The Chemical Basis of Life
All organisms are made
up of water, inorganic
ions, small molecules
(77% by weight) and
macromolecules (23%
by weight in E.coli).
white=hydrogen
red=oxygen
gray=carbon
yellow=phosphorus
blue=nitrogen
green=sulfur
Chemical Bonds
Atoms that make up a molecule are joined together by
Covalent Bonds, where electron pairs are shared between
atoms.
Atoms are most stable with a full outer electron shell
The number of bonds formed is determined by the
number of electrons needed to fill outer shell
Bond formation is accompanied by energy release
Breaking these covalent bonds requires energy
Examples: C-C, C-H or C-O covalent bonds require large
amounts of energy to break, so these bonds are stable under
most conditions
Fig. 2-1, Lodish et al., Mol. Cell Biol., 4th edition. WH Freeman
and Co., and Sumanas, Inc., 2000
Fig 2.1 Arrangement of electrons in
common atoms found in
biological molecules
Atoms can be joined by single bonds, or by bonds in which 2 pairs
of electrons are shared - double bond (O2); if 3 pairs are shared triple bond (N2)
The type of bond determines the shape of the molecular - atoms
joined by a single bond can rotate relative to one another; double &
triple bonds cannot . The double bond between the 2 carbon atoms
in Ethylene make the molecule rigid.
Fig. 2-3. Lodish et al., Mol. Cell Biol., 4th edition. WH Freeman and Co., and Sumanas, Inc., 2000
.
Polar and Non-polar molecules
In H2O (water), the - O-H bonds are polarized (one atom [O] is
partially negative; the other [H] is partially positive); water is
a polar molecule – and has an asymmetric charge distribution.
The water molecule has 2 polar –O-H bonds and therefore
has a dipole moment [a + charge separated from an equal –
charge]. This means that the area around the oxygen atom has
a mostly negative change and the areas around the hydrogen
atoms have a mostly positive charge.
Biologically important polar molecules have one or more
electronegative atoms - usually O, N, S and/or P). Because O is
more electronegative than H, shared electrons spend more time near
the O atom than the H atom.
Molecules without electronegative atoms & polar bonds (ex: C
& H) are nonpolar. These molecules are relatively inert.
Many biological molecules that we will study (proteins,
phospholipids, others) have both polar & nonpolar regions. This
influences what kind of bonds they can participate in.
δ, represents a partial charge
Fig. 2-5. Lodish et al., Mol. Cell Biol., 4th edition. WH Freeman and Co., and Sumanas, Inc., 2000
1
Noncovalent Bonds
Noncovalent bonds are very important in interactions between
molecules or different parts of a large biological molecule.
Fig 2.7,
Hydrogen bond
formation between
neighboring water
molecules
They are weaker than covalent bonds (require less energy to
break or make). Individual noncovalent bonds have low energies (~1 5 kcal/mole) and are easily broken & reformed.
They depend on attractive forces between positively &
negatively charged regions within same molecule or on two molecules
that are VERY close close to each other.
When many of them act together (in DNA, protein,
etc.), attractive forces add up & provide structure with stability.
(Cooperativity or “strength in numbers”)
Because they are weaker they are transient (temporary or short
lived) which explains why noncovalent bonds mediate the dynamic
interactions among molecules within the cell.
Noncovalent Bonds
Understanding noncovalent bonds and how and when they
work will help us to understand how one molecule interacts with
other molecules inside cells. For molecules to affect each other,
they must be close enough to form noncovalent bonds. There are
4 kinds of noncovalent bonds or interactions.
1. Ionic bonds (also called salt bridges) result from transfer
of electrons from 1 atom to another, leading to atoms with
positive & negative charges that attract each other. These
weak bonds can hold molecules together (ex: protein to DNA).
Also important between oppositely charged groups of a single
large molecule, such as inside protein centers where water is
not present.
3. Hydrophobic (water-fearing) interactions - not true
bonds since not usually thought of as attraction ,rather than a
chemical bond between hydrophobic molecules
Molecules with nonpolar covalent bonds lack
charged regions that can interact with water molecules & so are
insoluble in water
Hydrophobic molecules form into aggregates
minimizing exposure to water or other polar surroundings (ex: fat
on chicken soup).
