introduction

Carbohydrates are carbon compounds that contain large quantities of hydroxyl

groups. The simplest carbohydrates also contain either an aldehyde moiety (these
are termed polyhydroxyaldehydes) or a ketone moiety (polyhydroxyketones). All
carbohydrates can be classified as either monosaccharides, oligosaccharides or
polysaccharides. Anywhere from two to ten monosaccharide units, linked by
glycosidic bonds, make up an oligosaccharide. Polysaccharides are much larger,
containing hundreds of monosaccharide units. The presence of the hydroxyl groups
allows carbohydrates to interact with the aqueous environment and to participate in
hydrogen bonding, both within and between chains. Derivatives of the
carbohydrates can contain nitrogens, phosphates and sulfur compounds.
Carbohydrates also can combine with lipid to form glycolipids or with protein to
form glycoproteins.

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Carbohydrate Nomenclature

The predominant carbohydrates encountered in the body are structurally related to

the aldotriose glyceraldehyde and to the ketotriose dihydroxyacetone. All
carbohydrates contain at least one asymmetrical (chiral) carbon and are, therefore,
optically active. In addition, carbohydrates can exist in either of two conformations,
as determined by the orientation of the hydroxyl group about the asymmetric
carbon farthest from the carbonyl. With a few exceptions, those carbohydrates that
are of physiological significance exist in the D-conformation. The mirror-image
conformations, called enantiomers, are in the L-conformation.

Structure glyceraldehyde enantiomers

Structures of Glyceraldehyde Enantiomers

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Monosaccharides
The monosaccharides commonly found in humans are classified according to the
number of carbons they contain in their backbone structures. The major
monosaccharides contain four to six carbon atoms.

Carbohydrate Classifications

# Carbons Category Name Relevant examples

3 Triose Glyceraldehyde, Dihydroxyacetone

4 Tetrose Erythrose

5 Pentose Ribose, Ribulose, Xylulose

6 Hexose Glucose, Galactose, Mannose, Fructose

7 Heptose Sedoheptulose

9 Nonose Neuraminic acid, also called sialic acid

The aldehyde and ketone moieties of the carbohydrates with five and six carbons
will spontaneously react with alcohol groups present in neighboring carbons to
produce intramolecular hemiacetals or hemiketals, respectively. This results in the
formation of five- or six-membered rings. Because the five-membered ring structure
resembles the organic molecule furan, derivatives with this structure are termed
furanoses. Those with six-membered rings resemble the organic molecule pyran
and are termed pyranoses

Such structures can be depicted by either Fischer or Haworth style diagrams. The
numbering of the carbons in carbohydrates proceeds from the carbonyl carbon, for
aldoses, or the carbon nearest the carbonyl, for ketoses.

Cyclic Fischer projection of glucose Haworth projection of glucose

Cyclic Fischer Projection of α-D-Glucose

Haworth Projection of α-D-Glucose

The rings can open and re-close, allowing rotation to occur about the carbon
bearing the reactive carbonyl yielding two distinct configurations (α and β) of the
hemiacetals and hemiketals. The carbon about which this rotation occurs is the
anomeric carbon and the two forms are termed anomers. Carbohydrates can
change spontaneously between the α and β configurations: a process known as
mutarotation. When drawn in the Fischer projection, the α configuration places the
hydroxyl attached to the anomeric carbon to the right, towards the ring. When
drawn in the Haworth projection, the α configuration places the hydroxyl downward.

The spatial relationships of the atoms of the furanose and pyranose ring structures
are more correctly described by the two conformations identified as the chair form
and the boat form. The chair form is the more stable of the two. Constituents of the
ring that project above or below the plane of the ring are axial and those that
project parallel to the plane are equatorial. In the chair conformation, the
orientation of the hydroxyl group about the anomeric carbon of α-D-glucose is axial
and equatorial in β-D-glucose.

Chair form of glucose

Chair form of α-D-Glucose

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Disaccharides

Covalent bonds between the anomeric hydroxyl of a cyclic sugar and the hydroxyl
of a second sugar (or another alcohol containing compound) are termed glycosidic
bonds, and the resultant molecules are glycosides. The linkage of two
monosaccharides to form disaccharides involves a glycosidic bond. Several
physiogically important disaccharides are sucrose, lactose and maltose.

Sucrose: prevalent in sugar cane and sugar beets, is composed of glucose and
fructose through an α–(1,2)–β-glycosidic bond.

Structure of sucrose

Sucrose
Lactose: is found exclusively in the milk of mammals and consists of galactose and
glucose in a β–(1,4) glycosidic bond.

Structure of lactose

Lactose

Maltose: the major degradation product of starch, is composed of 2 glucose

monomers in an α–(1,4) glycosidic bond.

Structure of maltose

Maltose

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Polysaccharides

Most of the carbohydrates found in nature occur in the form of high molecular
weight polymers called polysaccharides. The monomeric building blocks used to
generate polysaccharides can be varied; in all cases, however, the predominant
monosaccharide found in polysaccharides is D-glucose. When polysaccharides are
composed of a single monosaccharide building block, they are termed
homopolysaccharides. Polysaccharides composed of more than one type of
monosaccharide are termed heteropolysaccharides.

