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Biol 2424 Human Phys
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Ch 2 BIOCHEMISTRY
Chemical rxs underlie all physiological processes: movement, digestion, the pumping of your heart, and even your
thoughts.
1. Living organisms are composed of matter. Matter is anything that occupies space, has mass, and can assume the
form of either a solid, liquid, or a gas.
2. We currently organize the matter of the universe into elements. An element is a substance that cannot be broken
down into simpler substances by chemical rxns.
Each box in the periodic table represents an element.
There are 92 elements that occur naturally, although scientists have made more (up to 112 named ones?).
Example: oxygen, silicon, aluminum, iron, nitrogen; referred to by element symbols O, Si, Al, Fe, N
3. Elements are atoms of the same type. An atom is the basic building block of matter, as in it cannot undergo
chemical change; it’s composed of electrons, protons, & neutrons (e-, p+, n).
Atoms lose or gain electrons to obtain stability.
- in the center of the atom is the nucleus that contains neutrons (neutral charge) & protons (positive charge), which
account for the element’s atomic weight. The negatively charged electrons have a negligible mass.
- shells are the spaces where electrons orbit the nucleus
- atomic number of an element is the number of protons (# of p = # of e, in neutral atom)
A neutron walks into a bar. "I'd like a beer" he says. The bartender promptly serves up a beer. "How much will that
be?" asks the neutron. "For you?" replies the bartender, "no charge." Ha. Ha.
4. If two or more elements combine, it results in molecule of that substance: H2, O2, etc.
5. When 2 or more different elements bind together, they form molecules of a compound.
H2O, CH4, NaCl.
Organic compounds contain carbon (e.g., C6H12O6)
Texts define organic compounds as having C, except for CO, CO2, & CO3. (Diamond & graphite are classified as
organic elements—they’re only 1 element: carbon). I would think it’s better to define organic compounds as
having C & H (“like pure cane sugar”), resulting in no exceptions.
Inorganic compounds don’t (e.g., NaCl)
Body contains both organic & inorganic substances that are necessary for survival.
Energy is needed by cells to do its fxs.
1. Energy is the capacity to do work.
2. Work is the movement of an object against some force.
e.g., kicking a soccer ball, pushing a car, moving an electron through a wire
3. Power is the rate at which work is done or energy is expended. How far you push a car per minute.
Types of Energy
First Law of Thermodynamics: the amount of energy in the universe is constant. Energy can take different forms; it
can be changed from one type into another, but cannot be made or destroyed. Wind energy can be converted to
electrical, etc.
forms that we’re concerned with
1. chemical energy: atomic bond changes O2 + 2H2 = 2H20
2. electrical energy: movement of charged particles (ions such as Ca+2, Na+, K+, Cl-, HCO3-, H+)
3. radiant energy: heat & light
When energy is changed from one form to another some may be transformed into a type that can’t be used for work of
that particular system. A car burns gas to move the cylinders to move the wheels, transforming chemical energy to
mechanical. Much of the energy is converted to heat & not all the gas burns totally down to CO2 & H2O. The heat is
dissipated to the atmosphere, and eventually, to outer space. Now how can we use it? It’s become inaccessible to the
earth’s energy budget.
Second Law of Thermodynamics: entropy is increasing, or the order of the universe is increasing towards disorder
(randomness). It’s slowing down & falling apart.
From a biological standpoint, all we need to know is that every time energy is transformed to do work, most is lost as heat,
so there’s always less usable energy available after a process is finished than when it started. The 10% rule of the food
web: it takes 10lbs of food to make one pound of you (not very efficient is it?). The efficiency of a machine or biological
system is excellent if it’s at 30%.
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Biological systems are highly organized both structurally & metabolically, so constant maintenance is required to keep up
this organization. This requires a constant supply of energy. Constant energy is needed to maintain homeostasis &
fight entropy. Every time energy is used by a cell to do work, most of that energy is dissipated as heat. If cellular energy
supplies are interrupted or depleted, illness and then death occur.
Forms of Energy
1. potential energy: stored energy, e.g., a battery, water behind a dam, boulder atop a cliff, or the ATP (adenosine
triphosphate) molecule of the body.
2. kinetic energy: energy of motion
As each object “falls” or moves, potential energy is converted to kinetic energy (kinesis = movement). Kinetic energy
can be chemical, radiant, or electrical. As water flows down from the dam, potential energy is converted to kinetic due
to the pull of gravity, and work can be done, such as turning turbines to convert some of the kinetic energy into
electrical. A match has potential chemical energy that can be converted to kinetic in the form of heat & radiant energy
(light) by adding a little heat (Lucky strike it, Baby! Oh, yeah!!).
