2. •Matter consists of chemical elements in pure form and in
combinations called compounds
•Organisms are composed of matter, which is anything
that takes up space and has mass
•Mass is the amount of matter in an object
•Weight is a measure of how strongly that mass is
pulled by gravity
•Matter is made up of elements, substances that cannot
be broken down to other substances by chemical
reactions
•A compound is a substance consisting of two or more
elements combined in a fixed ratio and has
characteristics different from those of its elements

3.  A compound
 Is a substance consisting of two or more elements
combined in a fixed ratio
 Has characteristics different from those of its
elements
+
Sodium Chloride Sodium Chloride

4. Essential elements
 Include
carbon, hydrogen, oxygen
, and nitrogen
 Make up 96% of living
matter
A few other elements
 Make up the remaining
4% of living matter

5.  The effects of essential element deficiencies
(a) Nitrogen deficiency (b) Iodine deficiency
Controlled experiment Enlarged Thyroid gland –
iodine is a trace element

6. Each element
 Consists of a certain kind of
atom that is different from those
of other elements
An atom
 Is the smallest unit of matter
that still retains the properties of
an element
Atoms of each element
 Are composed of even smaller
parts called subatomic particles

7.  Simplified models of an atom Neutrons, which
have no electrical
Cloud of negative Electrons charge
charge (2 electrons)
Protons, which are
Nucleus
positively charged
Electrons, which
are negatively
charged
(a) (b) In this even more simplified
This model represents the
electrons as a cloud of model, the electrons are
negative charge, as if we had shown as two small blue
taken many snapshots of the 2 spheres on a circle around the
electrons over time, with each nucleus.
dot representing an electron‘s
position at one point in time.

8.  The atomic number of an element
 Is the number of protons
 Is unique to each element
 Carbon has 6 protons, any atom with 6 protons is carbon
 The mass number of an element
 Is the sum of protons plus neutrons in the nucleus of an
atom
 Carbon can exist with 6, 7, or 8 neutrons – 12C, 13C, or 14C
 These are isotopes of carbon
 Is an approximation of the atomic mass of an atom

9.  Isotopes of a given element
 Differ in the number of neutrons in the atomic nucleus
 Have the same number of protons
 Radioactive isotopes
 Spontaneously give off particles and energy

10.  Can be used in biology
APPLICATION Scientists use radioactive isotopes to label certain chemical substances, creating
tracers that can be used to follow a metabolic process or locate the substance within an organism.
In this example, radioactive tracers are being used to determine the effect of temperature on the rate
at which cells make copies of their DNA.
TECHNIQUE
Ingredients including
Radioactive tracer Incubators
(bright blue)
Proliferation assay 10°C
1 2
15°C
3
20°C
Human cells
Ingredients for 4 5 6
25°C 30°C 35°C
1 making DNA are
added to human cells. One 7 8 9
ingredient is labeled with 3H, a 40°C 45°C 50°C
radioactive isotope of hydrogen. Nine dishes of cells
are incubated at different temperatures. The cells
make new DNA, incorporating the radioactive tracer
with 3H.
The cells are placed in test
2 tubes, their DNA is isolated, DNA (old and new)
and unused ingredients are
removed. 1 2 3 4 5 6 7 8 9

11. A solution called scintillation
fluid is added to the test tubes
3 and they are placed in a
scintillation counter. As the 3H
in the newly made DNA decays,
it emits radiation that excites
chemicals in the scintillation
fluid, causing them to give off
light. Flashes of light are
recorded by the scintillation
counter.
RESULTS The frequency of flashes, which is recorded as counts per minute, is
proportional to the amount of the radioactive tracer present, indicating the amount of new
DNA. In this experiment, when the counts per minute are plotted against temperature, it is
RESULTS
clear that temperature affects the rate of DNA synthesis—the most DNA was made at 35°C.
Optimum
Counts per minute
30 temperature
for DNA
(x 1,000)
20 synthesis
10
0
10 20 30 40 50
Figure 2.5 Temperature (°C)

12.  Glucose labeled with a radioactive isotope is
injected into the patient
 Chemically active areas can be seen on this PET
scan
Cancerous
throat
tissue

13.  Energy
 Is defined as the capacity to cause change
 Potential energy
 Is the energy that matter possesses because of its
location or structure
 The electrons of an atom
 Differ in the amounts of potential energy they possess
– because of their position

14.  Rows represent a new valence shell of electrons
 Valence shells have to be full before going to the next
level
 Maximum amount in valence shells: 2, 8, 8, 18, 18, 32
 Electrons like to be paired
 Groups S, D, P, and F
 Potassium: 1s12s22p63s23p64s1
 Energy Tree Spin rotation “Latice Energy”

15.  Columns represent similar chemical
characteristics
 Similar properties
 Similar chemical properties, melting point, boiling
point, freezing point, (ability to rust) oxidation etc.
 Copper, Silver, and gold are all in the same column
 What do they have in common?

