throughout the US, as the recommended daily intake is 6 teaspoons–making up only 5% of one’s daily caloric intake. However the average American not only consumes about 5 pounds of sugar a week, but also has an average of 22 teaspoons of sugar per day (one can of soda exceeds the limit, and processed foods can add any amount of sugar into their products to maximize taste). 

Paragraph 8

The consequences of such overconsumption clearly present as dental issues and obesity risk (health hazards of obesity are type 2 diabetes, high blood pressure, etc). Already, the average rate of obesity in the US has reached 36.5% and 17%  in children. New research also points to the connection of obesity (average caloric percentage of 25% from daily calories) and cardiovascular dangers, high cholesterol, diabetes, etc). This study was performed through two-year intervals that showed people with these higher sugar consumption rates to be three times as likely to die from cardiovascular issues. The FDA proposed the update of nutrition labels to solve the problem, however many companies loss touch with this movement because of their misleading advertisements. 

Paragraph 9

• Polysaccharide = macromolecule of hundreds to thousands of monomers bonded by dehydration synthesis 

• Starch = stores energy of plants through long chains of bonded glucose monomers

With lengths of many, many monomers long, polysaccharides are considered to be macromolecules, and they can act as storing or structural compounds with a cell. Starch is one type of polysaccharide that involves a chain of many glucose molecules bonded together  that is twisted into a helical shape, sometimes remaining singular and sometimes branching. Starches serve as the plant’s carbohydrate ‘bank’ or reserve of energy and building materials it can easily access. Capable of hydrolyzing starch (with the right enzymes), humans can consume forms of starch–rice, potatoes, corn, etc, and gain energy from it. 

Paragraph 10

• Glycogen = polysaccharide that also stores glucose (energy/resources) that can be accessed when needed

Stored in the liver and muscle cells where it can be easily broken down (hydrolyzed), glycogen acts as the animal form of a carbohydrate reserved, and is also formed by helical chains of glucose, however they are more branched than starch.  

Paragraph 11

• Cellulose = a polysaccharide that makes up the cell walls of plant cells

As it is present in all plants (helps make up the cell walls), cellulose is the most abundant organic compound. It is also formed through chains of glucose molecules, however the monosaccharides are flipped, alternating with its O at the top then bottom (in contrast starch and glycogen’s glucose are all oriented the same way). This allows hydrogen bonds to form between the OH and H’s, which arranges each glucose chain parallel to one another. This forms microfibrils with then become the strong structures in trees and lumber (with the help of other polymers). All animals (except some animals–cows and termites, bacteria, and fungi that recycle the cellulose back into the environment) lack the enzymes to hydrolyze cellulose, so humans are therefore unable to digest it and absorb cellulose’s nutrients. However, as insoluble fiber, cellulose helps with digestion (in nuts, vegetables, fruits, etc). 

Paragraph 12

• Chitin = another type of polysaccharide involved in an organism’s structures

Chitin is used by animals like insects and crustaceans to make their hard exoskeletons. The cell walls of fungi also have chitin. Most carbohydrates are hydrophilic because of the many hydroxyl groups present in the monosaccharides of its polymers. For example, cotton towels are very water absorbent because their cellulose is hydrophilic. This does not apply to all biological molecules.

Paragraph 13

• Lipids = type of biological molecule classified together for their hydrophobic properties

• Hydrophobic = water-fearing (nonpolar, so pushed away by cohesive water forces)

Lipids are distinguished from the other biological molecules not only because they are hydrophobic, but also because they are not polymers made of many repeated similar/identical monomers, or because they are macromolecules. There are four types of lipids, fats, phospholipids, steroids, and waxes.

Paragraph 14

• Fat = lipid of one glycerol and three fatty acid molecules

• Triglyceride = synonym for fat

• Glycerol = three carbons, each with a hydroxyl group

• Fatty acid = carboxyl group with 16-18 long hydrocarbon chain

Fats are hydrophobic because some of their monomers are hydrophobic. The singular glycerol molecule (three carbons with corresponding hydroxyl groups) itself is not hydrophobic. In fact its OH’s make it polar. However through dehydration synthesis with each hydroxyl of the glycerol and a fatty acid (acidic because of carboxyl group), totalling as three fatty acids, the hydrocarbon tail of these fatty acids have nonpolar bonds, making it hydrophobic. 