These interactions are important inside proteins and
inside membranes. They occur between hydrophobic side (R)
groups of amino acids in the protein interior away from H2O.
They are also important inside membranes where they occur
among the nonpolar lipid “tails” of phospholipid molecules.
2. Hydrogen (H) bonds - hydrophilic (water-loving); enhance
solubility of molecules in water, & interactions with water.
When H is bonded to an electronegative atom (ex: O or N), the
shared electron pair goes toward electronegative atom, so H is
partially positive. H can be shared between two electronegative
atoms.
H bonds occur between most polar molecules.
H bonds are important in determining structure & properties of
water, also between polar groups & large biological molecules
(like DNA)
Strong collectively, but weak individually (2 - 5 kcal/mole in
aqueous solutions)
Fig. 2.3
Noncovalent
ionic bonds
between
protein and
DNA,
noncovalent
H bonds
between the
2 strands of
the DNA
double
helix.
2
4. van der Waals interactions (forces) - hydrophobic groups can
form weak bonds with each other based on electrostatic interactions.
More than 1 kind of noncovalent bond usually occurs between 2
molecules
When 2 molecules are very very close together, if there is a
temporary shift in charge, then transient charge separations
(dipoles) result. This can be enough to attract 2 molecules to each
other.
These interactions are VERY weak (0.1 - 0.3 kcal/mole) & very
sensitive to distance; molecules must be close together & have
complementary shapes that will permit the 2 molecules to closely
approach each other.
These interactions are important biologically, for example in
interactions between antibodies and viral antigens , and between
enzymes and substrates.
Acids, Bases and Buffers
Acid - a molecule able to release (or donate) a hydrogen ion.
Whenever a hydrogen atom loses an electron, a proton dissociates &
is released. A proton can combine with other molecules to form
H3O+, H2O, etc.
Base - any molecule capable of accepting a hydrogen ion (proton).
Amphoteric molecule - a molecule that can serve as both an acid & a
base (usually has both a positive & negative charge); water and amino
acids are examples.
pH (measure of H+ concentration) = - log10 [H+]
In pure water, [H+] = [OH-] = ~10-7 M, or pH=7
Biological processes are very sensitive to pH changes since pH affects
the ionic state of biological molecules.
Drawing of theoretical interactions between 2 proteins: 2 ionic bonds, 1 H
bond, 1 large combination of hydrophobic and van der Waals interactions.
This is the situation for most molecular interactions and provides binding
specificity. Fig. 2-17. Lodish et al., Mol. Cell Biol., 4th edition. WH Freeman and Co., and Sumanas, Inc., 2000
Under physiological conditions, amino acid side (R)
groups are charged (ex: -COOH becomes -COO- and -NH2
becomes -NH3+). Even small pH changes can disrupt shape &
activity of an entire protein, messing up biological reactions
Buffers minimize pH fluctuations. They bind or release H+ &
OH- ions depending on conditions, thus protecting organisms
& their cells.
Example: pH of fluid within the cell is regulated by phosphate
buffer system (H2PO4- & HPO4-2)
Excess H+ ions bind HPO4-2; excess OH- ions neutralized by
protons derived from H2PO4
Intracellular fluid stays at pH 7.4
Biological molecules: importance of the carbon atom. Fig 2.9
Functional Groups – atoms that behave as a group and help
give organic molecules their properties.
Examples:
Hydroxyl group - —OH; aquires charge —OMethyl group - —CH3
Carboxyl group - —COOH; acquires charge —COOSulfhydryl group - —SH; react to form disulfide
bonds in polypeptides
Carbon atoms can form covalent bonds with as many as 4
other carbon atoms, or can form double bonds. Steroids like
cholesterol include rings. The -OH group provides a small
hydrophilic end. In membranes the larger, hydrocarbon portion
of cholesterol increases membrane fluidity.
Amino group - —NH2; acquires charge —NH3+
Phosphate group - —H2PO3; acquires charge —PO3-2
3
Four families of biological molecules and macromolecules
A. Amino acids and proteins
B. Carbohydrates (CH2O)n Energy reserves
C. Lipids – fats, fatty acids, steroids, phospholipids
D. Nucleotides and nucleic acids
Fig. 2.11
Fig 2.10, Monomers and Polymers of Macromolecules
Fig. 2.17,
Three polysaccharides
with identical sugar
monomers but
different shapes and
properties.
