Download (a) Electrons

Biochemistry
AP Biology
Mrs. Stahl
Intro. Video
• http://vimeo.com/83005599
A Chemical Connection to Biology
• Biology is the study of life
• Living organisms and their environments are
subject to basic laws of physics and chemistry
• One example is the use of formic acid by ants
to protect themselves against predators and
microbial parasites
Figure 2.1
Figure 2.1a
The Nature of Atoms
• Matter: Anything that has mass / takes up space.
• Atom: Small particles that make up matter.
• 1913- Niels Bohr and The Atomic Theory (electron
cloud and the model of the atom)
– Protons- positively charged
– Neutrons- neutral / no charge
– Electrons- negatively charged
– Nucleus- center where the protons and neutrons are
located.
– Electron Cloud- where the electrons roam.
Matter vs. Energy
Matter



Has mass & takes up
space
Affected by gravity
Consists of elements
and compounds
Energy





Moves matter
Potential, kinetic
Ability to do work
Conversions
Sound, light, heat
Elements and Compounds
• Matter is made up of elements
• An element is a substance that cannot be
broken down to other substances by chemical
reactions
• A compound is a substance consisting of two
or more elements in a fixed ratio
• A compound has characteristics different from
those of its elements
Figure 2.2
Sodium
Chlorine
Sodium chloride
The Elements of Life
• About 20–25% of the 92 elements are
essential to life (essential elements)
• Carbon, hydrogen, oxygen, and nitrogen make
up 96% of living matter
• Most of the remaining 4% consists of calcium,
phosphorus, potassium, and sulfur
• Six basic- CHONPS
• Trace elements are those required by an
organism in only minute quantities
An element’s properties depend on
the structure of its atoms
• Each element consists of unique
atoms
• An atom is the smallest unit of
matter that still retains the
properties of an element
Carbon
Hydrogen
Nitrogen
Major structural Major component Found in all
atom in all
of all organic
proteins and
organic molecules. molecules.
nucleic acids
Major nonliving
Key component in Most common
source is N2 in the
photosynthesis,
atom in the
atmosphere.
returned back to Universe.
Makes its way
the environment
into the food chain
through cellular
Enters biological via nitrogen fixing
respiration, and
systems largely
bacteria, which
decomposition.
bonded to oxygen convert it into a
in water.
usable form of N2
CO2 is the major
that can be used
nonliving source
Returned to the by producers and
of carbon in the
environment by passed on to
atmosphere.
decomposition
consumers in the
and water
food chain.
release.
Returned back to
the environment
through
decomposition and
denitrifying
bacteria (convert
nitrates in the soil
into atmospheric
nitrogen).
Oxygen
Phosphorus
Found in most
Found in all
organic molecules. nucleic acids
Sulfur
Found in all
proteins
Oxygen is in our
atmosphere, as
well as in our
water.
Major nonliving
source is found in
rocks.
Incorporated into
the food chain
through cellular
respiration and
returned back to
the environment
through
photosynthesis.
Used quickly to
store and release
free energy in
cells.
Decomposition
returns it back to
the environment.
Weathering
releases it back
into the soil, where
producers absorb
it and pass it
through the food
chain.
Decomposition
returns it back to
the environment.
Subatomic Particles
• Atoms are composed of subatomic
particles
• Relevant subatomic particles include
– Neutrons (no electrical charge)
– Protons (positive charge)
– Electrons (negative charge)
• Neutrons and protons form the
atomic nucleus
• Electrons form a cloud around the
nucleus
• Neutron mass and proton mass are
almost identical and are measured in
daltons. Also known as the atomic
mass.
Figure 2.4
Cloud of negative
charge (2 electrons)
Electrons
Nucleus
-
(a)
-
+
+
+
+
(b)
Atomic Number and Atomic Mass
• Atoms of the various elements differ in number
of subatomic particles
• An elements atomic number is the number of
protons in its nucleus. In a neutral atom it’s also
the number of electrons.
• An elements mass number is the sum of protons
plus neutrons in the nucleus
Figure 2.7a
2
Atomic number
He
4.003
Atomic mass
Element symbol
Electron
distribution
diagram
Helium
2He
Isotopes
• All atoms of an element have the same
number of protons but may differ in number
of neutrons
• Isotopes are two atoms of an element that
differ in number of neutrons
• Radioactive isotopes decay spontaneously,
giving off particles and energy
Radioactive Tracers
• Radioactive isotopes are often used as
diagnostic tools in medicine
• Radioactive tracers can be used to track atoms
through metabolism
• They can also be used in combination with
sophisticated imaging instruments
Figure 2.5
Cancerous
throat
tissue
Radiometric Dating
• The rate of decay = half-life, the time it takes for
one-half of the atoms in a sample to decay.