Paragraph 15

• Unsaturated fatty acid = a fatty acid with one or more double bonds between carbons (does not need as many hydrogens → unsaturated with hydrogens)

• Saturated fatty acid = a fatty acid with no double bonds (has as many hydrogens as possible → saturated with hydrogens)

• Trans fat = type of fat associated with certain health risks

When a double bond forms between the carbons in the hydrocarbon chain of a fatty acid, it creates a bend in that respective tail. This also means that the one less hydrogen (proportionate to how many double bonds) is present in the fat. As a result, when compacted, the kinks make it harder to stack onto each other, which keeps unsaturated fats liquid at room temperature. However, when there are no double bonds, the fatty acid is called a saturated fat because it has the most possible hydrogens. Additionally, as it has no bends from a double bond, saturated fatty acids can easily stack on top of one another, making it solid at room temperature. Unsaturated fats are found in fishes and plants while saturated fats are found in animal fat. ‘Partially hydrogenated fats’ refer to the addition of hydrogens to an unsaturated fat, causing it to become saturated. This process creates trans fats as well, which are harmful to the human body. 

Paragraph 16

• Adipose cell = type of cell that stores fat

Fats are used to efficiently store long-term energy in the body. It stores three times as much energy as polysaccharides. Animals enterprise this compacted nature of fats, as they move around, and store most of their energy as fat. In contrast, plants use only starch to store their energy, as the additional room does not affect their nonmotile lives. Fats are stored in adipose cells, which increase and decrease in size as fat enters or exits it. It is also harder to use the energy in fat because it is so densely energized/packed. However fat is not only important for energy reserves, as it also helps to insulate the body and protect and cushion vital organs. 

Paragraph 17

Partially hydrogenated fats, produced by adding hydrogens to unsaturated fat, were first invented in the 1890s as a supposedly healthier alternative to saturated fats, which research had linked to several health risks. It was thought that this new type of fat, in addition to unsaturated fat, were the best options. This then launched the market for partially hydrogenated fats to replace saturated fats, as they also kept for longer, and were also able to be heated multiple times (for example, frying things–margarine is a type of partially hydrogenated fat). But as new research showed, the ubiquity of the trans fat resulting from the partial hydrogenation process in 1990 seemed to be damaging public health even more than saturated fats had (for example, cutting out trans fats stopped one in five heart attacks). At first, the FDA required producers to list the presence of trans fats on their nutrient labels, then escalating to cities and states banning trans fats from restaurants and schools. Finally, in 2015 the FDA stated that all trans fats must be removed from food within three years, as it was not safe for the public. 

Paragraph 18

The research involved in establishing the effect of trans fats was done in two ways. The first–experimental, studied active participants with varying dietary levels of saturated, unsaturated, and trans fats and the changes in cardiovascular health. The projection was that an increase in trans fats would worsen such health. For ethical purposes, relatively fit people were studied, and only the cholesterol or intermediary risk factors were measured as to not actually give the participants a heart attack. 

Paragraph 19

The second way of conducting research is through observational studies. Observation allows a more comprehensive set of data to be collected over a longer period of time, including both disease and risk factors, as well as a more representative population. There are two types of observational studies, the first being retrospective. This looks into the past, where people have documented their current health status and then also add their past eating habits. Some of the data may not be accurate due to misremembered data and the fact that those who died of heart attacks are not included. The second way–prospective, looks into the future, as it has their participants progressively update their physical health, allowing data to be taken about lifestyle, including diet, habits, and also risk factors and disease. 

Paragraph 20

The Nurses’ Health Study was one of the major prospective studies that revealed the danger of trans fat. It began in 1997, overall recording the data of 120,000 female nurses. From 1980-1994 about 80,000 women were studied, where risk of coronary heart disease was estimated from consumption of varying forms of fat. Risk begins at a factor of 1, which shows no connection between the type of fat and coronary heart disease. Subsequently, any recorded value less than one means the risk decreases, and any value greater than one means the risk increases. For monounsaturated and polyunsaturated fats, risk of heart disease decreased with every 5% increase. 5% increases in saturated fats only had an increased risk of 17%. In contrast, trans fats have a 93% increased risk for every 2% intake increase, demonstrating how much of a threat trans fats poses. From advertising trans fat as a healthier alternative to saturated fat, the government has banned trans fat. This is an example of how a broadened understanding had revised and completely changed the policy.