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Glycogen

Glycogen is the major form of stored carbohydrate in animals. This crucial molecule
is a homopolymer of glucose in α–(1,4) linkage; it is also highly branched, with α–
(1,6) branch linkages occurring every 8-10 residues. Glycogen is a very compact
structure that results from the coiling of the polymer chains. This compactness
allows large amounts of carbon energy to be stored in a small volume, with little
effect on cellular osmolarity.
Structure of glycogen

Section of Glycogen Showing α–1,4– and α–1,6–Glycosidic Linkages

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Starch

Starch is the major form of stored carbohydrate in plant cells. Its structure is
identical to glycogen, except for a much lower degree of branching (about every
20–30 residues). Unbranched starch is called amylose; branched starch is called
amylopectin.

An Introduction to Protein Structure

Doug Brutlag

(You will need Adobe Acrobat Reader to read these papers)

Courses

Mike Levitts protein structure course:

http://stanford-online.stanford.edu/wintercourses/asp/coursePage.asp?
URL=http://ww.stanford.edu/wintercourses/sb228course.xml

Russ Altman's Algorithm Course

http://stanford-online/springcourses/asp/coursePage.asp?
URL=http://ww.stanford.edu/springcourses/bmi214course.xml
Introduction

Amino Acids

Peptide Bonds

Forces stabilizing Proteins

Van der Waals

Hydrophobic Force

Electrostatic Forces

Dipole moments

Hydrogen Bonds

Colvalent Bonds

Preferred Secondary Structure

References

Introduction
Proteins are more flexible than nucleic acids in structure because of both the larger
number of types of residues and the increased flexibility and lower charge density
of the polypeptide backbone. Proteins can serve many roles in the cell; as enzymes,
as structural components, membrane components, as templates, as substrates and
as products of reactions. Many aspects of protein metabolism are catalyzed and
regulated by the cell. These include their rates of expression, their translation, their
folding, their targeting to the proper cellular location and their degradation.
Proteins, and the functions they catalyze, are the end-product of the genes that
encode them. Some of the most important functions of proteins are to regulate the
expression of other proteins.

In this lecture we will discuss the components of proteins, their covalent structure,
their non-covalent interactions, higher order structures such as motifs and domains
and then give several examples of different types of protein folds. It will be
extremely useful for you to down load the Kinemage 4.2 program and the Proteach
Kinemage collection for reviewing the material presented in the class. Pointers to
the locations to obtain this program and the Proteach files are on the course Web
page.

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Amino Acids

The amino acid residues of proteins are defined by an amino group and a carboxyl
group connected to an alpha carbon to which is attached a hydrogen and a side
chain group R. The smallest amino acid, glycine, has a hydrogen atom in place of a
side chain. All other amino acids have distinctive R groups. Because the alpha
carbon of the other amino acids have four different constituents, the alpha carbon
atom is an asymmetric center and most naturally occurring amino acids are in the L
form.

Amino acids fall into several naturally occurring groups including hydrophobic,
hydrophilic, charged, basic, acidic, polar but uncharged, small polar, small
hydrophobic, large hydrophobic, aromatic, beta-branched, sulfur containing etc.
Hydrophobic amino acids, sometimes called non-polar amino acids, reside primarily
on the interior of the protein. Hydrophilic amino acids, sometimes called polar
amino acids, reside primarily on the exterior of the protein. Many amino acids will
fall into more than one group since each amino acid side chain has several
properties.

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Peptide Bonds

Amino acids are linked to each other by peptide bonds. Peptide bonds are formed
by the dehydration of the carboxyl group of one amino acid and the amino group of
the next. Because of the resonance structure of the electron orbitals on the amino
and carboxyl groups, the peptide bond is planar. The dihedral angle between the
amino group and the alpha carbon and the alpha carbon and the carboxyl group are
free to rotate and these angles are referred to as the phi-psi angles. Glycine, with
the smallest side chain, has the most conformational flexibility about the phi-psi
angles. Other amino acids are restricted in their rotation due to steric hindrance
from the side chains. The rotation of the dihedral angles of side chains about the
different bonds, referred to as chi-1, chi-2 etc., are also restricted for different side
chain elements. Proline, which in which the side chain is linked back to the
backbone is the most restricted; only two conformations are permitted.

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Forces determining protein structure

Several covalent and non-covalent forces determine protein structure. The list of
forces include (not exhaustive):

1) van der Waals interactions between immediately adjacent atoms: These non-
covalent forces result from the attraction of one atoms nucleus for the electrons of
another atom in a non-covalent form (no sharing of orbitals). These forces are much
weaker than covalent interactions and the interaction distances are much longer
than covalent bonds and much shorter than the other non-covalent interactions.
Van der Waals interactions occur at distances between 3 and 4 Å. They are very
weak beyond 5Å and electron repulsion prevents atoms from getting much closer
than 3Å. Van der Waals interactions are non-directional and very weak. However,
significant energy of stabilization can be obtained in the central hydrophobic core of
proteins by the additive effect of many such interactions.

