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Biochemistry Basics
Chapters 2 and 3
Subatomic Particles and the Atom
• Protons (+ charge) and
neutrons (neutral)
– found in the nucleus
• Electrons (- charge)
– Surround the nucleus in
a “cloud” or orbital
• Orbital
– the 3D space where an
electron is found 90% of
the time
– Each orbital can only fit
only 2 electrons
Isotopes
• Different forms of the same
element
• Have the same number of
protons, but different number
of neutrons
• May be radioactive
spontaneously giving off
particles and energy
Radioactive Decay and Half-Life
• The decay of radioactive elements
occurs at a fixed rate.
• The half-life of a radioisotope is the
time required for one half of the
amount of unstable material to
degrade into a more stable material.
• For example, a source will have an
intensity of 100% when new. At one
half-life, its intensity will be cut to
50% of the original intensity…. Etc.
• The half-life pattern is the same for
every radioisotope, the length of a
half-life is different. For example, Co60 has a half-life of about 5 years
while Ir-192 has a half-life of about
74 days.
• May be used to:
– date fossils
– as medical tracers
– to follow a
metabolic process
or locate a
substance within
an organism
APPLICATION
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.
TECHNIQUE
1
2
Ingredients including
Radioactive tracer
Incubators
(bright blue)
1
2
10°C
3
15°C
20°C
Ingredients for
Human cells
4
making DNA are
25°C
added to human cells. One
ingredient is labeled with 3H, a
7
40°C
radioactive isotope of hydrogen. Nine dishes of
cells are incubated at different temperatures. The
cells make new DNA, incorporating the radioactive
tracer with 3H.
The cells are placed in test
tubes, their DNA is isolated,
and unused ingredients are
removed.
5
6
30°C
35°C
8
9
45°C
50°C
DNA (old and new)
1 2 3
4
5 6
7
8 9
6
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
Figure 2.5
Counts per minute
(x 1,000)
The frequency of flashes, which is recorded as counts per minute, is proportional to
RESULTS
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.
30
20
Optimum
temperature
for DNA
synthesis
10
0
10
20 30 40 50
Temperature (°C)
7
Energy Levels
Third energy level (shell)
Second energy level (shell)
Energy
absorbed
First energy level (shell)
Energy
lost
Atomic
nucleus
Electrons have
more potential
energy the farther
they are from the
nucleus.
(b)
Figure 2.7B
An electron can move from one level to another only if the energy
it gains or loses is exactly equal to the difference in energy between
the two levels. Arrows indicate some of the step-wise changes in
potential energy that are possible.
8
Bonding – Covalent Bonds
Hydrogen atoms (2 H)
• Atoms bond
through
interaction of their
valence (outer
orbital) electrons
• Covalent bond
– electrons are
shared between
atoms and the
valence orbitals
overlap
In each hydrogen
atom, the single electron
is held in its orbital by
its attraction to the
proton in the nucleus.
1
When two hydrogen
atoms approach each
other, the electron of
each atom is also
attracted to the proton
in the other nucleus.
2
3
The two electrons
become shared in a
covalent bond,
forming an H2
molecule.
+
+
+
+
+
+
Hydrogen
molecule (H2)
Name
(molecular
formula)
Water (H2O).
Two hydrogen
atoms and one
oxygen atom are
joined by covalent
bonds to produce a
molecule of water.
Methane (CH4).
Four hydrogen
atoms can satisfy
the valence of
one carbon
atom, forming
methane.
Electronshell
diagram
Structural
formula
O
H
H
H
H
C
H
H
Spacefilling
model
Polarity
• Electronegativity
– Is the attraction of an atom
for electrons
• The more electronegative
an atom
– The more strongly it pulls
electrons toward itself
•
Because oxygen (O) is more electronegative than hydrogen (H),
shared electrons are pulled more toward oxygen.
This results in a
partial negative
charge on the
oxygen and a
partial positive
charge on
the hydrogens.
d–
O
d+
H
H
H2O
d+
Ionic Bonds
The lone valence electron of a sodium
atom is transferred to join the 7 valence
electrons of a chlorine atom.
