Understanding
Proteins
Primary Structure
 What
did holding hands represent?
 What was your left hand representing?
 What was your right hand representing?
 Why did we rearrange the amino acids
aka you?
 The holding of hands represents what?
 At the ends of our polypeptide chain,
what did we have?
 Why
did I pull you back and forth? What
does this represent?
Secondary Structure
 Why
did we “bend” the line of amino
acids?
And why did your arms going up and down
represent?
 What did the arms up reaching across the
bend and connecting thumbs represent?
Secondary Beta Pleated Sheet
So arms up on one side
were the double bonded
C from the carboxyl end
and the arms down were
the hydrogen from the
other sides amine group
(the up and down are not
relevant – just for the
simulation). (I had to add
the bend… use your
imagination  )
Secondary Structure
Points to understand:
 The Hydrogen bonds form at regular intervals,
between the backbone components.
 The Hydrogen bonds are “weak” compared to the
peptide bonds. *The number of the H bonds in the
entire structure does give strength to the structure
(so alone H are weak, a lot of them are stronger)
 The Hydrogen bonds and the pleats create a
regular structure from the amino acid chain.
 Note –can’t construct alpha helixes using students,
but can you visualize this structure?
Secondary Structure Alpha
Helix
Note this is not
showing R groups
Secondary Structure with both
Alpha helix and Beta pleated
sheet
Tertiary Structure
Points to understand:
 The “S” shaped hooks on the bungee cord
represent sulfur atoms. The tertiary structure is
formed when two sulfur atoms are joined
bonded together by the strong non-polar
covalent bond.
 S-S bonds form from the interactions between
the side chains – “R” groups.
 The S-S bond is more rigid than Hydrogen
bonds. This gives the protein structure more
rigidity and stability.
 The size of the loops created by the S-S bonds
depends on the location of the sulfur
containing amino acids (primary structure).
Tertiary Structure
Quaternary Structure

How did we represent this structure?
The two or more small polypeptide chains. The chains
could have been
positioned side by side or in other configurations. A
quaternary structure is formed when two or more
polypeptides come together to make the functional protein.

Points to understand:



Two or more separate polypeptides are needed for
this level of protein structure.
Each polypeptide has its own primary, secondary and
tertiary structure. Often these levels of structures provide
the fit between the different polypeptides in forming the
functional protein.
Genetic conditions such as Thalasemia occur when the
polypeptide units are not produced in equal amounts. The
result is that one polypeptide chain lacks a sufficient
number of partners to form the final functional protein unit.
Quaternary Structure
 What
determines a proteins shape?
The sequence of amino acids determines
the protein's shape - *** Why?
The sequence determines where an a helix
can form, where beta pleated sheets can
occur, where disulfide bridges are located,
where ionic bonds can form etc.
What effects proteins?
 Genetics
– example: forms of inherited
autosomal recessive blood disorders that
originated in the Mediterranean region. In
thalassemia, the disease is caused by the
weakening and destruction of red blood
cells. Thalassemia is caused by variant or
missing genes that affect how the body
makes hemoglobin.
Denature
 What
does it mean to denature a
protein?
 What factors cause denaturing?
Misc.
 Is
the environment inside a cell good for
protein folding?
 In the crowded environment inside a cell,
there are also specific proteins that aid in
the folding of other proteins
Chaperonins (or chaperone
proteins)

protein molecules that assist in the proper
folding of other proteins (Figure 5.24).
Chaperonins do not specify the final structure
of a polypeptide. Instead, they keep the new
polypeptide segregated from "bad
influences" in the cytoplasmic environment
while it folds spontaneously. The chaperonin
shown in Figure 5.24, from the bacterium E.
coli,is a giant multiprotein complex shaped
like a hollow cylinder. The cavity provides a
shelter for folding polypeptides.
http://click4biology.info/c4b/7
/pro7.5.htm


http://www.rothamsted.ac.uk/notebook/prot.
htm#III
Pictures and definitions from wikipedia and
Campbell book

Activity from J. Smith Indiana Academy

http://video.about.com/chemistry/Introducti
on-to-Amino-Acids.htm
Above video shows why carboxyl is acidic
and amine is basic* show just first part
