Chemical Basis of Life

I. Background
Chemistry is fundamental to understanding life. All matter is comprised of matter.
Chemical Elements and Compounds
1. Chemical elements, in pure and compound form, comprise matter
Terms:
Matteranything having mass and occupying space
Massa measure of the amount of matter that an object contains
Mass Weight
Weight is the measure of how strongly an object is pulled by earths gravity and consequently varies as a function of distance from the
earths center. Mass does not vary with its position.

2. Biologically Important Elements

a. 92 naturally occurring elements
b. 25 are essential for life
i. C, O, H and N96% of all living matter
ii. Ca, P, K, S, Na, Cl, Mg, and trace elementsremaining 4%
iii. Trace elementsalthough in very low quantities, are absolutely essential;
B, Cr, Co, Cu, F, I, Fe, Mn, Mo, Se, Si, Sn, V and Zn

3. Compoundstwo or more compounds combined in a fixed ratio

a. Compounds have unique emergent properties (NaCl has properties that differ from Na and Cl)

Atoms and Molecules

Terms:
Atomsmallest possible unit of matter that retains the physical and chemical properties of its element; all atoms of the same element share
the same chemical properties
1. Atomic structure determines the behavior of an element
a. Atoms are comprised of subatomic properties (many different types; three that are relatively stable)
i. Neutrons
ii. Protons
iii. Electrons

b. Subatomic Properties
Neutron Proton Electron
Charge No Charge +1 -1
Location Nucleus Nucleus Orbits Nucleus
Mass 1 dalton 1 dalton 1/2000 dalton

i. Nucleusdense core of the atom

ii. Nucleus is positively chargedneutrons and protons (positively charged) only
iii. Electrons are held in orbits by the electrostatic attraction to nuclear protons
iv. Daltonunit of mass equal to 1.67 x 10-24 g

Atomic Number
Atomic numberequal to the number of protons in a particular element
a. All atoms of a particular element have the same atomic number
b. Nomenclature: 11Na (sodium has 11 protons)
c. In a neutral atom, number of electrons equals number of protons

Mass Number
Mass numberthe number of protons and neutrons in a particular element
a. Nomenclature: 23Na (sodium has a total of 23 neutrons and protons)
b. Knowing both the atomic number and mass number, you can determine the number of neutrons (23 11 = 12)
c. Mass number is an approximate measure of the mass of an atom since proton and neutron mass are approximately 1 dalton (Na has
an atomic mass of approximately 23 daltons)
d. Number of protons in an atom is constant; number of neutrons varies (see below)

Atomic Weight
Atomic Weightthe weighed mean of the masses of an elements constituent isotopes

Isotope
Isotopethe of an element that have the same atomic number but different mass number
a. Isotopes of an element have the same number of protons and different number of neutron
b. In natural conditions, elements occur as mixtures of isotopes
c. Different isotopes of the same element react chemically in the same way
d. Isotopes can be radioactive

Radioactive Isotope
Radioactive Isotopean unstable isotope that spontaneously emits nuclear particles and/or energy (i.e., decays)
a. Loss of nuclear particles may transform one element into another
b. Isotopes have characteristic decay timeshalf-life.
c. Half-lifetime for 50% of radioactive atoms in a sample to decay

Biological Applications of Radioactive Isotopes

1. Dating of geological strata and fossils
a. Decay occurs at a fixed rate
b. Compare ratio of radioactive and stable isotopes in fossils with the ratio in living organisms (e.g., 14C and 12C)
2. Radioactive tracers
a. Course of biological reactions can be monitored or location of particular substances can be determined
b. Particular substances have unique chemistry (e.g., DNA) allowing specific labeling (e.g., 32P)
c. Treatment of cancercobalt
d. Specific technologies employ radioisotopes (e.g., PET)

Definitions:
Energyability to do work
Potential energyenergy stored by matter due to its position or location
a. Matter tends to move to the lowest state of potential energy
b. Exists in discrete unitsquanta (i.e., not infinitely divisible)

Energy Levels of Electrons

Electrons are negatively charged particles that orbit around the nucleus.
a. Equal in mass and charge
b. Involved in chemical reactions (only subatomic particle)
c. Have potential energy
d. Electrons have fixed potential energy states called electron shells
e. Electrons with the lowest potential energy are closest to the nucleus
f. Electrons with the highest potential energy are farthest from the nucleus
g. Electrons are not fixed in a single orbit but can move from one energy level to another, thereby gaining or losing potential energy.

Electron Orbitals
Orbitals are three-dimensional space where electrons will be found 90% of the time.
a. Statistical modelviewed as a three-dimensional probability cloud
b. Number of electrons in any given cloud can not exceed two
c. Energy levels
i. 1st energy level
(a) One spherical s orbital (1s orbital)
(b) 1st energy level can have a maximum of two electrons
ii. 2nd energy level
(a) Maximum of eight electrons
(b) One spherical s orbital (2s orbital)
(c) Three dumbbell-shaped p orbitals each oriented at right angles to the other two (2px, 2py, 2pz orbitals)
iii. Higher energy levels
(a) Contain s and p orbitals
(b) Additional orbitals with more complex shapes
d. Movement between energy levels requires gain (up) or loss (down) of energy.

Electron Configuration Determines an Atoms Chemical Properties.

