Proteins: Chapter 21
Objectives
 List 8 major functions of proteins and give an example of a protein that is
involved in each biological function
 Write out the structures for at least one amino acid which are
representative of an amino acid with a (1) nonpolar, (2) polar, but neutral,
(3) acidic and (4) basic R group. Also indicate the unique character of the
amino acids glycine, praline, and cysteine.
 Demonstrate the amphoteric character of amino acids by writing the
reactions for the zwitterions with an (1) acid or (2) base.
 Write out the reversible reaction for the oxidation of cysteine and indicate
how the production of cystine in a protein might stabilize the tertiary
structure of proteins.
 Draw the structure for a polypeptide, pointing out (1) peptide linkages, (2)
the chiral carbon atoms in the backbone, (3) the N- and C-terminal amino
acids, and (4) the R groups.
 Name the four levels of structure in proteins and briefly describe what
each is associated with.
 Indicate the 4 forces, which are involved in determining protein structure
and draw a representation of each.
 Characterize the secondary structures in alpha helix and B-pleated sheet
in terms of structure and the types of forces involved in each.
 Indicate what changes occur in proteins by the addition of specific
denaturation agents and list some practical applications of denaturation.
Why are proteins considered the most important of all biological compounds?
Structure
Catalysis
Movement
Transport
Hormones
Protection
Storage
Regulations
Classify proteins into two major types: fibrous proteins, which are insoluble in
water and are used mainly for structural purposes, and globular proteins,
which are more or less soluble in water and are used mainly for nonstructural
purposes.
The Building Blocks- Amino Acids
The 0 common amino acids found in proteins are called alpha amino acids and fit
the following basic structure:
The most important aspect of the R groups is their polarity and on that basis we
can classify amino acids into the four groups: nonpolar, polar but neutral, acidic
and basic (review table in book).
Which R groups are hydrophobic and which ones are hydrophilic?
When you look at the amino acids it is obvious that all of them are chiral except
for glycine. Nature makes only one of the two possible enantiomers and it is
virtually always the L form. D amino acids are extremely rare.
Zwitterions are compounds that have a positive charge on one atom
and a negative charge on another atom. Amino acids are zwitterions in
water solutions and in solid state. (UN-IONIZED AA does not actually exist!). As
expected, they are solids with high melting points and fairly soluble in water.
What happens when an amino acid is dissolved in water? When it is titrated with
an increasing amount of KOH?
The pH at which all the molecules have equal positive and negative charges is
known as the isoelectric point (pI).
Are amino acids amphiprotic? Can they act as buffers?
Cysteine: A Special Amino Acid- It is dimerized by mild oxidizing agents to
cystine-which in turn can be reduced to give two molecules of cysteine. What is
a disulfide bond?
Peptides and Proteins
How is a peptide bond formed? Show how to create a tripeptide.
What is a polypeptide? What is a residue? The C-terminal amino acid? The Nterminal amino acid?
Properties of Peptides and Proteins
The continuing pattern of peptide bonds is the backbone of the peptide or
protein molecules; the R groups are called the side chains. The 6 atoms of the
peptide backbone lie in the same plane, and the two adjacent peptide bonds can
rotate relative to one another about the C-N and C-C bonds.
The R groups mainly determine the chemical and physical properties of an amino
acid and collectively, the R groups mainly determine these properties in a
protein. At any pH above the isoelectric point, the protein molecules have a net
negative charge; at any pH below the isoelectric point, they have a net positive
charge. The water solubility of proteins depends on the repulsive forces between
the like charges on their surfaces. When proteins are at a pH where there is a
net positive or negative charge, the presence of these charges cause the protein
molecules to repel each. However, at the pI, where there is no net charge, the
repulsive forces are at there lowest and therefore the protein molecules can
aggregate and be precipitated from their solutions.
Four Levels of Organization
Primary describes the linear sequence of amino acids in the polypeptide chain.
How important is this sequence to the function of the protein?
Cytochrome c
Minor differences-still functions
insulin
Minor differences-consequences are
allergic rxn and also a change in
function
hemoglobin
A change in one aa-sickle cell anemia
Secondary refers to certain repeating patterns as a result of hydrogen bonding
between peptide bonds. Review alpha helices, beta pleated sheets, random coils,
and extended helix. Review the chemical connection on protein/peptide
conformation-dependent diseases.
