Adv an ced

Bio lo g y
Chemistry
Cla ssific atio n o f
Ma tter
 Elements
 pure substances made of only one type of atom
 Compounds
 pure substances made of two or more different
elements

Elements Compounds
Oxygen Dihydrogen oxide (H2O)
Sodium Sodium chloride (NaCl)
Lead Lead nitrate

2.1
 ???

 Turn to your neighbor

 Name four other elements

 Try to make two compounds from them
Em ergent Pr opertie s

Sodium Chloride Sodium Chloride

When elements are combined to form compounds new

properties are exhibited
Com mon Organi c
Elem en ts
 Carbon, hydrogen,
oxygen, and nitrogen
are essential
elements

 They make up 96% of

living matter

 The remaining
elements may are
also essential to life,
but in small quantity
2.2
De fic ie ncie s in
esse ntia l ele ments
Normal crop Abnormal growth

Goiter

Nitrogen deficiency Iodine deficiency

Deficiencies can lead to abnormal growth or disease

Cla ssic At omic Mo del

Electron Energy Levels

2.3
Ele ctron En ergy L eve ls
 Electrons move very fast in energy levels
called orbitals
 The orbitals represent the area where an
electron is most likely to be at a given moment

S orbital P orbitals D orbitals

2.3
 At omic Co mposit ion
Protons Neutrons Electrons

Location Nucleus Nucleus Electron orbital

Charge Positive (+) Neutral (0) Negative (-)

Mass 1 dalton 1 dalton 0.0005 daltons

1 dalton = 1 amu = 1.7 x 10-24 g

2.4
Th e Pe rio dic Ta ble

Atomic number

238
Chemical symbol U
92

Chemical name

Atomic Mass

2.4
Th e Pe rio dic Ta ble
 Atomic number = the number of protons

Because protons and neutrons have a

mass of 1 dalton...
 Mass number = the number of protons plus
neutrons

 Atomic mass = the average of all the

mass numbers for an element
2.4/2.5
 Ca lc ula tin g P/N /e
 Protons = atomic #
 Neutrons = mass # – atomic #
 Electrons = atomic # in a neutral atom

1. Atomic # = 92 = protons

238 P N e
U
92
3. Mass # = 238
92 146 92
5. Neutrons = 238-92

7. Electrons = protons = 92 2.5

 ???
 Find P/N/e for the following elements
P/N/e
 Fe 26/30/26

N 7/7/7
-1
 Cl 17/18/18

+1
 Na 11/12/10
Iso topes
 Isotopes have the same number of protons and
electrons, but different numbers of neutrons

 Some isotopes spontaneously give off energy

(radioactivity)

Isotopes of Carbon

12 14
6 C 6 C
2.6
Usin g i soto pes i n
rese arch
 Radioactive tracers
 The radioisotope are used to replace normal atoms
in a molecule
 The radioisotopes can then be traced using a
scintillation counter
 Radiocarbon dating
 Over time carbon 12 decays into carbon 14. The
amount of carbon 14 present in a fossil is a relative
estimate of its age.
 Useful up to ~50,000 years
2.7
Usin g Radioactiv e T racers
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.

Ingredients including
TECHNIQUE Radioactive tracer
(bright blue) Incubators
Ingredients for 1 2 3
1 making DNA are 10°C 15°C 20°C
added to human cells. One Human cells
4 5 6
ingredient is labeled with 3H, a 25°C 30°C 35°C
radioactive isotope of hydrogen. Nine dishes of cells
7 8 9
are incubated at different temperatures. The cells 40°C 45°C 50°C
make new DNA, incorporating the radioactive tracer
with 3H.

2 The cells are placed in test DNA (old and new)

tubes, their DNA is isolated,
and unused ingredients are 1 2 3 4 5 6 7 8 9
removed.
2.7
 3 A solution called scintillation fluid is
added to the test tubes 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 clear that temperature affects the rate of
DNA synthesis—the most DNA was made at 35°C.

