Homework questions to be emailed to valenciabiologyhw@gmail.com

1. State four elements essential to life that make up 96% of living matter
2. Describe the formation of a hydrogen bond and explain how it differs from a covalent or ionic bond
3. List 5 characteristics of water that are emergent properties resulting from hydrogen bonding
4. Explain how water's high specific heat, high heat of vaporization, and expansion upon freezing affect        both aquatic and terrestrial ecosystems
5. Explain how acids and bases affect the hydrogen ion concentration of a solution

CHAPTER 2
THE CHEMISTRY OF LIFE
WHAT ARE ATOMS
ANYWAY?

Figure 2.1 The hierarchy of biological order from atom to organism

All substances, non-living and living, are composed of matter
matter is composed of chemical elements
Matter is anything that occupies space and has mass
mass – the amount of a substance
is the same regardless of location
mass on earth = mass on moon
weight – the force gravity exerts of a substance varies with gravitation changes
mass on earth > mass on moon

Periodic Law
there is a recurring pattern in the properties of the elements when they are arranged in order of increasing atomic number

Chemical element
a substance which cannot be broken down into any other substance by ordinary chemical means
Each element consists of one type of atom
an element consists of atoms with the same atomic number and same chemical properties.
92 naturally occurring elements are recognized ranging from hydrogen, the lightest , to uranium, the heaviest

an additional 12 - 17 man-made elements have been created in the lab by bombarding elements with subatomic particles in devices known as particle accelerators .

distribution of elements (non-living vs. living)
in crust of earth (non-living)
9 elements constitute ~99% (by mass) of the earth’s crust except for oxygen, the most common elements inside organisms are not the elements most abundant in earth’s crust
for example, silicon, aluminum and iron constitute ~40% of the earth’s crust but are found only in trace amounts in the human body
Table 2.1 Naturally Occurring Elements in the Human Body

distribution of elements (non-living vs. living) in living organisms
of the 92 naturally occurring elements about 25 are essential to life
14 of which are found in organisms in any more than trace (>0.01%) amounts
trace elements are essential to at least some organisms, but only in minute quantities
some trace elements are required by all organisms and others are required by only certain organisms
Figure 2.3 The effects of essential-element deficiencies

of the 25 elements essential to life 11 are found in organisms in > than trace
4 make up ~96% of the human body
Carbon (C)
Hydrogen (H)
Oxygen (O)
Nitrogen (N)
7 make up remaining ~4% of human body calcium (Ca), phosphorus (P), potassium (K), sulfur (S), sodium (Na), chlorine (Cl), magnesium (Mg
Figure 2.8 Electron-shell diagrams of the first 18 elements in the periodic table

Each element has a symbol
the first letter or two of its English, Latin or German name
first letter is capitalized
examples
gold (Au) - from Latin word aurum
oxygen (O) - from English word oxygen

element = substance that can’t be broken down into any other substance by ordinary chemical means; atoms with the same atomic number and same chemical properties
molecule = a group of atoms held together by energy in a stable association
ex., two atoms of the element oxygen combine chemically to form a molecule of
oxygen (O2) compound = a molecule containing atoms of 2 or more elements combined in a fixed ratio

ex., water is a chemical compound consisting of molecules produced when 2
atoms of hydrogen combine with one atom of oxygen (H2O)
Compounds .. are much more common than pure elements few elements exist in a pure state in nature many consist of only two elements
ex., table salt (NaCl)
most compounds in living organisms contain at least 3 or 4 different elements mainly C, H, O, N

Compounds are described using a combination of symbols and numerals
chemical formula (or molecular formula)
structural formula
chemical formula or molecular formula = a shorthand method for describing the chemical composition of molecules and compounds consists of chemical symbols which indicate the types of atoms present and subscript numbers which indicate the ratios among the atoms
ex., chemical formula for water is H2O

note, when a single atom of one type is present it is not necessary to write 1
structural formula = another type of formula which shows not only the types and numbers of atoms in a compound but also their arrangement in a molecule
ex., structural formula for water is
H-O-H