Keratin-fibrous protein of hair, fingernails, horns, and wool- alpha helix
Silk- fibroin –exists primarily in B pleated sheets
Collagen- extended helix
Tertiary describes the overall conformation of the chain. In general, tertiary
structures are stabilized four ways
Covalent bonds-example is the disulfide bond
Hydrogen bonds- between polar groups in the side chains
Salt Bridges-occur between 2 amino acids with ionized side chains (ion-ion
attraction)
Hydrophobic interactions-nonpolar groups interacting together –this interaction is
usually weaker than H bonding or salt bridges, but, if it interacts over a large
area of the protein, cooperatively the many interactions are strong enough to
stabilize a loop or some other tertiary structure
(BE ABLE TO DESCRIBE AN EXAMPLE OF EACH!)
Chaperones are proteins that help newly synthesized proteins assume the
correct secondary and tertiary structures—so when do you think this occurs? In
the cytoplasm as the protein is being made on the ribosome or after it is
completely made?
Define proteomics—the concerted effort to catalogue all the proteins in their
various forms in a particular cell or tissue
The quaternary structure applies mainly to proteins containing more than one
polypeptide chain (subunit) and deals with how the different chains are spatially
related to each other. What type of bonding maintains quaternary structure?
Hemoglobin in adult humans is made of 4 chains (called globins): two identical
chains (alpha) of 141 amino acids residues each and two identical chains (beta)
of 146 residues each. Each globin chain surrounds an iron-containing heme unit,
the structure of which is shown in the textbook. Proteins that contain nonamino acid portions are called conjugated proteins and the this portion
is called a prosthetic group. In the fetus, hemoglobin contains two alpha and
two gamma chains (this form of hemoglobin has a greater affinity for oxygen
than the adult form—why do you think this is important to the fetus?)
Collagen –The soluble form of collagen (tropocollagen) is found in the fetus and
in young connective tissues. It is composed of 3 collagen polypeptides hydrogen
bonded together. The triple-helix units are further organized into a pattern called
the quarter-stagger arrangement, forming fibrils. The staggered
arrangement allows for the deposition of inorganic crystals of calcium
hydroxyapatite. The combination of crystals and collagen creates a hard material
that still has some springiness. The quarter-stagger alignment of tropocollagen
forms collagen fibrils and the twisting of these fibrils into a 5- or 6 strand helix
builds the collagen fibers. With aging, the triple helixes are covalently crosslinked and form insoluble collagen. This cross-linking consists of covalent bonds
that link together two lysine residues on adjacent chains of the helix. (review this
arrangement in the chemical connection provided in your textbook).
Actin, another protein responsible for providing structure, also has a quaternary
structure suited for this job. Review its structure and how it works to provide
structure to the inside of a cell and how it coordinates its activity with collagen
outside of the cell.
Integral Membrane Proteins transverse partly or completely a membrane
bilayer. About 1/3 of all proteins are integral membrane proteins. Such proteins
are composed of both hydrophobic and hydrophilic areas (Why?). GFP is a barrel
shaped integral membrane protein (find its structure via the Internet).
Glycoproteins- proteins with covalently attached carbohydrate side chains.
Examples include plasma proteins, ribonucleases, hormones such as
thyroglubulin, storage proteins such as ovalbumins, and protective proteins such
as immunoglobulins. Primarily they have two types of linkages: O-link
saccharides are bonded to an –OH group on the serine or threonine side chain
of the protein. The linkage is a glycoside bond (draw it!). Examples are mucins,
which line the respiratory and gastrointestinal tracts and also the cervix. They
help to protect the underlying cells from harmful environmental agents. (What is
the slime that covers fish lobsters)?
N-linked saccharides (-C-N-) This bond exists between the N of an aspargine
residue of the protein chain and the C-1 (anomeric carbon) of Nacetylglucosamine. Immunoglobulins are an example of N-linked saccharides. In
many cases, the function involved in adding N-linked saccharides to the protein
core is to make them more water-soluble and to facilitate their transport within
the cell. A special class of glycoproteins is the proteoglycans. These compounds
have a protein core, and the side chains are long polysaccharide chains made of
acidic polysaccharides. They are essential parts of the extracellular matrix that
provide strength, flexibility, and elasticity in tissues such as skin, cartilage,
and the cornea of the eye.
Denaturation
Protein conformations are stabilized in their native states by secondary and
tertiary structures and through the aggregation of subunits. Any physical or
chemical agent that destroys these stabilizing structures changes the
conformation of the protein. The process is called denaturation. Review the table
on Modes of Protein Denaturation.
Denaturing Agent
Affected Regions
Examples
Heat
6 M urea
Detergents
Acids, bases
Salts
Reducing agents
Heavy metals
Alcohols
Review the chemical connection on laser surgery and protein denaturation. What
is a fiberscope? How is it being used in the USA? Elsewhere in the world?
PROBLEMS
1. Go to www.geospiza.com and review the tutorial on Protein
structure.
In the book: 6, 7, 8, 10, 18, 24, 28, 33, 35, 39, 43, 48, 52, 58, 69, 73, 75