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Chapter 2
The Molecules of Cells
Pages 19-44
Matter
-a
substance that occupies
space and has ________;
- a substance composed of
_________
Atom
- the smallest unit of an _________
that possesses all the
characteristics of that element
- unit of an element that is not
easily divisible by ordinary
chemical means
Atom
• Composed of :
1 or more _________ (positive charge),
usually 1 or more neutrons (no charge),
and 1 or more __________
(negative charge)
Often the number of protons and electrons
are equal. The resulting atom has no net
charge.
similar to Fig. 2.2
____________
• a pure substance composed of only one kind
of atom
e.g. hydrogen (H), carbon (C), oxygen (O)
(See Blackboard for a list of chemical
symbols you should know.)
Different elements MUST have a different
number of protons in the nucleus
Isotope
• an atom of an element that differs in the
number of ____________ in the nucleus
e.g. Carbon 12 (12C) and Carbon 14 (14C)
both are carbon, must have 6 protons
12C has 6 protons and 6 neutrons
14C has 6 protons and 8 neutrons
____________ Isotope
• an unstable isotope; an atom that will
decay (change) into a different element
as subatomic particles are lost from the
nucleus
e.g.
14C
6p + 8n

14N
7p + 7n
+ 1e-
Ion
• an atom of an element that has gained
or lost one or more ___________
e.g. H+, Na+ - both have lost one
electron
Cl- - has gained one electron
outer electron is lost
_____________
• a substance composed of two or more
atoms; the atoms may be identical or
may be different elements (compound).
e.g.
water
H2O
glucose
C6H12O6
oxygen gas O2
Chemical Bond
• an attractive force between two atoms
• Three different types:
__________
______________
_____________
Ionic Bond
• the chemical bond that results from the
attractive force between two oppositely
charged _________
e.g. table salt
Na+- Cl-
Ionic bonds are not extremely strong.
Fig. 2.7
Covalent Bonds
• chemical bonds that result from two atoms
sharing one or more pairs of ____________;
produces a relatively strong bond
• Two types of covalent bonds:
Nonpolar covalent bond – the pair(s) of
electrons are shared equally
Polar covalent bond – the pair(s) of
electrons are not shared equally
Nonpolar covalent bond
Chlorine atoms share 1 pair of electrons
similar to Fig. 2.8
Polar covalent bonds
O and H do not share electrons equally
similar to Fig. 2.9
O and H have partial charges due
to polar covalent bonds
O
H
Pg. 26
H
_____________ Bond
• an attractive force between two atoms
with opposite partial charges
• The atoms are not ions, the partial
charges result from the atoms being
polar covalently bonded to some other
atom.
• weak bonds, but very important in
living systems
O forms hydrogen bonds with H
BETWEEN water molecules
Fig. 2.9
Properties of water
• very good __________ for polar substances
• water molecules are adhesive and cohesive
• takes a lot of energy to warm (high heat
capacity) or vaporize (high heat of
vaporization) water
• ice (solid water) is ________ dense than
liquid water
________________
- the substance is attracted to
water; will form H bonds with water;
contains some polar covalent bonds
________________
- the substance is repelled by
water; will not form H bonds with
water; contains mostly nonpolar
covalent bonds
Hydrophilic – e.g. glucose
O-H bond is polar covalent
A fatty acid – all the C-C and
C-H bonds are nonpolar covalent
see also
Fig. 2.20
Will this molecule form any H bonds
with water?
See page 110 in Chapt. 6
____________ – the loss of one or
more electrons from an atom or
molecule
_____________ – the gaining of
one or more electrons from an atom
or molecule
Usually linked; referred to as
oxidation/reduction (redox) reactions
Oxidation/reduction is important in
living systems because energy is
transferred from molecule to molecule
with the electrons.
Oxidation – loss of
e
and _______
Reduction – gaining of e- and
energy
NADox +
lower energy
e
+
+
H
 NADHre
higher energy
Acid
- a substance that releases _________
ions when placed in solution
e.g. HCl  H+ + Cl-
________
- a substance that combines with H+ or
releases OH- when placed in solution
e.g. HCO3- + H+  H2CO3
NaOH  Na+ + OH-
_____
- a measure of the hydrogen ion
concentration of a solution
- ranges from 0 to 14
0 – the most acidic, lots of H+ 14 –
the least acidic, very few H+
(most alkaline or basic)
7 – neutral, neither acidic or
basic
pH is the negative logarithm of
the hydrogen ion concentration
Based on logarithms, each whole number
change represents a 10-fold change in H+.
pH 6 is ______ more acidic than pH 7
Negative log is why larger pH numbers
represent lower acidity.
100 = 1
10-1 = 0.1
10-2 = 0.01
10-14 = 0.000,000,000,000,01
__________
- a substance, that within a certain range,
maintains a constant pH by combining
with H+ when mixed with an acid, or
releasing H+ when mixed with a base
- Buffers do not necessarily maintain a
pH of 7.
H2O + CO2  H2CO3  HCO3- + H+


Organic Chemistry
“Organic chemistry nowadays almost
drives me mad. To me it appears like a
primeval tropical forest full of the most
remarkable things, a dreadful endless
jungle into which one does not dare enter
for there seems to be no way out.”