Each element consists of one kind of atom, which is different from the atoms of other elements
the name "atom" comes from a Greek word meaning "indivisible"
an atom is the smallest unit of matter that still retains the properties of an element
atoms are composed of many types of subatomic particles
protons neutrons electrons

some others, discussed primarily by physicists
protons (p) type of charge = single positive
where found = nucleus of the atom
relative mass = 1.007 daltons, approximately 1 dalton
neutrons (n) type of charge = neutral, no charge
where found = nucleus of the atom
relative mass = 1.009 daltons, approximately 1 dalton
electrons (e) type of charge = single,
where found = orbiting the nucleus

electrons (e)
type of charge = single, negative
relative mass = 1/1840 dalton, (1/2000) contribution to overall mass of atom considered negligible
where found = orbiting the nucleus
Electron orbitals can be various shapes, but usually illustrated as concentric circles for purposes of simplicity

electrons orbit the nucleus at nearly the speed of light
its not possible to precisely locate the position of any individual electron at any given time
a particular electron can be anywhere at a given point in time, from close to the nucleus to infinitely far away from it

Electron orbitals
arrangement of electrons in their orbits is the key to the chemical behavior of an atom !
PROPERTIES OF ATOMS
SOLIDS, LIQUIDS AND GASES
BASED ON PROTONS IN THE NUCLEUS AND ELECTRONS ON ORBITALS ACTING AS COUNTERBALANCE.
ATOMS HAVE PROTONS, NEUTRONS AND ELECTRONS
CHARACTERISTICS OF ATOMS
ATOMS HAVE THE SAME NUMBER OF PROTONS AS ELECTRONS
THE ATOMIC NUMBER IS THE NUMBER OF PROTONS
THE NUMBER OF PROTONS AND NEUTRONS = ATOMIC WEIGHT
ATOMS WITH DIFFERENT NUMBER OF NEUTRONS ARE CALLED ISOTOPES
Figure 2.4 Simplified models of a helium (He) atom
Figure 2.8 Electron-shell diagrams of the first 18 elements in the periodic table

All atoms of a particular element have the same unique number of protons
this is the element’s atomic number
atomic number = the number of protons in the atom’s nucleus (also the number of electrons if an atom has a neutral charge)
top number in box for element in periodic table
An atom’s mass number or atomic mass is the sum of the number of its protons and neutrons

atomic mass = equal to the sum of the masses of an atom’s protons & neutrons
measured in daltons (also in AMU = atomic mass units)
1 gram = 602 million million billion daltons
also referred to as atomic weight
bottom number in box for element in periodic table
1 Dalton is 1/12 mass of Carbon atom (12)

Figure 2.8 Electron-shell diagrams of the first 18 elements in the periodic table

Atoms consist of protons, neutrons and electrons
Some elements have variant forms called isotopes
atoms of the same element that vary in neutron number and atomic mass have same numbers of protons and electrons but different numbers of neutrons

isotopes of carbon
carbon 12C – nucleus consists of 6 protons, makes up ~99% of naturally occurring C
carbon 13C - nucleus has 7 neutrons, makes up ~1% of naturally occurring C
carbon 14C- nucleus has 8 neutrons, occurs only in minute quantities

Isotopes can be stable
nuclei remain permanently intact such as the 12C and 13C isotopes of carbon
unstable (or radioactive)
nuclei decays spontaneously, giving off particles and energy such as the 14C isotope of carbon

Radioactive isotopes can be
harmful to life by damaging molecules in cells, especially in DNA
the particles and energy thrown off by radioactive atoms can break apart the atoms of molecules cause abnormal connections between atoms to form

Radioactive isotopes can have beneficial uses
living cells can’t distinguish between radioactive and non-radioactive isotopes
serve as biological spies, monitoring the fate of atoms in living systems
medical uses such as x-ray, radiation therapy, PET imaging
carbon dating = determining the ratios of the different isotopes of carbon, use known half-life, calculate age
ISOTOPES
DIFFERENT FORM OF ATOM
MORE NEUTRONS
CARBON 12/CARBON 14
C12; 6e,6n,6p/ C14: 6e,8n,6p
MEASURES 1/2 LIFE/LOSS OF n
ATOMS: DIFFERENT NEUTRON #
USE:RADIOACTIVE DATING, MRI’S