In the human body, the controlled released of the potential energy from food is used to do work, as in utilizing
kinetic energy. Work is not just walking, talking, & reading, but also secreting mucus, building an enzyme, or
producing a nerve impulse. The controlled release of energy in the body is essential for life. Energy can be measured
like matter, and energy changes can be used to understand matter changes in the body.
Other energy considerations:
Because cells are composed of macromolecules (CLiP On), as well as inorganic molecules, we need to investigate
the following:
- how are macromolecules held together by chemical bonds, which in turn hold cells together, & eventually our
entire body
- chemical rxs involve the formation & breaking of chemical bonds that involve energy
- to obtain energy from macromolecules to maintain homeostasis, bonds have to be broken
- to store energy, bonds have to be formed
Mnemonic:
CLiP oN some macromolecules—never leave home without them:
Carbohydrates, Lipids, Proteins, Nucleic Acids (DNA, RNA, & ATP)
Chemical Bonds
There are 3 major types of chemical bonds: ionic, covalent, & hydrogen bonds. Each result from the attractive forces
between atoms that improves their stability.
Atoms are most stable when their outer electron shells are full. The octet rule: 8 electrons in the outer shell provide a
more stable energy configuration for the atom. An atom will gain or lose electrons or share depending on how many are in
its outer shell. The exception is the first shell, which requires only two electrons, as in the small atom of hydrogen.
Elements that already have a full outer shell don’t react readily with other elements & are called inert elements.
1. Covalent Bonds: are formed when adjacent atoms share pairs of electrons between them to obtain stability. In terms
of metabolic rxs, covalent bonds are the strongest type.
Example: Carbohydrates or H2O. Organic compounds form mostly covalent bonds.
2. Ionic Bonds: electrons are “donated by one atom & taken by another.” This bond is formed between cations &
anions, as a result of electrostatic attraction (the yin & yang of electrical attraction). In terms of metabolic rxs, ionic
bonds are weak. Ionic bonds join atoms together to form an ionic compound. An ion is an element that has an
electrical charge due to an unequal number of e’s compared to the p’s.
cation = electron donator, so has a positive charge
anion = electron acceptor, so has a negative charge
E.g., putting salt in water results in the cation Na & anion Cl: NaCl  Na+ (aqueous) + Cl- (aq)
Ionic bonds are mainly an electrical attraction between ions & are subject to dissolution in water, which is polar.
Generally inorganic compounds form ionic bonds.
3. Hydrogen Bonds: are a weak bond type. They’re temporary & form as a result of polar (weak electrical attraction)
between Hydrogen & Oxygen (or Nitrogen). Hydrogen bonds are common in water & DNA.
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CHEMICAL RXS: forming and/or breaking bonds; Metabolism = biological chemical rxs
1. * Energy can be stored in bonds.
* It takes energy to break a bond.
* Energy is released when a bond is formed.
2. A + B (reactants)  C + D (products)
3. Essentially are carried out as a consequence of the rearrangement of e’s to achieve greater stability
4. the more stable the atoms participating in the chemical bond, the more difficult it will be to break.
In many biological processes, the breaking of that bond will eventually release energy that we can use for some useful
purpose. However, sometimes you have to feed a little energy into the system to get the bond to break.
Let's say that I poured gasoline all over the front of the room. What would happen? There's oxygen in the air. Why
doesn't it ignite? Because the rx needs something to make it go up (heat). A match provides the energy necessary to
start the rx. This is called activation energy. To break a chemical bond, you have to add in some energy, called the
activation energy to get things going.
activation energy + A + B  C + D + bond energy + heat
Types of Chemical Rxs
1. catabolic (decomposition) rx: the breakdown chemical rxs of metabolism.
“Catastrophic Occurrence?: Cats cannibalize carcasses. Holy, feline furry frenzy, Batman!”
AB  A + B
CH4 C + 4H
e.g., digestion of a cheezboogercheezboogercheezbooger & Pipsi
energy is released as bonds break = exothermic rx, heat is released
2. anabolic (synthetic) rx: the making or "building up" of chemical rxs of metabolism
A + B  AB
4H + O2 2H2O
energy "goes in" (endothermic); heat is absorbed & new molecules are formed
What do anabolic steroids do?
3. reversible rx: AB  A + B occur under special conditions. (“You’ve got me jerkin’ back & forth….”)
- If energy is needed and/or products A or B, then the rx will proceed to the right.
- If energy is in excess along with A & B, then storage may be accomplished by having the rx proceed to the left.
Special requirements may be needed to achieve the rx: heat, H2O, pressure, enzymes, vitamins, minerals, or
other catalysts.
