Download Biol 1020 Ch. 2 Chemistry

Chapter 2: Chemistry (!)
In many ways, life can be viewed as a complicated
chemical reaction.
Modern models of how life works at all levels typically
have at least some aspect of chemistry as a major
component or underpinning.
Therefore….
You must understand chemistry to understand life (and
to pass this course)!
.
Chapter 2: Chemistry

Elements and Atoms

Describing Atomic Combinations

Chemical Bonds Hold Molecules
Together and Store Energy

Chemical Equations Describe
Chemical Reactions

Oxidation-Reduction Reactions (redox
reactions) Are Common in Biological
Systems
.
Chapter 2: Chemistry

Elements and Atoms

Describing Atomic Combinations

Chemical Bonds Hold Molecules
Together and Store Energy

Chemical Equations Describe
Chemical Reactions

Oxidation-Reduction Reactions (redox
reactions) Are Common in Biological
Systems
.
•
Describe the difference between the
terms “element” and “atom”.
•
What are chemical symbols, and what is
the periodic table?
•
Draw a model of a neutral atom with
atomic number 6 and atomic mass 12.
.
Elements and Atoms
http://serc.carleton.edu/images/usingdata/nasaimages/periodic-table.gif
.
Elements and Atoms
elements – substances that cannot be further broken down into
other substances (at least by ordinary chemical reactions)


every element has a chemical symbol (H for hydrogen, O for
oxygen, etc.); this is most familiar from the periodic table

there are 92 naturally occurring elements, from hydrogen up to
uranium
http://serc.carleton.edu/images/usingdata/nasaimages/periodic-table.gif
.
Elements and Atoms

O, C, H, N ~ 96% of living mass

Ca, P, K, S, Na, Cl, Mg, Fe - consistently present in
small amounts

several trace elements
.
Elements and Atoms
atom = smallest unit of an element


electron: little mass; -1

proton: ~1 mass unit; +1

neutron : ~1 mass unit

nucleus: protons and neutrons
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Elements and Atoms
atomic number = # of protons


periodic table arranged largely according to
atomic number
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Elements and Atoms
atomic mass ≈ protons + neutrons


isotopes:# of protons same, # of neutrons different
.
•
Describe the difference between the
terms “element” and “atom”.
•
What are chemical symbols, and what is
the periodic table?
•
Draw a model of a neutral atom with
atomic number 6 and atomic mass 12.
.
•
Draw a model of a neutral atom with
atomic number 6 and atomic mass 14.
•
Compare with the previous atom that
you drew and discuss isotopes.
.
Fig. 2.3
.
Elements and Atoms
atomic decay

alpha, beta, and/or gamma radiation


many uses and dangers

DNA mutations
decay rates are averages



used for measuring time
radioisotopes: most unstable isotopes
.
•
Draw a model of a neutral atom with
atomic number 6 and atomic mass 14.
•
Compare with the previous atom that
you drew and discuss isotopes.
.
•
What are electron orbitals?
•
What is the valence shell?
•
How does the valence shell relate to
chemical reactivity of an atom?
.
Elements and Atoms
electrons occupy orbitals


ATOMS: # of electrons = # of protons

orbitals: electrons energy levels, location probabilities

electron shell: orbitals with similar energies
.
Elements and Atoms
.
Elements and Atoms

valence shell: filled by highest-energy electrons

valence electrons involved in chemical interactions
“rule of eight”
.
•
What are electron orbitals?
•
What is the valence shell?
•
How does the valence shell relate to
chemical reactivity of an atom?
.
Chapter 2: Chemistry

Elements and Atoms

Describing Atomic Combinations

Chemical Bonds Hold Molecules
Together and Store Energy

Chemical Equations Describe
Chemical Reactions

Oxidation-Reduction Reactions (redox
reactions) Are Common in Biological
Systems
.
•
Draw a Venn diagram for the following
terms:
molecule
compound
•
Then place the following in the diagram:
O2
NaCl
H2O
.
Describing Atomic Combinations
molecule – has covalent bonds


one or more elements
examples: O2, H2O

smallest unit of a molecular substance

differs in properties from its elements
.
Describing Atomic Combinations
compound - two or more different elements combined


may just be ratios, not fixed numbers

differs in properties from its elements

may have ionic bonds
.
Describing Atomic Combinations
chemical formula - number of atoms of each element

molecular formula for molecules

examples: H2O, CO2, O2, C6H12O6
simplest ratio for ionic compounds (NaCl, etc.)

structural formula - arrangement of atoms

examples:


water
H─O─H

carbon dioxide
O═C═O

molecular oxygen
O═O
.
•
Draw a Venn diagram for the following
terms:
molecule
compound
•
Then place the following in the diagram:
O2
NaCl
H2O
.
•
Discuss moles, atomic mass units, and
Avogadro’s number.
•
Why use moles instead of just mass?
•
Discuss the water and glucose problem
(will be given in class).
.
Describing Atomic Combinations

molecular mass = sum of the atomic masses in molecule

mole: # molecules for gram amount to = atomic mass
Example:


water has molecular mass 1+1+16 = 18

mole of water has a mass of 18 g
mole is simply a conversion factor


Avogadro’s number, is 6.02 x 1023 atoms or molecules
.
•
Discuss moles, atomic mass units, and
Avogadro’s number.
•
Why use moles instead of just mass?
•
Discuss the water and glucose problem
(will be given in class).
.
Chapter 2: Chemistry