Na
Na
Sodium atom
(an uncharged
atom)
Cl
Cl
Chlorine atom
(an uncharged
atom)
Each resulting ion has a completed
valence shell. An ionic bond can form
between the oppositely charged ions.
+
–
Na
Cl
Na+
Sodium on
(a cation)
Cl–
Chloride ion
(an anion)
Sodium chloride (NaCl)
• Covalent bonds are stronger than ionic bonds
• Covalent and Ionic bonds are intramolecular
forces of attraction because they are within
molecules
Intermolecular Forces
• intermolecular forces of attraction exist
between molecules
• Van der Waals Interactions
– Forms when atoms and molecules are
very close together
– Occurs because electrons are in
constant motion and may accumulate
by chance on one part of the molecule.
The result is “hot spots” of positive and
negative charge.
– very weak
• hydrogen bonds
– form when the slightly negative O or N that is
bonded to a slightly positive H is attracted to the
slightly positive H of a neighbouring molecule
– strongest intermolecular forces
Water
(H2O)
d –O
Hd +
H
d+
d–
N
Ammonia
(NH3)
H
d+
Figure 2.15
H
H
d+
A hydrogen
bond results
from the
attraction
between the
partial positive
charge on the
hydrogen atom
of water and
the partial
negative charge
on the nitrogen
atom of
ammonia.
Morphine affects
pain perception
and emotional
state by
mimicking the
brain’s natural
endorphins
Carbon
Nitrogen
Hydrogen
Sulfur
Oxygen
Natural
endorphin
Morphine
(a) Structures of endorphin 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
endorphin
Brain cell
Figure 2.17
Morphine
Endorphin
receptors
(b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell
recognize and can bind to both endorphin and morphine.
18
Bicarbonate Buffer System
When excess hydrogen ions are added to the reaction is shifted to the left. This means
that some of the added hydrogen ions will react with the bicarbonate ions to produce
carbonic acid and the carbonic acid will dissociate into carbon dioxide and water as
shown below.
When hydrogen ions are removed from the reaction, the reaction will shift to the
right. More carbon dioxide will combine with water and more carbonic acid will be
produced and more hydrogen ions and bicarbonate ions will be produced.
Water
• highly polar because of asymmetrical shape
and polar covalent bonds
• The polarity of water molecules results in
hydrogen boding
d–
Hydrogen
bonds
+
+
d–
+
Figure 3.2
d–
+
d–
Surface Tension: A
force that occurs at
the surface of the
water so it behaves
as if there is a film on
top.
Cohesion: Water
molecules are attracted
to one another (between
O and H of neighbouring
molecules) so water
evaporating from leaves
of a plant will pull up
other water molecules
Density: Water is
most dense at 4C,
which is less dense
than water. Aquatic
life can survive
throughout the winter
Universal
Solvent: able to
dissolve many
polar substances
(e.g. salt, sugar,
etc.)
High heat of
vaporization: In
order for water to
reach a gaseous
state, it must
absorb a great
deal of heat from
surroundings
Adhesion:
water
molecules are
attracted to
other
molecules (e.g.
nutrients)
High Specific Heat
Capacity: the amount of
heat required to raise the
temperature of a
substance by 1C. It takes
a lot of energy to increase
or decrease temperature.
Large bodies of water
moderate the
temperature on land.