Glucose subunits in 3
different types of
linkages.
Fig. 2.12, The Structures of Sugars.
Sugar (monomers) can be joined together by covalent glycosidic
bonds to form disaccharides (ex: sucrose) or short chains called
oligosaccharides. Polysaccharides are polymers of sugar unit
monomers joined by glycosidic bonds.
Fig. 2.19, Fats and fatty acids.
a-triglyceride, b-stearic acid,
c-tristeareate [another
triglyceride or neutral fat], dlinseed oil containing 2
different unsaturated fatty
acids due to C=C bonds
(yellow kinks).
Glycogen is branched
Starch is helical
Cellulose is linear
bundles
Fig 2.22, Phosphatidylcholine, a phospholipid. It is amphipathic.
Nonpolar, dissolve in
organic solvents like
chloroform but don’t dissolve
in water. Fatty acids have a
hydrophilic end (ex: glycerol)
and a hydrophobic end (HC
chains) and so are termed
amphipathic.
4
Proteins: General Information
Proteins: Building blocks (monomers) amino acids
Composed of H, C, O, N & usually S or P; very large
macromolecules; polymers of amino acids (the monomers, linked
together by peptide bonds)
• Traits & functions - more varied role than other molecules in
organisms (enzymes, structural or both); carry out almost all cell
activities; typical cell has ~10,000
• Catalyze and accelerate rate of metabolic reactions
Cytoskeletal elements serve as structural cables, provide
mechanical support in & out of cells
Hormones, growth factors, gene activators - regulators
Membrane receptors & transporters - determine what cell
reacts to, what can leave, enter cell
Contractile elements - biological movements
Antibodies and toxins, Form blood clot
• Transport substances from one part of body to another .
Composed of H, C, O, N & usually S or P; very large
macromolecules; polymers of amino acids (the monomers, linked
together by peptide bonds)
Proteins have more varied roles than other molecules in organisms.
They carry out almost all cell activities; typical cell has ~10,000
• Catalyze and accelerate rate of metabolic reactions
• Cytoskeletal elements serve as structural cables, provide
mechanical support in & out of cells
• Hormones, growth factors, gene activators – regulators
• Membrane receptors & transporters - determine what cell reacts
to, what can leave, enter cell
• Contractile elements - biological movements
• Antibodies and toxins, Form blood clot
• Transport substances from one part of body to another .
Amino acids:
20 unique amino acids, differ in their R groups
All 20 have the same general structure
Generalized Amino Acid
R
H
O
N
H
C
H
C
Generalized Amino Acid
Physiological pH
H R
O
H
OH
+
N
C
H H
R = Radical or Side Group
C
O
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
Fig ure 2.24
Fig. 2.24 Formation of a peptide bond. Proteins are always
synthesized in the amino-to-carboxyl direction.
Fig. 2.26 Amino acid
structures – 4 types,
get their properties
from their side R
groups:
Polar charged
Polar uncharged
Nonpolar
Other
Character of amino R
groups is very
important to protein
structure & function;
R groups determine
what kind of
noncovalent bonds
can form
2 ways that protein structures are shown. The protein is Ras,
its substrate shown in blue, is guanosine diphosphate. On the
right is the water-accessible surface: + charges are blue and –
charge are red. Charges are not evenly distributed, and the
surface is very bumpy.
Fig. 3-5. Lodish et al., Mol. Cell Biol., 4th edition. WH Freeman and Co., and Sumanas, Inc., 2000
5
Other amino acids: in addition to the 20 essential amino acids, other
amino acids are sometimes found in polypeptides (ex:
hydroxyproline, hydroxylysine).
From alterations of R groups of the 20 amino acids after their
incorporation into polypeptide. [post-translational modification]
The changes greatly change properties & function of a
protein, increasing or decreasing its solubility or modifying its
interaction with other molecules. Why?
Conjugated proteins - involve another type of molecule attached
covalently or noncovalently to the protein
Nucleoproteins - protein + nucleic acids
Lipoproteins - protein + lipids
Glycoproteins - protein + carbohydrate
Various low-molecular-weight materials, like metals & metalcontaining groups, are often attached
Protein structure
The sequence of amino acids in the protein (polypeptide)
determines its structure and all its properties. The amino acid
sequence in referred to as the primary structure of the protein.