Optimum
30 temperature
Counts per minute

for DNA
synthesis
(x 1,000)

20

10

0
10 20 30 40 50
Temperature (°C)
2.7
Usin g Radioactiv e T racers

 Bone scans use

technetium as a
radioactive tracer
 It concentrates in
areas of high blood
flow and inflammation

98

Post. Ant.
43 Tc
Metastatic Bone Carcinoma 2.7
 Ele ctrons a nd e nergy

Third energy level • Electrons closer to

the nucleus are held
Energy
Second energy level absorbed
tightly
• They have less
potential for motion
First energy level
as a result
Energy • The further from the
lost nucleus the more
Nucleus potential energy
electrons have

ENERGY = MOTION 2.8

 ???

 When light is emitted (such as turning on

a light bulb) electrons change energy
levels

 Do the electrons move toward the

nucleus or away from it?
Va le nce electrons

 Valence electrons
 Are those in the outermost, or valence shell
 Determine the chemical behavior of an atom

2.9
 Ele ctron Sh ell
Dia grams
Helium
Hydrogen 2 Atomic number
2He
He
1H
Atomic mass 4.00 Element symbol
First Electron-shell
2 e’s shell diagram

Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon

3Li 4Be 3B 6C 7N 8O 9F 10Ne

Second
8 e’s shell

Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine Argon

11Na 12Mg 13Al 14Si 15P 16S 17Cl 18Ar

Third
18 e’s shell

2.10
 Val ence El ectr ons and
Chem ical Propert ies

 Atoms need full outer energy levels to be

stable (8 electrons)
 Atoms form bonds to fill their outer
energy levels
 Atoms with the same number of valence
electrons have similar bonding properties

2.9
Lewi s ( electron) Dot
Formu la s

 Show the atom’s H

chemical symbol
 Show the atom’s C
valence electrons as
dots
O

H O H
 ???

 Draw Lewis Dot Structures for:

N F

H 2O Cl 2
Co va le nt Bo nds

 Formed when two atoms share a pair of

electrons
 Electrons are shared so that each atom
has a full outer energy level
Formati on of a coval ent 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. Representing Covalent
Bonds

3 The two electrons H H Lewis Dot Structure

become shared in a
covalent bond, + +
forming an H2 H H Structural Formula
molecule.
Hydrogen
molecule (H2)
 Single and double bonds
Name Electron- Structural Space-
(molecular shell formula filling
formula) diagram model

Hydrogen (H2).
Two hydrogen
H H
atoms can form a
single bond.

Oxygen (O2).
Two oxygen atoms
share two pairs of O O
electrons to form
a double bond.

•Single bond - the sharing of one pair of valence electrons

•Double bond - the sharing of two pairs of valence electrons

Co va le nt c ompounds
Name Electron- Structural Space-
(molecular shell formula filling
formula) diagram model

Water (H2O).
Two hydrogen
atoms and one O H
oxygen atom are
joined by covalent H
bonds to produce a
molecule of water.

Methane (CH4).
Four hydrogen
atoms can satisfy H
the valence of
one carbon
H C H
atom, forming
methane.
H
 Po la r v s. No n-p olar
 Electronegativity
 Is the attraction of an atom for the electrons in a
covalent bond
 The more electronegative an atom
 The more strongly it pulls shared electrons
toward itself
 In a Non-polar Covalent Bond
 The atoms have similar electronegativities
 Share the electron equally
2.11
Highly e le ctronegat ive
at oms
 Fluorine
 Oxygen
 Chlorine
 Nitrogen
Po la r Co va le nt Bonds
 In a polar covalent bond
 The atoms have differing electronegativities
 Electrons are shared unequally
Because oxygen (O) is more electronegative than hydrogen (H),
shared electrons are pulled more toward oxygen.
δ–

This results in a
partial negative
charge on the
oxygen and a
partial positive
O charge on
the hydrogens.

H H
δ+ δ+
H2O 2.11
Weak Bo nds
 Hydrogen bonds
 Form when a hydrogen atom bonded to one
electronegative atom is attracted to another
electronegative atom δ– δ+

Water H
(H2O) O A hydrogen
bond results
from the
H attraction
between the
δ+ partial positive
charge on the
δ–
hydrogen atom
of water and
Ammonia the partial
(NH3) N negative charge
on the nitrogen
H H atom of
δ+ H δ+ ammonia.