• In radiometric dating, scientists measure the ratio
of different isotopes and calculate how many halflives have passed since the fossil or rock was
formed.
• Half-life values vary from seconds or days to billions
of years.
Example- Carbon 14
• Carbon dating of fossils.
– Half-life of 5, 730 years
– A sample of carbon-14 today would contain .5 g of
carbon-14 after 5,730 years.
– .25 g after 11,460 years
– .125 g after 17,190 years
– Allows scientists to pinpoint when materials formed.
The Energy Levels of Electrons
• Energy is the capacity to cause change or the ability to
do work.
• Potential energy is the energy that matter has because
of its location or structure.
– Ex- grapefruit: If you hold a grapefruit in your hand, above
the ground= posses potential energy.
– If you drop the grapefruit and it falls, PE decreases.
– Carry it to the top of a building, PE increases.
• The electrons of an atom differ in their amounts of
potential energy
• An electrons state of potential energy is called its
energy level, or electron shell
Energy Levels
• Each one corresponds with a specific amount
of energy.
• Every atom has a ladder of potential energy
values.
• Electrons that are on different levels but the
same distance from the nucleus, have the
same energy.
(a) A ball bouncing down a flight
of stairs provides an analogy
for energy levels of electrons.
Third shell (highest energy
level in this model)
Second shell (next highest
energy level)
First shell (lowest energy
level)
Atomic
nucleus
(b)
Energy
absorbed
Energy
lost
Electron Distribution and Chemical
Properties
• The chemical behavior of an atom is determined by the
distribution of electrons in electron shells.
• We cannot pinpoint the location of any given electron
at any time. Electron could be anywhere.
• Orbital- area around the nucleus that contains only two
electrons.
• The periodic table of the elements shows the electron
distribution for each element.
• Oxidation- when electrons are transferred from one
atom to another.
• Reduction- the gain of an electron.
Figure 2.7
Hydrogen
1H
Atomic number
2
He
Atomic mass
First
shell
4.003
Helium
2He
Element symbol
Electron
distribution
diagram
Lithium
3Li
Beryllium
4Be
Boron
5B
Carbon
6C
Nitrogen
7N
Oxygen
8O
Fluorine
9F
Neon
10Ne
Sodium
11Na
Magnesium
12Mg
Aluminum
13Al
Silicon
14Si
Phosphorus
15P
Sulfur
16S
Chlorine
17Cl
Argon
18Ar
Second
shell
Third
shell
Figure 2.7a
2
Atomic number
He
4.003
Atomic mass
Element symbol
Electron
distribution
diagram
Helium
2He
Figure 2.7b
Hydrogen
1H
First
shell
Helium
2He
Lithium
1Li
Beryllium
4Be
Boron
5B
Carbon
6C
Second
shell
Sodium
11Na
Third
shell
Magnesium Aluminum
12Mg
13Al
Silicon
13Si
Nitrogen
7N
Oxygen
8O
Fluorine
9F
Neon
10Ne
Phosphorus
15P
Sulfur
16S
Chlorine
17Cl
Argon
18Ar
Second
shell
Third
shell
• Valence electrons are those in the
outermost shell, or valence shell
• The chemical behavior of an atom is
mostly determined by the valence
electrons.
• Elements with a full valence shell are
chemically inert (moving or acting
slowly or not at all).
• If the outer shell isn’t full, then the
element is reactive.
How does oxidation / reduction help
organisms?
• Organisms store their chemical energy in high
energy electrons that get transferred from
atom to atom, gaining and losing, in order for
internal reactions to occur.
• Used to burn sugars such as glucose, an fatty
acids in the fats we eat.
Chemical Bonds
• Molecule: group of atoms held
together by energy in a stable
association.
• Compound: molecule of more than
one element.
• Chemical bonds: opposites attract
and molecules come together.
Bonds and Interactions
Name
Basis of Interactions
Strength
Covalent Bond
Sharing pairs of electrons
Strongest Bond
Ionic Bond
Attraction of opposite
charges. NaCl = table salt
Hydrogen Bond
Sharing of H atom
Hydrophobic Interaction
Forcing of hydrophobic
portions of molecules
together in presence of
polar substances
Van der Waals forces
Weak attraction between
atoms due to oppositely
polarized electron clouds.
Weak
The Molecule That Supports All of Life
• Water is the biological medium on Earth. Oceans make up
71% of Earth.
• Water is the only common substance to exist in the natural
environment in all three physical states of matter.
• The structure of the water molecule allows it to interact with
other molecules and this was true in the beginning when
other molecules would around and interact.
