Download DP Chemistry Standard Level

DP Chemistry Standard Level
Option B.2
By: Alexander Burant
Table of Contents (Click where you
want to go)
Structure of Proteins
Condensation Reactions
Electrophoresis
Secondary Structures
B.2 Proteins and Enzymes
What you should understand by then end of this presentation:
• Understand what proteins and amino acids are
• Understand protein structures
• How does its shape affect function in metabolic processes
• How pH, temperature, and heavy metals affect enzyme
activity
• The use of chromotography
By the end I should be able to:
• Deduce structural formulas of reactants and products
• Explain solubilities and melting points of of zwitterions
• Apply relationships between charge, pH and isoteric point
for amino acids and proteins
Terms to keep in mind
Zwitterion: a dipolar ion that has both a positive
and negative charge but overall neutral.
• Zwitterions are not dipoles
– Zwitterions are commonly called inner salts
– Overall, they are neutral but contain regions with
positive and negative charges.
– Overall, a zwitterion is neutral
Terms to keep in mind
• Amphoteric: can have properties of both acids
and bases
• Buffers: solutions that can resist changes in pH
• Isoelectric point: a point that is electrically
neutral
To understand proteins, we need to
understand amino acids
Amino acids are acids, obviously, that are
comprised of an NH2 and a COOH. Amino acids can
be called the building block of nearly all biological
structures.
What’s so special about them?
• They form many of the biological structures such
as muscles, cells and tissue
• Most importantly, they can bond together in a
condensation reaction to make long chains called
a polypeptide. They do this in a condensation
reaction
Condensation Reactions
• This are reactions when two molecules come together to make a larger
one as a smaller one is released.
Notice in this
amino acid that in
blue, we have an
OH molecule.
Notice that the red
portion of the
molecule on each
amino acid has a
single bond with the
blue. This mean that
each amino acid can
ditch the other.
Notice that the C=O
And N-H bonded together
Notice
in this
This
then
means that H2O
amino to
acid
Needs
bethat
released.
in blue, we have
an H molecule.
2-amino acids
• The previous example is that of a dipeptide
and water
• If another amino acid was added then it would
be tripeptide
• There are many combinations of these
peptide chains which gives us the great
variance of amino acids.
FYI: 2-amino acids have another name by α – amino acids
What Exactly are Proteins?
IB Language: Proteins are large macromolecules
made up of chains of 2-amino acids formed by
condensation reactions.
Let’s break this definition down put it in english
IB Language: Proteins are large macromolecules made up of
chains of 2-amino acids formed by condensation reactions.
• Macromolecule: a really big molecule
• Amino acid
• Condensation Reactions: This is when two typically larger
molecules come together and in the process release a smaller
molecule (typically water)..
What do proteins do?
• The enzymes of the proteins are a catalyst for
man of the reactions in the body
• Structure in the body
• Energy source
• Some are hormones
• Some are carrier molecules such as
hemoglobin that carries oxygen in our cells.
Protein Structure
• Recall that proteins are chains of the 2-amino acids.
• Imagine that proteins are like headphones and you just put them in your
pocket.
– What happens to them?
– This same concept occurs to proteins
• The entanglement of proteins give them 3D shapes which affect functions.
• The structure is affects by the same forces as regular molecules such as
hydrogen bonding and van der Waals’ force.
– The Primary structure is the condensation reaction itself ie the long chain of
amino acids.
– Secondary structure of protein bond via intramolecular hydrogen bonding.
– Tertiary Structure can be held together by Vander Waals’ force, hydrogen
bonding, and ionic attractions due to ionic groups.
• This controls the function of the protein and can be held together by disulfide bridges
and hydrogen bonding
Secondary Structures
• Think of the head phone analogy
– Long headphone chords get tangled
– So do long chains of enzymes
• The chains create different structures due to the
intramolecular forces we have previously learned
about.
• In secondary structures, this “entanglement”
occurs from hydrogen bonding
– Remember that hydrogen bonding is not actual
bonding but an attraction of hydrogen to highly
electronegative molecules.
Secondary Structures Continued
• Remember what a hydrogen bond actually is.
• The highly electronegative atom, bonded with a hydrogen, “hogs”
the electrons which leaves the partially positive hydrogen to be
partially attracted to other electronegative atoms.
• Now image a long chain of amino acids, the lone hydrogens will
want to bind somewhere else on the chain which creates the helix
formation. This fancy word for this is α-helix. It looks like this
Another Type of Secondary Structure
• Β-pleated sheet is another form of bonding
where the atoms form a sheet by hydrogen
bonding
How do we analyze proteins?
• In order to analyze, the proteins must be broken down
by HCl
• Paper Chromatography
– The unknown amino acid is placed near the bottom of the
chromatography paper.
– The paper is placed in a solvent which causes the amino
acids to rise
– Different amino acids move up the paper at different rates
• Electrophoresis
– The structure of the amino acid determines pH which is
called the isoelectric point
Electrophoresis?
• Amino acids change structure at different pH levels
• Lets think this through as to what happens when an amino acid is
places in a solution with low pH
– What does this mean?
– A low pH means a high concentration of H+ or low?
– These extra protons latch on to the amino acid
• What happens at a high pH
– A solution with high pH mean more H+ or OH– What will happen to the protons on the amino acid?
• Will the soltuion with OH- abundance accept H+ or donate?
• The solution will accept H+ so it can make water, not donate H+ leaving an
unstable oxygen.
• With this knowledge, we can say that amino acids act as buffers
• Now each amino acid will find the spot where it finds its unique pH
level and this is called the isoelectric point.
Electrophoresis
• Since each amino acid has its own isoelectric point
• The acids are placed in a gel with a specific pH where a
potential difference is applied to it (fancy way of saying
it is hooked up to a battery or another source of
electricity).
• The acids move across the gel at different rates.
• They are sprayed and then identified
• How do we know which way they move?
– Remember that opposites attract
– A negatively charged molecule will move toward the
positive electrode.