ENERGY FLOW IN CHEMICAL RXS
1. Endergonic rxs (“in work”) are chemical rxs that require an input of energy to produce molecules with higher free
energy than the reactants = energy absorbing (endothermic) = contain more potential energy in their chemical bonds
than did the reactants.
- In order to produce glucose from carbon dioxide & water (plant work), energy must added (sunlight), but then we
(burp!) can get a lot of energy out of glucose to fight against entropy!!!
Isn’t photosynthesis the keenest?
2. Exergonic rxs (“out work”) are chemical rxs that release energy (exothermic), thus forming products that contain less
free energy than the reactants, but they also provide energy that can be harvested for other uses. The combustion of
glucose to carbon dioxide and water releases energy in the form of heat.
e.g., ATP + H2O  ADP + Pi + H+ + energy
3. Exergonic rxs that convert food molecules into carbon dioxide & water in cells are coupled to endergonic rx that form
ATP (adenosine triphosphate). Some of the chemical bond energy in glucose is therefore transferred to the "high
energy" bonds of ATP (energy currency of the cell). The breakdown of ATP into adenosine diphosphate (ADP) and
an inorganic phosphate (PO4-) group results in the liberation of energy. The energy liberated by the breakdown of
ATP is used to power all cell processes. ATP is thus the "universal energy carrier" of the cell.
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FACTORS INFLUCENCING THE RATE OF CHEMICAL RXS
For atoms & molecules to react chemically, they must collide with enough force to overcome the repulsion
between their electrons.
- Interactions between valence shell electrons—the basis of bond making & breaking—cannot occur over long
distances.
- The force of collisions depends on how fast the particles are moving!!!
- Solid, forceful collisions between rapidly moving particles are much more likely to cause rxs than are those in which
the particles graze each other.
1. Heat: Adding heat to a substance (increasing its temperature) increases the kinetic energy of its particles, and thus, the
number of collisions & the force of their collisions. Therefore, chemical rxs proceed more quickly at higher heat levels.
When heat decreases (T drops), particle movement & rxs occur more slowly.
2. Particle Size: Smaller particles move faster than larger ones at a given T, and therefore, tend to collide more frequently
& forcefully. Hence, the smaller the reacting particles, the faster a chemical rx goes at a given temperature &
concentration.
3. [ ]: Rxs progress most rapidly when the reacting particles are present in high concentrations, because the larger the
number of randomly moving particles in a given space, the greater the chance of successful collisions. As the
concentration of reactants declines during a reaction, chemical equilibrium eventually occurs, unless additional
reactants are added or products are removed from the rx site.
4. Volume Size/Surface Area Availability – concentration or molecular solute density is dependent on a given volume;
given a high enough concentration, if the area of rx is increased, more rxs will take place per second
5. Catalysts: Although many rxs that occur in non-living systems can be speeded up simply by heating, drastic increases
in body T are life threatening, because important biological molecules are destroyed. Still, at normal body T, most rxs
would proceed far too slowly to maintain life were it not for the presence of catalysts.
Catalysts are substances that increase the rate of chemical rxs without themselves becoming chemically
changed or part of the product. Molecules called enzymes are biological catalysts. The presence of enzymes is the
single most important factor determining the rate of chemical rxs in living systems. Almost all enzymes are proteins.
Other substances “help” enzymes; coenzymes are organic compounds, many of which are made from vitamins.
Cofactors are cations that aid in enzyme function, such as Mg & Ca.
BIOCHEMISTRY: Two compound classes—both are essential for life.
1. organic compounds contain carbon (& hydrogen) and are covalently bonded compounds.
Texts define organic compounds as having C, except for compounds such as CO, CO2, CO3. [ Even diamond &
graphite are considered organic substances (not compounds!)—they’re just the element carbon bonded in various
ways. ] If I had my way, I’d define organic compounds as have C & H (like pure cane sugar), so there would be no
exceptions.
2. inorganic compounds essentially everything else, including water, salts, acids, & bases.
INORGANIC COMPOUNDS
Water is the most important inorganic material for living systems, making up 60-80% of the cell, and thus, 60-80% of
you, you Rascally Dog, you!
Characteristics of Water (the special properties of water are what make life possible)
1. Water is polar & exhibits hydrogen bonding—these characters are what give it a high heat capacity, high
heat of vaporization, make it a universal solvent, & make it highly reactive. Water’s boiling point is much
higher & its freezing point is much lower than expected for its atomic weight, because of its polarity & hydrogen
bonding. One would not even predict it to be polar, but the electron shells interact an unusual way, yielding a
lower than expected hydrogen bond angle.