Figure 2.6 A PET scan, a medical use for radioactive isotopes

Electrons
Electrons orbit the nucleus of the atom
The arrangement of electrons in their orbits, or energy shells, is the key to the chemical behavior of an atom
electrons vary in the amount of energy they possess
the farther the electron is from the nucleus, the greater its energy
electrons are quite far from the nucleus
Figure 2.9 Energy levels of an atom’s electrons

as a result nuclei of 2 atoms never get close enough to interact with each other (in
nature)
electrons, not protons or neutrons, determine chemical behavior
isotopes of an element (which have the same # & arrangement of electrons, but different # of neutrons) behave the same chemically
ELECTRON PROPERTIES
ELECTRONS ATTRACTED BY THE NUCLEUS ARE REPELLED BY EACH OTHER.
ELECTRONS MOVE THRU CLOUD LIKE ORBITALS
ENERGY LEVELS ARE THE DISTANCE FROM THE ATOMIC NUCLEUS: CLOSE/LOW: FAR/HIGH
Figure 2.11 Electron orbitals
Figure 2.9 Electron orbitals
MORE THINGS ABOUT
ELECTRONS
ELECTRONS FILL LOWEST ENERGY LEVELS FIRST
ELECTRONS ARE 2,8,8,18ETC.
ENERGY LEVEL FILLED IS MORE STABLE, LIKE THE INERT ELEMENTS. (He,Ne,Ar,Rn).
IONS ARE ATOMS THAT HAVE LOST OR GAINED ELECTRONS
Figure 2.7 Energy levels of an atom’s electrons
Figure 2.9 Energy levels of an atom’s electrons
MORE THINGS ABOUT
ELECTRONS
THE CHEMICAL BEHAVIOR OF AN ATOM IS DETERMINED BY ITS ELECTRON CONGIGURATION AND ACTUALLY ITS PROPERTIES DEPEND MOSTLY ON THE NUMBER OF ELECTRONS IN ITS OUTERMOST shell. These are valance electrons (in a valance shell).

Atoms with complete outer shells are unreactive...won't react with other atoms it encounters..inert elements.
But, those with incomplete outer valance shells,
will interact with certain other atoms in a way that each partner will complete its valance shell by either
..

sharing or
transferring its valance electrons.
This causes the atoms to stay close together and the attractions are called chemical bonds.

VALENCE ELECTRONS … by D. Edgar Murray
Why is an atom just happy as hell
When it has a completely filled outer shell?
Electrons must be like a tasty snack
Which atoms can eat to fill their lack,
If they can't have a full shell with no empty spaces
They'll share with their neighbors on a part-time basis …..
ELECTRONEGATIVITY

THE MEASURE OF AN ATOM'S ATTRACTION FOR ELECTRONS OF A COVALENT BOND IS CALLED ITS ELECTRONEGATIVITY. The more electronegative an atom, the more strongly it pulls shared electrons toward itself.
FORMS OF BONDING
IONIC BONDS
IONS = ELECTRONS GAINED OR LOST.
A TRANSFER OF ELECTRONS
SODIUM AND CHLORINE =NaCl
SODIUM LOSES 1 ELECTRON
CHLORINE GAINS 1 ELECTRON
Figure 2.14 Electron transfer and ionic bonding
Figure 2.15 A sodium chloride crystal
The emergent properties of a compound
COVALENT BONDS

PAIRS OF ELECTRONS SHARED
C-C-C OR C-H OR C=C OR C=H
CAN HAVE TRIPLE BONDS
SYMMETRICAL CHARGES: NON-POLAR COVALENT
ASYMMETRICAL CHARGES: POLAR COVALENT SUCH AS H20
Figure 2.10 Formation of a covalent bond
Figure 2.12 Covalent bonding in four molecules
Figure 2.13 Polar covalent bonds in a water molecule
Figure 2.17 Molecular shapes due to hybrid orbitals
CHEMICAL REACTIONS
SYNTHESIS (DEHYDRATION )
REMOVES WATER, BUILDS MOLECULES, ASSEMBLES.
ANABOLISM REACTION A + B = AB
REACTANTS = PRODUCTS
AA + AA = PEPTIDE (-WATER)
PEPTIDE + PEPTIDE = DIPEPTIDE
Unnumbered Figure (Page 38) Chemical reaction between hydrogen and oxygen

