1.

Proteins
a. Linear polymers built of monomer units called amino acids which are linked end to
end
b. Contain a wide range of function groups
c. Can interact with one another and with other biological macromolecules to form
complex assemblies
d. Some proteins are quite rigid, whereas others display considerable flexibility
2. Levels of Protein Structure
a. Primary
b. Secondary
c. Tertiary
d. Quaternary
3. Basic Amino Acid Structure
a. -carbon is chiral (except G)
b. Primary amines (except P)
i. By convention, the amino end is taken to be the beginning of a polypeptide
chain, and so the sequence of amino acids in a polypeptide chain is written
starting with the amino-terminal residue
ii. Keep amine on the left side
c. Zwitterions
i. Charged ion, but overall is neutral
ii. Amino group weak base
iii. Carboxyl group weak acid
iv. Ionization state depends on pH
d. Tetrahedral structure
4. Stereoisomers
a. L vs. D
i. In living organisms, only L exists
5. Amino Acid Classification
a. Nonpolar/Hydrophobic
i. Aromatic, aliphatic and/or sulfur groups
ii. GAVLIMP TP
1. Glycine
2. Alanine
3. Valine
4. Leucine
5. Isoleucine
6. Methionine
7. Proline
8. Tryptophan
9. Phenylalanine
b. Polar
i. Neutral
1. OH- or an amide
a. SomeTimes Cats Try A Growl
i. Serine
ii. Threonine
iii. Cysteine
1. Forms disulfide bonds via oxidation
2. Insulin 2 peptide chains linked by disulfide bonds
iv. Tyrosine
v. Asparagine
vi. Glutamine

ii. Basic
1. N that can accept an H+
a. Life Always Has
i. Histidine
1. Histidine ionization histidine can bind or release
protons near physiological pH
ii. Arginine
iii. Lysine
iii. Acidic
1. CO2H that can donate H+
a. A Goal
i. Aspartate
ii. Glutamate
6. Titration Curves
a. pI (isoelectric point) the pH at which the number of positive and negative
charges on a population of molecules is equal (i.e. no net charge)
i. pI = (pK1 + pK2)/2
7. Bonds
a. Peptide bonds are planar, locked at those positions with no rotation
i. Planar because it is partially a double bond
ii. In cis and trans, trans is usually more favorable except for in proline
iii. The bond resonates between a single bond and a double bond; because of
this double-bond character, rotation about this bond is prevented and thus
the conformation of the peptide is constrained
b. Phi () and psi () can rotate freely about the N-C and C-carbonyl bond
respectively
i. The freedom of rotation about two bonds of each amino acid allows proteins
to fold in many different ways
c. Ramachandran diagram
i. Graphs all of the angles that they can rotate
8. Levels of Protein Structure
a. Primary Structure
i. Linear polypeptide chain
1. Backbone
a. Repeating
b. H-bonding potential
2. Side chains
ii. Size varies
1. 50-2000 amino acids27,000!
iii. Precisely defined amino acid sequence
1. Specified by gene
b. Secondary Structure & Strand
i. Non-linear
ii. 3-Dimensional
iii. Formed by a regular pattern of hydrogen bonds between the peptide N-H and
groups of amino acids that are near one another in the linear sequence Paul
& Corey
iv. -helix
1. Rod-like structure
2. A tightly coiled backbone forms the inner part of the rod and the side
chains extend outward in a helical array
3. It is stabilized by H-bonds between the NH and CO groups of the main
chain
4. H-bonding is very regular, repeating, and alternating

5. Essentially all -helices form right-handed helices, some left-handed

helix proteins however, do exist
v. -pleaded
1. Strands have a little more flexibility and the angles are found over
longer distances
2. Composed of two or more polypeptide chains called strands
3. Orientation and hydrogen bonding pattern of strands gives rise to flat
or twisted sheets
4. Parallel sheets buried inside, while anti-parallel sheets occurs on the
surface
a. Parallel adjacent strands run in the same direction
b. Anti-parallel - adjacent run in opposite directions
vi. Loops
1. Polypeptide chains can change direction by making reverse turns and
loops
a. Reverse turn ( turn or hairpin turn)
c. Super-secondary structure
i. Association of secondary structures
1. , greek key helix-loop-helix
d. Domains
i. Larger associations of 2 or more secondary structures
1. 35-200 amino acids
ii. Independent folding unit of tertiary structure
iii. Also known as a fold
e. Tertiary structure
i. Non-linear
ii. 3-dimensional
iii. Global but restricted to the amino acid polymer
iv. Formed and stabilized by:
1. Hydrogen bonding
2. Covalent (disulfide) bonding
3. Hydrophobic packing toward core and hydrophilic exposure to solvent
v. Functional and energetically favorable
f. Quaternary structure
i. Associations of tertiary structures
9. Factors that influence the conformational equilibria of peptide chains are:
a. Planarity of peptide bonds
i. Conformations are defined by dihedral angles phi and psi
b. Hydrogen bonding of amide carbonyl groups to N-H donors
c. Steric crowding of neighboring groups
d. Repulsion and attraction of charged groups
e. Hydrophilic and hydrophobic character of substituent groups
10.Structural Classification of Proteins (SCOP)
a. All alpha helical
b. All beta structure
c. Mixed alpha/beta
d. Mixed alpha + beta
e. Other
11. Types of Protein Structure related to Protein Function
a. Globular
i. Water-soluble, roughly spherical
ii. Hydrophilic nature
iii. Often stable structures
iv. Show a quite variety of protein structures
v. They do not aggregate into macroscopic structure