2. High heat capacity: it absorbs & releases large amounts of heat before changing appreciably in temperature itself.
- assists in T regulation by lessening the effect of internal (cellular) & external environmental stresses.
- distributes heat in the body (Feeling toasty today, Punk?!)
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3. High heat of vaporization: when water changes from a liquid to a gas it absorbs large amounts of heat to break
the H bonds that hold water molecules together.
- assists in cooling the body as sweat evaporates from our skin. Having eccrine sweat glands almost all over our
integument is a unique human trait & vital for cooling what in particular?
4. Universal solvent: can dissolve oodles of organic & inorganic molecules.
- important for rxs because biological molecules do not react chemically unless they are in solution, and virtually all
chemical rxs occurring in the body depend on water's solvent properties.
- excellent transport mechanism for nutrients, gases, wastes in ECF, ICF, blood plasma, & urine
- needed to form lubricants: mucus of respiratory passages, vagina, pleural & peritoneal fluid, etc.
5. Reactivity: important as a reactant itself—not just a solvent
- foods are broken down by adding a H2O molecule to each bond to be broken = hydrolysis rxs.
- when large molecules such as carbs. or proteins are synthesized, a water molecule is removed for every bond
formed = dehydration synthesis.
SALTS, ACIDS, BASES, & BUFFERS
Salts, acids, & bases are electrolytes, that is they ionize & dissociate into their components in water and can then
conduct an electrical current.
SALTS: are ionic compounds (involve the transfer of electrons) containing cations other than H + and anions other than
OH- (hydroxyl ions). Salts, such as calcium carbonate, calcium phosphate, NaCl, KCl, & Na2SO4, are involved in
the formation of teeth & bones, nerve impulse conduction, & muscle contraction.
ACIDS: substances that dissociate into hydrogen ions (H+) & anions in detectable amounts in water. Usually have
a sour taste and can react with many metals or "burn" a hole in your rug. Because a hydrogen ion is just a
hydrogen nucleus, or "naked" proton, acids are also defined as proton donors.
When acids are dissolved in water, they release hydrogen ions (protons) & anions. The anions have little or no effect
on acidity; it is the concentration of protons that determines the acidity of a solution.
For example: hydrochloric acid (HCl), an acid produced by stomach cells that aids digestion, dissociates into a
proton & a chloride ion: HCl  H+ (cation) + Cl- (anion)
Other acids found or produced in the body:
- acetic acid (HC2H3O2, abbr. as HAc); aka vinegar
- sulfuric acid (H2SO4)
- carbonic acid (H2CO3) forms when CO2 dissolves in body fluids
- fatty acids, keto acids, & phosphoric acid
- The molecular formula for an acid is easy to recognize because the hydrogen is always written first
- Acids lower the pH of a solution.
- Essential compounds for digestion, circulation, etc.
BASES: bases: generally substances that dissociate into hydroxyl ions (OH-) & cations in water or proton
acceptors.
For example: dissociation (ionization) of sodium hydroxide (NaOH) produces a hydroxyl ion & a sodium ion; the
hydroxyl ion may then bind to (accepts) a proton present in the solution; this produces water and simultaneously
reduces the acidity of the solution.
NaOH  Na+ (cation) + OH- (hydroxyl ion) and then: OH- + H+  H2O
Bases have a bitter taste, feel slippery on your fingers (break lipids down), & are proton acceptors. Common inorganic
bases include the hydroxides, such as magnesium hydroxide (milk of magnesia) & NaOH (lye).
- the bicarbonate (HCO3-) ion is an important base in the body, is particularly abundant in blood, where it constitutes
the alkaline reserve of the body; HCO3- + H+ +  H2CO3
- Ammonia (NH3), a common waste product of protein breakdown in the body, is also a base. It reacts with free H + to
form an ammonium ion: NH3 + H+  NH4+
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- Bases raise the pH of a solution.
- essential for blood transport, digestion, & waste excretion
ACID-BASE CONCENTRATION: the pH Scale indicates the acidity/alkalinity of a solution. [ ] = concentration of
1. The greater the number of hydrogen ions in solution, the more acidic the solution; conversely, the greater the [ OH- ]
(& thus the lower the [ H+ ]), the more basic or alkaline, the solution. The [ H+ ] in various body fluids is measured in
pH units.
2. The idea for a pH scale was devised by a Danish biochemist and part-time beer brewer named Soren Sorenson in
1909. He was searching for a convenient means of checking the acidity of his alcoholic product to prevent its
spoilage by bacterial action. (The growth of many bacteria is inhibited under acidic conditions.)