Electron configuration is the distribution of electrons in an atoms electron shells.
Elements (first 18; first three rows) of the periodic table:
a. Ordered by atomic number
b. Outermost shell of these atoms never has more than four orbitals (2s and 2px, 2py, 2pz) or eight electrons
c. Electrons assume the lowest potential energy state first (i.e., lower electron shells before higher; electrons 1 and 2 into 1s)
d. Electrons are added to p orbitals singly, then paired
e. Outer shells may only be partially filled
i. Example: 8O has eight electrons

1s 2s 2px 2py 2pz

Electrons 2 2 2 1 1

Valence Electrons
Valence electrons are the electrons in the outermost shell. The chemical properties of an atom depend on these electrons.
a. Octet rulevalence shell is complete when it contains eight electrons (except H and He).
b. An atom with a complete valence shell is inert or unreactive
c. Noble gases (e.g., helium argon, and neon) are inert in their elemental state
d. Atoms without complete valence shells are chemically reactive and can form chemical bonds until eight electrons fill the valence
shell
e. Atoms with the same number of electrons exhibit similar chemical behavior
f. In general, valence electrons are responsible for an atoms binding capacity.

Molecules
Atoms combine by chemical binding to form molecules. Atoms with incomplete valence shells tend to fill those shells by interacting with
other atoms. The consequence of this interaction may be the formation of a chemical bond.
Terms:
Chemical bondattraction that holds a molecule together
Moleculetwo or more atoms held together by chemical bonds
Types of Chemical Bonds
1. Covalent bondchemical bond between atoms formed by sharing a pair of valence electron

a. Strong chemical bond (e.g., H2, O2, N2)

Structural versus molecular formulas

Structuralrepresents the atoms and the bonding within a molecule (e.g., H-H); the line represents the bond)
Molecularnumber and type of atoms but no indication of arrangement of bonds (e.g., CH 4)

b. Single covalent bondsbond formed by sharing a single pair of valence electrons

c. Double covalent bondsbond formed by sharing two pairs of valence electrons
d. Triple covalent bondsbond formed by sharing three pairs of valence electrons
e. Double and triple bonds are rigid and do not allow rotation
Terms:
Valencenumber of covalent bonds that must be formed to complete the outer electron shell (i.e., bonding capacity of an atom)
Examples:
Valence
H 1
O 2
N 3
C 4
S 2

Compounda pure substance composed of two or more elements combined in a fixed ratio (e.g., H 2O, CH4)

Electronegativityatoms ability to attract and hold electrons

a. The greater an atoms electronegativity, the more strongly it attracts shared electrons
b. Scale:
Electronegativity
O 3.5
N 3.0
S 2.5
C 2.5
P 2.1

2. Types of Covalent Bonds--Nonpolar and polar

Nonpolar covalent bondbond formed by equal sharing of electrons between atoms

a. Occurs when the electronegativity of two atoms is roughly equal (e.g., CH 4)
b. Molecule made of one element usually have nonpolar covalent bonds

Polar covalent bondbond formed by an unequal sharing of electrons between atoms

a. Occurs when the electronegativity of two atoms is different
b. Shared electrons spend more time in proximity to the atom with higher electronegativity
c. For H2O, the oxygen is strongly electronegative. The electrons spend more time near the oxygen atom, creating localized
charges. The hydrogen have a partial positive charge and the oxygen a partial negative charge (see next lecture).

3. Ionic Bonds
Terms:
Ioncharged atom or molecule
Anionan atom that has gained one or more electrons from another atom and has become negatively charged; a negatively charged ion
Cationan atom that has lost one or more electrons and has become positively charged; a positively charged ion
Ionic bondbond formed by the electrostatic attraction made possible by the complete transfer of an electron from a donor atom to an
acceptor
a. Attraction results from the strength of electronegativity
b. Ionic bonds are strong in crystal form but weak in water
c. Ionic compounds are called salts

Electronegativity continuum:
LOW Nonpolar covalentPolar covalentIonic HIGH

4. Weak Chemical Bonds

a. Types:
i. Hydrogen bonds
ii. Van der Waals forces
iii. Hydrophobic interactions
b. Temporary associationsbonds that form briefly and reversibly (e.g., receptor binding)
c. Occur between different molecules or differents parts of a single large molecules
d. Help stabilize tertiary structure of large molecules

Hydrogen Bonds
Hydrogen bonds are formed by the charge attraction when a hydrogen atom covalently bonded to a one electronegative atom is attracted to
another electronegative atom.
a. 20X easier to break than covalent bond
b. Charge attraction between oppositely charged parts of polar molecules
Van der Waal Interactions
Occur when molecules are very close and asymetries result in neighboring electron clouds.

Biological Function is Related to the Shape of the Molecule

Molecules have characteristic sizes and shapes.
For many molecules, biological function depends on molecular shape. Receptor binding generally involves spatial conformation.
Molecular shape is determined by nature of bonds.
a. Molecules with two atoms can only be linear
b. Molecules with more than two atoms can have complex shapes
c. Bond formation results in rearrangement of valence shells.

Bonds are Created and Broken by Chemical Reactions

Chemical reaction is the process by which the composition of matter is changed by making or breaking chemical bonds.
a. Reactants into products
b. Matter is conserved; reactant atoms are only rearranged
c. Most reactions are reversible
d. Reaction rate is affected by the relative concentration of reactants and products
e. Chemical reactions proceed in both directions
f. When chemical equilibrium is reached, the rate of forward and reverse reaction are equal and the relative concentration of reactants
and products stop changing

II. Inorganic Chemistry: Water

Correlational support for the view that water contributes to the fitness of the environment to support life:
1. Life is likely to evolved in water
2. Living cells are comprised of 70-95% water
3. Water covers 75% of the earths surface
4. Water naturally occurs in all three physical states of matter (i.e., solid, liquid and gas)

Waters properties result from its unique structure and molecular interactions.
Polarity
Water is a polar molecule (see last lecture).
1. Water has four valence orbitals that are aligned in a tetrahedron.
2. Two corners of the tetrahedron are orbitals with unshared pairs of electrons and weak negative charge
3. Two of the corners are occupied with H atoms in polar covalent bonds with O.
4. Because O is strongly electronegative, shared electrons with H spend more time around the O atom, creating a weak positive charge
near the Hs.

