Download Protein Structure

Levels of Protein Structure
• Why is the structure of
proteins (and the other organic
nutrients) important to learn?
Protein Structure - Introduction
• The multiplicity of functions
performed by proteins arises from the
huge number of different 3D shapes
they adopt: function follows
structure; function is determined by
structure
• Proteins are the most structurally
complex and functionally
sophisticated molecules known
Review
• Amino acids are the subunits
(monomers, building blocks) of
proteins
• Defining property: all have a
carboxyl (COOH) (carboxylic acid)
group and an amino group (NH2)
bonded to the alpha carbon
• Amino acids in a sequence are also
called residues
Review
• The bond that forms between two amino
acids is called the peptide bond
–Formed between the carbon of the
carboxyl group on one amino acid and
the nitrogen of the amino group on the
adjacent amino acid
–**This bond is covalent
• There are twenty standard amino acids
found in proteins
–Bacteria, plants, animals
Polypeptide Backbone
• The backbone of proteins (remember:
also called polypeptides) consists of
repeating sequence of atoms
N-C-C-N-C-C-N-C-C-N…
• Only the alpha Carbon, Nitrogen
of the amino group, and Carbon of
carboxyl group is considered in the
backbone
R Groups/Radical/Variant/
Side Chains
• The chemical versatility of the R
group of amino acids is vital to the
function of proteins
• R groups are also called side chains
–They are not involved in
peptide bonding but are what
give each amino acid its
unique properties
Quick chem: Electronegativity
• Polarity is caused by the
electronegativity of atoms: the
tendency of an atom in a
bond to attract electrons
towards itself.
• Highly electronegative atoms are, in
order:
F > O > N > Cl
Carbon and hydrogen have similar
electronegativities so the CH bond is
not polarized.
Quick Chem: Polar vs. Nonpolar
• Polar bond:
when electrons
are not shared
equally
between atoms
in a molecule
• Nonpolar:
electrons are
shared
Quick Chem: Hydrogen Bonding
• When a bond forms between an
electronegative atom, usually
Oxygen or Nitrogen, and a
hydrogen bonded to another
electronegative atom
• These bonds can occur between two
molecules (like water) or within the
same molecule (like DNA and like you
will see with proteins…)
Level 1: Primary Structure a.k.a
Amino Acid Sequence or Primary Sequence
• The primary structure of a protein is
simply the order in which the amino
acids that make up the protein are in
–The sequence of aa in a protein
• “The one dimensional first step in
specifying the three dimensional structure
of the protein” 
–All of the information required for a
polypeptide chain to fold is contained in
its amino acid sequence
Example of Primary Structure
• Gelatin:
Ala-Gly-Pro-Arg-Gly-Glu-4Hyp-Gly-Pro
Primary Structure
• Each of the thousands of known
proteins has its own particular
amino acid sequence
• Because each aa ca be used many
times, and there is no length
restriction, the possible number
of combinations is HUGE
Level 2: Secondary Structure
• Secondary structures have repetitive
patterns caused by the hydrogen
bonding
• So it’s one part of the backbone
being attracted to another part
of the backbone
–Side chains are NOT part of the
secondary structure
Common Secondary Structure:
The Alpha Helix
• Alpha Helix: in which every
backbone N-H group
hydrogen bonds to the
backbone C=O group of the
amino acid four residues
earlier
Common Secondary Structure:
Beta Sheet
• Hydrogen bonding between
the backbone carbonyl (C=O)
of an amino acid in one
strand and the backbone
amide N-H of a second amino
acid in another strand
Secondary Structure
• Many regions of
different secondary
structure can be
present in the same
protein molecules
Primary and Secondary Structure
• Primary structure: linear
sequence of aa's
• Secondary structure: - regular,
recurring folding of the protein
backbone due to H-bonding
Importance of the Chemical
Characteristics of the Side Chain
• The twenty amino acids found in
proteins are classified based on
the chemical characteristics of
their side chains:
polar/nonpolar, basic/
acidic, aromatic, positively
charged/negatively charged
Tertiary Structure
• Arrangement of
secondary structures +
side chains
Protein Level 3: Tertiary Structure
• The tertiary structure is the final specific
geometric shape that a protein assumes.
• This final shape is determined and
stabilized by a variety of bonding
interactions between the side chains
of the amino acids
• These bonding interactions between side
chains may cause a number of folds,
bends, and loops in the protein
chain; different fragments of the same
chain may become bonded together.
Interactions Between Side
Chains that Contribute to
Tertiary Structure
• We will learn three types of bonding
interactions between side chains
including: hydrogen bonding, salt
bridges, disulfide bonds; and the
effect of polarity of side chains
on structure
Ionic Bonds/Salt Bridges
• The reaction is simply the transfer
of a H+ (positive ion); the
attraction of the positive and
negative charges; (ionic
bonding).
• The interaction of the acid and
base side chains; these are used in
the salt formation.
Disulfide Bonding
Polarity of Side Chains
• A critical factor governing the folding
of any protein is the distribution of its
polar and nonpolar side chains
• Nonpolar side chains tend to be
forced together in an aqueous
environment; aggregate in interior
of protein molecule
• Polar side chains arrange themselves
near the outside of the molecule
Quaternary Structure
• The combination of two or more
polypeptide chains forming one
complete unit
• The interactions between the
chains are not different from
those in tertiary structure; are
distinguished only by being
interchain rather than
intrachain
Tertiary Structure
• Three main classes of proteins
correlate with typical tertiary
structures:
• Globular: the polypeptide chain
folds up into a compact shape like a
ball with an irregular surface; water
soluble
• Fibrous: relatively simple, elongated
structure; insoluble in water
• Membrane proteins: insoluble; beta
barrel, alpha helical,etc
• Primary: sequence of amino
acids in the protein
• Secondary: hydrogen bonding
b/w backbone groups
• Tertiary: interactions of side
chains
• Quaternary: two or more
polypeptide chains
• http://www.youtube.com/watch?v=lijQ3a8yUY
Q
“Cool” things about proteins
• Blood type is based on the proteins present in
each
• Luminol detects blood proteins
• Antibiotics interfere with protein synthesis in
bacteria
Application
• In a protein 146 aa long, a valine
(hydrophobic R group) is
substituted for a glutamic acid
(acidic R group) at position 6.
What is/are the effects of this
substitution?