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2) Hydrophobic force: The hydrophobic force is really a negative non-covalent

force. The presence of hydrophobic side chains in aqueous solution induces the
formation of structured water (clathrate cages of water molecule form, like
miniature ice crystals about the hydrophobic side chains). This reduction in entropy
of the water molecules is a very unfavorable resulting in a strong force to keep
hydrophobic side chains buried in the interior of the protein. The hydrophobic force
is one of the largest determinants of protein structure. Most secondary structural
elements we will discuss have an amphipathic nature, one hydrophobic side and
one hydrophilic side because the structure lies on the surface of the protein.

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3) Electrostatic forces: The attraction of oppositely charged side chains can form
salt-bridges that stabilize secondary and tertiary structures. The electrostatic force
is quite strong, falling off as the square of the distance between the charged atoms.
It also depends heavily on the dielectric constant of the medium in which the
protein is dissolved. It is strongest in a vacuum and 80 fold weaker in water and
weaker still at elevated salt solutions. Water and ions can shield electrostatic
interactions reducing both their strength and distance over which they operate.

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4) Dipole moments. Dipole moments are caused by pairs of charges separated by

a larger distance than permitting a salt- or ion bridge. The dipole moment gives rise
to an electric field along the entire length of a structural element. Dipole moments
are often used by proteins to attract and position charged substrates and products.
The peptide chain naturally has a dipole moment because the N-terminus carries
about 1/2 a positive charge and the C-terminus carries about 1/2 unit of negative
charge. The alpha helix is known to carry a partial negative charge at its C-terminus
and a positive charge at its N-terminus. In order to help neutralize this charge
distribution, alpha helices often have acidic residues near their N-terminus and a
basic residue near their C-terminus.

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5) Hydrogen bonds: Hydrogen bonds occur when a pair of nucleophilic atoms

such as oxygen and nitrogen share a hydrogen between them. The hydrogen may
be covalently attached to either nucleophilic atom (the H-bond donor) and shared
with the other atom (the H-bond receptor). H-bonds are directional and their
strength deteriorates dramatically as the angle changes. Hydrogen bonds do not, in
general, contribute to the net stabilization energy of proteins because the same
groups that hydrogen bond to each other in a native protein structure, can
hydrogen bond to water in the denatured state. However, hydrogen bonds are
extremely important because of their directionality, they can control and limit the
geometry of the interactions between side-chains. This is shown most dramatically
in patterns of hydrogen bonding between the carboxyl groups and the amino groups
in the peptide backbone that give rise to alpha helix and beta strand conformations.

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6) Covalent bond distances and torsion angles: The major properties of the
covalent bonds hold proteins together are their bond distances and bond angles. In
particular, the bond angles between two adjacent bonds on either side of a single
atom, or the dihedral angles between three contiguous bonds and two atoms
control the geometry of the protein folding. The preferred dihedral angles for
different secondary structural elements are discussed below.

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Preferred secondary structures

Alpha helices are the most well known element of protein structure, proposed by
Pauling and confirmed in the first structure determined, myoglobin, alpha-helices
have distinctive patterns of hydrogen bonding and phi-psi angles. They are
generally between 5 and 20 residues in length, but some proteins and coiled-coil
structures can be considerably longer. The carboxyl groups of the backbone
hydrogen bond to the amino group of a residue four amino acids distant along the
chain. Alpha helices generally have a pitch of about 3.5 residues per turn, but there
are forms of helices with tighter (3 residues per turn) and longer (4 residues per
turn).

Alpha helices can be coiled about them selves in both two coil, three coil and four
coil (four helix bundle) conformations. Alpha helices can exist internal in proteins
(generally hydrophobic), on the surface of proteins (amphipathic) or in membranes
(hydrophobic). Alpha helices can span membranes either singly or in groups.

Beta-strands are an extended form in which the side chains alternate on either side
of the extended chain. The backbones of beta-strands hydrogen bond with the
backbone of an adjacent beta strand to form a beta-sheet structure. The strands in
a beta sheet can be either parallel or anti-parallel and the hydrogen-bonding
pattern is different between the two forms. Anti-parallel beta stands are often linked
by short loops containing 3-5 residues in highly characteristic conformations. Longer
loops are occasionally found where the loop plays an important role in substrate
binding or an active site. The antigen-combining site of the immunoglobulins is an
important example of this.

Beta sheets can be internal to a protein (largely hydrophobic) or on the surface in

which case they are amphipathic, with every other amino acid side chain alternating
between hydrophobic and hydrophilic nature.

The peptide backbone is constrained by steric hindrance, and hydrogen bonding

patterns that limit its torsional angles (phi-psi angles) to certain limits. Plots of phi
versus psi dihedral angles for amino acid residues are called Ramachandran plots.
One can tell if the backbone is following a helical or a an extended beta strand
structure based on the values of the phi-psi angles over a length of backbone
(usually 3-4 residues is sufficient).