Due to hydrogen bonding, water has a high level of structural organization.

1. Individual polar water molecules are held together by hydrogen bonds.

2. The localized charges on one water molecule are attracted to opposite charges on other water molecules.
3. Since there are four orbitals carrying weak charges, water molecules can form hydrogen bonds with four neighboring water
molecules.

From waters polarity and capacity to form hydrogen bonds, a number of properties emerge:
Cohesive Behaviorcohesion results from the tendency of a substance (e.g., water) to be held together by hydrogen bonds
1. Though transient, the number of hydrogen bonds at any given time gives water more structure than other liquids.
2. Hydrogen bonding holds water column together in plants, counteracting the downward pull of gravitywater adheres to vessel
walls.
3. Surface tensionmeasure of the difficulty to stretch or break the surface of a liquid
a. At the air/water interface, surface water molecules are hydrogen bonded to each other and to other molecules below the
surface
b. Relative to other liquids, water has a greater surface tension
c. Surface tension causes water to bead (i.e., the shape with smallest area to volume ratio the permits hydrogen bonding)

High Specific Heat

Terms:
Kinetic energyenergy of motion
Heattotal kinetic energy due to molecular motion in a body of matter
Temperaturemeasure of heat intensity due to the average kinetic energy of molecules in a body of matter
Celsius (C) Fahrenheit (F)
Water Boils 100 212
Human Body Temperature 37 98.6
Room Temperature 23 72
Water Freezes 0 32

Conversion Between Celsius and Fahrenheit:

C = 5(F 32)/9
F = [9C/5] + 32
K = C =273
Calorie (cal)amount of heat required to raise one gram of water one degree Celsius (amount of heat released when one gram of water
cools one degree Celsius)
Kilocalorie (kcal)amount of heat required to raise one kilogram of water one degree Celsius (amount of heat released when one kilogram
of water cools one degree Celsius)
Specific heatamount of heat that must be absorbed or lost for one gram of a substance to change its temperature one degree Celsius
Specific heat of water1 cal/g/C

Water has a high specific heat (i.e., it resists temperature changes when it absorbs or releases heat).
Keep in mind that heat is a measure of energy resulting from molecular movement. Since hydrogen bonding limits waters capacity to
move, these bonds must be disrupted to permit water molecules to move faster (increase temperature). To break (form) a bond, energy must
be absorbed (released). As a result of hydrogen bonding among water molecules, it takes a relatively large heat loss or gain for each 1C
change in temperature.
Biological Implications
The combination of waters high heat capacity and its prevalence in the environment act as a heat sink.
1. Energy absorbed during the day and summer only moderately warms large bodies of water.
2. This energy is released during the night and winter.

Waters heat capacity also contributes to:

1. Relative stability of the temperature of the marine environment
2. Milder climate of coastal areas
3. Regulation of body temperature
Heat of Vaporization
Terms:
Vaporizationtransformation of a liquid into a gas
Heat of vaporizationquantity of heat required for 1 gram of liquid to be converted into gas
Evaporative coolingcooling of a liquids surface when liquid evaporated

1. Molecules with sufficient kinetic energy can overcome the mutual attraction of molecules in a liquid and escape into the air.
2. For water to evaporate, energy is required to break hydrogen bonds.
3. Relative to other liquids, water has a high heat of vaporization (540 cal/g or 2260 J/g; Joule=0.239 cal)
4. Molecules at a liquids surface with the greatest kinetic energy are most likely to escape into gaseous form. The average kinetic
energy (i.e., temperature) of the remaining molecules is lower.
Biological Implications
1. Evaporative cooling moderates the Earths climateevaporation of tropical surface water helps to dissipate absorbed solar energy
2. As moist tropical air (i.e., air with molecules of high kinetic energy) moves towards colder climates, heat is released as water
condenses into rain (liquid)
3. Some animals can regulate body temperature by evaporative cooling

Density of Solid Water

Water is less dense in solid than liquid form. This characteristic is the result hydrogen bonding.
1. As water cools (i.e., loses kinetic energy) it contracts.
2. Water is densest at 4C.
3. From 4C to freezing (0C), water expands, becomes less dense and floats.
4. The densest water can be found at the bottom of a body of water, the least dense at the surface, and water with intermediate density
lying in the middle.
5. Keeping in mind that temperature is a measure of kinetic energy (i.e., measure of heat intensity due to the average kinetic energy of
molecules in a body of matter), as kinetic energy is reduced, capacity to move is also reduced (i.e., direct relationship). At warmer
temperatures, waters kinetic energy permits hydrogen bonds to be broken. At near freezing temperatures, water no longer has the
necessary kinetic energy to break hydrogen bonds.
6. When each water molecule has four hydrogen bonds, a crystalline lattice is formed. As a crystal, each molecule is maximally
separated. (Density is a measure of the number of molecules within a given physical space. For water, molecules are maximally
separated in the solid form and therefore it is least dense.)
Biological Implications
1. Deep bodies of water do not freeze solid from the bottom up.
2. The process of freezing releases energy to the water lying below the solid water. This in effect insulates (warms) the liquid water
near the newly forming ice.
3. Dampens seasonal changes. Energy associated with the formation or breaking of hydrogen bonds, moderates temperature of the
environment during seasonal changes.

