Download The Chemical Level of Organization

Chapter 2
Atoms
Chemistry is the science that
investigates matter and its interactions
 Atoms are the basic particles of matter

 Matter is anything that takes up space and
has mass
○ Matter occurs in 3 states: solid, liquid, and gas
○ All matter is composed of elements which
cannot be broken down or changed
○ The smallest, stable unit of matter is the atom
Atomic Structure

Atoms contain 3 types of subatomic
particles: protons (positive electrical
charge), neutrons (uncharged), and
electrons (negative electrical charge)
 Number of protons in an atom is its atomic
number
 Protons and neutrons are found in the
nucleus, the center of the atom
 Electrons orbit the nucleus forming the
electron cloud (represented as a spherical
electron shell)

Isotopes are atoms of a given element that
differ in terms of the number of neutrons in the
nucleus
 Isotopes can only be distinguished from each other
by their mass number (number of protons and
neutrons in the nucleus)
 Unstable isotopes are radioactive

Atomic weight is the average mass of an
element’s atoms
 Takes into account the mass of subatomic particles
and relative proportions of any isotopes

Electrons are located in the electron shell
 The number of electrons in an atom’s outer shell
determines the chemical properties of that element
 The first shell (ring) can contain 2 electrons and
every ring after can contain up to 8
 If the outer ring is full then the atom is stable
Chemical Bonds

Chemical bonds are forces formed by
atom interactions
 The atoms most important to biology are the
unstable ones because they interact and
form larger structures
 Bonding produces molecules (chemical
structures with more than one atom bonded
via sharing electrons) and compounds
(chemical substances made up of atoms of
2 or more elements)
Chemical Bonds (cont.)

Ionic bonds
 Ions are atoms or molecules with an electric charge (positive
charge = cations and negative charge = anions)
 Ionic bonds are chemical bonds created by the electrical
attraction between anions and cations
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Covalent bonds
 A strong bond that involves the sharing of electrons
 Can be single or double
 Nonpolar covalent bonds = neutral bonds because of equal
sharing
 Polar covalent bonds = unequal sharing between atoms

Hydrogen bonds
 Weak attraction between a slight positive charge on the
hydrogen atom of one polar covalent bond and a weak negative
charge on an O or N atom of another
 Too weak to create molecules, but can alter shape and pull
other molecules together
Decomposition, Synthesis, and
Exchange Reactions
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Cells stay alive by controlling chemical reactions
Chemical reactions are when new bonds are formed between
atoms or when existing bonds are broken.
Basic energy concepts
 Work is movement or change in the physical structure of matter
○ Walking or running
 Energy is the capacity to perform work
○ There are 2 major types of energy:
 Kinetic energy is energy in motion (falling)
- Used to perform work
 Potential energy is stored energy (stretched spring or charged battery)
○ Energy cannot be destroyed, it can only be converted
 During each conversion some energy is released as heat (an increase in random
molecular motion)
 The temperature of an object is directly related to the average kinetic energy of its
molecules
 Heat can’t completely be converted to work or any other form of energy; cells can’t
capture it or use it
Types of Reactions

Decomposition reactions
 Breaks down a molecule into smaller fragments (digestion)
○ AB
A+B
 Decomposition reactions involving water are important in the breakdown of
complex molecules in the body
○ Hydrolysis involves one of the bonds in a complex molecule being broken, and
the components of a water molecule being added to the resulting fragments
 A – B – C – D – E + H2O
A – B – C – H + HO – D – E
 Catabolism refers to the decomposition reactions of complex molecules within
cells
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Synthesis reactions
 Synthesis is the opposite of decomposition; larger molecules are made from
smaller components
○ A+B
AB
 Always involves the formation of new chemical bonds
 Dehydration synthesis (condensation) is the formation of a complex molecule
by the removal of water
○ A – B – C – H + HO – D – E
A – B – C – D – E + H₂O
 Anabolism is the synthesis of new compounds in the body

Exchange reactions
 In an exchange reaction, parts of the reacting molecules are shuffled
○ AB + CD
AD + CB
Reversible Reactions

Many important biological reactions are
freely reversible
 A+B
AB
This equation means that 2 reactions
are happening simultaneously, one
synthesis and one decomposition
 At equilibrium the rates of the 2
reactions are balanced

