Weston

Holzinger - Understanding Biochemistry

Primary Structure
O O O O
|| || || ||
+H N C CO- +H N C CO- +H N C C
3
+ 3 3 N C CO- + H2O
| | | | |
R R R
H R
The linking of amino acids by their carboxylate and amino group is termed _______________ structure.
o This is a ______________________ synthesis reaction (produces ____________).
o The resultant CN bond is called a _________________ linkage. This is a __________________ bond.
Therefor, we name these chains as di, tri, and poly__________________.
o Previously we mentioned each amino acid having two acid/base functional groups.
Assuming all non-ionic R groupds, we see that there are _____ of these on a dipeptide.
Tripeptide: ________. Any polypeptide: ________
If the polypeptide below consisted of: PheAlaGluLysGlyAla
Then you would identify there being ______ acid/base functional groups.
Because there is an automatic ____ from the ends, and _____ AA with groups.

O O O O O O
|| || || || || ||
+H3N C C N C C
N C C N C C N C C N C C O-
| | | | | | | | | | |
R H R
H R H R H R H R

It is important to note unique characteristics of the peptide bond.
o Chemical structure notes that the nitrogen has an unbound electron pair. Since the oxygen
is double bonded to the carbon, it will pull on this electron pair to relieve tension.
Therefor the CN bond acts much like a ________________________, which cannot rotate.
(this is due to _________________ hindrance).
This sharing of the electrons produces several ___________________ structures.
These non-rotatable connections are called _________________________.
o There is always ______ less amid plane or peptide linkage than the number of AAs.
The polypeptide above has _____ amino acids and therefor _____ amid planes.
o The connection between amid planes is by a carbon connected only by single bonds.
This is called the __________ carbon of the amino acid. It allows rotation of the chain.
It is also important to note the number of possible polypeptides that could be made from a certain
list or set number of amino acids.
o When using each amino acid only once we can use the mathematical term, _________________.
This is written as n!.
The polypeptide above could produce ______ unique chains using each AA only once.
o If you can use the same amino acid multiple times, it would be calculated as ______.
If you make a 6 AA chain using any number of 3 different AAs, you could end up with
______ different possibilities.
Protein Primary Structure 1.2.J
 Weston Holzinger - Understanding Biochemistry

Secondary Structure
O
O
||
||
C N C C
C
N | | |
| H R
R H R R
Once the order of amino acids is set, they start connecting further.
O The ____________________, formed during the primary structure, has an
O ||
exposed oxygen and hydrogen atom.
|| N C C o When lined up these would be expected to form
C | |
____________________ bonds.
C R
N | o Thus secondary structure could be simplified as:
|
H R the connection of _______________________
R H R with _________________________________.

O
This can take two forms.
||
O o The first, seen on the right, is the most commonly used
|| N C C N C R

secondary structure in humans, known as an _______________.
C | | |
R C In this structure, an amino acid will hydrogen bond
H R
H to the _______ one from it.
This creates a very tightly wound coil that forces the
O R groups to protrude _______________, and hide the
O || constant portions of the molecule.
|| N C C This is seen best from an axial view.
C C | | R Thus the polypeptide will take on the properties of
N | the ________________ during a certain segment, even
H R
R | R though all amino acids have hydrophilic portions.
H In a transmembrane protein you would expect an
alpha helix with hydrophilic R groups on the ________
R and hydrophobic ones in the ________________ in order
R
to wedge the protein in the biphospholipid
R
membrane.
R o The second one mentioned is a beta-pleated sheet.
This is not discussed in detail in this class.
R
o There are other formations but, again, are not discussed.
R When bonds are formed, we generally see a _____________________ of
R energy (often in the form of heat).
R
o Therefor, when a peptide chain forms its secondary
R structure, we would expect that process to be _______thermic.
The alpha helix is the ___________ energy state.

Protein Secondary Structure 1.2.K

 Weston Holzinger - Understanding Biochemistry
Tertiary Structure

CH2(CH2)12CH3

O
||
CO +H3NCH2

CH2S-H
H-SCH2

CH2S--------SCH2

Only one free part of the amino acid is left to form bonds: the ____________________.
This happens in ___________________ structure.
It is then when we truly have a functional protein because it has a 3d shape.
o We know the several different types of R groups that an amino acid can have. Now we will
revisit a few of those with special names/properties upon bonding.
o Hydrophobic R groups are especially important in ________________ proteins, and also in
making rounded segments of the chain.
o Ionic R groups with opposite charges will _________________.
This is termed as an _____________________ interaction, and often called a _________________
o Sulfhydryl groups are found only in the amino acid _______________.
These can form a covalent, ____________________ linkage.
It is the content of many of these in human hair that gives it a unique burning smell.
Tertiary structure is the __________________ of the three talked about so far.
o Thus it is the most susceptible to breaking. The process of breaking the tertiary structure is
called _______________________.
This can be caused by physical effects: such as _____________.
This happens in the case of a hair perm. The heat temporarily breaks the
bonds. Then when they reform, they remain
But also chemical effects: such as __________.
An example of this is the fermentation of ___________. The lactic acid from the
lactose catabolism _____________ the pH. This makes some of the protein
insoluble in water, and separates the cheese from the whey.
Protein Tertiary Structure 1.2.L
 Weston Holzinger - Understanding Biochemistry
Quaternary Structure

Quaternary structure is also a bond between R groups, like tertiary, but is between two different
polypeptide chains.
o It is important to note that not all proteins have a quaternary structure. Some are
comprised of a single polypeptide chain.
o Therefore we would consider these to be int____molecular bonds.
o Since the weight is so considerably large, this is generally the _________________ of the
structures.
Protein Conformations
There are two predominant forms of protein.
______________________
these are generally more rounded and bulky.
One example is _______________________.
______________________
these are long and usually built for strength.
One example is _______________________.
Structure Review:

Structure Strength
Bond Type Between Key Terms
(1-4)

Primary


Secondary


Tertiary


Quaternary

Protein Quaternary Structure 1.2.M