Water as a Solvent
Terms:
Solutiona liquid consisting of a completely homogeneous mixture of two or more substances
Solventdissolving agent of a solution
Solutesubstance dissolved in a solution
Aqueous solutionsolution in which is the solvent
Hydrophobicwater fearing; non-water soluble compounds; generally nonpolar compounds with symmetric charge distribution
Hydrophilicwater loving; water soluble compounds
1. Ionic compoundsheld together by ionic bonds formed by electrostatic attraction following the complete transfer of an electron
from a donor atom
2. In polar solvents, the charged region of the polar molecule has an electrical attraction to charged ions
3. Water surrounds he individual charged ions, shielding them from each other
4. Polar solvents also have affinity for oppositely charged regions of other polar molecules

Quantitative Properties of Aqueous Solutions:

1. Solute Concentration
2. pH
Terms:
Molecular weightsum of the weight of all atoms in a molecule
Moleamount of a substance that has a mass in grams numerically equivalent to its molecular weight in daltons
E.g.: Sucrose (C12H22O11)
Atomic Weight Number of Atoms
C 12 dalton 12 144 dalton
H 1 dalton 22 22 dalton
O 16 dalton 11 176 dalton
Molecular Weight 342 dalton
Therefore, one mole of sucrose is equal to 342 grams.
Molaritynumber of moles of solute per liter of solution
To make a 1M solution of sucrose, weigh out 342 grams of sucrose and add water until the total volume equals 1 liter.
Why do we use moles?
1. From a practical standpoint, grams are more convenient (1 gram = 1.67 x 10 24 dal)
2. One mole of any substance will have the same number of molecules (6.02 x 10 23)
3. Substances can be combined in fixed ratios based on number of molecules

Dissociation of Water
An individual water molecule is comprised of two hydrogen atoms in covalent bonds with an oxygen atom. The hydrogen atom is usually
shared in a hydrogen bond between two water molecules. Occasionally, the hydrogen atom will shift from the oxygen atom to which it is
covalently bound to the unshared orbitals of the oxygen to which it is hydrogen bonded.
Details:
1. Only a hydrogen ion (proton with a +1 charge) is transferred, not the electron
2. The transferred proton binds to an unshared orbital of the second water molecule forming a hydronium ion (H3O+)
3. The water molecule that lost a proton has a net negative charge and is called a hydroxide ion (OH-)
4. The ionization reaction is reversible and exists in an equilibrium where most of the H 2O is not ionized.
Reaction:
H2O + H2O H3O+ + OH-
By convention, this reaction is expressed as the dissociation of water into H+ and OH-:
H2O H+ + OH-

[H+] and pH
Acids and Bases
At equilibrium in pure water at 25C:
1. The number of H+ ions is equal to the number of OH- ions ([H+] = [OH-])
2. Under these conditions there are very few water molecules that are dissociated1 out of 5.54 x 108). The concentration of
hydronium and hydroxyl ions is 1 gram of ions per each 1.0 x 10 7 liters or 1 x 10-7 M.
Acids
By definition, an acid is a substance that increases the relative [H +] of a solution.
Acids combine with OH- to form H2O.

Bases
By definition, a base is a substance that decreases the relative [H +] of a solution; alternately, bases increase [OH-].
E.g.,:
Acid: HCl H+ + Cl-
Base
Direct Reduction: NH3+ + H+ NH4+
Indirect Reduction: NaOH Na+ + OH-
OH- + H+ H2O

Solution
Neutral [H+] = [OH-]
Acidic [H+] > [OH-]
Basic [H+] < [OH-]

Strong Acids and Bases

1. Completely dissociate in water
2. Single arrow indicates a complete dissociation
HCl H+ + Cl-
Weak Acids and Bases
1. Partially and reversibly dissociate
2. Indicated by a double arrow

Measuring acidity: pH scale

1. In any aqueous solution [H+][OH-] = 1 x 10-14
a. Neutral: [H+] and [OH-] = 1 x 10-7
b. In an acidic solution where [H+] = 1 x 10-5, [OH-] = 1 x 10-9
c. In a basic solution where [H+] = 1 x 10-9, [OH-] = 1 x 10-5
2. The pH scale measures degree of acidity.
a. It ranges from 0 to 14.
b. pH = -log10 of the [H+] expressed in moles per liter
c. pH of 7 is a neutral solution
d. pH < 7 is an acidic solution
e. pH > 7 is a basic solution
f. Each 1unit change in pH represents a 10-fold increase in [H+]

How much greater is the [H+] in a solution with a pH of 2 (-log10 1 x 10-2) than one with a pH of 6 (-log10 1 x 10-6)? Answer: 10,000 (1/100
vs. 1/1,000,000)

3. Most biological systems have pHs ranging from 6 to 8 (a fairly narrow range). Exception: pH of stomach acid is 1.5.

Buffers
Buffers are substances that minimize changes in pH. In biological systems with narrow pH ranges, buffers are very important.
1. Buffers are combinations of H+-donor and H+-acceptor forms in a solution of weak acids or bases.
2. Function by accepting H+ ions from solution when in excess and by donating H + ions to the solution when they have been depleted.

H2CO3 HCO3- + H+
1. H2CO3 is a weak acid and acts as a H+-donor
2. HCO3- is a weak base and acts as a H+-acceptor
3. In response to a rise in pH, reaction shifts to the right with the production of hydrogen ion (H+)
4. In response to a decrease in pH, reaction shifts to the left
E.g.:
HCl + Na HCO3 H2CO3 + NaCl
NaOH + H2CO3 Na HCO3 + H2O

Acid Precipitation
Rain, snow or fog more strongly acidic than pH 5.6.
Primarily due to sulfur oxides and nitrogen oxides produced by combustion of fossil fuels. In the atmosphere, these oxides react with water
in the air to form acids.
Acid precipitation:
1. Lowers soil pH, affecting mineral solubility.
2. Lowers pH of lakes and ponds
III. Organic Chemistrya branch of chemistry that specializes in the study of carbon compounds
Terms:
Organic moleculesmolecules containing carbon
Vitalismbelief the life force is not governed by chemical or physical laws; prior to the 19 th century, organic compounds could not be
artificially synthesized
Mechanismnatural phenomena are governed by chemical and physical laws
1. Mainstream biological favors this view.