Enzymes and Activation Energy
Most chemical reactions do not occur spontaneously, or they
occur so slowly that they are of no value to cells
 For reactions to proceed, enough energy must be provided to
activate the reactants

 The amount of energy required to start to start a reaction is the
activation energy

Cells use enzymes to speed up reactions that support life
because cells can’t handle the harsh requirements reactions
normally need
 Enzymes are types of catalysts (compounds that accelerate chemical
reactions without themselves being permanently changed)
 Enzymes promote chemical reactions by lowering activation energy
requirements
 Lowering activation energy affects rate, not direction or products

Reactions absorb and release energy
 Reactions that release energy are exergonic
 Reactions that absorb energy are endergonic
Inorganic Compounds
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Nutrients are essential elements and
molecules obtained from the diet
Metabolites include all molecules synthesized
or broken down by chemical reactions inside
our bodies
Inorganic compounds are small molecules that
generally do not contain carbon and hydrogen
atoms
 Water, carbon dioxide, oxygen, inorganic acids and
bases, and salts

Organic compounds are mostly carbon and
hydrogen atoms, they can be larger & more
complex than inorganic compounds
Physiological Systems Depend on Water
Water is the single most important
constitute of the body
 3 important general properties of water:

 Water is an essential reactant in the
chemical reactions of living organisms
 Water has a very high heat capacity (the
ability to absorb and retain heat)
 Water is an excellent solvent
Body Fluid pH

pH is the concentration of hydrogen ions
in a solution
 It appears as a number between 0 and 14
○ Water is a 7 = neutral
○ Below 7 is acidic and above 7 is basic
(alkaline)
 Blood and most bodily fluids normally range
from 7.35 to 7.45
○ Below 7 produces a coma and above 7.8
causes uncontrollable, sustained muscular
contarctions
Acids, Bases, and Salts

An acid is any substance that breaks apart in
solution to release hydrogen ions
 Strong acids dissociate completely
○ Stomach acid

A base is a substance that removes hydrogen
ions from a solution
 Strong bases dissociate completely
○ Drain openers

Weak acids and bases do not dissociate
completely
 The body contains weak bases that are important in
counteracting acids produced during cellular
metabolism
Acids, Bases, and Salts (cont.)

Salts
 An ionic compound consisting of any cation
except a hydrogen ion and any ion except a
hydroxide ion
○ They are held together by ionic bonds and
dissociate easily in water
 Salts are examples of electrolytes, inorganic
compounds whose ions can conduct an
electrical current in solution

Buffers and pH
 Compounds that stabilize pH by either removing
or replacing hydrogen ions
 Antacids and baking soda
Carbohydrates

Carbs are organic molecules that contain
carbon, hydrogen, and oxygen in a ratio
near 1:2:1
 Includes sugars and starches which make up
about half the typical US diet
 Most important as sources of energy
Carbs are one of the 4 major classes of
organic compounds
 3 major types of carbs: monosaccharides,
disaccharides, and polysaccharides

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Monosaccharides (simple sugars)
 Carb containing from 3-7 carbon atoms
 Includes glucose; the most important “fuel” for the body
 Dissolve quickly and are rapidly distributed

Disaccharides
 2 monosaccharides joined together
 Sucrose

Polysaccharides
 Larger carb molecules that result when repeated
dehydration synthesis reactions add additional
monosaccharides or disaccharides
 Starches and cellulose
 Not easily broken down
 Glycogen (animal starch)
○ A polysaccharide made of interconnected glucose
○ Stored in muscles as an energy reserve of glucose
Lipids
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Contain a carbon-to-hydrogen ratio of 1:2
Familiar lipids include fats, oils, and waxes
Most are insoluble in water, but special
transport mechanisms carry them in the
circulating blood
Provide about 2x as much energy as carbs
when broken down in the body
The major types of lipids are fatty acids,
fats, steroids, and phospholipids

Fatty Acids
 Long chains of carbon atoms with attached hydrogen
atoms that end in a carboxylic acid group (-COOH)
 Only the carboxyl end dissolves in water
 Saturated fatty acids have only single bonds between
their carbons and unsaturated have 1+ double bonds

Fats
 Fatty acids + glycerol = fat
○ Triglyceride = 3 fatty acids + glycerol
 Energy reserves and insulation