Fredrich Wohler 1835
Organic Chemistry
- the study of ___________ containing
compounds
Organic molecule
- a molecule synthesized by living
organisms (no longer useful)
- a molecule containing 2 or more carbon
atoms (What about methane, CH4?)
- a molecule containing at least the
elements ________ and __________
Functional Groups
- parts of organic molecules
•
•
•
•
•
Hydroxyl group
Methyl group
Carboxyl (acidic) group
Amino group
Phosphate group
-OH
-CH3
-COOH
-NH2
-PO3
Can you identify the functional groups?
Can you identify the functional groups?
_____________, -COOH
Can you identify the functional groups?
__________, -CH3
Can you identify the functional groups?
_____________, -OH
Can you identify the functional groups?
______________, -PO3
Can you identify the functional groups?
__________, -NH2
Families of Organic Molecules
•
•
•
•
Carbohydrates
Lipids
Proteins
Nucleic Acids
Note – this list does not contain all the different
kinds of organic molecules
____________________
• Contain only C, H and O
• Lots of hydroxyl groups
• Three groups we’ll look at
Monosaccharides – simple sugars
Disaccharides – made from 2
simple sugars
Polysaccharides – polymers of
simple sugars
_____________
- a large molecule composed of
repeating subunits, monomers
e.g. polysaccharides, proteins,
DNA, plastics, etc.
Monosaccharides – simple sugars
• Contain only C, H, and O
• Ratio of these three elements is:
___C : ___H : ___O
• Lots of hydroxyl groups, -O-H
• Dissolve easily in water. Why?
e.g. glucose or fructose, C6H12O6
ribose, C5H10O5
_________________
• Composed of 2 simple sugars bonded
together
• C:H:O ratio not quite 1:2:1
e.g. sucrose, C12H22O11, made from
joining glucose and fructose, both
C6H12O6
Easily digested to simple sugars
Fig. 2.16
Dehydration aka
______________________
• Contain only C, H and O
• Ratio not 1C:2H:1O, but still contains
lots of O
• Size limits solubility in water
e.g. starch and cellulose are both
polysaccharides made from only glucose
starch – easily digested
cellulose – undigestible by most
organisms
similar to Fig. 2.17
similar to Fig. 2.19
__________
• Usually contain only C, H and O
• Ratio of C:H:O nowhere near 1:2:1
lots of C and H, relatively little O
• 4 types we’ll look at:
Fatty Acids
Glycerides
Phospholipids
Steroids
Fatty Acids
• Consist of a carboxyl group and a
____________________ chain
similar to Fig. 2.20
________________ Fatty Acids
• at least 2 H atoms bonded to each of the C
in the hydrocarbon chain
from Fig. 2.20
Common in animal fats; solid at room temperature
_________________ Fatty Acids
• One or more C atoms in the hydrocarbon chain
have less than 2 H atoms bonded to them.
from Fig. 2.20
Common in vegetable oils; liquid at room temp.
Trans fats - partially hydrogenated vegetable oils,
not typically made by living organisms
Glycerides
• Glycerol and 1, 2 or 3 ________ _____
(mono-, di-, or triglycerides)
How are they synthesized?
How do you digest them?
Dehydration
similar to Fig. 2.20
When did your great grandmother use hydrolysis of
triglycerides?
Will this molecule form any H bonds
with water?
Fig. 2.20
Is it hydrophilic or hydrophobic?
________________
• A diglyceride + phosphate group + R group
• Lipid end is hydrophobic
• Phosphate and R group end is hydrophilic
• Form the basic structure of all cell
membranes
similar to Fig. 2.21
Steroids
•
•
•
•
•
Non-fatty acid lipids
Contain only lots of C, H and little O
Behaves like other lipids
e.g. _________________
Absolutely necessary –
e.g. cell membranes, sex hormones
similar to
Fig. 2.22
Proteins
• Contain __________, in amino groups
• Made from long chains of amino
acids
• Very diverse group of molecules;
very diverse functions
• Shape is extremely important
Amino Acids
• An _________ group and a
____________ group bonded to
the same carbon atom
• Differ in the R group attached to
the central carbon atom
Amino Acids
• All proteins made from different
combinations of the same 20 amino
acids
• Humans have 8 (children 9)
_____________ amino acids –
must be present in diet
similar to Fig. 2.23
Polypeptide
• A small polymer of ______ _____;
part of a protein molecule.
• Peptide bonds – a covalent bond
between the carboxyl group of one
amino acid and the amino group of
the following amino acid.
• Synthesis? Digestion?
Dehydration
similar to
Fig. 2.24
_______________
• A change in the shape of a molecule.
• Shape is very important in organic
molecules, especially proteins.
e.g. frying an egg; sickle-cell anemia
_____________ _______
• An organic molecule composed of
long chains of nucleotides.
e.g. DNA, RNA
Nucleotides
• An organic molecule composed of:
1 or more phosphate groups,
a 5-carbon sugar,
and a _______________ base
similar to Fig. 2.26
Adenosine Triphosphate - ______
• A nucleotide involved in most of the
reactions in which energy is transferred
in living organisms
• Composed of Adenine (N-base), 5-C
sugar and three phosphate groups
similar to Fig. 2.27