Chapter 2
CHEMISTRY
1
WHY is there a
CHEMISTRY chapter in
my Biology book?
• Structure and function of all living things are
governed by the laws of chemistry
• QUESTION: What examples can you give of how
chemistry is involved in biology?
• Understanding the basic principles of chemistry
will give you a better understanding of all living
things and how they function!
2
CHEMISTRY- The science of the composition,
structure, properties, and reactions of matter
• Matter
• is anything that has weight and takes up
space
• Elements
• are the basic building blocks of matter that
cannot be broken down by chemical means
• Atoms
• are the smallest units of an element that
retain the element’s physical and chemical
properties.
• These bond together to form molecules
3
Elements
• Pure substances than
cannot be broken down
into simpler substances
• Periodic Table categorizes
elements and shows
trends
• Currently, there are 118
elements, 92 which occur
naturally
4
Biologists love CHONPS most of all!
• 90% of the mass of living things are composed
of combinations of 4 elements: O,C, H, & N
• Throw in P and S and you can make almost
any combination of organic molecules!
– Carbs
– Lipids
– Nucleic acids
– Amino acids, proteins
5
Atoms
• Simplest part of an element that retains all
properties of that element
• Too small to see so we make up models to help us
understand the structure of atoms and predict how
they will act
• Subatomic particles:
• Neutrons have a neutral charge
• Protons are positively charged
• Neutrons and protons make up the nucleus
• Electrons are negatively charged and orbit
around the nucleus
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2.1 From atoms to molecules
Subatomic particles of atoms
Normally, #e = #p = #n
HOWEVER, some atoms of certain elements may have
“extra” neutrons in their nucleus…
…this will slightly change their atomic _________; they
are called ______________
2.1 From atoms to molecules
Isotopes
• Isotopes are atoms that Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
have the same atomic
number but a different
atomic mass because the
number of neutrons differ
larynx
• Examples: 14C/12C, 127I, 131I
thyroid gland
trachea
• Radioactive isotopes are
useful in dating old objects,
sterilizing food, imaging
body organs and tissues
through x-rays and killing
cancer cells
a.
• Types of radiation can be harmful
b.
by damaging cells and DNA
a: © Biomed Commun./Custom Medical Stock Photo; b(patient): Courtesy National Institutes of Health
and/or causing cancer
8
(NIH); b(brain scan): © Mazzlota et al./Photo Researchers, Inc.
Different elements are used in
medical contrast imaging
Iodine
Barium
9
2.1 From atoms to molecules
Molecules
• Most elements do not exist by
themselves in nature but rather
like to combine with other
elements
• “Molecules” are made of atoms
that are bonded together
• Can be made of the same atom or
different atoms
Compounds
• A molecule is formed when two or more atoms join together
chemically.
• Example, oxygen gas, O2
• A compound is a molecule that contains at least two different
elements. All compounds are molecules but not all molecules are
compounds.
• Ex: WATER. 2 H atoms + 1 O atom = 1 H2O molecule
• Chemical properties of compounds are often very different than the
elements alone (2 gases = liquid)
• “Chemical reactions”- chemical bonds can be broken, atoms can be
rearranged, and new chemical bonds are formed!
11
Types of Chemical Bonds
• Most bonding takes place because atoms are most
chemically stable when their outermost energy levels
are filled
• “Octet” rule
• Ex: Fluorine (7 outer e-)
• Covalent bonds:
– Strong bonds
– Shared electrons, simulate a full outer orbital
12
Ionic Bonds
•
•
•
•
Create ions
Na becomes (Na+) = loses eCl becomes (Cl-)= gains an eCreate electrical charges: when + and – charges
attract, ionic bonds are created
13
States of Matter
• SOLID: molecules are tightly linked; little movement and
definite shape
• LIQUID: molecules are less tightly linked; moves more freely
than solids; conforms to container
• GAS: molecules are usually not attracted to one another;
move very fast; fills the entire volume of a container
14
WATER
• Living things are 70-80% water by weight
• Most chemical rxns in living things take place
in aqueous environments (either inside or
outside the cells)
• Water is needed to dissolve and transport
nutrients, gases, etc. around us (blood, tissue
fluid, saliva, sweat, etc)
15
2.2 Water and living things
What are the properties of water?
• Liquid at room temperature
• Liquid water does not change temperature
quickly
• High heat of vaporization
• Frozen water is less dense than liquid water
• Molecules of water cling together, “cohesion”
and to other polar substances “adhesion”
• A good solvent for other polar (+/-) molecules
Water is a covalently bonded
molecule that is also POLAR
(has +, - regions)
• 2 Hydrogen atoms bond with an Oxygen atom at an
angle
• Region of the molecule where the O atom is located has a
slightly neg.(-) charge, while the regions of the molecule where
the two H+ atoms are have a slightly positive charge.
• Oxygen has a greater “custody” of the shared electrons
17
Hydrogen Bonds
• Hydrogen Bonds: negative part of the water molecule
(O) forms a bind with the positive charge of the H
atoms
– Relatively weak, singly, but rather strong collectively
– Cause H2O molecules to cling together & to other
substances!