“Like Dissolves Like”
• ionic compounds dissolve in water because
the ions separate
• Hydration shell
• However, molecules do not need to be ionic to
dissolve in water
• polar covalent molecules (eg: sugars, alcohols)
can dissolve in water, but large nonpolar
molecules (eg: oils) do not
• small nonpolar molecules (eg: O2, CO2) are
slightly soluble and need soluble protein
molecules to carry them (eg: hemoglobin
transports oxygen through the blood)
• hydrophilic – “water-loving;” dissolves in
water
– e.g. polar or ionic molecules, carbohydrates, salts
• hydrophobic – “water-fearing;” does not
dissolve in water
– e.g. non-polar molecules, lipids
Acids and Bases
• acid – donates H+ to water; pH 0-7
• base –donates OH- to water (or H3O); pH 7-14
• neutralization reaction – the reaction of an
acid and a base to produce water and a salt
(ionic compound)
Strong and Weak Acids/Bases
• strong acids and bases – ionize completely
when dissolved in water
– HCl(aq) (100% H3O+(aq))
– NaOH(aq) (100% OH-(aq))
• weak acids and bases – ionize only partially
when dissolved in water
– CH3COOH(aq) (1.3%  H3O+(aq))
– NH3(aq) (10%  OH-(aq))
Functional Groups
• Functional groups are
the parts of molecules
involved in chemical
reactions
• They Are the chemically
reactive groups of atoms
within an organic
molecule
• Give organic molecules
distinctive chemical
properties
Estradiol
HO
Female lion
OH
CH3
CH3
O
Figure 4.9
OH
CH3
Testosterone
Male lion
27
• Six functional groups are important in the
chemistry of life
– Hydroxyl
– Carbonyl
– Carboxyl
– Amino
– Sulfhydryl
– Phosphate
28
Some important functional groups of organic
compounds
FUNCTIONAL
GROUP
HYDROXYL
CARBONYL
CARBOXYL
O
OH
(may be written HO
C
C
OH
)
STRUCTURE In a hydroxyl group (—OH),
a hydrogen atom is bonded
to an oxygen atom, which in
turn is bonded to the carbon
skeleton of the organic
molecule. (Do not confuse
this functional group with the
hydroxide ion, OH–.)
O
The carbonyl group
( CO) consists of a
carbon atom joined to
an oxygen atom by a
double bond.
When an oxygen atom is doublebonded to a carbon atom that is
also bonded to a hydroxyl group,
the entire assembly of atoms is
called a carboxyl group (—
COOH).
29
Names of Compounds
HYDROXYL
NAME OF
COMPOUNDS
CARBONYL
Alcohols (their specific
names usually end in -ol)
CARBOXYL
Ketones if the carbonyl group is Carboxylic acids, or organic
within a carbon skeleton
acids
Aldehydes if the carbonyl group
is at the end of the carbon
skeleton
EXAMPLE
H
H
H
C
C
H
H
H
OH
H
C
H
C
H
H
Ethanol, the alcohol
H
O
C
H
C
OH
H
present in alcoholic
beverages
H
Acetone, the simplest ketone
H
Figure 4.10
C
O
H
H
C
C
H
H
Acetic acid, which gives vinegar
its sour tatste
O
C
H
Propanal, an aldehyde
30
Functional Groups
AMINO
SULFHYDRYL
H
N
PHOSPHATE
(may be written HS
H
The amino group (—NH2)
consists of a nitrogen atom
bonded to two hydrogen
atoms and to the carbon
skeleton.
Figure 4.10
O
SH
)
O P OH
OH
The sulfhydryl group
consists of a sulfur atom
bonded to an atom of
hydrogen; resembles a
hydroxyl group in shape.
In a phosphate group, a
phosphorus atom is bonded to four
oxygen atoms; one oxygen is
bonded to the carbon skeleton; two
oxygens carry negative charges;
abbreviated P . The phosphate
group (—OPO32–) is an ionized
form of a phosphoric acid group (—
OPO3H2; note the two hydrogens).
31
Chemical Properties of Functional
Groups
• Functional groups possess certain chemical properties that they
impart to the molecules to which they are attached.
Hydroxyl  Polar – hydrophilic
– Water molecules are attracted to hydroxyl group, dissolves in
water (e.g. sugars have hydroxyl groups)
δ-
δ+
Carboxyl  Polar – hydrophilic
– Carboxyl group is a source of hydrogen ions (H+) and therefore
makes the molecule acidic
32
• Amino
– Act as a base, picking up protons (H+) from the surrounding
solution
• Sulfhydryl  Help stabilize structures of proteins
• Phosphate  Transfer of energy between organic molecules
(ATP)
33
Test your Knowledge
1. Identify the functional groups in the following molecules.
G3P
Aspartame
Aspirin
2. Which of the above molecules are soluble in water?
Explain.
3. Which of the above molecules can act as a base? an
acid? Explain.
4. Explain the significance of one of the functional groups
on G3P.