The genome (DNA) contains instructions for the amino acid
sequences. Sickle cell anemia – one amino acid change in Hb:
valine [nonpolar] instead of glutamic acid [charged, polar]
Secondary structure refers to the conformation or shape of
parts of the polypeptide chain. These conformations are present
in most proteins. The alpha (α) helix and beta (β)-pleated sheet
are secondary structures that are stabilized by H bonds between
amino acids of the same polypeptide chain.
Alpha helices give strength and rigidity to that part of the
protein – wool has many alpha helical regions. Beta-pleated
sheets give flexibilty and resistance to tensile (pulling) forces.
Silk has mostly beta-pleated sheets as its secondary structure.
Parallel ÎÎÎÎ
ÎÎÎÎ
Antiparallel ÎÎÎÎ
ÍÍÍÍ
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
Fig ure 2.30
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Fig. 2.30 Alpha helix. R groups are on the outside of the helix.
Some α helices are amphipathic [have both hydrophilic and
hydrophobic regions].
Karp/CELL & MOLECULAR BIOLOGY 3E
Fig ure 2.31
Fig. 2.31 Beta-pleated sheet. Sheets in the same polypeptide can
run either parallel or antiparallel. R groups extend up and down,
out of the sheet.
Tertiary structure – conformation of the entire protein. Its 3D shape,
stabilized by noncovalent bonds. Most intracellular proteins are
globular while extracellular and structural proteins are more fibrous.
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
Figure 2.32
Fig. 2.32. Ribbon model of ribonuclease. Arrows indicate N-terminal to
C-terminal direction. Green, loops and turns. Blue, disulfide bonds. Loops
and turns of the polypeptide chain connect the alpha helices and beta sheet
regions of the protein.
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
Fig ure 2.35
Fig. 3.35, Noncovalent bonds maintain protein conformation.
6
In green, an
immunoglobulin
domain in Neu
Protein domains and motifs
Domains - proteins are often composed of 2 or more
distinct modules or structural units (domains) that
fold independently of one another; often these
represent parts of the protein that have separate
functions
In pink, a
membranespanning domain
Tissue
plasminogen
activator
DOMAINS
Schematic diagrams of some proteins, showing their modular or
domain nature. The epidermal growth factor domain, EGF in
orange Fig. 3-10. Lodish et al., Mol. Cell Biol., 4 edition. WH Freeman and Co., and Sumanas, Inc., 2000
th
Motifs are smaller regions of proteins, commonly
occurring substructures that are combinations of α
helices and β strands
Proteins like these with more than 1 domain may have arisen
during evolution by fusion of genes coding for different ancestral
proteins; each domain once was separate molecule
Domain mix-match creates proteins with unique combinations of
activities
MOTIFS
Proteins are dynamic structures and small changes occur within
proteins.
Internal movements can be studied with NMR, and we see
constant thermal motion in molecules.
Examples:
random, small fluctuations in bond arrangement
shifts in H bonds
waving of external side chains (R groups)
aromatic ring rotation about single bonds (in Phe, Tyr)
Figure 2.37
Figure 2.38
The coiled coil [left] motif in myosin. 2 α helices wrapped around
each other. The β barrel motif [right] of triose phosphate isomerase,
with β strands of the barrel viewed from the side
Quaternary Structure & Multiprotein Complexes
Quaternary (4°) structure is the linking of polypeptide chains
to form multisubunit functional protein via intermolecular R group
interactions. Requires more than 1 polypeptide chain.
Multiprotein complexes – made up of different
proteins, each with a specific function, that become physically
associated to form a much larger complex.
• Efficient – since proteins are physically associated, product of
one enzyme can be passed directly to next enzyme in sequence;
prevents dilution in cell's aqueous medium
• Some associations are stable; some not
• Stabilized by noncovalent bonds
A hemoglobin molecule, composed of 2 α-globin chains and 2 βglobin chains joined by non-covalent bands. Each globin can bind 1 O2
molecule. Binding of O2 to 1 polypeptide causes a change in
conformation in the other globins that makes them bind O2 more tightly.
Each polypeptide binds heme [in red], an iron-containing complex that
actually binds the O2.
Figure 2.40b
Often interactions between proteins in the complex are regulated
by changes like phosphate addition to key amino acids.