Paragraph 21

• Phospholipid = polymer of one glycerol molecule, phosphate group, and two fatty acids

Phospholipids are different from fats because instead of having a third fatty acid, phospholipids have a phosphate group attached. Also, the second fatty acid is unsaturated as it has a double bond.

Paragraph 22

When in an aqueous solution or surrounded by water, lipids form a double layered membrane, as its hydrophobic tail (hydrocarbon chains), which clusters together with other phospholipids away from the water, and the hydrophilic heads (the glycerol, phosphate, and r group) face out towards the water. Some types of proteins are involved with the membrane that forms from phospholipids. 

Paragraph 23

• Steroids = lipids formed by four fused rings of carbon (3 6-carbon and 1 5-carbon)

• Cholesterol = a type of steroid that is found in animal cell membranes, contributing to production of other hormones (sex hormones)

Steroids are another type of lipid, however they are not made of glycerol or fatty acids; instead every steroid molecule shares the same basic carbon skeleton of four fused rings–the attached chemical groups are responsible for variation among steroids. Cholesterol, for example, has hydroxyl and carbonyl functional groups as well as a hydrocarbon chain attached. Cholesterol is a steroid in animals (in cell membranes) used to help produce important hormones.

Paragraph 24

• Anabolic steroids = synthetic steroids that have similar structures to testosterone

• Anabolism = process of body making substances

Because anabolic steroids have a similar shape to testosterone–a steroid hormone that increases muscle and bone growth (mainly during puberty) and also produces masculine characteristics, so too, do anabolic steroids have similar effects on muscle building. Medically, it is used to treat anemia and muscle-destroying diseases.

Paragraph 25

Athletes can use anabolic steroids to increase the rate of muscle growth and performance. However, there are many side effects that include mood swings, depression, impact liver health, and reduce male sex hormone production. As a result, that also causes more consequences. For women, use of steroids can give rise to pronounced masculine traits and disruption of their menstrual cycles. The US congress, professional authorities, and school athlete programs have banned the use of synthetic steroids, using drug testing and punishment to maintain the health and fairness of competitors. However many trainers, coaches, etc continue to give their athletes anabolic steroids.  

Paragraph 26

• Proteins = polymers of bonded amino acids

As a result of their wide variation and diversity, proteins participate and regulate almost all dynamic functions in the body. Enzymes are vital to the body’s chemical reactions because they are catalysts (for example, lactase, maltase, and sucrase help make and break down those carbs). Signaling proteins, or hormones, help to control the rate of body activities by acting as messengers–these messages are then received by receptor proteins in the cell membrane that implement or pass on the hormone’s information. Transport proteins also in the cell membrane bring nutrients and sugar into the cell. Defensive proteins patrolling your bloodstreams (like antibodies) defend against antigens. Contractile proteins make up most of your muscle mass, and structural proteins form the ligaments and tendons that keep your joints and muscles operational. For example collagen, a type of structural protein, makes up about 40% of the body’s protein because it is connective tissue. 

Paragraph 27

A protein’s function is tied directly to its structure, as its particular shape allows it to complete its specific function. Proteins are mostly carbon, hydrogen, nitrogen, and oxygen. However the sulfur bonds present, although few, form stabilizing bonds within the protein. Most enzymes and other proteins have a globular shape (rounded, compact). Fibrous proteins are longer and thinner, and are the structural proteins (hair, connective tissue, etc). Classification of proteins with globular and fibrous labels are quite general, as each protein also has its own unique shape. The specific way the protein is folded creates grooves and structures that allow it to attach to the molecule it needs to accomplish its function. Most proteins need this recognition system because they operate based on recognizing and binding to a specific molecule. 

Paragraph 28

• Denaturation = process of a protein unfolding

When a protein denatures, its specific folding and therefore shape is lost, also removing its ability to function. This shows how important structure is to function, especially for proteins. Without the ability to operate, misshapen proteins can damage the body in the forms of degenerative diseases like Alzhimer’s, mad cow disease, etc. This usually happens because the amino acid chain making up the protein was not folded properly during its immediate arrangement after being made. Infectious proteins that have been mis-folded in such a way are called prions. They are infectious because they cause similar proteins to also mis-fold/become misshapen. It is key to recognize that the three dimensional structure of proteins is the only way they are able to fulfill their functions. 