Elements and Atoms

Describing Atomic Combinations

Chemical Bonds Hold Molecules
Together and Store Energy

Chemical Equations Describe
Chemical Reactions

Oxidation-Reduction Reactions (redox
reactions) Are Common in Biological
Systems
.
•
What is a covalent bond?
•
What do polar and nonpolar mean for
covalent bonds?
•
Give an example of each.
.
Chemical Bonds Hold Molecules
Together and Store Energy

outermost shell (valence electrons) determine chemistry

filled shells: rule of 8
.
Chemical Bonds Hold Molecules
Together and Store Energy
chemical bonds are based on filling valence shells


reduced energy state

bond energy amount required to break bond
.
Chemical Bonds Hold Molecules
Together and Store Energy
strong chemical bonds


covalent bonds – electrons shared

ionic bonds – ions of opposite charge
.
Chemical Bonds Hold Molecules
Together and Store Energy
covalent bonds

electrons shared in pairs

1 pair is a single covalent bond

double and triple also possible

carbon forms four total
.
Chemical Bonds Hold Molecules
Together and Store Energy
covalent bonds

give definite shapes

spacial arrangements of
shared orbitals
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Chemical Bonds Hold Molecules
Together and Store Energy
covalent bonds

nonpolar: equal sharing

polar: unequal sharing

polar if one nucleus holds a
stronger attraction on the
electron pair

polar molecules have
regions with partial charges
.
•
What is a covalent bond?
•
What do polar and nonpolar mean for
covalent bonds?
•
Give an example of each.
.
•
What are ions?
•
What are cations and anions?
•
What is an ionic bond?
•
Give an example of an ionic bond.
.
Chemical Bonds Hold Molecules
Together and Store Energy
ionic bonds
ion: atom that has gained or lost at least one net
electron


cations - lost one or more; +charge

anions - gained one or more; -charge

–ide indicates an anion
polyatomic ions can also form


covalently bound atoms that lose or gain electrons or
protons

only polyatomic ions can lose or gain protons
.
Chemical Bonds Hold Molecules
Together and Store Energy
ionic bonds

ionic bond: cation/anion attraction

ionic compound: substance with ionic bonds
.
Chemical Bonds Hold Molecules
Together and Store Energy
ionic bonds

polar substances, such
as water, tend to
dissolve ionic
compounds

hydration –
surrounding ions with
the ends water
molecules with the
opposite (partial) charge
.
•
What are ions?
•
What are cations and anions?
•
What is an ionic bond?
•
Give an example of an ionic bond.
.
•
What are hydrogen bonds?
•
Draw an example.
.
Chemical Bonds Hold Molecules
Together and Store Energy
hydrogen bonds

d+ with d-

d+ charge is usually H

weak interaction
.
Chemical Bonds Hold Molecules
Together and Store Energy
hydrogen bonds
common and important in living things


water forms them

weak means relatively easy to manipulate

collectively, hydrogen bonds can be very strong – they hold
together the two strands of DNA, for example
.
•
What are hydrogen bonds?
•
Draw an example.
.
Chemical Bonds Hold Molecules
Together and Store Energy
In aqueous systems (such as living organisms), the
effective relative bond strengths are:
covalent bond > ionic bond > hydrogen bond
.
Chapter 2: Chemistry

Elements and Atoms

Describing Atomic Combinations

Chemical Bonds Hold Molecules
Together and Store Energy

Chemical Equations Describe
Chemical Reactions

Oxidation-Reduction Reactions (redox
reactions) Are Common in Biological
Systems
.
•
Discuss the chemical equations in the
notes and the terms there (reactant,
product, equilibrium).
.
Chemical Equations Describe
Chemical Reactions





Reactants are written on the left
Products are written on the right
an arrow (
) is used to show the direction the
reaction proceeds
C6H12O6 + 6 O2
6 CO2 + 6 H2O + Energy
double arrows (
) indicate equilibrium reactions
- i.e. reactions proceeding at simultaneously in both
directions
N2 + 3 H2
2 NH3
Sometimes, different lengths of double arrows are
used to indicate which direction is favored
CO2 + H2O
H2CO3
.
•
Discuss the chemical equations in the
notes and the terms there (reactant,
product, equilibrium).
.
Chapter 2: Chemistry

Elements and Atoms

Describing Atomic Combinations

Chemical Bonds Hold Molecules
Together and Store Energy

Chemical Equations Describe
Chemical Reactions

Oxidation-Reduction Reactions (redox
reactions) Are Common in Biological
Systems
.
•
What is a redox reaction, and how does
it relate to movement of electrons and
movement of energy?
•
What gets oxidized/reduced in the
following:
–
–
•
making NaCl
rusting iron
What gains/loses energy in each case?
.
.
Oxidation-Reduction Reactions Are Common
in Biological Systems
example: rusting

4 Fe + 3 O2

during the process iron atoms (Fe) become iron ions (Fe3+):
4 Fe

2 Fe2O3
4 Fe3+ + 12 e-
on the flip side, the oxygen atoms gain electrons
3 O2 + 12 e-
6 O2-
.
Oxidation-Reduction Reactions Are Common
in Biological Systems

oxygen is common oxidizing agent (hence “oxidation”)

redox in biological systems

very important in photosynthesis, respiration, more
electrons are less easily lost from molecules than from
atoms


molecules typically will lose the equivalent of a complete
hydrogen atom when oxidized (proton as well as electron)

counting charge changes alone is not sufficient – look for
movement of electrons , includes complete H equivalent
.
•
What is a redox reaction, and how does
it relate to movement of electrons and
movement of energy?
•
What gets oxidized/reduced in the
following:
–
–
•
making NaCl
rusting iron
What gains/loses energy in each case?
.