18
Water’s polarity is responsible for
some of its unique properties:
Cohesion• Water molecules are attracted
(+/-) to other nearby water
molecules; bonds them
together
• Surface tension = cohesive
forces between water
molecules are strong enough
to act as if their was a "skin" in
the water surface
19
Water Properties
Adhesion• Water is attracted (+/-) to other substances.
• meniscus = adhesive forces between water
molecules and glass
20
Water Properties
• Water is very important in temperature
regulation - resists quick temperature changes
and maintains homeostasis!
• H2O has a very high specific heat- which
means it can absorb or lose a large amount of
heat energy before its temperature changes.
• Thus, water has a moderating effect on
temperatures (ex: body temp).
21
Water Properties
• Water is less dense as a solid
• As liquid water cools, it’s molecules slow
down and come closer together, until they
reach 4°C.
• Below 4°C (approaching 0°C) they stop
moving, and hydrogen bonds become fixed,
rigid, and push apart, opening up spaces
between the molecules
– This is why ice floats, frozen bottles and
pipes burst
22
Water is a almost-universal solvent
• Water is extremely important to all living
things, so the chemistry of living things
often involves the study of solutions
• The polar (+/-) nature of water makes it a
great solvent for other polar compounds to
dissolve in.
• Hydrophilic or hydrophobic?
• What types of substances mix well with
water?
23
Know your terms
• Solution: mixture in which
substances are uniformly
distributed in another
substance
– Solutions can be mixtures of
liquids, solids, or gases
• Solute:
• Solvent:
• Concentration [ ]:
measurement of the amount of
solute dissolved in a fixed amount
of solvent
• Saturated?
• Aqueous solutions:
24
2.2 Water and living things
Acids and bases
• Acids are substances that dissociate and release hydrogen
ions (H+)
• Ex:
HCl  H+ + Cl-
• Bases are substances that take up hydrogen atoms or release
hydroxide ions (OH-)
Ex:
NaOH  Na+ + OH-
Dissociation: molecules come apart when enough “pull” is exerted
• Pure water dissociates into H+ and OH- equally (hydrogen and
hydroxide)
H2O
H+ + OH-
Acids and Bases – the pH scale
• Acidity and Alkalinity is a measure of the relative amount of
OH- and H+ ions in a solution!
• pH= measure of how many H+ ions are in a solution
• Pure water has equal OH- and H+ ions in solution; pH of 7.0
• Acidic solutions have H+ > OH- ions
– pH is below 7.0
– Sour
• Basic solutions have H+ < OH- ions
– pH is above 7.0
– slippery and bitter
26
Working scale is between 0 and 14 with 7 being neutral
A pH below 7 is acidic and above 7 is basic
The concentration of ions between each whole number
is a factor of 10
Buffers
• …are chemical substances that neutralize small
amounts of either an acid or a base added to a
solution
• Most chemical rxn’s in living organisms are
controlled by pH, therefore...
• Buffers are very important for homeostasis.
– If blood pH drops below 7.0 (acidosis), it could be fatal
– If blood pH goes above 7.7 (alkalosis), it could be fatal
• If our blood did not contain a buffering system,
we would not be able to drink and eat
acidic/basic foods!
Bicarbonate
28
Organic Compounds
• All compounds discovered can be classified
into two broad categories: inorganic and
organic
• "Organic" =
• The compounds of life consist of primarily 6
elements: "CHONPS"
29
Chemistry of CARBON is the
chemistry of LIFE!
• Carbon forms the “backbone” (framework) of
all organic molecules
• C has four e- in its outermost energy level, but
needs 8 to fill it, so it readily forms covalent
bonds!
30
Carbon, the basis for life
• Carbon likes to bond, with other atoms and
with itself
• single bonds• double bonds• triple bonds31
Simple & Complex Molecules
• Molecules are often built up from smaller, simpler molecules:
MONOMERS
• Monomers bond together to produce: POLYMERS
• Large polymers are called: MACROMOLECULES
• Dehydration reaction – the removal of water that allows
subunits to link together into larger molecules
• Hydrolysis reaction – the addition of water that breaks larger
molecules into their subunits
32
There are Four Major Classes of Organic
Compounds:
CARBOHYDRATES (= ENERGY)
• - The most abundant organic compounds in nature
- C:H:O = approx. 1:2:1
Monosaccharides - simple sugars; "building blocks of all
carbs"
• C6H12O6
Three main monosaccharides:
• glucose- main source of energy for cells
• fructose- sugar in fruits and honey (the sweetest
monosaccharide)
• galactose- sugar in milk and yogurt
33
Carbohydrates, cont’d
Disaccharides - two
monosaccharides bonded
together by dehydration
rxn’s (form glycosidic bonds)
Examples:
• glucose + fructose = sucrose
(common table sugar)
•glucose + galactose = lactose
(major sugar in milk)
34
2.4 Carbohydrates
What are “complex” carbohydrates?