Example: E. coli pyruvate dehydrogenase - 60 polypeptide
chains constituting 3 different enzymes; a stable multiprotein
complex whose enzyme activities catalyze reaction series
connecting 2 metabolic pathways: glycolysis & TCA cycle
7
Figure 2.45
Denaturation and refolding of ribonuclease. Top left, native
enzyme containing disulfide bonds (red=S), and many noncovalent
bonds not shown. Refolding occurs after the denaturing agents are
removed.
Figure 2.43
Protein folding – one possible series of steps
1. generation of much of 2° structure (α-helix & β-pleated sheet)
2. soluble protein folding then driven by hydrophobic bonds; nonpolar
groups forced into central core
3. Polypeptide is collapsed into compact state (molten globule) that
resembles native protein, but molten globules still lack many R group
bonds that maintain final 3° structure
4. noncovalent bonds between R groups (tighter packing) & covalent
disufide bonds = native state
Molecular chaperones
Proteins that help other proteins fold properly into their final
3D conformation. Not specific for a single protein.
Chaperones can sense misfolded proteins.
They appear to work by binding exposed hydrophobic patches
on surfaces of partially folded intermediates, preventing them
from reaggregating into incorrect structures.
They provide an environment that allows folding & provide
no information essential for the process, so proteins still selfassemble.
Nucleic Acids – the third class of biopolymers
Primarily involved in storage & transmission of genetic information
May also be structural (rRNA) or
catalytic (ribozymes)
Nucleotides are their subunits,
phosphodiester bonds join nucleotides together, in a 5’-to-3’
orientation
Experimental Pathways, Figure 4
Illustration of proposed steps in molecular chaperones
GroEL-GroES-assisted folding of a polypeptide.
DNA / RNA Differences: 1
5' CH
2
5' CH
2
OH
O
1'
3'
O
OH
4'
H H
OH
H H
2'
OH
H
Deoxyribose
OH
4'
1'
H H
3'
H H
2'
OH
OH
Ribose
In DNA the sugar is deoxyribose, in RNA the sugar is ribose
All nucleotides have a common structure
Fig. 4-1. Lodish et al., Mol. Cell Biol.,
4th
edition. WH Freeman and Co., and Sumanas, Inc., 2000
DNA / RNA Differences: 2
DNA is usually double-stranded; RNA is almost always singlestranded.
8
Figure 2.48
DNA / RNA Differences: 3
The nitrogen-containing bases in DNA are A, T, G, C; in
RNA they are A, U, G, C. No U in DNA, no T in RNA.
Purines have 2 rings.
Adenine (A)
Guanine (G)
Pyrimidines have 1 ring.
Thymine (T)
Uracil (U)
Cytosine (C)
In double-stranded DNA, a
T is always paired with an
A, and a C is always paired
with a G.
Fig. 2.49, Nitrogenous bases in nucleic acids
Double-stranded DNA forms a right-handed double helix, due to
the geometry of the sugar-phosphate backbone of DNA. The helix
has a major groove and a minor groove.
Fig. 4-5. Lodish et al., Mol. Cell Biol., 4th edition. WH Freeman and Co., and Sumanas, Inc., 2000
A single strand of DNA containing 3 bases:
cytosine (C), adenine (A) , and guanine (G).
Fig. 4-3. Lodish et al., Mol. Cell Biol.,
and Co., and Sumanas, Inc., 2000
4th
edition. WH Freeman
Each nucleic acid molecule has
a 5’-PO4 end and a 3’-OH end.
Synthesis is from 5’-to-3’
Sometimes when proteins noncovalently bind to DNA, it causes
the DNA to bend. Here, when the TATA box-binding protein
binds to DNA it affects the winding and direction of the double
helix. Fig. 4-7. Lodish et al., Mol. Cell Biol., 4 edition. WH Freeman and Co., and Sumanas, Inc., 2000
th
Denaturation and renaturation of double-stranded DNA molecules
(Breaking and reforming noncovalent hydrogen bonds)
Fig. 4-8. Lodish et al., Mol. Cell Biol., 4th edition. WH Freeman and Co., and Sumanas, Inc., 2000
RNA can assume complex shapes. A ribosomal RNA from a
bacterial small ribosomal subunit. This is a single molecule
Figure 2.50a
with lots of H bonds (yellow regions).
9