Paragraph 29

• Amino acid = monomer of protein

Amino acids are made up of an amino group (NH₂), carboxyl group (COOH) which gives an amino acid its acidic properties, a central carbon atom, where a hydrogen is attached above and a variable R group is attached below. The R group is an umbrella term for the various arrangements and combinations of carbon atoms and functional groups (glycine only has one H for its R group) that distinguish each amino acid from the other. As a result, the amino and carboxyl group, central carbon, and additional hydrogen all make up the amino acid’s backbone. 

Paragraph 30

These R groups are so significant because they determine if the amino acid is hydrophobic or hydrophilic. All of these depend on the end atoms of the R group. Hydrophobic amino acids have nonpolar C–H bonds at the end of the R group. The R groups of hydrophilic amino acids have either polar or charged. OH groups have polar covalent bonds, and any negatively charged O at the end of carboxyl groups are acidic because they have released their H+ ion (increases the acidity. Alternatively, and the NH₂ groups in basic amio acids are able to accept an additional proton (just H+ ion), giving it a negative charge. This turns the NH₂ into a NH₃, although it depends on how many bonds the nitrogen already has. A nitrogen atom have make three covalent bonds, however this acceptance of an additional proton is done through the pair of electrons not involved in covalent bonds. Also, the backbone of an amino acid is usually portrayed in its ionized form, where the carbozyl group has lost its H+ ion, and the amino group has accepted it. 

Paragraph 31

• Peptide bond = the bond connecting two amion acids through dehydration synthesis (results in a dipeptide)

• Polypeptide = chain of 100-1,000 amio acids

Amino acids link to each other through dehydration synthesis, bonding the C of a cayboxyl group of one amino acid to the N of a amino group of another amino acid. Two bonded amion acids are called a dipeptide, and the continuation of adding amion acids forms a polypeptide. Despite the fact that there are only 20 different types of amio acids, there are countless types of polypeptide chains (eventaully form unique proteins) because any variation in the seuqence of the amino acids creates a different polypeptide. Also, each chain is at least 100 amino acids long, so there is a lot of variation between just these 20 amino acids. 

Paragraph 32

• Disulfide bridge = specific name in some proteins for a covalent bond between two sulfur atoms

There is a key distinction between polypeptide chains and a protein, because a polypeptide must first be elaborately folded so it can form into a protein. This folding process is where the R groups come in, because the hydrophobic or hydrophilic properties it gives to the amion acids. Those hydrophobic amino acids will gather together in the interior of a protein, away from the external water. Conversely the hydrophilic amino acids arrange themselves outside, allowing the protein to be dissolved as a result. Additionally, ionic and hydrogen bonds that form between hydrophilic amino acids also determine a protein’s shape. A type of covalent bond between sulfur atoms also affects the protein’s shape, called a disulfide bridge. 

Paragraph 33

• Primary structure = specific sequence of amino acids within one polypeptide chain

• Secondary structure = folding/coiling of the polypeptide chain into particular pattern

• Tertiary structure = the folded, three dimensional shape of the secondary structure

• Quaternary structure = two or more tertiary structures arranged together

First, protein structure begins with a singular polypeptide chain, which, according to its sequence of amino acids and how hydrogen bonds form within its backbone, will form on of two secondary structures (alpha helix or beta pleated sheet). The tertiary structure involves the influence of the R group, and hydrophobic/hydrophilic interactions. This results in a particular folded polypeptide, including its alpha helices/beta pleated sheets. Hydrogen, ionic, and covalent (disulfide bridges) also create the specific folding in tertiary structures.  Finally, the quaternary structure invovles multiple tertiary structures, which are also influenced by hydrogen bonding, resulting in the protein’s final, unique shape. (Stage where protein becomes fully functional, though some proteins can operate as a tertiary structure).

Paragraph 34

The cell is a membrane-enclosed workhouse of constantly occurring chemical reactions. All of these reactions involve the transformation of both matter and energy.