DECOMPOSITION REACTIONS
HYDROLYSIS ADDS WATER
CATABOLISM/SPLITS CMPDS.
AB + WATER = A + B
DIGESTION
PROTEIN + WATER = AA + AA
REDOX REACTIONS
TRANSFER OF ELECTRONS
LOSE OR GAIN ELECTRONS

Hydrogen bond
A weak electrostatic link between an electronegative atom (such as oxygen) and a hydrogen atom which is linked covalently to another electronegative atom; hydrogen bonding is what makes water stick to itself.
hydrogen bonds[1].swf

Multiple hydrogen bonds
hold the two strands of the DNA double helix together
hold polypeptides together in such secondary structures as the alpha helix and the beta conformation;
help enzymes bind to their substrate;
help antibodies bind to their antigen
help transcription factors bind to each other;
help transcription factors bind to DNA
Chapter 3
Water and the Fitness of
the Environment
Figure 3.1 A view of earth from space,

The importance of water
Water is the single most abundant component of cells and organisms. 75-85% of a cell is water (10-20 in spores and dry seeds).
The polarity of water molecules are caused by the angles that hydrogen atom bond to the oxygen atom (104.50), making the oxygen atom electronegative (d-).

WATER Chp 3
Life began in water and evolved there 3 billion years ago. Most cells contain 70%-90% water with water covering 3/4 of out planet.
While the water molecule mentioned above is simple, on the whole it is neutral except for the unequal distribution of electrons which form regions of slight + charges near the hydrogen atoms and slight negative charges near the oxygen atom. The polarity of its bonds giving opposite charges on opposite ends of the molecule makes it known as a polar molecule.

Overview: The Molecule That Supports All of Life
Water is the biological medium here on Earth
All living organisms require water more than any other substance

•Water is the most common and yet unusual substance in the universe
• Solutions vs. mixtures
– exclusion of salts in freezing water
– dissolving water in air and air in water

•• Molecular properties
– Electronic structure
– Electrical polarity
– cohesion and adhesion
• Surface Properties
– Surface tension
– Capillarity

•Thermal properties
– density vs. temperature
– heat capacity
– Heat of fusion and vaporization

• Air is warmer near the surface because air can hold more water vapor in solution
It gets cooler at higher elevations because air can hold less water vapor in solution

•Electronic structure
• When hydrogen combines with oxygen to form water, the electrons shared by hydrogen go to the two half empty p orbitals.
• This results in an asymmetrical charge distribution that creates an electrical dipole across the molecule.

•• The side of the molecule nearest the hydrogen atoms will exhibit a slight + charge, while the side opposite will exhibit a slight (–) charge.
• This gives the water molecule a range of very abnormal physical properties, that make water the most useful substance on our planet.

Concept 3.1: The polarity of water molecules results in hydrogen bonding
The water molecule is a polar molecule

This property accounts for the cohesiveness, the temperature-stabilizing capacity and the solvent properties of water.
Moderation of Temperature
Water moderates air temperature
By absorbing heat from air that is warmer and releasing the stored heat to air that is cooler
Heat and Temperature
Kinetic energy
Is the energy of motion
Heat
Is a measure of the total amount of kinetic energy due to molecular motion
Temperature
Measures the intensity of heat
Water’s High Specific Heat
The specific heat of a substance
Is the amount of heat that must be absorbed or lost for 1 gram of that substance to change its temperature by 1ºC
Water has a high specific heat, which allows it to minimize temperature fluctuations to within limits that permit life
Heat is absorbed when hydrogen bonds break
Heat is released when hydrogen bonds form

Specific heat...amount of heat that must be absorbed or lost for 1g of the substance to change 1'C. Water has a high specific heat and tends to absorb more heat to warm it and hold heat longer to cool it. Heat must be absorbed to break the H bonds and heat is released when H bonds are formed so a calorie of heat causes a very small change in temperature because the energy is being used to disrupt H bonds before the molecules can start moving faster.

Having so much water on earth, having so much water in organisms, rapid temperature changes tend not to occur in organisms and bodies of water...helping control the climate! It also takes a lot of energy to vaporize water. However the evaporation cools because all the hot molecules left!