2.13
δ+
Weak Bo nds
 Van der Waals interactions
 Occur when temporarily positive and negative
regions of molecules attract each other

The gecko’s “spiderman” grip is due to Van der Waals attractions

2.13
Weak b onds are
esse ntia l
 Weak chemical bonds
 Reinforce the shapes of large molecules
 Help molecules adhere to each other

2.13
Ionic Bonds
 Electron transfer between two atoms
creates ions
 Ions
 Are atoms with more or fewer electrons
than usual Cl
-1

 Are charged atoms

 An anion
 Is negatively charged ions
 A cation
 Is positively charged
2.12
Ionic Bonds
 An ionic bond
 Is an attraction between anions and cations
2 Each resulting ion has a completed
1 The lone valence electron of a sodium
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–
Na Cl
Sodium on Chloride ion
Sodium atom Chlorine atom
(an uncharged (an uncharged (a cation) (an anion)
atom) atom)

Sodium chloride (NaCl)

2.12
Mo lecula r shape and
function
 The precise shape of a molecule
 Is usually very important to its function in the
living cell
 Determines how biological molecules
recognize and respond to one another with
specificity

2.15
Mo lecula r shape and
function Carbon Nitrogen

Natural Hydrogen Sulfur

endorphin Oxygen

Structures of endorphin Morphine

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
Binding to endorphin
endorphin Morphine
receptors
Endorphin receptors on the
surface of a brain cell
recognize and can bind to
both endorphin and Endorphin
morphine. Brain cell
receptors
2.15
Th e Formatio n of
Bo nds w ith Ca rbon
 Carbon has four valence electrons
 This allows it to form four covalent bonds
with a variety of atoms

2.16
The bondin g ve rsati lit y of
carbon
 Carbon forms many diverse molecules

Name and Molecular Structural Ball-and- Space-

Comments Formula Formula Stick Model Filling
Model
H
(a) Methane CH4 H C H
H

H H
(b) Ethane
C2H6 H C C H
H H

(c) Ethene H H
C2H4 C C
(ethylene) H H

2.16
 Versa til ity of Carbon
 The electron configuration of carbon
 Gives it covalent compatibility with many
different elements
Hydrogen Oxygen Nitrogen Carbon
(valence = 1) (valence = 2) (valence = 3) (valence = 4)

H O N C

2.16
Car bon S kele ton Var iation

 Carbon chains
 Form the skeletons of most organic molecules
 Vary in length and shape
H H H H H
(a) Length H C C H H C C C H
H H H H H
Ethane Propane
H
H C H
H H H H H H
(b) Branching H C C C C H H C C C H
H H H H H H H
Butane Isobutane
H H H H H H
H H
(c) Double bonds H C C C C H H C C C C H
H H H H
1-Butene 2-Butene
H H H
H C H
(d) Rings H C C H H C C H
H H C
H C C H
C C C
2.16
Cyclohexane Benzene
Functional Gr oups
 Functional groups OH
CH3
Estradiol
 Are the chemically
reactive groups of
atoms within an HO
organic molecule
Female lion

OH
 Give organic Testosterone CH3

molecules distinctive CH3

chemical properties
O

Male lion

2.17
 Functional Gr oups
FUNCTIONAL HYDROXYL CARBONYL CARBOXYL
GROUP
O
C
OH O OH

(may be written HO) C

NAME OF
Alcohols Ketones or Aldehydes Carboxylic Acids
COMPOUNDS

EXAMPLES
H H H O H O
H C C OH H C C H C C
H OH
H H H C H
Ethanol, the alcohol H
present in alcoholic H Acetic acid, which gives
beverages vinegar its sour tatste
Acetone, the simplest 2.17
ketone
 Functional Gr oups
FUNCTIONAL
GROUP AMINO SULFHYDRYL PHOSPHATE

H O
N
O P OH
H SH OH
(may be written HS)

NAME OF
Amines Thiols Organic Phosphates
COMPOUNDS

EXAMPLES O H H H H OH OH H O

C C N H C C SH H C C C O P O−

HO H H H H H O−
H H

Glycine Ethanethiol Glycerol phosphate

2.17