Carbon
1. Atomic number of 6 (6 protons and 6 electrons)
2. Carbon has 4 valence electrons.
3. Does not normally form ionic bonds
4. Completes outer shell by forming 4 covalent bonds; tetravalent electron configuration

Tetravalent electron configuration

1. Permits the formation of large, complex molecules
2. Carbon is oriented in the center from which the molecule branches in four directions
3. Permits carbon to covalently bind with many different elements, most commonly:
Hydrogen Oxygen Nitrogen Carbon
Valence 1 2 3 4
Atomic # 1 8 7 6
4. Determines organic molecules three dimensional shape (e.g., four single covalent bonds creates a tetrahedron)

Carbon Skeletons
Organic molecules often include long chains of carbons covalently linked together. These carbon skeletons may vary in:
1. Length
2. Shape
3. Number and location of double bonds
4. Nature of other covalently bound elements
Hydrocarbonscontain only carbon and hydrogen
1. Major component of fassil fuels
2. Since C-H and C-C bonds are nonpolar, hydrocarbons are hydrophobic

Isomers
Isomercompounds sharing the same molecular formula but with different structures and therefore have different properties
Types of isomers:
1. Structural isomersisomers that differ in the covalent arrangement of their atoms
a. Number of possible isomers increase with carbon skeleton size
b. May also differ in location of double bonds
2. Geometric isomersshare the same covalent partners but differ in spatial arrangements
a. Double bonds prevent free rotational around central axis
b. Result in subtle differences in biological activity
3. Enantiomersisomer with mirror images of each other (l-isomer and d-isomer)
a. Possible when four different atoms or groups of atoms are bonded to the same carbon (i.e., asymmetric carbon)
b. There are two different possible spatial arrangements of the four groups around the asymmetric carbon
c. Usually, only one form is biologically active.

Functional Groups
There are a number of small groups of atoms that are frequently bonded to the carbon skeleton of organic molecules. These groups are
known as functional groups.
Functional groups:
1. Have specific chemical and physical properties
2. Are regions of organic molecules that are commonly chemically reactive
3. Exhibit common properties independent of which organic molecule it is bonded to
4. Their number and arrangement determine the unique chemical properties of organic molecules

Hydroxyl Group
Hydroxyl group consists of a hydrogen atom bonded to an oxygen atom, which in turn is bonded to carbon (-OH).
Properties:
1. Polar; O-H is a polar covalent bond
2. Water soluble; water can form a hydrogen bond to the polar hydroxyl group
3. Organic compounds with hydroxyl groups are called alcohols

Carbonyl Group
Carbonyl group consists of a carbon atom double bonded to an oxygen atom (-CO).
1. Polar; the oxygen atom can be involved in hydrogen bonds
2. Water soluble
3. Functional group found in sugars
4. If the carbonyl group is off the end of the carbon skeleton, it is referred to as an aldehyde.
5. If the carbonyl group is at the terminal end of the carbon skeleton, it is referred to as a ketone.

Carboxyl Group
Carboxyl group consists of a carbon double bonded to one oxygen atom and single bonded to the oxygen of a hydroxyl group (-COOH).
1. Polar and water soluble; covalent bond between oxygen and hydrogen is so polar that the hydrogen reversibly dissociates as H +. This
polarity results from the combined effect of the two electronegative oxygen atoms bonded to the same carbon.
2. Since it donates protons, it is an acid. Compounds with this functional group are called carboxylic acids.

Amino Group
Amino group consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton (-NH2).
1. Polar and water soluble
2. Acts as a weak base; the unshared pair of electrons on the nitrogen can accept a proton, giving the amino group a +1 charge.
3. Compounds with this functional group are called amines.

Sulhydryl Group
Sulfhydryl group consists of an atom of sulfur bonded to an atom of hydrogen (-SH).
1. Participates in disulfide bridges that stabilize the tertiary structure of macromolecules
2. Compounds with this functional group are called thiols.

Phosphate Group
Phosphate group is the dissociated form of phosphoric acid (H 3PO4).
1. Polar and water soluble
2. Dissociation of two hydrogen atoms leaves the phosphate group with a negative charge (-2)
3. Important for cellular energy storage

Methyl Group
Methyl group consists of carbon bonded to three hydrogen atoms (-CH3).
1. Nonpolar and hydrophobic
2. Contribute to the tertiary structure of macromolecules

Macromolecules
Integral themes in biological systems exemplified by macromolecules:
1. There is a natural structural hierarchy of structural level in biological organization.
2. Due to the interactions among subunits at lower organizational levels, new properties emerge as you move up the structural hierarchy.
3. Form fits function.

Polymerslarge molecules consisting of many identical or similar subunits connected together

A. Macromolecules are polymers.
Terms:
Polymerlarge molecules consisting of many identical or similar subunits connected together
Monomersubunit or building block of a polymer
Macromoleculelarge organic polymer
1. Four classes of macromolecules in living organisms
a. Carbohydrates
b. Lipids
c. Proteins
d. Nucleic acids
2. Small set of monomers is the basis for an immense variety of polymers
a. All macromolecules are constructed by 40-50 different monomers
b. Diversity results from the unique combination of these subunits

How are macromolecules formed?

