Download - Review basic molecular chemistry and organic chemistry in preparation for a course in genetics
Non-water part of living
things are 98% CHNOPS
• Carbon
• Hydrogen
• Oxygen
• Nitrogen
• Phosphorus
• Sulfur
An atom is made up of protons and neutrons located in a central nucleus
• The nucleus is surrounded by electrons
In an uncharged atom, the number of electrons equals the number of protons.
Electrons are arranged in shells. The outermost shell determines the chemical
properties of an atom. In most atoms, a full outer shell can hold eight
electrons.
• Atoms whose shells are not full tend to interactwith other atoms and gain, lose, or shareelectrons
Figure 2.6
HYDROGEN (H)
Atomic number = 1
CARBON (C)
Atomic number = 6
NITROGEN (N)
Atomic number = 7
OXYGEN (O)
Atomic number = 8
Electron
Outermost electron shell (can hold 8 electrons)
First electron shell (can hold 2 electrons)
Element Symbol Atomic
number
Electrons to
share = number
of covalent
bonds
Molecule formed
with hydrogen
Hydrogen H 1
Oxygen O 8
Nitrogen N 7
Carbon C 6
Element Symbol Atomic
number
Electrons to
share = number
of covalent
bonds
Molecule formed
with hydrogen
Hydrogen H 1 1
Oxygen O 8
Nitrogen N 7
Carbon C 6
Element Symbol Atomic
number
Electrons to
share = number
of covalent
bonds
Molecule formed
with hydrogen
Hydrogen H 1 1 H2 H H
Hydrogen
molecule
Oxygen O 8
Nitrogen N 7
Carbon C 6
• Atoms whose shells are not full tend to interactwith other atoms and gain, lose, or shareelectrons
Figure 2.6
HYDROGEN (H)
Atomic number = 1
CARBON (C)
Atomic number = 6
NITROGEN (N)
Atomic number = 7
OXYGEN (O)
Atomic number = 8
Electron
Outermost electron shell (can hold 8 electrons)
First electron shell (can hold 2 electrons)
Element Symbol Atomic
number
Electrons to
share = number
of covalent
bonds
Molecule formed
with hydrogen
Hydrogen H 1 1 H2 H H
Hydrogen
molecule
Oxygen O 8 1, 2, 3,
4, or 5 ?
Nitrogen N 7
Carbon C 6
Clicker question How many bonds does oxygen form?
Element Symbol Atomic
number
Electrons to
share = number
of covalent
bonds
Molecule formed
with hydrogen
Hydrogen H 1 1 H2 H H
Hydrogen
molecule
Oxygen O 8 2
Nitrogen N 7
Carbon C 6
Element Symbol Atomic
number
Electrons to
share = number
of covalent
bonds
Molecule formed
with hydrogen
Hydrogen H 1 1 H2 H H
Hydrogen
molecule
Oxygen O 8 2 H20 H H
water O
Nitrogen N 7
Carbon C 6
• Atoms whose shells are not full tend to interactwith other atoms and gain, lose, or shareelectrons
Figure 2.6
HYDROGEN (H)
Atomic number = 1
CARBON (C)
Atomic number = 6
NITROGEN (N)
Atomic number = 7
OXYGEN (O)
Atomic number = 8
Electron
Outermost electron shell (can hold 8 electrons)
First electron shell (can hold 2 electrons)
Element Symbol Atomic
number
Electrons to
share = number
of covalent
bonds
Molecule formed
with hydrogen
Hydrogen H 1 1 H2 H H
Hydrogen
molecule
Oxygen O 8 2 H20 H H
water O
Nitrogen N 7 1, 2, 3,
4, or 5?
Carbon C 6
Clicker question How many bonds does nitrogen form?