Evaporative Cooling
Evaporation
Is the transformation of a substance from a liquid to a gas
Heat of vaporization
Is the quantity of heat a liquid must absorb for 1 gram of it to be converted from a liquid to a gas
Evaporative cooling
Is due to water’s high heat of vaporization
Allows water to cool a surface

Insulation of Bodies of Water by Floating Ice
Solid water, or ice
Is less dense than liquid water
Floats in liquid water
Since ice floats in water
Life can exist under the frozen surfaces of lakes and polar seas
The Solvent of Life
Water is a versatile solvent due to its polarity
It can form aqueous solutions

As a solvent
Terms...a liquid that is a mixture of two or more substances sis called a solution. The dissolving agent of a solution is the SOLVENT, and the substance that is dissolved is the SOLUTE. If water is the solvent, then the solution is called an AQUEOUS SOLUTION.

Water can also interact with polar molecules such as proteins

 While there is no universal solvent, water is one of the best and guess why? That's right, the Hydrogen bonds. Example: put salt in the water, the hydrogen regions (+) surround the chlorine atoms (-) and the oxygen (-) surround the sodium (+). and non-ionic compounds can form weak H bonds with the water as long as they are polar.
If the substance has an affinity for water, its said to be HYDROPHILIC (cotton absorbs H2O without dissolving) and some have no affinity to water (HYDROPHOBIC) because of the nonpolar bonds (especially C--H bonds). (See table 3.1 P46).

Hydrophilic and Hydrophobic Substances
A hydrophilic substance
Has an affinity for water
A hydrophobic substance
Does not have an affinity for water
Solute Concentration in Aqueous Solutions
Since most biochemical reactions occur in water
It is important to learn to calculate the concentration of solutes in an aqueous solution
A mole
Represents an exact number of molecules of a substance in a given mass
Molarity
Is the number of moles of solute per liter of solution

These attractions tend to hold the molecules together in a hydrogen bond which makes the water COHESIVE. The bonds are short lasting because they are so weak but collectively hold it together providing such possibilities as water reaching through the force of gravity through small pores through plants to leaves. Adhesion to the walls of the vessels also aid this process. The surface tension is a measure of how difficult it is to break the surface of a liquid.
Cohesion
Water molecules exhibit cohesion
Cohesion
Is the bonding of a high percentage of the molecules to neighboring molecules
Is due to hydrogen bonding

WATER ON GLASS WATER ON PLASTIC
WATER WITH WATERp
Cohesive force changes physical properties
• In the liquid state water molecules form chains that are constantly breaking up and reforming.This increases the viscosity of water.

•Cohesive and adhesive forces
• The polarity of water causes water molecules to be:
– electrically attracted to each other = cohesive force
– electrically attracted to molecules of another species (such as glass) = adhesive force

Surface tension
Is a measure of how hard it is to break the surface of a liquid
Is related to cohesion

•Surface tension Surface tension
• Molecules located at the air-water interface will be attracted to both air and water molecules.
• The sum of all these force vectors is creates a net downward force.
• The result is that the surface acts as an elastic "skin."
• The tensile strength of this skin to intrusion and tearing is called the surface tension.

Water expands when it freezes. Water is one of the few substance that is less dense as a solid than a liquid (ice floats). The H bonds are the reason for this and above 4'C, it is like other substances, contracting when cool and expanding when warm but when water starts to freeze,,the molecules aren't moving fast enough to break the H bonds and the crystal lattice the molecules get locked in keep the molecules far enough apart to make ice about 10% less dense than water at 4'C

The hydrogen bonds in ice
Are more "ordered" than in liquid water, making ice less dense

Water molecules are cohesive --
Hydrogen bonds form between the hydrogen atoms and the oxygen atoms of water molecules and are responsible for its high boiling point, high specific heat, and high heat of vaporization.

Water has a high temperature-stabilizing capacity -- Specific heat is the amount of heat a substance absorb per gram to increase its temperature 10C. The specific heat of water is 1.0 calorie per gram.
Water has a high heat of vaporization, the amount of energy required to convert one gram of a liquid into vapor.