3. The pH scale is defined by the concentration of hydrogen ions in a solution, expressed in moles per liter. The
pH scale runs from 0-14 and is logarithmic; each successive change of one pH unit represents a 10 fold change in
hydrogen ion concentration.
4. At a pH of 7, the number of hydrogen ions equals the number of hydroxyl ions, and the solution is said to be neutral
(neither acidic nor basic). Pure distilled water has a pH of 7.
5. Solutions with a pH lower than 7 are acidic, the H+ ions outnumber the OH- ions. The lower the pH, the more acidic
the solution. A solution with a pH of 6 has 10x as many H+ ions as a solution with a pH of 7; pH of 3 indicates a [ H+
] 10,000x greater than that of a neutral solution.
6. Solutions with a pH higher than 7 are basic or alkaline, and the relative [ H+ ] decreases by a factor of 10 with each
higher pH unit. Thus, solutions with a pH of 8 & 11 have, respectively, 1/10 and 1/10,000 the number of hydrogen
ions present in a solution of pH 7. Notice that the smaller the [ H+ ], the greater the [ OH- ] becomes & vice versa.
1. gastric acid pH 1-2
2. lemon juice pH of 2
3. vinegar & cola, about pH 3
4. tomatoes & grapes pH 4
5. vagina (lactic acid) pH 3.5-4
6. urine pH 5-8
7. saliva & milk pH 6.5
8. distilled H2O pH7
9. semen & blood pH 7.4
10. egg white pH 8
11. pancreatic secretions pH 8
12. sea water pH 8.4
13. baking soda pH 8.5
14. soaps pH 10
15. household ammonia pH 11.5-11.9
16. chemical hair removers pH 12.5 (NaOH)
BUFFERS
1. It is critical for homeostasis (maintenance of a constant internal environment) that the concentration of hydrogen
ions (H+) in the blood be maintained within a narrow range of around pH 7.0 to 7.8. If the pH goes below or above
these limits, death results, because most enzymes cannot operate properly if the pH is outside this range.
Enzymes are necessary to perform nearly all bodily processes.
2. Even though the body produces tremendous quantities of acid each day through cellular activities such as
metabolism & respiration, blood pH usually remains within the range 7.35-7.45, which is made possible by the
action of various buffering compounds.
3. A buffer resists abrupt & large swings in pH by taking up excess H+ or OH- to keep the pH relatively constant. It
does this by releasing H (acting as an acid) when the pH begins to rise and by binding with protons (acting as a
base) when the pH drops.
4. Proteins, phosphates, & bicarbonates provide the major buffer systems in animals.
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Biol 2424 Human Phys
MACROMOLECULES
In all living cells, molecules combine by chemical bonds to form large molecules known as macromolecules. These
macromolecules all contain carbon, whose unique structure allows macromolecules to assume a great variety of shapes
& very large sizes.
There are 4 Groups of Organic Macromolecules:
Carbohydrates, Lipids, Proteins, Nucleic Acids
Mnemonics:
CLiP oN some macromolecules—never leave home without them.
Main elements of your body: You CHO CaN P a lot of NaClS, Mggie K. = You sure can micturate a lot of sodium
chlorides, Maggie Kay: Carbon, Hydrogen, Calcium, Nitrogen, Phosphorus, Sodium, Chloride, Sulfur, Magnesium,
& Potassium.
[ Principal elements by weight % in body: O (65); C (18.6); H (9.7); N (3.2); Ca (1.8); P (1.0); K (0.4); Na (0.2); Cl (0.2); Mg (0.06); S (0.04); Fe (0.007); I (0.0002);
Trace elements: Si, F, Cu, Mn, Zn, Se, Co, Mo, Cd, Cr, Sn, Al, & B. ]
In living organisms, the properties of these macromolecules & their interactions form:
- the subcellular structures (organelles, membranes) of cells.
- facilitate the chemical rxs that are the basis for all physiological processes and for life itself. (Ta Da.)
CARBOHYDRATES (carbo + hydro = “carbon + water”)
This is a group of molecules that includes sugars & starches; they represent 1-2% of cell mass.
- General formula (CH2O)n and can exist in a chain of carbons or a ring of carbons.
- Primary source of energy for cells.
- Used for structural purposes in the cell membrane & in organelles.
- Used to store energy in the form of starch (plants) & glycogen (animals).
Types of Carbohydrate molecules
monosaccharides: theses are simple sugars that consist of only 1 sugar molecule, e.g., glucose, galactose, &
fructose. Monosaccharides are the structural units of other sugars. They are linked together when an H+ from
one and an OH- from another leave to form H2O. This is called dehydration synthesis. Monosaccharides are
used to build disaccharides & polysaccharides.
disaccharides: are 2 monosaccharides bonded together
sucrose = glucose + fructose;
maltose = glu + glu;
lactose (milk sugar) = glu + galactose
polysaccharides: are long chains of monosaccharides linked together.
