PROTEINS




Proteins are the most abundant molecule.
Proteins are polymer organic molecules (called peptides) consisting of many amino acids bonded
together.
Amino Acids: Monomers or building blocks of all proteins.
All proteins are made from the 20 different amino acids.
The basic structure of a generalized amino acid is shown above.
(Memorize this!)

Every amino acid contains the same parts:
a) Amino group (NH2)
b) Carboxyl group (COOH)
c) R-group: variable- 20 R-groups, so only 20 amino acids. (makes each amino acid different)
The Formation of Proteins




Peptide bonds: Bond formed when 2 amino acids bond by condensation (dehydration) synthesis.
The OH of the carboxyl group (-COOH) of one amino acid reacts with the H of the amino group of the
other.
Joining two amino acids is called a dipeptide.
Joining three or more amino acid is called a polypeptide
Know how to draw this and label where the peptide bond is (See blue arrow).
[Another Protein Synthesis Diagram]
Dipeptide- 2 amino acids joined by peptide bond.
Polypeptide- many amino acids bonded together.
Protein Conformation/ Structure




Protein conformation-shape of the protein molecules
When a cell makes polypeptides, the structure determines its function (shape very important to
function)
Denaturation: protein shape altered with changes in pH, temperature. Change in shape alters activity
of enzyme. Enzymes function within a narrow range of these factors.
There are 4 levels of protein structures.
o Primary
o Secondary
o Tertiary
o Quaternary
Levels of Protein Structure
1) Primary structure:
a. Sequence of amino acids in a linear chain
b. Single polypeptide chain with amino acids connected by peptide bonds. (No H-bonds between
nearby amino acids!)
c. Since the R group of amino acids interact with other R groups, therefore the primary structure is
important to determining the secondary and tertiary.
d. If the amino acid sequence is incorrect, the protein will not function. Even if it’s just one
difference!
e. The sequence is determined by DNA.
2) Secondary structure:
a. Formed when a primary structure folds upon itself.
b. Single polypeptide chain. H- bonding to side groups of amino acids several places away, forms
folded or coiled structure.
c. There are two basic shapes
i. Alpha helix (α-helix)-hair, wool, horns feathers
ii. Beta pleated sheet (β-pleated sheet)-silk
iii. Random coils
3) Tertiary structure:
a. Includes the folding of secondary structures to form a globular (round and compact) protein shape
b. Caused by interaction of R groups in the amino acids
c. Held together by many different bonds
d. Hydrophobic groups cluster together on the inside of the protein
e. Enzymes are examples of globular proteins. The precise folding of the polypeptide chain creates
the “active site” so that the reaction can take place
Bonds include:





ionic bonds or salt bridges (between acidic negatively charged and basic positively charged side groups)
hydrogen bonds (between -COOH and -NH2 and -OH groups on side chains)
hydrophobic forces between non polar side groups
disulphide bridges (S-S)- strong covalent bonds - between thiol groups on pairs of the amino acid cysteine
Dipole-dipole (polar) and London dispersion forces.
4) Quaternary structure:
a. Involves the combination of different polypeptide
chains
b. Two or more polypeptide chains linked to form complex 3-D structure.
c. Not all proteins form a quaternary structure.
d. Bonds include H-bonds, disulfide bridges, ionic, covalent and hydrophobic forces
e. Example: Hemoglobin
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
[Protein Structure #1] ---- [Protein Structure #2]
Types of interactions


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

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)

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

H –bond – attractive force between hydrogen and another electronegative element (ex O)
****Denaturation: using extremes of pH or temperature to alter the
shape of a protein (breaks some bonds)
Fibrous vs Globular Proteins

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
* Protein Solubility
GLOBULAR PROTEINS
Tightly folded; compact
*Soluble in water
Tertiary structure most significant
Functional (they do something)
Hemoglobin, enzymes, antibodies,
hormones
-
9 of the 20 amino acids are nonpolar (hydrophobic)
The remaining 11 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