Terms:
Polymerizationchemical reactions that link two or more small molecules to form larger molecules with repeating structural units
Condensation Reactionpolymerization reaction which form covalent links producing net removal of a water molecule for each covalent
bond formed
Hydrolysisreaction that breaks covalent bonds between monomers by the addition of a water molecule
Condensation Reaction

1. During the reaction, one monomer loses a hydroxyl ion (OH -) and the other loses a hydrogen ion (H+).
2. Water production is indirect (process will be discussed during metabolism lecture).
3. Process requires energy.
4. Process requires biological catalysts or enzymes.
Hydrolysis
1. Hydrogen from water bonds to one monomer, hydroxyl to the adjacent monomer.

Carbohydrates
Carbohydratesorganic molecules made of sugars and their polymers
1. Monosaccharidesmonomer building block of carbohydrates
2. Polymers are made by condensation reactions
3. Carbohydrates are classified by the number of simple sugars they contain

Monosaccharides
Monosaccharides are simple sugars in which C, H, and O occur in the ratio of 1:2:1 (CH 2O).
1. Major nutrient source for cells; glucose is the most common
2. Photosynthetic organisms produce glucose from CO2, H2O and sunlight
3. Energy is stored in sugars chemical bonds and this energy is harvested by cellular respiration
4. Other organic molecules are made from the carbon skeletons of sugars
5. Sugars are the monomer used to make di- and polysaccharides

Characteristics of sugars
1. An OH is attached to each carbon except one, which double bonded to an oxygen
a. Aldehyde--double bonded oxygen is on the terminal carbon (e.g., glucose)
b. Ketone-- double bonded oxygen is within the carbon skeleton (e.g., fructose)
2. Carbon skeleton varies in size from three to seven carbons.
Classification # of Carbons Example
Triose 3 Glyceraldehyde
Pentose 5 Ribose
Hexose 6 Glucose
3. Sugars have asymmetric carbons which allow the formation of enantiomers (e.g., glucose and galactose).
a. Small differences in spatial arrangement between isomers affect molecular shape which confers distinctive biochemical
properties.
4. In aqueous solutions, many monosaccharides form ring structures. The ring structure is favored in chemical equilibrium.

Disaccharides
Disaccharides are double sugars that consist of two sugars joined by a glycosidic linkage.
Glycosidic linkagecovalent bond formed by a condensation reaction between two sugar monomers (e.g., maltose).
Disaccharide Monomers
Maltose Glucose + Glucose Used in beer fermentation
Lactose Glucose + Galactose Present in milk
Sucrose Glucose + Fructose Table sugar

Polysaccharides
Polysaccharides are macromolecules that are polymers of a few hundred or thousand monosaccharides.
1. Formed by enzyme mediated condensation reactions
2. Important biologically
a. Energy storagestarch and glycogen
b. Structural supportcellulose and chitin

Storage polysaccharides
1. Starchglucose polymer; storage polysaccharide in plants
a. Helical glucose polymer with " 1-4 linkages
b. Storage granules in plants called plastids
c. Simplest form: amylose (unbranched)
d. Amylopectinbranched polymer
e. Grains and potatoes are a common source
2. Glycogenglucose polymer; storage polysaccharide in animals
a. Large glucose polymer (" 1-4 and $ 4-6 linkages) with a higher degree of branching than amylopectin
b. Stored in muscle and liver

Structural Polysaccharides
1. Celluloselinear unbranched polymer of glucose ($ 1-4 and $ 4-6 linkages)
a. Structural component of plant cell walls
b. Differs from starch based on the nature of its glycosidic linkages (" vs. $)
c. Differences in glycosidic linkage result in unique three-dimensional shapes and physical properties
d. Hydrogen bonding between cellulose molecules forms bundles called microfibrils that reinforce the cell wall
e. Can not be digested by animals; no enzyme to digest the $ 1-4 linkage

2. Chitinstructural polysaccharide that is a polymer of an amino sugar

a. Exoskeleton of arthropods
b. Cell walls of some fungi
c. Nitrogen containing group replaces OH on carbon 2

Lipids
Lipids are a diverse group of water insoluble organic compounds. They dissolve in nonpolar solvents. Important groups include fats,
phospholipids and steroids.

Fats
Fats are macromolecules constructed from glycerol (a three carbon alcohol) and fatty acid (carboxylic acid).

Glycerol (structure)
Fatty acid (structure)
1. Composed of a carboxyl group on one end and an attached hydrocarbon chain (tail)
2. Carboxyl functional group (head) has properties of an acid
3. Hydrocarbon tail usually consists of an even number of carbons (16-18 are common)
4. Nonpolar C-H bonds make the molecule hydrophobic and not water soluble
5. Ester bondbond formed between the OH group on glycerol and the carboxyl group
6. Each of glycerols three OHs can form ester bonds
7. Triaclyglycerola fat composed of three fatty acids bonded to one glycerol by ester linkages
8. Characteristics:
a. Insoluble in water
b. Variation is due to the fatty acid composition
c. Fatty acids in a fat may be the same or vary
d. Fatty acid vary in length
e. Fatty acids may vary in the number and position of double bonds
Saturated Fat Unsaturated Fat
No double bonds in the fatty acid tail Has double bonds (one or more)
Carbons in skeleton are bonded with maximum Carbon double bond does not allow close packing at
number of Hs room temperature
Solid at room temperature Liquid at room temperature
Butter, lard, grease Olive, corn or peanut oil

9. Functions:
a. Energy storage (C-H bond is energy rich)
 b. Take up less space than carbos; therefore more compact reservoir for energy storage
c. Insulation
d. Cushioning

Phospholipds

Phosholipids contain glycerol, two fatty acids and a phosphate group and usually a small chemical group attached to the phosphate group.
1. Third glycerol carbon is attached to a negatively charged phosphate group
2. There is usually a small (usually charged or polar) molecule attached to the phosphate group
3. Phospholipids can be quite diverse based on the nature of the fatty acids and phosphate attachements
4. Contain both a hydrophobic and hydrophilic group which affects its interaction with water
5. Form micellestails away from water, heads towards
6. Major component of cell membranes; bilayer with head towards aqueous environments and tails held together by interactions
between tails

Lipids have four fused rings of carbon with various functional groups attached.
Cholesterol is a common steroid. It is a precursor for other steroids including sex hormones and bile acids.