- usually used to store energy for the cells or provide limited structural purposes = cell membrane
- plant starch = amylose
- plant structural carbohydrate = cellulose
- animal starch = glycogen
- formed by dehydration synthesis between monosaccharides & disaccharides.
- broken down when water is added in hydrolysis reactions, but not as easily catabolized as disaccharides.
Uses for Carbohydrates
1. Due to large #'s of covalent bonds, high amounts of energy are held.
The most commonly used molecule to provide cellular energy is glucose.
2. May be used in the formation of cell structures.
Example: Ribose and deoxyribose in RNA & DNA, which are nucleic acids.
3. Polysaccharides are used for longer term energy release storage, because they are less soluble in water than mono
& disaccharides.
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LIPIDS (fats) are organic compounds that contain (CHO) carbon, hydrogen, & oxygen, but have much fewer oxygen
molecules than carbohydrates. They’re insoluble in water, but dissolve readily in other lipids and in organic solvents, such
as alcohol, chloroform, ether, & soap. This makes them very useful as structural components of cells.
lipid molecules fxs:
1. energy storage for cells
2. insulation & protection of organs
3. production, transportation, and storage of hormones & vitamins
4. provide structure of cell membranes (having a fence is a basic necessity in the evolution of life)
Lipids yield 9kcal, whereas carbs & proteins yield 4kcals of energy; lipids are much more efficient molecules for energy
storage.
TYPES OF LIPIDS: trigylcerides, phospholipids, & steroids
1. Triglycerides: or neutral fats are known as fats, waxes, & oils. They are composed of two types of building blocks:
- 3 fatty acid chains and a glycerol molecule linked together by dehydration synthesis.
- Triglycerides are the body's most concentrated source of usable energy fuel, and when they are broken down, they
yield large amounts of energy, about 3.5x more than in simple sugars.
- To have an equivalent amount of energy storage by just using carbohydrates would add about 70lbs to your body.
- The long hydrocarbon chains make fats nonpolar molecules. Because polar & nonpolar molecules do not interact,
oils & fats don’t dissolve in water (remember H2O is polar).
- Well suited for storing energy fuel in the body and are found primarily in fat deposits of the hypodermis, where they
insulate the deeper body tissues from heat loss and protect them from mechanical trauma/impact/jolts.
- Women are usually better English channel swimmers than men due to their thicker subcutaneous fat layer, which
helps insulate them from the bitterly cold water. How else does it make them better “channel” swimmers?
Triglycerides may be solid (fats) or liquid (oils) depending on the temperature. How solid a tryglyceride is at a given
temperature depends on 2 factors:
1. The length of its fatty acid chains
2. Its degree of saturation.
Carbon containing compounds with only single covalent bonds are referred to as saturated molecules; all carbon atoms
bonded to four other atoms—this is the “BAD” type that encourages fatty deposits in vessels.
- Organic molecules that contain one or more double or triple bonds are said to be unsaturated or
polyunsaturated. “GOOD” type
- Triglycerides with short fatty acid chains and/or unsaturated fatty acids are liquid at room T and are typical of
plant lipids, as in the oils we use for cooking: corn, olive, peanut, sunflower, etc.
- Triglycerides with long fatty acid chains and/or more saturated fatty acids are common in animal fats such as
butter fat, and muscle fat, which are solid at room T.
Saturated fats have been implicated as substances that encourage the deposit of fatty substances on artery walls, leading
to arteriosclerosis (hardening of the arteries). As a result, margarine made from polyunsaturated fats has been promoted
as a product that allows us to "have our cake & eat it too." But is margarine less harmful than butter????
2. Phospholipids
Are modified triglycerides composed of polar phosphorus head, & 2 nonpolar fatty acid tails.
Diagram phospholipid:
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- Phosphorus head is polar, making it hydrophilic—water loving or it dissolves in water.
- Fatty acid tails are nonpolar or hydrophobic—water hating or does not dissolve in water.
- Important component of cell membranes to regulate what goes in & out of cells.
- Fxn as surfactants (decrease surface tension) to prevent lungs from collapsing and reduces surface tension of cell
membrane. Breathe into/out of a plastic bag; now try doing it with a wet one to represent the pulmonary alveoli.
How important are surfactants?
3. Steroids
- Structure is much different than the above, but they are still in this category, because they are nonpolar & water
soluble.
