Transcript Chapter 2

Chapter 2
THE MOLECULES OF
CELLS
PAGES 18-44
Matter
A SUB STA N C E THA T
O C C UP I ES SP A C E A N D HA S
M A SS;
- A S UB STA N C E C O M P O SED O F
A TO M S
-
Atom
- THE SMALLEST UNIT OF AN
ELEMENT
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 protons (positive charge),
usually 1 or more neutrons (no charge),
and 1 or more electrons
(negative charge)
Often the number of protons and electrons are
equal. The resulting atom has no net charge.
Fig. 2.2
Element
 a pure substance composed of only one kind
of atom
e.g. hydrogen (H), carbon (C), oxygen (O)
(See 1114 webpage 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
neutrons 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
Radioactive 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
+ 1e7p + 7n
Ion
 an atom of an element that has gained or lost one or
more electrons
e.g. H+, Na+ - both have lost one electron
Cl- - has gained one electron
Molecule
 a substance composed of two or more atoms; the
atoms may be identical or may be different elements.
e.g. water
H2O
glucose
C6H12O6
oxygen gas O2
Chemical Bond
 an attractive force between two atoms
 Three different types:
Ionic
Covalent
Hydrogen
Ionic Bond
 the chemical bond that results from the attractive
force between two oppositely charged ions
e.g. table salt
Na+ - Cl-
Ionic bonds are not extremely strong.
Covalent Bonds
 chemical bonds that result from two atoms
sharing one or more pairs of electrons;
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
Fig. 2.6
Polar covalent bonds
O and H do not share electrons equally
FIG.
2.6
O and H have partial charges due to polar
covalent bonds
Pg. 26
Hydrogen 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. 2.8
Hydrophilic
- the substance is attracted to
water; will form H bonds with water;
contains some polar covalent bonds
Hydrophobic
- 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
Fig. 2.17
A fatty acid – all the C-C and
C-H bonds are nonpolar covalent
Fig. 2.22
WILL THIS MOLECULE FORM
ANY H BONDS WITH WATER?
Oxidation – the loss of one or more
electrons from an atom or molecule
Reduction – the gaining of one or
more electrons from an atom or
molecule
Usually linked; referred to as
oxidation/reduction reactions
Oxidation/reduction is important
in living systems because energy
is transferred from molecule to
molecule with the electrons.
Oxidation – loss of e- and energy
Reduction – gaining of e- and
energy
NADox + e- + H+  NADHre
lower energy
higher energy
Acid
- a substance that releases hydrogen
ions when placed in solution
e.g. HCl  H+ + ClBase
- a substance that combines with H+
when placed in solution
e.g. HCO3- + H+  H2CO3
pH
- 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 10X more acidic than pH 7
Negative log is why larger numbers represent
lower acidity.
100 = 1
10-1 = 0.1
10-2 = 0.01
10-14 = 0.000,000,000,000,01
Buffer
- 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 carbon 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 carbon and hydrogen
Functional Groups
- parts of organic molecules
 Hydroxyl group
 Methyl group
 Carboxyl (acidic) group
 Amino group
 Phosphate group
-OH
-CH3
-COOH
-NH2
-PO3
Families of Organic Molecules
 Carbohydrates
 Lipids
 Proteins
 Nucleic Acids
Carbohydrates
 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
Polymer
- 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:
1C : 2H : 1O
 Lots of hydroxyl groups, -O-H
 Dissolve easily in water. Why?
e.g.
glucose or fructose, C6H12O6
ribose, C5H10O5
Disaccharides
 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
Polysaccharides
 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
Lipids
 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 hydrocarbon
chain
Fig. 2.22
Saturated Fatty Acids
 at least 2 H atoms bonded to each of the C in the
hydrocarbon chain
Fig.
2.22 in animal fats; solid at room temperature
Common
Unsaturated Fatty Acids
 One or more C atoms in the hydrocarbon chain
have less than 2 H atoms bonded to them.
Fig.
2.22 in vegetable oils; liquid at room temp.
Common
Glycerides
 Glycerol and 1, 2 or 3 fatty acids
(mono-, di-, or triglycerides)
How are they synthesized?
How do you digest them?
Phospholipids
 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
Steroids
 Non-fatty acid lipids
 Contain only lots of C, H and little
O
 Behaves like other lipids
 e.g. cholesterol
 Absolutely necessary –
e.g. cell membranes, sex
Proteins
 Contain nitrogen, 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 amino group and a carboxyl
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)
essential amino acids – must be
present in diet
Polypeptide
 A small polymer of amino acids;
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?
Denaturation
 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
Nucleic Acids
 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 nitrogenous base
Adenosine Triphosphate - ATP
 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