Proteins
Polypeptide chainpolymers of amino acids arranged in particular linear sequences and linked by peptide bonds.
Proteins are macromolecules that consist of one or more polypeptide chain organized in three-dimensional space.
1. Proteins makeup 50% of cellular dry weight
2. Functions:
a. Structural support
b. Storage
c. Transport (e.g., hemoglobin)
d. Signaling (e.g., neurotransmitters)
e. Signal transduction (e.g., receptors)
f. Movement (e.g., contractile proteins)
g. Defense (e.g., antibodies)
h. Catalysis of biochemical reactions
3. Vary extensively in structure
4. Comprised of 20 amino acids

Amino Acids
Proteins are made up of amino acids. Amino acids (most) consist of an asymmetric carbon, called the alpha carbon, which is covalently
bonded to:

1. Hydrogen atom
2. Carboxyl group
3. Amino group
4. Variable R groupthis is specific to each amino acid and confers that amino acids unique properties

At biologically relevant pHs, both the amino and carboxyl group are ionized.
Amino acids can exist in three ionic states. The state is determined by the pH of the solution.
1. Cation (-NH3+)
2. Zwitterion (-NH3+, COO-)
3. Anion (COO-)
Amino acids can be grouped by the properties of their side chains.
1. Nonpolar side groups (hydrophobic); less soluble in water
2. Polar side groups (hydrophilic); soluble in water
a. Uncharged polar
b. Charged polar
(i) Acidic side groups; Dissociated carboxyl group gives this group a negative charge
(ii) Basic side groups; amino group with an extra proton gives this group a positive charge

Polypeptide chains are polymers formed from amino acids monomers by peptide bonds.
Peptide bondcovalent bond formed by a condensation reaction that links the carboxyl group of one amino acid to the amino group of
another

1. Polaritypeptides have ends:

a. N-terminusamino group end
b. C-terminuscarboxyl group end
2. Backbonerepeating sequence of N-C-C-N-C-C-N
3. Lengthfrom a few monomers to thoussands
4. Unique linear sequences

Conformation of a protein confers function

Protein conformation is the three-dimension shape of a protein.
Native conformation is the functional conformation found under normal physioogical conditions.
1. Occurs spontaneously, usually due to hydrophobic interactions
2. Enables recognition and bonding between proteins and other molecules
3. Stabilized by chemical bonding and weak interactions between neighboring parts of the protein molecule
4. Conferred by the linear organization of the amino acids

Levels of protein structure

1. Primary
2. Secondary
3. Tertiary
4. Quaternary (two or more polypeptide chains)

Primary
Primary structure is the unique sequence of amino acids.
1. Determined by genes
2. Slight change in primary sequence alters protein conformation and function
3. Sequencing
a. Developed by Sanger
(i) Complete digest to determine relative proportion of aas
(ii) partial digest and overlap mapping to determine sequence

Secondary
Secondary structure is the regular coiling and folding of a peptide backbone.
Types:
1. Alpha helix
2. Beta pleated sheet

Tertiary
Tertiary structure is the three-dimensional shape of a protein. Results from folding of R groups and their interactions with the aqueous
environment.
Covalent and weak interactions contribute to tertiary structure.
Weak interactions:
a. Hydrogen bonding between polar side groups
b. Ionic bonds between charged side chains
c. Hydrophobic interactions between nonpolar side chains in a proteins interior
Covalent linkage:
a. Disulfide bridges; strong bond that reinforces conformation

Quaternary structure
Interaction between and among several polypeptide chains

Nucleic Acids
Genes, an organisms heritable units, are comprised of nucleic acids.
Types of nucleic acids:
1. Deoxyribonucleic acid (DNA)
a. Makes up genes that indirectly direct protein synthesis
b. Contain information for its own replication
c. Contains coded information that programs all cell activity
d. Replicated and passed to next generation
e. In eukarotic cells, it is found primarily in the nucleus
2. Ribonucleic acid (RNA)
a. Functions in the synthesis of proteins coded for by DNA
b. Messenger RNA (mRNA) carries encoded genetic message from the nucleus to the cytoplasm
c. Information flow:
DNA RNA Protein
d. Sequence:
(i) In the nucleus, genetic message is transcribed from DNA into RNA
(ii) RNA moves into the cytoplasm
 (iii) Genetic message is translated into a protein

Nucleic acids are polymers of nucleotides linked together by condensation reactions.

Nucleotidebuilding block of nucleic acids; comprised of a five-carbon sugar covalently bonded to a phosphate group and a nitrogenous
base.

1. Pentose--5-carbon sugar
a. Two types:
(i) Ribosefound in RNA
(ii) Deoxyribosefound in DNA; lacks -OH group on carbon 2
2. Phosphateattached to carbon 5 of the sugar
3. Nitrogenous base; two families:

a. Pyrimidinesix member ring comprised of carbon and nitrogen

(i) Cytosine (C)
(ii) Thymine (T); only found in DNA
(iii) Uracil (U); only found in RNA
b. Purinefive member ring fused to a six member ring
(i) Adenine (A)
(ii) Guanine (G)

Functions of nucleotides:
1. Monomer for nucleic acids
2. Energy transfer (e.g., ATP)

3. Electron receptors in enzyme controlled redox reactions (e.g., NADPH)

Nucleic acids
1. Formed by phosphodiester linkages; bond between the phosphate of one nucleotide and the sugar of another
2. Backbone consists of repeating pattern of sugar-phosphate-sugar-phosphate
3. Varying nitorgenous bases are attached to the backbone
4. Genes are represented by linear sequence of nitrogenous bases which in turn is the unique code for linear sequence of amino acids
in a protein.