Steroids
 Large lipid molecules composed of four connected rings
of carbon atoms
 They differ in the carbon chains that are attached to the
basic structure
 Cholesterol is the best-known steroid

Phospholipids
 Consists of a glycerol and 2 fatty acid linked to a nonlipid
group by a phosphate group
 The most abundant lipid components of cell membranes
Proteins
The most abundant organic components of the human body and in
many ways the most important
 Accounts for about 20% of the total body weight
 Protein function

 Support (structural proteins)
○ Create a 3D framework for the body
 Movement (contractile proteins)
○ Responsible for muscle contraction
 Transport
○ Transport proteins carry lipids, minerals, and gases through the blood
 Buffering
○ Prevent dangerous changes in pH
 Metabolic Regulation
○ Enzymes speed up chemical reactions in living things
 Coordination and Control
○ Protein hormones can influence metabolic activities of every cells or affect the
function of specific organs or organ systems
 Defense
○ Waterproof proteins form the skin, hair, and nails and protect us from the
environment. Antibodies protect us from disease. Clotting proteins restrict
bleeding.
Protein Structure
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Proteins are long chains of organic molecules called amino
acids
There are 20 different amino acids that are the building blocks
of proteins
Each amino acid consists of a central carbon atom bonded to
a hydrogen atom, an amino group (-NH2), a carboxylic acid
group (-COOH), and a variable R group or side chain
The name amino acid refers to the presence of an amino
group and a carboxylic acid group
The amino acids are strung together like beads, with the
carboxylic acid group of one attached to the amino group of
another via a peptide bond
Peptides are molecules made up of amino acids held together
by peptide bonds.
 Polypeptides containing more than 100 amino acids are proteins
In a globular protein, like myoglobin, peptide chains fold back
on themselves creating a rounded mass
 The shape of a protein determines its function
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Alanine (Ala)
Valine (Val)
Leucine (Leu)
Isoleucine (Ile)
Proline (Pro)
Methionine (Met)
Phenylalanine
(Phe)
Tryptophan (Trp)
Glycine (Gly)
Serine (Ser)
Threonine (Thr)
Cysteine (Cys)
Asparagine (Asn)
Glutamine (Gln)
Tyrosine (Tyr)
Asparic Acid (Asp)
Glutamic Acid
(Glu)
Lysine (Lys)
Arganine (Arg)
Histidine (His)
DNA and RNA
Nucleic acids are large organic molecules
composed of carbon, hydrogen, oxygen,
nitrogen, and phosphorus
 The 2 classes of nucleic acids are:

 Deoxyribonucleic Acids (DNA)
○ Determines our inherited characteristics as well as
all aspects of body structure and function
 Ribonucleic Acids (RNA)
○ RNA cooperate to form specific proteins using the
information provided by DNA
Structure of Nucleic Acids

Made up of subunits called nucleotides
 Each nucleotide contains a sugar, a phosphate group,
and a nitrogenous base
○ Sugar = 5 carbon (ribose or deoxyribose)
○ Nitrogenous bases = adenine, guanine, cytosine, thymine
(DNA), or uracil (RNA)
ATP (Adenosine Triphosphate)
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
The energy that powers a cell is obtained by the
breakdown of organic molecules
A high-energy bond is a covalent bond that stores
an unusually large amount of energy
 When the bond is later broken, the energy is later
released under controlled conditions

In our cells, a high-energy bond usually connects a
phosphate group to an organic molecule creating a
high-energy compound
 The most important is ATP
○ Made of AMP plus 2 phosphate groups or ADP plus 1
phosphate group
 ADP to ATP is the primary method of energy storage, and
the reverse reaction is the primary method of release
○ ADT + phosphate group + energy
ATP + H2O
Introduction to the Microscope
Types
 Care
 Parts
 Focusing

Types of Microscopes

Light Microscope
 The models found in most
schools, use compound lenses to
magnify objects. The lenses bend
or refract light to make the object
beneath them appear closer.
Common magnifications: 40x,
100x, 400x
 *Oil Immersion lenses can
improve quality of focus and
magnification

Types of Microscopes

Stereoscope
 This microscope allows for binocular (two eyes)
viewing of larger specimens.

Scanning Electron Microscope
 Allow scientists to view a universe too small to be
seen with a light microscope. SEMs do not use light
waves; they use electrons (negatively charged
electrical particles) to magnify objects up to two
million times.