Paragraph 35

• Energy = ability to do work (cause change)

• Kinetic energy = the energy of motion

• Thermal energy = type of kinetic energy in the random movements of atoms/molecules

• Heat = transfer of thermal energy between objects

• Potential energy = energy stored in an object’s location or structure

• Chemical energy = potential or stored energy in chemical bonds

Energy can be defined as the capacity to change things, or otherwise do work. The first of the two main energy types, kinetic energy refers to the energy present in motion, specifically the ability for that motion to be transferred to another object. For example, riding a bike involves the motion of your pedaling legs, which then turns the gears and wheels, moving the entire bicycle. Thermal energy involves the random movements of atoms/molecules. Heat describes the transfer of thermal energy. Light is another type of kinetic energy. The second main energy type is potential energy, which has to do with the object’s position or structure. A ball held above the ground has potential energy because it has the potential to move after being released (from gravity). Subsequently, the potential energy of chemical bonds (chemical energy) comes from the potential work that can be done by breaking or making those chemical bonds.

Paragraph 36

• System = thing being observed by scientist

• Surroundings = whatever is not being observed (rest of the universe)

• Thermodynamics = the study of energy transformations

• First law of thermodynamics = energy can be neither created nor destroyed, only transformed or transferred

• Entropy = measure of disorder (proportional to amount of unavailable energy) 

• Second law of thermodynamics = the universe’s entropy increase with every energy conversion

As energy cannot be produced, according to the first law of thermodynamics, then only energy transformations are possible.  The study of such–thermodynamics, reveals how things like plants are only able to convert one form of energy (light energy) into another (chemical energy). Additionally, whenever an energy conversion occurs, some of that energy is converted to thermal energy, and is therefore unavailable to further do work. Entropy is the form of measurement used to describe how much energy is unavailable. The second law of thermodynamics tells us that the entropy of the universe increases with each energy conversion. 

Paragraph 37

• Cellular respiration = process of getting energy from the chemical energy in organic molecules

Energy conversions like that of a car, use the explosive energy from gasoline and roxygen to move the pistons and then the wheels–however the byproducts that are released, (carbon dioxide, oxygen) are accompanied by a lot of thermal energy, which had been lost from the energy conversion. Only 25% of energy from this reaction is actually used to move the car. Additionally, cells exhibit this same increase of entropy through cellular respiration, where it only gains 34% of the reaction’s energy. Although there is 66% energy entropy or disorder, biological order remains; it is involved by the cell’s intake of organized forms of matter/energy, such as glucose, which is then broken down to create ATP. As a result, cellular respiration trades ordered reactants for disorder byproducts with its surroundings. 

Paragraph 38

• Exergonic reaction = a chemical reaction that releases energy

• Endergonic reaction = a chemical reaction that absorbs energy

Chemical reactions are classified in one of two ways–the first are exergonic reactions, which release energy by beginning with chemical energy-rich reactants that are then broken down into low-energy products. All that other energy from the reactant is released as thermal energy. Burning wood is an example of such–it takes the energy-rich cellulose in it and breaks it down into carbon dioxide and water, releasing the rest of the energy as light and heat. Cellular respiration also involves the breakdown of glucose into carbon dioxide and water (goal is to produce ATP for the cell), however it is more of a gradual process. Endergonic reactions, the second type, absorb energy from its surroundings by beginning with low-energy reactants and ending with energy-right products. Photosynthesis does this, as it constructs glucose–high in chemical energy, from water and carbon dioxide–both low in energy. The additional energy in the product comes from the sun’s light energy. 

Paragraph 39

• Metabolism = all of the chemical reactions in an organism

• Metabolic pathway = series of chemical reactions that either constructs a complex molecule, or deconstructs a complex molecule. 

• Energy coupling = when the energy from exergonic reactions (energy released) is used to fuel endergonic reactions (that released energy absorbed)

Cells constantly perform both exergonic and endergonic reactions. The sum of these reactions is known as metabolism. Each of these reactions makes up the various metabolic pathways of the cell, which describe both types of reactions. For example, the energy from fats and carbohydrates are released by exergonic reactions, which is then absorbed by the endergonic reactions which transform that ingested energy into ATP, etc. (energy coupling)

Paragraph 40

• ATP = adenosine triphosphate; the fuel for most cellular activity

• Phosphorylation = process of moving third phosphate group from ATP to another molecule

The reason ATP is used as the main energy source for cells is because of the unstable nature of its triphosphate bonds. Each phosphate group is negatively charged, so they all repel one another, allowing the hydrolysis to occur very easily. Thus, similar to spring, the third phosphate group easily breaks off (ATP becomes adenosine diphosphate), where the energy (phosphate group) from that exergonic reaction is then used in an energy couple to power another endergonic reaction through phosphorylation. 