1. Unique, compact tertiary structures

b. Fibrous
i. Elongated
ii. Insoluble
iii. Regular repeating structures
iv. Secondary structure forms the dominant structure
v. Either alpha-helices or beta-pleaded sheets
vi. Structural or supportive role in the body
c. Membrane
i. Constitute about 25% of all the proteins
ii. Very little known about membrane protein structures
iii. Roles:
1. Transport of molecules/ions in or out of cells
2. Cell recognition, receptors, cell to cell communication
iv. Amino acid side chains of transmembrane segments must be non-polar
v. Helices and beta-barrels peptide bonds participate in hydrogen-bonding with
the lipid bilayer
d. Unfolded
12.
How do proteins fold properly?
a. Experiment
i. Christian Anfinsens work on the enzyme ribonuclease revealed the relation
between the amino acid sequence of a protein and its conformation
1. Took the protein out of the cell and unfolded the proteins by breaking
all of the disulfide bonds with a reducing agent to reduce the sulfide
bond
2. We are not exactly sure how denaturants work, but instead of the
protein forming H-bonds, the H-bonds form with urea
a. They replace water as the molecule solvating the protein and
are then able to disrupt the van der Waals interaction stabilizing
the protein structure
3. He took the native (active protein) and added urea to denature it (this
form does not chew the RNA) and then later removed the urea. He
assays the protein again and then it becomes active again and folds on
its own
4. You can also have some of the disulfide bonds bond the wrong way or
order
ii. Experiments showed that the information needed to specify the catalytically
active structure of ribonuclease is contained in its amino acid sequence
iii. The process was driven by the decrease in free energy as the scrambled
conformations were converted into the stable, native conformation of the
enzyme
b. Denaturants
i. Compete with polypeptide to gain hydrogen bonds to destroy secondary
structure of protein
ii. Increases non-polar side chain solubility in water
13.
Proteins fold by progressive stabilization of intermediates rather by
random search
a. Levinthals Paradox
i. Imagine a single 100 aa protein sequence and assume each aa has 3 possible
conformations and that each transition would take 0.1 picosecond.
ii. It would take 10^10 seconds to try all of the combinations
b. The essence of protein folding is the tendency to retain partly correct intermediates
c. Folding funnel

i. The surface for the overall process of protein folding can be visualized as a
funnel
ii. As the free energy of the population of protein molecule decreases, the
proteins move down into narrower parts of the funnel and fewer conformation
are accessible
iii. At the bottom is the folded state with its well-defined conformation

14.

15.

iv.
Cumulative selection
a. A monkey randomly poking at a key board could type a sentence from Shakespeare
in a few thousand keystrokes if the correct letters are retained
b. Protein folding occurs by cumulative selection
i. Partly correct folding intermediates are retained because they are slightly
more stable than unfolded regions
Energy Landscape

a.
16.

17.

Intrinsically Disorder Proteins (IDPs)

a. These proteins, completely or in part, do not have a discrete 3-D structure under
physiological conditions
The Protein Trinity

a.

18.

19.

20.

21.

22.

23.

Metamorphic Protein Structure

a. Appear to exist in an ensemble of structures of approximately equal energy that are
in equilibrium
b. Small molecules or other proteins may bind to a particular member of the
ensemble, resulting in a complex having a biochemical function that differs from
that of another complex formed having a biochemical function that differs from that
of another complex formed by the same bound to a different partner
c. An example is cytokine lymphotactin
Do protein in the cell the same as in the test tube?
a. Proteins are synthesized in cells from an N to C terminal direction
b. Proteins are synthesized in the cytoplasm, but they have to find their final place in
the cell
c. Additional evidence suggests that protein folding/translocation requires assistance
(i.e. catalysis) in the cell
i. Mutant cells defective in certain proteins can lead to the accumulation in the
cells of misfolded and aggregated proteins
ii. Eukaryotes can be expressed in prokaryotes but they often misfold and
aggregate in the bacterial cells and form structures called inclusion bodies
In vivo protein folding
a. Chaperonins escorts the proteins and prevent it from folding until it emerges
completely from the ribosome
i. They lead them to the GroEL (ATPase) with a big hollow center and put a cap
on it.
ii. ATP is used to chain with the conformation of GroEL
Post Translational Modifications (PTMS)
a. Phosphorylation
b. Glycosylation
c. Ubiquitination
d. S-Nitrosylation
e. Methylation
f. N-Acetylation
g. Lipidation
h. Proteolysis
Protein modifications formation or breakage of covalent bonds
a. Disulfide bond formation
b. Addition of small moiety
i. Phosphorylation, glycosylation, methylation, hydroxylation, etc.
c. Truncation
i. Self-cleavage
1. Viral capsid protease (SCP)
2. Intramolecular chaperones
ii. Cleavage of signal sequences signal peptidases
iii. Protein splicing inteins
iv. Intramolecular cleavage
d. Addition of ubiquitin or ubiquitin-like protein
Protein Functions
a. Enzymes
b. Storage
c. Transport
d. Contractile
e. DNA binding
f. Defense
g. Toxins
h. Regulatory

24.
a.
b.
c.
d.
e.
f.

Enzymes
Oxidoreductases
Transferases
Hydrolases
Lyases
Isomerases
Ligases