Transcript chemistry of living things

Unit One
Science Basics
&
Chemistry of Living Things
Science Basics
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The Scientific Method – a series of steps used
to learn new information about a specific
topic; usually consists of five steps
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1. State Problem
2. Formulate Hypothesis
3. Experiment
4. Analyze Results
5. Make Conclusion
Science Basics
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Hypothesis – educated guess (usually very
little previous knowledge on the topic)
Theory – statement/idea based on a large body
of supporting evidence
Scientific Law – accepted as fact by the
scientific community
The only way scientific thought is advanced is
through objective unbiased experimentation
Matter and the Elements
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Matter is anything that has mass and takes up
space
An Element is a pure form of matter that
cannot be broken down into a simpler form
An Atom is the smallest unit of any element
that still retains the physical and chemical
properties of said element
An atom consists of three subatomic particles:
Protons, Neutrons, and Electrons
More about the Atom
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At the center of an Atom is the Nucleus
The Nucleus contains both Protons and
Neutrons
Electrons orbit around the nucleus in
pathways that are not very well defined; they
are referred to as orbitals and/or shells
Protons are positive (+), Electrons are
negative (-), and Neutrons have no charge
More about the Atom
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Protons and Neutrons are much more massive
than Electrons
It can be stated that the mass of an Atom is due
almost entirely to the presence of Protons and
Neutrons (the mass of Electrons is negligible)
Due to the above fact, Atomic Mass/Mass
Number takes into account the mass of Protons
and Neutrons
Atomic Number is the total number of Protons
in an Atom
The Periodic Table of the Elements
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A systematic chart used to assist in the study of
chemical reactions between Atoms and
Molecules
Initially developed by Mendeleev (Russian) in
the late 1800’s; his chart organized Elements by
Atomic Mass
http://www.aip.org/history/curie/periodic.htm
It was later determined the best way to organize
Elements was via Atomic Number
More on the Periodic Table
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Each Element has a Shorthand Representation that
consists of either one or two letters:
Sulfur
S
Neon
Ne
A row is called a Period and a column is called a
Group
Elements are listed from left to right by ascending
Atomic Number
There are three categories of elements: Metal,
Metalloid, & Nonmetal
http://www.chemicalelements.com/
Basic Chemistry
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How an atom interacts with other atoms is determined
by the electrons; therefore, the chemical behavior of
the atom is due to the actions of the electrons
All atoms seek to be chemically stable by attempting
to obtain 8 electrons in their outer shell called the
Valence Shell
Those “pathways” mentioned earlier are areas in
which the electrons travel while orbiting the nucleus.
The pathways are often referred to as Orbitals
In order for an atom to achieve the desired chemical
stability it will attempt to either gain or lose electrons
from the orbitals of the valence shell
Helium
Carbon
Basic Chemistry
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The orbitals in which electrons are commonly
found are the “S”, “P”, “D”, and “F”
The S orbital can have up to 2 electrons
The P orbital can have up to 6 electrons
The D orbital can have up to 10 electrons
The F orbital can have up to 14 electrons
Ions
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Atoms in which the number of electrons does not
equal the number of protons are Ions
If an atom has fewer electrons than protons it is
positively charged (the + protons outnumber the
– electrons); these are called Cations
If an atom has more electrons than protons it is
negatively charged (the –electrons outnumber the
+ protons); these are called Anions
He+ (cation), Cl- (anion)
Isotopes
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Atoms of an element that have different
numbers of neutrons are called Isotopes
Isotopes of an atom of a specific element have
the same atomic number (# of protons) but
different mass number (protons + neutrons)
Radioactive Isotopes are used in medicine to
detect and treat cancer, and they are used to
determine the approximate age of fossils
Molecules
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A Molecule is a group of atoms held together
by the energy of interacting electrons
There are 2 categories of bonds that electrons
form when interacting with eachother:
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Ionic Bonds – unequal sharing of eCovalent Bonds – equal sharing of e
Because covalent bonds involve the sharing of
electrons, single, double, and triple bonds exist in
order to optimize the presence of the electrons in an
attempt to fill the valence shell of each atom
Molecules
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The atoms of most inorganic (nonliving)
substances form ionic bonds, whereas, the atoms
of most organic (living) substances form
covalent bonds
Examples of elements which are commonly
found in organic substances are: Carbon,
Hydrogen, Oxygen, Nitrogen, and Phosphorus
Examples of elements which are commonly
found in inorganic substances are: Aluminum,
Chlorine, Lead, Silver, and Gold
Molecules
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Hydrogen bonds are weak chemical bonds
that play a special role in biology
Two key properties of hydrogen bonds cause
them to play an important role in biological
molecules: they are weak, and as a result of
their weakness, they are highly directional
The bottom line is that hydrogen bonds
stabilize the shapes of many important
biological molecules
Water and Hydrogen Bonds
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Polar molecules other than water are called
Hydrophilic because they are attracted to the
hydrogen bonds of water
Nonpolar molecules are called Hydrophobic
because they are repelled by the hydrogen
bonds of water
If polar molecules dissolve in water they are
Soluble
Water Formulas
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The Chemical Formula for water is H2O
The Structural Formula for water is:
Ionization of Water