16.  Energy levels
 Are represented by electron shells
These
Third energy level (shell)
electrons are
more likely to
Second energy level (shell) _
Energy
_ “do
absorbed something”
_
First energy level (shell)
Energy
+ lost
Atomic
nucleus

17.  The chemical behavior of an atom – what it does
 Is due to its electron configuration and distribution
 The periodic table of the elements
 Shows the electron distribution for all the elements
Hydrogen 2 Atomic number Helium
He 2He
1H 4.00 Element symbol
Atomic mass
First Electron-shell
shell diagram
Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon
3Li 4Be 3B 6C 7N 8O 9F 10Ne
Second
shell
Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine Argon
11Na 12Mg 13Al 14Si 15P 16S 17Cl 18Ar
Third
shell
Figure 2.8

18. Valence electrons
 1. Are those in the outermost, or valence shell
 2. Determine the chemical behavior of an atom

19.  Are the three-dimensional space where an electron is found
90% of the time
 Each electron shell
 Consists of a specific number of orbitals
Electron orbitals.
Each orbital holds
up to two electrons. x Y
Z
1s orbital 2s orbital Three 2p orbitals 1s, 2s, and 2p orbitals
Electron-shell diagrams.
Each shell is shown with
its maximum number of
electrons, grouped in pairs.
(a) First shell (b) Second shell (c) Neon, with two filled shells
(maximum (maximum (10 electrons)
2 electrons) 8 electrons)

20.  A covalent bond
 Is the sharing of a pair of valence electrons

21.  Formation of a covalent bond
Hydrogen atoms (2 H)
1 In each hydrogen
atom, the single electron
is held in its orbital by + +
its attraction to the
proton in the nucleus.
2 When two hydrogen
atoms approach each
other, the electron of
each atom is also + +
attracted to the proton
in the other nucleus.
3 The two electrons
become shared in a
covalent bond, + +
forming an H2
molecule. Hydrogen
molecule (H2)
Figure 2.10

22.  A molecule
 Consists of two or more atoms held together by
covalent bonds
 A single bond
 Is the sharing of one pair of valence electrons
 A double bond
 Is the sharing of two pairs of valence electrons

23. Name Electron- Structural Space-
(molecular shell formula filling
formula) diagram model
(a) Hydrogen (H2).
Two hydrogen H H
atoms can form a
single bond.
(b) Oxygen (O2).
Two oxygen atoms
share two pairs of O O
electrons to form
a double bond.
Figure 2.11 A, B

24.  Covalent bonding in compounds
Name Electron- Structural Space-
(molecular shell formula filling
formula) diagram model
(c) Water (H2O).
Two hydrogen
atoms and one O H
oxygen atom are
joined by covalent H
bonds to produce a
molecule of water.
(d) Methane (CH4).
Four hydrogen
atoms can satisfy H
the valence of
one carbon
atom, forming H C H
methane.
H
Figure 2.11 C, D

25.  Electronegativity
 Is the attraction of a particular kind of atom for the
electrons in a covalent bond
 The more electronegative an atom
 The more strongly it pulls shared electrons toward
itself
 In a nonpolar covalent bond
 The atoms have similar electronegativities
 Share the electron equally – carbon/hydrogen

26.  In a polar covalent bond
 The atoms have differing electronegativities
 Share the electrons unequally Oxygen, nitrogen,
and phosphorous
Because oxygen (O) is more electronegative than hydrogen (H),
shared electrons are pulled more toward oxygen.
have large nuclei
– which attract the
electrons strongly.
This results in a
partial negative
charge on the
oxygen and a
partial positive
O charge on
the hydrogens.
Figure 2.12 H H
+ +
H2O

