Biochemistry:
 How do you calculate number of protons, neutrons, and electrons using
atomic number and atomic mass?
o Number of protons are equal to the atomic number
o Number of electrons are equal to the atomic number in a neutral atom
o Number of neutrons are equal to the atomic mass minus the atomic
number
 How protons, neutrons and electrons affect the atom
o Number of neutrons can affect the mass of an atom – if an atom exists
with differing number of neutrons, then there are isotopes of that atom
o Number of protons is what identifies the atom; if there are more protons
than electrons, then the atom has become a positively charged ion
o Number of electrons, particularly the valence electrons (electrons in the
outer energy level) affect how an atom will form bonds with other
atoms. Atoms want to be stable, and having a full outer energy level is
what makes them stable. Atoms can gain/lose electrons or share
electrons to form bonds with other atoms to become stable. If an atom
has more electrons than protons, then it has become a negatively
charged ion.
 What are isotopes?
o Atoms that differ in their atomic mass because they differ in the number
of neutrons.
 Chemical bonds – ionic v. covalent v. hydrogen
o Ionic bonds are formed when atoms gain or lose electrons, becoming
positively or negatively charged ions that are attracted to one another.
o Covalent bonds are formed when atoms share electrons
o Hydrogen bonds are formed between adjacent molecules, such as
between water molecules. The hydrogen on one molecule is attracted to
a negatively charged atom on an adjacent molecule. This often happens
due to polarity (molecules having charged ends)
o Hydrogen bonds form between adjacent water molecules, between the
hydrogen on one molecule, and the negatively charged atom on an
adjacent molecule. See the dotted lines below.
o Hydrogen bonds can form between the hydrogen on one molecule and a
negatively charged atom on ANY other kind of molecule – not just
water.
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Why do atoms in ionic bonds have unequal numbers of
electrons/protons?
o In an uncharged atom, the number of protons (+ charged) and electrons
(- charged) are equal. In the process of forming an ionic bond, electrons
are gained/lost, resulting in an unequal number of protons and
electrons, resulting in charges to the atom (they become ions)
Which molecules are covalently bonded
o You don’t need to know this
What are compounds and how are they formed?
o Compounds are formed when atoms of different elements are bonded
together
Acids and bases
o Acids are solutions that have a greater percentage of hydrogen ions
than they have hydroxide ions. They have a pH lower than 7.
o Bases are solutions that have a greater percentage of hydroxide ions
than they have hydrogen ions. They have a pH greater than 7.
o Solutions that are neutral have equal amounts of hydrogen and
hydroxide ions.
How is water a polar substance
o Water is a molecule that is covalently bonded within, however due to
the difference in size between the hydrogen atoms and oxygen atoms,
the ends of the molecule have slight charges to it. The electrons spend
more time rotating around the oxygen atom, giving it a slight negative
charge due to the negative charge on electrons. The hydrogen ends of
the molecule have slight positive charges due to the proton.
o Would be told whether something is polar; do not need to have a list of
things that are polar memorized
Properties of water
o Water is liquid at room temperature (due to hydrogen bonding)
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o Universal solvent for polar compounds (like dissolves like – polar
substances can dissolve other polar substances along with substances
that are ionically bonded)
o Water molecules are cohesive (polarity causes water molecules to be
attracted to one another and stick together as a result)
o Temperature of water changes slowly
o High heat of vaporization
o Frozen water is less dense so ice floats (hydrogen bonding gets looser in
colder temperatures)
Relationship between properties of water
o Water is a polar molecule, which causes water molecules to be attracted
to one another through hydrogen bonding (it is cohesive). This causes
surface tension, and causes water to repel substances that are nonpolar.
Structures of the compounds
o Carbohydrates – compounds of carbon, hydrogen, and oxygen; in rings
 Monosaccharides – 1 ring (simple sugar)
 Disaccharides – 2 rings (simple sugar)
 Polysaccharides – 3 or more rings
 Starch
 Cellulose – cell walls of plants
 Glycogen
o Lipids – compounds of carbon, hydrogen, and oxygen
 Made of 3 fatty acids and a glycerol
o Proteins – made of amino acids, which are molecules made from carbon,
hydrogen, oxygen, nitrogen, and sometimes sulfur
o Nucleic acids – made of nucleotides, which include a phosphate group,
sugar, and nitrogen-containing base
Roles of the organic molecules
o Carbohydrates
 Quick and short-term stored energy
o Lipids
 Stored energy, hormones, insulation
o Proteins
 Build living tissue, enzymes, antibodies, absolute last source of
energy
o Nucleic acids
 Molecules of inheritance
Peptide bond
o Holds 2 amino acids together. Found between the carboxyl group of
one amino acid and the amino group of the other. Look for the carbon
double-bonded to an oxygen, then find the nitrogen that this carbon is
attached to. Between that carbon and nitrogen is the peptide bond.
Results in formation of dipeptide or polypeptide (proteins).
Dipeptide
o Two amino acids joined together
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What is the difference between hydrolysis and condensation?
o Condensation occurs when two smaller molecules join together to build
a bigger molecule, removing a water molecule in the process.
o Hydrolysis occurs when a bigger molecule is broken down into two
smaller molecules, adding a water molecule in the process
ID compounds
o Monosaccharides – 1 ring
o Disaccharides – 2 rings
o Polysaccharides – 3 or more rings
o Lipid – looks like a giant letter “E”
o Saturated fat – long chain of carbon, hydrogen, and oxygen, with all
single bonds between the carbons
o Monounsaturated fat – long chain of carbon, hydrogen, and oxygen,
with one double bond between 2 carbons
o Polyunsaturated fat – long chain of carbon, hydrogen, and oxygen, with
2 or more double bonds between the carbons
o Amino acid – compounds of carbon, hydrogen, oxygen, and 1 nitrogen.
Within the amino acid are a carboxyl group (-COOH), amino group (NH2), and R group (part that varies)
o Protein – compound of carbon, hydrogen, oxygen, and multiple
nitrogens