- All steroids have the same basic structure: 3 six carbon rings joined to 1 five carbon ring.
- The most important steroid is cholesterol. We get some from our diet, being in animal products such as eggs,
meat, & cheese. What digestive organ makes cholesterol?
- Cholesterol has earned "bad press" because of its role in arteriosclerosis, but it is absolutely essential for human life.
Vital to homeostasis, it’s found in cell membranes (cell recognition) and is the raw material of vitamin D, steroid
hormones of the adrenal cortex & gonads, and bile salts.
- Steroid hormones include the sex hormones estrogen & testosterone for reproduction.
- Cortisol & aldosterone aid in regulating metabolism & ridding wastes from the body.
Diagram testosterone:
PROTEINS compose 10-30% of cell mass and are the basic structural materials of the body. However, not all proteins
are construction materials; many proteins play vital roles in ensuring normal cell function. Proteins have the
most varied fxs of any molecules in the body.
1. Proteins are long chains of amino acids held together by special chemical bonds called peptide bonds.
Amino acids are the building blocks of proteins.
–NH2 = amino group
–COOH = carboxyl group
R = fx group
proteins can be polar or nonpolar
Diagram:
Generic Amino Acid
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2. There are 20 different types of amino acids. There are nine essential amino acids (cannot be manufactured by our
body), so are “essential” in our diet: histidine, leucine, isoleucine, lysine, methionine, phenylalanine, threonine,
tryptophan, & valine.
3. When 2 or more amino acids are joined together a dipeptide is formed
tripeptide = 3-9 amino acids
10-100 = polypeptide
Amino acid chains with 100+ are proteins; usually 100's or 1,000's of amino acids in a protein.
4. The structure of a protein can be described at 4 levels.
1. Primary = straight chain of amino acids
2. Secondary = can be a helical structure (like DNA) or a pleated sheet (paper fan), due to side group attraction
(hydrogen bonding).
Fibrous proteins are pleated sheets or long helical strings, water insoluble, & usually have structural purposes:
collagen, elastin, & keratin
3. Tertiary = helix bends & coils on itself; e.g., myoglobin, which stores O2 in muscle.
4. Quaternary = 2 or more polypeptide chains form a folded & twisted structure and attach to other molecules; e.g.,
hemoglobin, which transports O2.
Globular proteins are functional, having tertiary or quaternary structure, are water soluble, and act as carriers for
insoluble lipids, serve as enzymes, cell messengers (hormones & neurotransmitters), and as defense molecules to fight
invaders. Enzymes are catalysts, lowering activation energies to speed up chemical rx rates. Enzymes are what make life
possible at T & P levels at (or near) the earth’s surface.
Proteins can be combined with lipids or sugars to form lipoproteins or glycoproteins.
When proteins lose their 3-D structure or conformation, they are said to denature.
- When exposed to extreme heat or acidity, the chemical bonds begin to break, and the protein loses it structure.
When this happens, the protein is “broken”—it will no longer fx. Structural proteins are a lot more stable than
functional proteins.
- The change is irreversible.
- Example: The change that you see when you fry or boil an egg (primarily the protein albumin) is a good example.
You cannot restore the egg to its original form. There’s a good reason to worry about a high fever.
ENZYMES: PROTEIN CATALYSTS
1. One of the most important uses for proteins is as biological catalysts. Catalysts are substances that reduce the
amount of activation energy needed to break or form bonds, which speeds up the rx rate.
2. Just about every rx in a cell requires a different enzyme. There are tens of thousands of rxs in a cell, so we need
tens of thousands of enzymes.
3. Increase rx rates. A catalyst is not altered by the rx (conformation doesn't change). Catalysts do not
change the final result of a rx.
4. Enzymes lower the activation energy of chemical rxs. The activation energy is the amount of energy needed by
the reactant molecules to participate in a rx. If you don't have enzymes, only a small amount of the collisions have
enough activation energy for a rx to take place. By lowering the activation energy, enzymes allow a larger
proportion of the reactants to form bonds, thus increasing the rx rate.
5. Can be important in medical diagnosis; e.g., indicate cancer, heart attack, pancreatic, osteological, or hepatic
diseases; in a heart attack, damaged cardiac cells release enzymes into the blood.
CONTROL OF ENZYME ACTIVITY
Diagram: Enzyme Activity versus T
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Remember protein enzymes have a specific 3-D shape (conformation) that is determined by the amino acid sequence,
and ultimately, by the genes. The specificity of an enzyme can be high (only one molecule) or low (acts on a group of
molecules). Enzyme names indicate fx & usually end in –ase. Some enzymes have an active & inactive form. Often the
ending –ogen is used for the inactive form; e.g., pepsinogen is the inactive form of pepsin. Why even make an inactive
enzyme form??