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Water can be broken apart into two ions:
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H+ and OHH+ is a Hydrogen Cation
OH- is a Hydroxide Anion
H+ equals acidic
OH- equals basic
The way to measure the acidity or basidity of a
substance is by using the pH scale
pH Scale – “Percentage of Hydrogen”
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The scale ranges from 0 to 14
O to 6.9 is acidic, with 1 and 2 being very acidic
7 is neutral (neither acidic or basic)
7.1 to 14 is basic, with 13 and 14 being very
basic
Again, if there are many hydroxide anions (OH-)
in solution, then the solution is basic
If there are many hydrogen cations (H+) in
solution, then the solution is acidic
pH Scale
pH Scale and Buffers
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In order to change the pH of a solution, a buffer
can be added
A buffer is a solution of known pH that can lower
or raise the pH of the solution in question
Buffers do the above by either absorbing or
releasing H+ cations into solution
Buffers are important in that they keep solutions
from becoming too acidic or too basic; buffers
keep solutions’ pH in an acceptable range
Monomers and Polymers
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Organic Molecule – a molecule formed by
living organisms that consist of a carbon
backbone with other elements bonded to it
All four categories of macromolecules, which are
organic, are made from monomers that combine
to form polymers
Macromolecules – very large molecules that are
necessary for the maintenance of the structure
and function of the cell
Monomer – a subunit or “train car” that when
connected to others forms a polymer or “train”
Monomers and Polymers
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Polymer – a large molecule composed of many
subunits (“train cars”)
All four categories of macromolecules connect
their monomers (subunits) in the same way:
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“Dehydration Synthesis” – making polymers from
monomers
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OH group is removed from one subunit and an H group is
removed from the other subunit
Both the OH and H groups together compose water (H2O);
this is why this process is called “Dehydration”
An enzyme (protein) is used to facilitate this reaction
Monomers and Polymers
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To breakdown a polymer the opposite of
Dehydration Synthesis occurs and is called
“Hydrolysis”
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Hydrolysis – reducing a polymer to its monomer
parts
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An OH and H group are added to opposite sides of a
subunit , therefore causing the polymer to be broken
into its monomer parts
Proteins
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Monomer = Amino Acid
Polymer = Protein
20 common amino acids which differ by their
functional group
Amino Acids are linked by “Peptide Bonds”
(a type of covalent bond), and are formed via
Dehydration Synthesis
Long chains of amino acids linked by Peptide
Bonds are called “Polypeptides”
Proteins
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The way in which proteins function is
determined by the shape of the protein, which in
turn, is determined by what monomers bond with
each other
There are four levels of protein structure that
determine functionality:
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Primary – long chain
Secondary – long chain folds
Tertiary – long chain folds and twists
Quaternary – more than one polypeptide chain
Proteins
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Proteins can only function in a specific range in
reference to temperature and pH
If the temperature is too high, or the environment is
too acidic (low pH), then the protein unfolds and no
longer functions = “Denatured”
Proteins are extremely important because they
serve as the “local government”: they ensure the
proper function of the cell
Tertiary Proteins are Enzymes
Enzymes act as catalysts, which govern cellular
reactions
Proteins
Nucleic Acids
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Monomer = Nucleotide
Polymer = Nucleic Acid (RNA & DNA)
The 5 Carbon Sugars of each Nucleotide are
linked by Phosphate Groups to form
Polynucleotide Chains = RNA and DNA
RNA is found in viruses, and both RNA and
DNA are found in other species
RNA is single-stranded
DNA is double-stranded
Nucleic Acids
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Polynucleotide Chains (RNA and DNA)
function is essentially that of a library:
these macromolecules possess all the
information necessary to both form an
individual and maintain that individual
throughout life
Nucleic Acids
Carbohydrates
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Monomer = Simple Carbohydrate
Polymer = Complex Carbohydrate
Carbohydrates purpose is to serve as an energy
supply for cells, and in some cases
(polysaccharides), to serve as a structural support
to organelles in cells
Simple Carbohydrates
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Monosaccharides – one monomer/subunit, Glucose is an
example C6H12O6
Disaccharides – two monomers/subunits linked together
via dehydration reaction, Lactose is an example
Carbohydrates
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Complex Carbohydrates
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Polysaccharides – long polymer chains; Starch,
Glycogen, Chitin, and Cellulose
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Starch (plants) and Glycogen (animals) are storage
macromolecules for energy when energy is not
immediately needed by the organism’s cells
Cellulose (plants) and Chitin (animals) are
carbohydrate macromolecules that assist with
structural support of organelles within the organism’s
cells
Carbohydrates
“Glucose”
Lipids
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Monomer = Fatty Acids and Glycerol
Polymer = Lipid or “Triglyceride”
Lipids are “Fats”
They are not soluble in water because of the
chemistry of their structure
They are soluble in oil
Lipids are composed primarily of Carbon and
Hydrogen atoms bonded to each other
Lipids
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Saturated Fat – each carbon is bonded to as
many hydrogen atoms as is possible
Unsaturated Fat – not every carbon is bonded
to all hydrogens as is possbile, and therefore,
double and triple bonds form between carbon
atoms
Lipids serve as long term energy storage for
cells, and also serve as the primary component
of all cells plasma membrane (barrier to
outside world)
Lipids