• Polysaccharides are made of
many carbon rings
• Cell stores energy it doesn’t
need by converting
monosaccharides into
disaccharides/polysaccharides
• Starch is the storage form in
plants
•
• Glycogen- is the storage form
in animals
– stored in liver and muscles- once
storage is full, glycogen turns to fat!
The Role of Enzymes in Starch Digestion
(Amylase)
• Monosaccharides- soluble in water & CAN pass through cell
membrane by diffusion
• Disaccharides- are soluble in water and CANNOT pass through
the cell membrane (too BIG!)
– when a cell needs energy, disaccharides are broken down into its
monomers by hydrolysis!
• Polysaccharides- are NOT soluble in water and CANNOT pass
through the cell membrane without a series of hydrolysis rxn’s!
36
2.5 Lipids
What are lipids?
• Molecules that do not dissolve in water
• Used as energy storage molecules, insulation,
cushion
• Found in cell membranes
• Found as fats and oils, waxes, phospholipids
and steroids
2.5 Lipids
How are fats and oils different?
• Fats
– Usually animal origin
– Solid at room temperature
– Function as long-term energy storage, insulation from heat
loss and cushion for organs
• Oils
• Usually plant origin
• Liquid at room temperature
2.5 Lipids
What is the structure of fats and oils?
• TRIGLYCERIDES: A glycerol molecule and 3 fatty acid
tails
2.5 Lipids
Understanding fats when reading a
nutrition label
• Recommendation for total
amount of fat for a 2,000
calorie diet is 65g
• Be sure to know how many
servings there are
• A % DV of 5% or less is low
and 20% or more is high
• Try to stay away from trans
fats
• Would you eat the food on
the right? Why or why not?
Trace elements: Are required by an organism in only minute quantities
Make up the remaining 4% of living matter
Table 2.1
• The effects of essential element deficiencies
Figure 2.3
(a) Nitrogen deficiency
(b) Iodine deficiency
2.5 Lipids
What is the structure of a
phospholipid?
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
• The structure is similar
to a triglyceride.
• One fatty acid is
replaced by a polar
phosphate group.
• Phospholipids are the
primary components of
cellular membranes.
polar
head
inside cell
nonpolar
tails
outside cell
a. Phospholipid structure
Figure 2.19 Structure of a phospholipid.
b. Membrane structure
2.5 Lipids
What are steroids?
• A lipid
• Structure is four fused
carbon rings
Important steroids:
Cholesterol, testosterone,
estrogen, progesterone,
cortisol
2.6 Proteins
What are proteins?
• Large and often complicated molecules
• Make up skin, muscles, pigments, antibodies,
hormones & enzymes
• Hundreds of thousands of different kinds in
each cell
• Mostly C,H,O, & N
• Composed of amino acid monomers (20 AA
groups in total)
• Can denature, change in shape, that causes
loss of function
2.6 Proteins
What do amino acids look like?
2.6 Proteins
What do the levels of organization
look like?
• Support: keratin (hairs, nails) , collagen (ligaments, tendons,
skin)
• Transport: channel proteins allow certain molecules through
cell membranes; hemoglobin transports oxygen (RBC)
• Defense: antibodies are protein made by WBC
• Hormones: regulate cell metabolism and growth (ex: insulin)
• Motion: muscle tissue made of contractile proteins (actin &
myosin)
• Enzymes: catalyze chemical reactions in cells
48
ENZYMES are important proteins
• Many chemical reactions in living cells (and organisms) are
regulated by ENZYMES
• Enzymes are globular proteins in living systems that mediate
metabolic reactions (make and break chemical bonds)
– Metabolism: the series of energy exchanges and chemical reactions
that occur in living systems (cells, organisms)
– catabolic activities = breakdown of larger molecules into smaller;
AB ==> A + B
– anabolic activities = synthesis of larger molecules from smaller ones;
A + B ==> AB
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2.7 Nucleic acids
What are nucleic acids?
• Made of nucleotide
subunits
• Function in the cell to
make proteins
• Directs traits and
behaviors
• Includes RNA and DNA
NUCLEIC ACIDS
• Nucleic acids are long chains (polymers)of
nucleotides
• Nucleotides are the monomers of nucleic acids
Each nucleotide includes a nitrogenous base, 5-C sugar, and
phosphate group
52
DNA: Deoxyribonucleic acid
• Contains genetic
information
• Composed of:
1) Deoxyribose sugar
2) Phosphate group
3) 4 different “base" groups:
Adenine, Guanine, Cytosine,
and Thymine
53
RNA: Ribonucleic acid
• Stores and transfers genetic information for
making proteins from nucleus to ribosomes
• Like DNA, RNA is composed of nucleotides:
1) Ribose sugar
2) Phosphate group
3) 4 different “base" groups: Adenine, Guanine,
Cytosine, and Uracil
• DNA IS DOUBLE STRANDED AND RNA IS
SINGLE STRANDED!
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Summary of the macromolecules