Transmission Electron Microscope
 Also uses electrons, but instead of scanning the
surface (as with SEM's) electrons are passed
through very thin specimens.
Parts of a Microscope
Magnification

Your microscope has 3 magnifications:
Scanning, Low and High. Each objective
will have written the magnification. In
addition to this, the ocular lens
(eyepiece) has a magnification. The total
magnification is the ocular x objective
Magnification
Ocular Lens
Total
Magnification
Scanning
4x
10x
40x
Low Power
10x
10x
100x
High Power
40x
10x
400x
General Procedures
1. Make sure all backpacks and junk are
out of the aisles.
 2. Plug your microscope in to the
extension cords. Each row of desks
uses the same cord.
 3. Store with cord wrapped around
microscope and the scanning objective
clicked into place.
 4. Carry by the base and arm with both
hands.
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Focusing Specimens
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1. Always start with the scanning objective. Odds are, you
will be able to see something on this setting. Use the Coarse
Knob to focus, image may be small at this magnification, but
you won't be able to find it on the higher powers without this first
step. Do not use stage clips, try moving the slide around until
you find something.
2. Once you've focused on Scanning, switch to Low Power.
Use the Coarse Knob to refocus. Again, if you haven't focused
on this level, you will not be able to move to the next level.
3. Now switch to High Power. (If you have a thick slide, or a
slide without a cover, do NOT use the high power objective). At
this point, ONLY use the Fine Adjustment Knob to focus
specimens.
4. If the specimen is too light or too dark, try adjusting the
diaphragm.
5. If you see a line in your viewing field, try twisting the
eyepiece, the line should move. That's because its a pointer,
and is useful for pointing out things to your lab partner or
teacher.
Drawing Specimens
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1. Use pencil - you can erase and shade areas
2. All drawings should include clear and proper
labels (and be large enough to view details).
Drawings should be labeled with the specimen
name and magnification.
3. Labels should be written on the outside of
the circle. The circle indicates the viewing field
as seen through the eyepiece, specimens
should be drawn to scale - ie..if your specimen
takes up the whole viewing field, make sure
your drawing reflects that.
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Example:
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Making a Wet Mount
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1. Gather a thin slice/piece of whatever your
specimen is. If your specimen is too thick, then the
cover slip will wobble on top of the sample like a seesaw, and you will not be able to view it under High
Power.
2. Place ONE drop of water directly over the
specimen. If you put too much water, then the cover
slip will float on top of the water, making it hard to
draw the specimen, because they might actually float
away. (Plus too much water is messy)
3. Place the cover slip at a 45 degree angle
(approximately) with one edge touching the water
drop and then gently let go. Performed correctly the
cover slip will perfectly fall over the specimen.
How to Stain a Slide
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1. Place one drop of stain (iodine, methylene
blue..there are many kinds) on the edge of the cover
slip.
2. Place the flat edge of a piece of paper towel on
the opposite side of the cover slip. The paper towel
will draw the water out from under the cover slip, and
the cohesion of water will draw the stain under the
slide.
3. As soon as the stain has covered the area
containing the specimen, you are finished. The stain
does not need to be under the entire cover slip. If the
stain does not cover as needed, get a new piece of
paper towel and add more stain until it does.
4. Be sure to wipe off the excess stain with a paper
towel.
Cleanup
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1. Store microscopes with the scanning
objective in place.
2. Wrap cords and cover microscopes.
3. Wash slides in the sinks and dry
them, placing them back in the slide
boxes to be used later.
4. Throw cover slips away.
Troubleshooting

Occasionally you may have trouble with working your
microscope. Here are some common problems and
solutions.
 1. Image is too dark!
○ Adjust the diaphragm, make sure your light is on.
 2. There's a spot in my viewing field, even when I move the
slide the spot stays in the same place!
○ Your lens is dirty. Use lens paper, and only lens paper to
carefully clean the objective and ocular lens. The ocular lens
can be removed to clean the inside.
 3. I can't see anything under high power!
○ Remember the steps, if you can't focus under scanning and
then low power, you won't be able to focus anything under
high power.
 4. Only half of my viewing field is lit, it looks like there's a half-
moon in there!
○ You probably don't have your objective fully clicked into place.