Inheritance is based on the replication of the DNA double helix

1. DNA consists of two nucleotide chains wound in a double
2. Sugar-phosphate backbone is on the outside of the helix
3. The polynucleotidee strands of DNA are held together by hydrogen bonding between paired nucleotide bases and by van der Wall
attraction between stacked bases
4. Base pairing rules:
a. A always with T
b. G always with C
c. In RNA, A always with U
5. The two strands are complementary and can serve as templates for new complementary strands
6. Most DNA molecules are long (often thousands or millions of bases)

Inorganic molecules

Inorganic molecules do not contain carbon and were not synthesised from a biological origin (oxides of carbon and carbonates are
exceptions)
Certain inorganic molecules play important roles in maintaing living organisms

Oxygen and Carbon Dioxide

Oxygen is needed in most organisms to release energy from organic molecules (via aerobic respiration)
Organic molecules are synthesised by plants from an inorganic stock of atmospheric carbon dioxide (via photosynthesis)
These two processes are in many ways inter-related, with O2 being released by photosynthesis and CO2 being released by respiration

The Role of Oxygen and Carbon Dioxide in Living Organisms

Minerals
Mineral nutrients are the chemical elements required by living things other than the four main elements of organic molecules (C, H, O, N)
Phosphorus is a part of nucleic acids, cell membranes and ATP
Sulphur is found in certain amino acids and can play an important role in the structure and function of proteins
Calcium is important in the growth and development of bones and teeth
Sodium and potassium are involved in neuronal signalling (nervous communication)
Iron is found in red blood cells and is necessary for the transport of oxygen in blood
Magnesium is found in chlorophyll, which is required for photosynthesis

Water
Living organisms usually consist of approximately 70 - 90% water as it functions as the fluid medium that bathes the cells and tissues
Water has a specific structure with associated properties that are critical for the maintenance of living organisms

Structure of a Water Molecule:

Water (H2O) is made up of two hydrogen atoms covalently bound to an oxygen atom
 While this bonding involves the sharing of electrons, they are not shared equally
The oxygen atom, having more protons (+ve), attract the electrons (-ve) more strongly (i.e. the oxygen has a higher electronegativity)
Thus the oxygen atom becomes slightly negative and the hydrogen atoms become slightly positive

Hydrogen Bonding between Water Molecules:

Covalently bonded molecules that have a slight potential charge are said to be polar
The slightly charged regions of the water molecule can attract other polar or charged compounds
Water molecules can associate via weak hydrogen bonds (F/O/N bonding with H)

Structure and Bonding of Water Molecules

Properties of Water:
Water has a high specific heat capacity
It can absorb a lot of energy with little change in form due to the extensive hydrogen bonding, making water a good medium for metabolic
reactions
It also has a high heat of vaporisation - this allows sweat to be an efficient form of evaporative cooling
Water is very cohesive
Because water molecules are polar, they will form intermolecular associations with each other (cohesion) and other polar molecules
(adhesion)
This allows water to travel up the stems of plants (against gravity) without requiring high levels of energy for transport
It also means water has a high surface tension, allowing small insects to walk along the surface of water without disturbing its integrity
Water is the 'universal' solvent
Water, due to its polarity, can dissolve other polar substances as well as ionic compounds (but not non-polar substances)
While individual water molecules cannot sufficiently weaken and break the intramolecular attraction between ions, large enough quantities
can
This makes water a very efficient transport medium for hydrophilic ('water-loving') substances, but not hydrophobic substances
Water is less dense as a solid
Unlike most substances, water expands when frozen to ice (the arrangement of water molecules in an ice crystal creates empty spaces)
This is important as it means ice will float on water - this prevents the oceans from freezing over when surface temperatures are sub-zero

Organic molecules

What Is Organic Chemistry?

Life is based on carbon; organic chemistry studies compounds in which carbon is a central element.

The properties of carbon make it the backbone of the organic molecules which form living matter.

o Carbon is a such a versatile element because it can form four covalent bonds.

o Carbon skeletons can vary in length, branching, and ring structure.

o The functional groups of organic molecules are the parts involved in chemical reactions.

o Organic molecules important for life include relatively small monomers as well as large polymers.

Which Organic Molecules Are Important for Life?

Carbohydrates are a class of important organic molecules that provide energy and structure.

o Sugars are the building blocks of carbohydrates.

o There are 4 types of complex carbohydrates found in animals or plants.

Lipids are a large class of hydrophobic organic molecules.

o Triglycerides (typically called fats) are made of glycerol plus fatty acids; saturated fats have been linked to heart disease.

o Phospholipids contain a polar group and are amphipathic; they form cellular membranes.

o Steroids have a characteristic ringed structure; they include cholesterol and sex hormones.

Proteins are crucial to life and perform a wide range of functions.

o Amino acids are the building blocks of polypeptide chains which fold to form proteins.

o Shape is critical for protein function and creates specific regions called domains; a protein that is denatured loses its
domains and the ability to function.

o Protein denaturation causes proteins to unfold and clump in a random configuration; understanding the denaturation
process helps in understanding the structure of intact proteins.

o Proteins can combine with other macromolecules to form lipoproteins and glycoproteins.

Nucleic acids are the primary information-bearing molecules of life.

o Nucleotides, the building blocks of nucleic acids, are also important as energy carriers.
o The nucleic acid DNA is composed of two chains of nucleotides in a helical structure; RNA is a similar nucleic acid of equal
importance.