PROTEINS
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Proteins are an extremely important molecule
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About 50% of a cell’s dry weight is protein
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Proteins are polymers (called polypeptides) composed of repeating
monomer units called amino acids
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All proteins are manufactured from the 20 different amino acids
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Every amino acid contains the same parts:
-an amino group (NH2)
-a carboxyl group (COOH)
-a hydrogen
-a specific R group (side chain)
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Each of these parts is attached to a central carbon atom:
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Each amino acid has a different side chain (R group)  this is what makes
each amino acid distinct
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The properties of amino acids reflect the properties of the individual R
groups. Example: R groups can be polar, non-polar
The Formation of Proteins
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Proteins are formed by the linking of amino acids through a dehydration
synthesis reaction
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The carboxyl group of one amino acid reacts with the amino group of the
next amino acid
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Specifically, the –OH of the carboxyl combines with one an H of the
amino group:
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The bond between the amino acids is called a peptide bond
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The joining of two amino acids yields a dipeptide
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Three or more amino acids form a polypeptide
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Proteins always have an amino group on one end and a carboxyl group on
the other end.
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Linking several amino acids together produces a repeating sequence of
atoms along the chain (N-C-C-N-C-C-)
Protein Conformation/Structure
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Protein conformation – shape of the protein molecule
When a cell makes polypeptides the structure of the polypeptide will
determine its function (structure determines function)
The shape therefore is very important for the function
There are 4 levels of protein structure:
1) Primary
2) Secondary
3) Tertiary
4) Quaternary
1)
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Primary Structure
sequence of amino acids in a linear chain
each protein has a unique sequence of amino acids
since R groups of the amino acids can interact with other R groups, this
sequence affects secondary and tertiary structure.
 if the sequence of a polypeptide molecule is incorrect the protein will
not function (example: Insulin consists of 51 amino acids. If even
ONE of those amino acids is substituted for a different one, the
protein shape may be altered and the protein will not work!!)
 sequence is determined by the genetic code found in DNA
2) Secondary Structure
 Formed when a primary structure folds upon itself
 the twisting and bending occurs because of interactions within the chain
itself (ex. H-bonding)
 There are two basic shapes  a) alpha helix ( α-helix)
b) beta pleated sheet ( β -pleated sheet)
 you can also have a random coil
ALPHA HELIX- found in the proteins of hair, wool, horns, feathers
BETA PLEATED SHEET- found in silk
3) Tertiary Structure
 Involves the folding of secondary structures to form a globular (round,
compact) protein shape
 Caused by interactions between the R groups in the amino acids
 Held together by many bonds (H-bonds, dipole-dipole, London, ionic,
covalent) (ex of covalent = disulfide bride  bond forms between S of
one amino acid and S of another amino acid)
 Hydrophobic groups cluster together on the inside of the protein
 Hydrophilic groups tend to be on the exterior of the protein
 Enzymes are globular proteins. The precise folding of the polypeptide
chain creates the “active site” so that the reaction can take place.
4) Quaternary Structure
 Involves the combination of different polypeptide chains.
 Many proteins (particularly large globular ones) are made of more than
one polypeptide chain.
 The polypeptide chains are held together by: H-bonds, disulfide bridges,
ionic, covalent, hydrophobic forces
 Example: hemoglobin (O2 carrier in blood)
The “heme group” :
- contains an iron atom, and is where the oxygen binds to hemoglobin.
- It is an example of a “prosthetic group” or a “cofactor”: a non-amino
acid part of a protein.
- Proteins with prosthetic groups are called “conjugated proteins”.
Ex: chlorophyll
Fibrous vs Globular Proteins
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Proteins can be fibrous or globular
Shape
Solubility
Organization
Function
Examples
FIBROUS PROTEINS
long
Insoluble in water
Secondary Structure most
significant
Structural
Collagen, keratin, myosin
GLOBULAR PROTEINS
Tightly folded; compact
*Soluble in water
Tertiary structure most
significant
Functional (they do something)
Hemoglobin, enzymes,
antibodies, hormones
* Protein Solubility
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8 of the 20 amino acids are nonpolar (hydrophobic)
The remaining 12 are polar (hydrophilic)
For globular proteins, the hydrophobic amino acids cluster together in
the interior of the protein leaving the polar ones on the exterior (see
tertiary structure)
This allows the protein to dissolve in water
If a protein contains less non-polar amino acids, the less soluble it will
be.
Functions of proteins
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Proteins have many diverse structures and therefore many functions
(structure determines function)
Function
Enzymes
- Assisting in chemical
reactions.
- Globular Proteins
Hormones
- Chemical messengers
Defense
- Protection against
disease
Structure
- Support
Transport
- Transport other
substances
Examples
Digestive enzymes help breakdown the different
polymer molecules.
AMYLASE: breaks starch into maltose
Insulin, a hormone, helps regulate concentration
of sugar in the blood
Antibodies, help fight micro-organisms like
bacteria and viruses
Collagen is, a main component of connective
tissue like ligaments and tendons and is an
important part of your skin
Hemoglobin, the iron containing protein of blood,
transports oxygen throughout the body. Other
proteins help to move substances across cell
membranes
Other functions…
Type of Protein
Receptor Protein
Function
Response of a cell
to chemical stimuli
Storage Protein
Storage of amino
acids
Contractile Protein
Movement
Examples
Receptors in nerve cells detect
chemical signals from other nerve
cells
Casein, the protein of milk, stores
amino acids used for developing
baby mammals
The proteins of muscle allow for
movement
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R groups interact uniquely causing the polypeptide chains to bend and
fold:
Example:
-oppositely charged R groups attract
-similarly charged R groups repel
-hydrophobic R groups move away from water (that surrounds
proteins in cells)
-hydrophilic R groups move towards water
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London forces – weak attractive forces between molecules resulting from
the small, instantaneous dipoles that occur because of varying positions
of electrons during their motion about nuclei (at some instant, there are
more electrons on one side of the atom than the other)
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Dipole-Dipole forces – attractive force resulting from the tendency of
polar molecules to align themselves such that the positive end of one
molecule is near the negative end of the another molecule
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H –bond – attractive force between hydrogen and another
electronegative element (ex O)
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Hemoglobin
-oxygen carrying molecule in the blood
-composed of 2 alpha helixes and 2 beta sheets
-binding of O2 to any one of the subunits of hemoglobin induces a
conformational change in that subunit
-because the subunits fit snugly together, this change induces the
positions of the 2 alpha and 2 beta sheets to rearrange
-in this new conformation it becomes easier for the other subunits to
bind oxygen
-this increases the affinity for oxygen, making oxygen binding more likely
-at the centre of the hemoglobin molecule exists a system of
hydrocarbon rings called a porphyrin ring system (known as the heme
group)
-at the centre of the heme group is an iron molecule (this is the part that
binds to oxygen and gives blood its red colour)
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Myoglobin
-oxygen carrier in muscle cells
-has a higher affinity for oxygen than hemoglobin
-thus oxygen moves from hemoglobin (in capillaries) into muscle cells
ensuring efficient transfer of oxygen from blood to tissue