Element Symbol Atomic
number
Electrons to
share = number
of covalent
bonds
Molecule formed
with hydrogen
Hydrogen H 1 1 H2 H H
Hydrogen
molecule
Oxygen O 8 2 H20 H H
water O
Nitrogen N 7 3
Carbon C 6
Element Symbol Atomic
number
Electrons to
share = number
of covalent
bonds
Molecule formed
with hydrogen
Hydrogen H 1 1 H2 H H
Hydrogen
molecule
Oxygen O 8 2 H20 H H
water O
Nitrogen N 7 3 H
NH3 N H
Ammonia H
Carbon C 6
• Atoms whose shells are not full tend to interactwith other atoms and gain, lose, or shareelectrons
Figure 2.6
HYDROGEN (H)
Atomic number = 1
CARBON (C)
Atomic number = 6
NITROGEN (N)
Atomic number = 7
OXYGEN (O)
Atomic number = 8
Electron
Outermost electron shell (can hold 8 electrons)
First electron shell (can hold 2 electrons)
Element Symbol Atomic
number
Electrons to
share = number
of covalent
bonds
Molecule formed
with hydrogen
Hydrogen H 1 1 H2 H H
Hydrogen
molecule
Oxygen O 8 2 H20 H H
water O
Nitrogen N 7 3 H
NH3 N H
Ammonia H
Carbon C 6 1, 2, 3,
4, or 5?
Clicker question How many bonds does carbon form?
Element Symbol Atomic
number
Electrons to
share = number
of covalent
bonds
Molecule formed
with hydrogen
Hydrogen H 1 1 H2 H H
Hydrogen
molecule
Oxygen O 8 2 H20 H H
water O
Nitrogen N 7 3 H
NH3 N H
Ammonia H
Carbon C 6 4
Element Symbol Atomic
number
Electrons to
share = number
of covalent
bonds
Molecule formed
with hydrogen
Hydrogen H 1 1 H2 H H
Hydrogen
molecule
Oxygen O 8 2 H20 H H
water O
Nitrogen N 7 3 H
NH3 N H
Ammonia H
Carbon C 6 4 CH4 H
Methane H C H
H
• Atoms in a covalently bonded molecule mayshare electrons equally, creating a nonpolarmolecule
• If electrons are shared unequally, a polarmolecule is created
• In a water molecule, oxygen exerts a strongerpull on the shared electrons than hydrogen
–This makes the oxygenend of the moleculeslightly negativelycharged
–The hydrogen end ofthe molecule isslightly positivelycharged
–Water is therefore apolar molecule
(Ğ) (Ğ)
(+)(+)
• The charged regionson water moleculesare attracted to theoppositely chargedregions on nearbymolecules
–This attractionforms weak bondscalled hydrogenbonds
Hydrogen bond
Consequences of water’s
H bonding
• Surface tension
• Capillary action
• High specific heat
• Takes much energy to melt and to
evaporate
• Ice floats Simple parts, new qualities - emergent
properties.
• Molecules in ice are farther apart than those inliquid water
Hydrogen bond Hydrogen bond
LIQUID WATER
Hydrogen bonds constantly
break and re-form
ICE
Hydrogen bonds are stable
Carbon bonds to other carbons
H H
H C C H
H H
H H H
H C C C H
H H H
Propane C3H8
Ethane C2H6
H H H H H H H
H C C C C C C C H
H H H H H H H
And much longer chains
Ethylene C2H4
Carbon can make double bonds
C C
H
H H
H
H C C H
Acetylene C2H2
=Ethyne
Carbon can make triple bonds
Ways of depicting propane
H H H
H C C C H
H H H
C C C
“Carbon backbone”
Assumes the correct number of
hydrogens are attached.
C3H8
Chemical formula
Gives no structural information.
CH3-CH2-CH3
Isomers: Same formula, different structure
H H H H
H C C C C H
H H H H
Butane
C4H10 C C C C
Isobutane
C4H10
C C C
C
C
C C C
Isobutane,
other views,
rotated or
bent differently.
C
C C
C
How many pentane isomers?
Pentane: C5H12
Bigger molecules, many possible isomers
A. 2
B. 3
C. 4
D. 5
E. 6
Clicker question
There are three pentane isomers, C5H12
c-c-c-c-c
c c-c-c-c
c c-c-c
c
c-c-c-c c
c c-c-c
c
c c
c-c-c
c c-c-c-c
c-c c c
c
Not
C5H10
1.
2.
3.
=
= = =
A chiral molecule has 2 mirror images
These are called stereoisomers or
enantiomers Same formula and same structure,
but like right and left hands.