Paragraph 41

ATP is needed for cellular work for all of its various functions. Endergonic synthesis chemical reactions depend on the energy released when ATP loses its third phosphate group. Transport proteins are able to bring certain nutrients (against concentration gradient) into the cell through phosphorylating the transport protein. Additionally, when an ATP connected to a moto protein is hydrolyzed, it then results in the protein’s contraction (change in shape). Because each cell uses and makes about 10 million ATP’s each second, ATP is a renewable energy source. First, it must be synthesized in an endergonic reaction that takes an ADP and combines it with a phosphate group. After that, the ATP can then be hydrolyzed in an exergonic reaction, allowing that released energy to then power whatever synthesis reaction. Energy for the synthesis of ATP comes from cellular respiration, however it is still renewable because all the ADP formed by those exergonic reactions can be repurposed during the cycle to become new ATP’s.

Paragraph 42

• Activation energy = amount of energy needed to weaken bonds so chemical reaction can occur

• Enzyme = biological catalysts that increase rates of reaction by lowering activation energy

Chemical reactions do not occur spontaneously (order to disorder, high-energy to stability) because activation energy is needed to get the reactants in a state where they can rearrange themselves. That amount of energy needed acts as a barrier to chemical reactions–the activation energy must be high enough to weaken the reactant’s chemical bonds that they are easily changed. Conversely, because activation energy thresholds are so high, it is impossible for all the life-essential chemical reactions to occur by themselves. INcreasing the overall energy of that entire system by heating it could increase reaction rate, however it may also end up killing the cell (denatures proteins too) in addition to speeding up some unnecessary chemical reactions. That is why enzymes are used to specifically catalyze (lowering the activation energy) needed chemical reactions (almost all proteins, some are RNA molecules)

Paragraph 43

• Substrate = specific reactant that enzyme catalyzes

• Active site = groove where the substrate binds to

Enzymes work by forming the weakened-bond environment that allows a chemical reaction to occur. In this way, what might’ve taken years or not at all, can be done in seconds by enzymes (hydrolysis of sucrose with sucrase into glucose and fructose). Enzymes, as proteins with a unique 3D structure, and specific to each reaction. The substrate of an enzyme has a certain shape, which must fit into the active site of the enzyme for the reaction to occur. Because the unique structure of each enzyme and their active site must match only each other, an enzyme’s function is specific to the specific substrate it acts on. 

Paragraph 44

• Induced fit = change in shape of active site from binding of substrate that prompts catalyzing of the reaction

The catalytic cycle first begins with the empty active site. When the enzyme binds to its substrate, the active site’s shape changes, adjusting so that it fits around the substrate more snuggly (like a handshake). Subsequently, that change in shape can either itself weaken the substrate’s bonds, or it may bring certain amino acids into position so that those can catalyze the reaction. The reaction then occurs–exergonic or endergonic (ex. Sucrose reacts with water to break down into glucose and fructose). After reacting, the active site releases the substrate, readying itself to perform the same reaction. Each cycle, an enzyme is capable of catalyzing thousands or millions of substrates.

Paragraph 45

All enzymes have specific environmental conditions that allow them to have optimal performances. As a type of protein, the structure of enzymes directly influences its functionality. Temperature, the average thermal energy of a system, impacts the movement of particles, and most enzymes work best 35-40 degrees celsius. There are some exceptions for certain organisms that have evolved to survive in harsh environments (Taq polymerase). pH also affects the enzymes, as an unbalanced pH may denature the enzyme. Most enzymes prefer almost neutral environments (6-8), although some have different requirements (pepsin at 2). 

Paragraph 46

• Cofactor = an inorganic compound that improves an enzyme’s functioning 

• Coenzyme = cofactor made of organic molecules

Cofactors are important because they help enzyme functioning by participating in catalysis through also binding to the active site. Cofactors are inorganic compounds, while cofactors made of organic compounds are called coenzymes. Vitamins can function as either coenzymes themselves or are used to make them. (Folic acid is a coenzyme for nucleic acid enzymes). Additionally, a cell must constantly regulate which enzymes are active and not, otherwise it would be too chaotic while every single possible chemical reaction is happening. Such control is exerted through the transcription of certain enzymes (genes are turned on or off depending on what is needed).