The rate of enzyme-catalyzed rxs increases with increasing T, up to a maximum. Why do the rxs increase?
At a few degrees above body T, proteins start to denature (lose their conformation), & the rate of the rxs that they catalyze
therefore decreases & then ends. Humans often cook food. Why? What’s the biological advantage?
2. Each enzyme has optimal activity at a characteristic pH, which is called the pH optimum for that enzyme.
Example: the pH in the stomach has to be around 2 for pepsin to digest proteins; trypsin from the pancreas has to be
in a pH of around 9 to effectively digest starches.
Diagram: Enzyme Activity versus pH
3. Many enzymes need cofactors for activity (enzyme “helpers”)
- coenzymes are cofactors derived from water-soluble vitamins.
- cofactors transport H+ and small molecules from one enzyme to another.
- Other cofactors are ions such as Ca+2, Mg+2, & selenium
- enzymes that use these cofactors cause a conformational change in the enzyme and allow it to bind with their
substrates.
- Others form temporary bonds between the enzyme & its substrate when the enzyme-substrate complex is formed.
HOW DO ENZYMES WORK?
1. The reactants in an enzyme-catalyzed rx called the substrates of the enzyme fit into a specific pocket in the
enzyme called the active site.
2. By forming an enzyme-substrate complex, substrate molecules are brought into proper orientation & existing
bonds are weakened.
3. This allows new bonds to be more easily formed:
A + B (reactants)  C + D (products)
4. The old model, the lock-and-key model of enzyme activity, was that there was an exact fit of substrates on the
enzyme’s binding site. We now know that enzymes don’t make an exact fit, but as the binding site of the enzyme
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& substrates begin to interact, the binding site changes shape to fit more closely to the substrates: induced-fit
model. The binding site is intermediate in shape to accommodate “reactants or products,” so the same enzyme
can be used for reversible rxs.
NUCLEIC ACIDS: (DNA & RNA) composed of carbon, oxygen, hydrogen, nitrogen, phosphorus, & nucleotides, their
basic structural units. Nucleotides, such as NADH, FADH2, & NADPH, are made of a phosphate group, 5C sugar, & base.
Nucleic acids are the largest molecules in the body.
Nucleic acids include 3 major molecule classes:
1. deoxyribonucleic acids = DNA
2. ribonucleic acids = RNA
3. adenosine triphosphate = ATP
4. Each consists of a nitrogenous base, a pentose sugar, & a phosphate group.
5. There are 5 different types of nitrogenous bases: adenine, guanine, cytosine, thymine, & uracil
uracil is found only in RNA and replaces thymine: A, G, C, T/U
DNA is found in the nucleus of the cell in chromatin/chromosomes where it constitutes the genetic material, or genes.
It has 2 fundamental roles:
1. It replicates itself before a cell divides, ensuring that the genetic information in the daughter cells is identical.
2. Provides instructions for building every protein in the body. By providing the directions for protein synthesis, DNA
determines what type of organism you will be—frog, human, or tree—and directs your growth & development
according to the information it contains. Although we have said that enzymes govern all chemical rxs, remember
that enzymes, too, are proteins formed at the direction of DNA.
RNA is located chiefly outside the nucleus. It’s manufactured inside the nucleus and brought outside into the cytoplasm.
Consider it a “molecular slave” of DNA. RNA decodes DNA’s message & transfers the message so orders can be carried
out. RNA carries out the orders for protein synthesis issued by DNA.
3 types of RNA:
1. mRNA = messenger RNA
2. tRNA = transfer RNA
3. rRNA = ribosomal RNA
ATP (adenosine triphosphate) is the "energy currency of the cell" that’s used either as a source of energy or a place to
store energy for future use.
The rx ATP  ADP + Pi releases energy or requires energy.
DNA & RNA STRUCTURE:
1. DNA is a coiled, double-stranded helix or ladder. The rungs are composed of nucleotides A, G, C, & T. Its backbone or “uprights” of the ladder is composed of the phosphate & deoxyribose groups that are coiled into a spiral
staircase-like structure called a double-helix.
A always binds with T, and G always with C. These are called complementary bases and are bonded with
hydrogen bonds (which are easily broken, so that DNA can be copied or read). Contained in chromatin in the cell's
nucleus. Chromatin condenses into chromosomes when a cell divides. A gene is a specific sequence of bases in
DNA that code for a particular amino acid.
2. RNA molecules are single strands of nucleotides. RNA bases are A, G, C, & U (which replaces T). Its sugar is
ribose.