27.  In some cases, atoms strip electrons away from their
bonding partners
 Electron transfer between two atoms creates ions
 Ions
 Are atoms with more or fewer electrons
than usual
 Are charged atoms
 An anion
 Is negatively charged ions
 A cation
 Is positively charged

28.  An ionic bond
 Is an attraction between anions and cations
1 The lone valence electron of a sodium 2 Each resulting ion has a completed
atom is transferred to join the 7 valence valence shell. An ionic bond can form
electrons of a chlorine atom. between the oppositely charged ions.
+ –
Na Cl Na Cl
Na+ Cl–
Sodium on Chloride ion
Na Cl
(an anion)
Chlorine atom (a cation)
Sodium atom
(an uncharged (an uncharged
Figure 2.13 atom) atom) Sodium chloride (NaCl)
In water (our bodies) these ionic bonds do not hold  so we
have ions (very important to cells)

29.  Ionic compounds
 Are often called salts, which may form crystals
Not called molecules
Na+
Cl–
Figure 2.14

30.  Several types of weak chemical bonds are important
in living systems (in aqueous environments)
 Ionic bonds
 Hydrogen bonds
 Van der Waals interactions
 Occur when transiently positive and negative regions of
molecules attract each other only when they are very close
 Hydrophobic interactions

31.  A hydrogen bond
 Forms when a hydrogen atom covalently bonded to
one electronegative atom is also attracted to another
electronegative atom
– +
Notice water Water H
is polar!
(H2O) O A hydrogen
bond results
These molecules
H
from the
attraction
are hydrophilic
Remember between the
 water-loving
+ partial positive
cells are in an –
charge on the
aqueous
hydrogen atom
of water and
So are ions.
Ammonia the partial
environment. (NH3) N negative charge
on the nitrogen
H H atom of
+ H + ammonia.
Figure 2.15
+

32. Sharing in covalent bond formation can be unequal (polar). Large atoms
like oxygen or nitrogen have large nuclei with powerful positive charges.
These nuclei tend to pull the electrons so that they spend more time
around the large nuclei (O), leaving the molecule with a partial negative
charge in that area and a partially positive charge
around the smaller nuclei (H).
These molecules are polar.
The weak attraction between
these partial charges is called
a hydrogen bond.
Water is a polar compound
and many of it’s important
qualities is due to it’s polarity
and it’s ability to form hydrogen bonds between water molecules
and between water and other molecules and ions.

33.  Several types of weak chemical bonds are important
in living systems (in aqueous environments)
 Ionic bonds
 Hydrogen bonds
 Van der Waals interactions
 Occur when transiently positive and negative regions of
molecules attract each other only when they are very close –
more to do with fit.
 Hydrophobic interactions

34. Non-polar

35. Hydrophobic interactions
The polypeptide
backbone is hydrophilic
water
but the hydrogen bonds
keep the backbone
internal,
with hydrophobic amino hydrophobic
acids facing out –
interacting with the fatty
acids of the membrane.
water

37.  Weak chemical bonds
 Determine and reinforce the shapes of large molecules
 Help molecules adhere to each other
 The precise shape of a molecule
 Is very important to its function in the living cell
 Is determined by the positions of its atoms’ valence
orbitals

38. This gives each molecule,
no matter how small or
large, a specific shape and
a characteristic chemical
nature. Space-filling Ball-and-stick Hybrid-orbital model
model model (with ball-and-stick
Unbonded
model superimposed)
Electron
pair
O O
H H H H
Water (H2O) 104.5°
H H
C C
H H H H
Methane (CH4) H H

39. Carbon Nitrogen
Hydrogen Sulfur
Molecular shape Oxygen
Natural
determines how endorphin
Morphine
biological molecules
recognize and
respond to one
another with
specificity
(a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds to
receptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match.
Natural
endorphin Morphine
Brain cell Endorphin
receptors
(b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell
recognize and can bind to both endorphin and morphine.

40. A Chemical reaction
 Is the making and breaking of chemical bonds
 Leads to changes in the composition of matter
Chemical equilibrium
 Is reached when the forward and reverse reaction rates
are equal
In the cell, enzymes make and break covalent bonds.
Only in rare cases can a covalent bond be broken
without an enzyme.

41.  Convert reactants to products
+
2 H2 + O2 2 H2O
Reactants Reaction Product
No change in
Chemical equilibrium -
concentration of
the forward and reverse reactants or
reaction rates are equal product.