Proteins have many diverse structures and therefore many functions (structure determines function)
Function
Enzymes
- Assisting in chemical
reactions.
- Globular Proteins
Hormones
- Chemical messengers
Examples
Digestive enzymes help breakdown the different polymer molecules.
AMYLASE: breaks starch into maltose
Defense
- Protection against
Antibodies, help fight micro-organisms like bacteria and viruses
Insulin, a hormone, helps regulate concentration of sugar in the blood
disease
Structure
- Support
Transport
- Transport other substances
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
Storage Protein
Contractile Protein

Function
Response of a cell to
chemical stimuli
Storage of amino
acids
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
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
LIPIDS:


Lipids are a diverse group of molecules
This category of molecules includes:
-fats (triglycerides)
-phospholipids
-steroids
-waxes

All lipids have a common characteristic: they are all hydrophobic (insoluble in water) (do not mix
with water)
Consist mostly of C-H atoms in a non-polar bond arrangement

Functions of Lipids:
a) store a large amount of energy
Excellent long-term energy storage
Concentrated source of energy – 1 g of fat contains more than twice as much energy as 1 g of
carbohydrate (9 kcal/g vs. 4 kcal/g in carbs)
b) phospholipids are the structural component of membranes
c) Steroids
o Built by a carbon skeleton consisting of four fused hydrocarbon rings
o Cholesterol is one type of steroid
o Cholesterol is also the building block of testosterone and estrogen (hormones that control
development of sexual characteristics)
o Cholesterol is important in maintaining the fluidity of cellular membranes but too much
can cause heart problems
d) waxes provide protective coating for plants to prevent water loss
o contain 1 phosphate, 1 glycerol, 2 fatty acids
e) insulators for animals (keeps animals warm by preventing loss of heat)
f) facilitate (help) the digestion & metabolism of other nutrients
g) help the absorption and transport of vitamins A,D,E,& K
Types of Lipids:
A. Triglycerides (fats) = glycerol + three fatty acids
 They are nonpolar (don't dissolve well in water). Only the ends of the fatty acids can be attracted to water.
 They tend to form circular blobs in water with the nonpolar glycerol inside, the fatty parts facing to water.
 A triglyceride is formed through a condensation reaction.
[How Triglycerides are Formed]
Saturated: all single bonds (many C-H bonds), hard, animal fats
Unsaturated: some double bonds (less C-H bonds), liquid, plant oils
Saturated fat:
- there are only single bonds between the carbons in the fatty acid chains.
- As a result, the carbons are “saturated” or completely surrounded by hydrogens and are bonded
to 4 other elements.
- Saturated fats take up less space and therefore are more dense.
- They tend to be solid at room temperature
- Ex: animal fats (such as in meat), butter
Unsaturated fat:
- There is at least 1 double bond between two
carbons in a fatty acid chain.
- As a result, the carbons are “unsaturated” –
they are NOT completely surrounded by
hydrogens and are bonded to less than 4
other elements.
- This produces a “kink” or bend in the
molecule which causes the molecule to take
up more space, making it less dense. As a
result, they tend to be liquid at room
temperature.
- Ex: vegetable oils, fish oils
..----B. Phospholipids:



comprise cell membranes & soaps (Made of glycerol + 2 fatty acids + 1 phosphate )
Polar PO4 faces outward to extracellular fluid and toward the cytoplasm
Nonpolar fatty acids face inward
[Polar nature of phospholipids]
C. Steroids: have a ring structure
a) lipid hormones
b) cortisone
c) cholesterol
d) vitamins (Vit. D)
e) anabolic steroids
D. Waxes
 Waxes consist of a long-chain fatty acid linked through an ester oxygen to a long-chain alcohol.
 Their strongly hydrophobic nature allows them to function as water repellents on the leaves of

some plants, on feathers, and on the cuticles of certain insects.
Waxes also serve as energy-storage substances in plankton (microscopic aquatic plants and
animals) and in higher members of the aquatic food chain.
Know how to Identify and Draw the Following Lipid Subunits: ----------