• Water’s unique emergent properties help make Earth suitable
for life.
• Life began in the water for two billion years before moving
onto land.
• About 2/3 or 67% of our bodies are made up of water. Crucial
for adequate growth, development, and reproduction to
occur.
What is the difference between a
tropical rainforest biome and a desert
biome?
• Rainforests have the most biodiversity and
productivity on land because of the large
amount of rainfall.
• Deserts seem dead and lifeless, that is until
the rain comes.
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Polar covalent bonds in water
molecules result in hydrogen bonding
• In the water molecule, the electrons of the polar
covalent bonds spend more time near the oxygen
than the hydrogen.
• The water molecule is thus a polar molecule:
the overall charge is unevenly distributed. Oxygen is
partially negative and hydrogen is partially positive.
• Polarity allows water molecules to form hydrogen
bonds with each other.
• Although they are weak bonds, they are important in
DNA replication, protein structure, and the chemical
organization of living systems.
Figure 3.2
−
Hydrogen
bond
+
+
Polar covalent
bonds
−
−
+
+
−
Draw into
your
notes!
Hydrogen Bonds
• Can form between any hydrogen atom that is
covalently bonded to an atom that has a strong
attraction for electrons.
• Each water molecule can form a max of four
hydrogen bonds with four other water molecules.
• Single hydrogen bond is weaker than single
covalent / ionic bond.
• Groups of hydrogen bonds are very strong.
Water is the Universal Solvent
• Does the dissolving
• When an ionic compound is dissolved in water, each ion
is surrounded by a sphere of water molecules called a
hydration shell
• Solvent: substance present in the greatest amount
• Solute: substance present in lesser amounts
• Solution: a mixture of two or more substances
• Ex- Kool-aid, sugar, and water
– Solvent= water
– Solutes= sugar and Kool-aid
– Solution= all mixed together and the distribution is even
throughout
Figure 3.7
−
Na+
+
+
−
+
−
−
Na+
+
Cl−
Cl–
−
+
+
−
−
−
−
+
−
+
−
Figure 3.8
Water
soluble
protein
δ+
δ−
δ−
+
Properties of Water
•
•
•
•
•
•
Cohesion and Surface Tension
Adhesion and Capillary Action
High Specific Heat
High Heat of Vaporization
Capillary Action
Low Density of Ice
Cohesion
• When the polarity of water allows water
molecules to be attracted to each other.
• Hydrogen bonds the water molecules
together.
• Surface Tension- The molecules at the surface
are hydrogen bonded to molecules below
them.
• Example: Insects walking on water, drops of
water on a penny
Adhesion
• The attraction between different substances, for
example, between water and plant cell walls.
– Example- meniscus in a graduated cylinder or wet
microscope slides stick together
• Capillary Action- Movement of liquid through a
narrow passage. Allows transport of water against
gravity from roots to leaves.
– Ex- water moving up a straw, water moving up a plant
from the roots to the leaves.
BioFlix: Water Transport in Plants
Animation: Water Transport
Heat
• Kinetic Energy = energy of motion
• Heat= total amount of energy in a system
• Temperature= measure of the average kinetic
energy of molecules
• Calorie= the amount of heat needed to raise
the temperature of water by 1 C
High Specific Heat
• Hydrogen bonds absorb heat when they break
and release heat when they form, minimizing
temperature changes.
• Defined as: the amount of heat that must be
absorbed or lost for 1 g of that substance to
change its temperature by 1°C
• The specific heat of water is 1 cal/g/°C
• Water resists changing its temperature because
of its high specific heat. Takes longer to heat up
and longer to cool down.
• Crucial for maintaining homeostasis
• Water’s high specific heat can be traced to
hydrogen bonding
– Heat is absorbed when hydrogen bonds break
– Heat is released when hydrogen bonds form
Why do organisms have a high water
content?
• To maintain a constant internal temperature
• If we didn’t have a high water concentration
then the heat generated by the chemical
reactions inside our cells would destroy the
cells if the heat wasn’t absorbed by the water
inside them.
Heat of Evaporation
• Evaporation is transformation of a substance
from liquid to gas
• Heat of vaporization is the heat a liquid must
absorb for 1 g to be converted to gas
• As a liquid evaporates, its remaining surface
cools, a process called evaporative cooling
• Evaporative cooling of water helps stabilize
temperatures in organisms and bodies of water.
For example sweating releases excess water.
Videos
• http://www.youtube.com/watch?v=0eNSnj4Zf
Z8
• http://www.youtube.com/watch?v=WpXHpXK
Ztws
• http://www.youtube.com/watch?v=8O8PuMki
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Review of Acids & Bases
• http://www.bozemanscience.com/acidsbases-ph/