•capacity Thermal properties: Heat capacity
• Heat capacity of water is the energy that is needed to raise the temperature of 1 gram of water by 1 degree Celsius.
1 cal/gm ºC
• Heat of fusion = 80 cal/gram
• Heat of vaporization = 580 cal/gram
Thermal property: Phase change
580 cal/gm released
580 cal/gm absorbed

Water is an excellent solvent. A solvent is a fluid in which another substance, called the solute, can be dissolved.
Hydrophobic: water fearing
Hydrophilic: water loving
The solubilization of sodium chloride because water molecules form spheres of hydration.
Figure 3.7 A water-soluble protein

• When water freezes it forms a three-dimensional honeycomb structure that excludes most ions in the water solution.
Capillarity
• adhesive force between water and glass forces the water to climb up the glass (against gravity)
• This also happens in soils at the water table, a capillary fringe forms where water is held up by surface tension near the surface, water infiltrates by gravity and capillarity action.
The pH Scale
The pH of a solution
Is determined by the relative concentration of hydrogen ions
Is low in an acid
Is high in a base
Figure 3.8 The pH scale and pH values of some aqueous solutions

The pH scale measures acids and bases..and what is being measured is....acids the number of H+ or Hydrogen ions in water. Bases, the number of OH- or hydroxide ions...which decreases the amount of H+ ions.
The scale is 1-14 with 7 as neutral meaning H+=OH- and is 7 on the scale. If the pH is higher than 7...7.1-14, the solution is alkaline or basic. A pH less than 7...6.9-1, is acidic.
one unit of pH= a tenfold change of the concentration of Hydrogen ions..

Effects of Changes in pH

Concept 3.3: Dissociation of water molecules leads to acidic and basic conditions that affect living organisms Water can dissociate
Into hydronium ions and hydroxide ions
Changes in the concentration of these ions
Can have a great affect on living organisms
Reaction producing hydroxide and hydronium ions
Acids and Bases
An acid
Is any substance that increases the hydrogen ion concentration of a solution
A base
Is any substance that reduces the hydrogen ion concentration of a solution

Living matter is very sensitive to pH and most cells (exceptions noted) operate best at nearly neutral pH and do not function well with fluctuations and thus, the body has many mechanisms which stabilizing the fluids.
The Threat of Acid Precipitation
Acid precipitation
Refers to rain, snow, or fog with a pH lower than pH 5.6
Is caused primarily by the mixing of different pollutants with water in the air

Acid precipitation
Can damage life in Earth’s ecosystems

Buffers
The internal pH of most living cells
Must remain close to pH 7
Are substances that minimize changes in the concentrations of hydrogen and hydroxide ions in a solution
Consist of an acid-base pair that reversibly combines with hydrogen ions

BUFFERS are the chemical substances able to bond to H+ ions thereby removing them from solution when their concentration starts to rise/or release H+ions into solution when the concentration begins to fall. Many chemical reactions in living organisms do release or use H+ ions.

Why pH is important
Chlorine sanitizers produce the sanitizing HOC1 (hypochlorous acid) by combining with water. The killing power of the hypochlorous acid released in this reaction depends very heavily on the acidity or alkalinity the pH - of the water in which the reaction takes place. (PH is the measure of acidity or alkalinity of a solution. It ranges from 0 [acid] to 14 [alkaline]. PH is important because hypochlorous acid (HOC 1) exists in water in an equilibrium.

Here's the equation: HOC1 = H + + OC1
Depending on the pH of the water, the HOC1 can be come H + + OC1 -(two separate ions) or the H + + OC1-can unite to become HOC1.
At low pH levels (7,2 and down) the highest percentage of sanitizing oxygen and chlorine will be combined with hydrogen in the HOC1 form. The equation will be shifting leftward, so to speak. At first glance, this might seem

good, since it is HOC1 that does the germ killing. But here's the catch ... in this acid environment, the HOC1 will dissipate rapidly, and can cause eye irritation and corrode metallic pool fixtures and pumps.
Conversely, at high pH levels (7,7 and up), too much of the sanitizer will be in the separated form: H + + OC1_. This greatly reduces its sanitizing ability. The ideal distribution is about 50-50, that is, 50% of the germ-killing oxygen and chlorine in the combined HOC1 form and 50% in the free OC1-form.

This equilibrium occurs at a pH of 7,5. That's why it's so important to keep pool water in the 7,2-7,6 pH range. This range is easier to attain than trying for exactly 7,5 all the time, and it still provides a good distribution of HOC1 and OC1_,