Transcript Freeman 1e: How we got there

Chapter 3
Macromolecules
Chemical Bonding and Water
in Living Systems
Strong and Weak Chemical Bonds
• Covalent bonds (Figure 3.1) are strong
bonds that bind elements in macromolecules.
Covalent Bonding
• Weak bonds—such as hydrogen bonds
(Figure 3.2), van der Waals forces, and
hydrophobic interactions—also affect
macromolecular structure, but through more
subtle atomic interactions.
Hydrogen Bonding
• A variety of functional groups containing
carbon atoms are common in biomolecules
(Table 3.1) and in the folding of complex
biomolecules.
An Overview of
Macromolecules and Water as
the Solvent of Life
• Understanding the relative composition of a
bacterial cell (Table 3.2) helps us to
understand the metabolic needs of the
organism.
• The bacterial cell is about 70% water, with
over one-half of the dry portion being made
up of protein and one-quarter being made up
of nucleic acids.
• Proteins (Figure 3.3a) are polymers of
monomers called amino acids. Nucleic acids
(Figure 3.3b) are polymers of nucleotides and
are found in the cell in two forms, ribonucleic
acid (RNA) and deoxyribonucleic acid
(DNA).
• Lipids (Figure 3.3d) have both hydrophobic
(nonpolar) and hydrophilic (polar)
properties. They play crucial roles in
membrane structure and as storage depots for
excess carbon.
• The cohesive and polar properties of water
promote chemical interaction and help shape
macromolecules into functional units.
PART II Noninformational
Molecules
Polysaccharides
• Sugars combine into long polymers called
polysaccharides.
• The relatively simple yet eloquent structure
of the polysaccharides (Figure 3.4) and their
derivatives (Figure 3.5) makes them the most
abundant natural polymer on Earth and allows
them to be used for metabolism, as a
component of information transfer molecules
(Figure 3.8), and for cellular structure.
Nucleotides
• Glycosidic bonds (Figure 3.6) combine
monomeric units (monosaccharides) into
polymers (polysaccharides), all with a carbonwater (carbohydrate) chemical composition
approaching (CH2O)n.
• The two different orientations of the
glycosidic bonds that link sugar residues
impart different properties to the resultant
molecules. Polysaccharides can also contain
other molecules such as proteins or lipids,
forming complex polysaccharides.
Lipids
• Lipids are amphipathic—they have both
hydrophilic and hydrophobic components.
This property makes them ideal structural
components for cytoplasmic membranes.
• Simple lipids (triglycerides) are composed
of a glycerol molecule with fatty acids
(Figure 3.7) covalently linked in ester
(Bacteria) or ether (Archaea) bonds.
• Many lipids draw their polar characteristics
from complex, non–fatty acid groups
connected to carbon 1 or 3 of glycerol (Figure
3.7).
Informational Molecules
Nucleic Acids
• The nucleic acids deoxyribonucleic acid
(DNA) and ribonucleic acid (RNA) are
macromolecules composed of monomers
called nucleotides. Therefore, DNA and RNA
are polynucleotides. Without a phosphate, a
base bonded to its sugar is referred to as a
nucleoside.
• All nucleotides have a phosphate group and
a five-carbon sugar, with the sugar being
ribose (–OH at carbon 2) in RNA or
deoxyribose (–H at carbon 2) in DNA (Figure
3.10).
• It is the primary structure, or order, of
pyrimidine and purine bases (Figure 3.9)
connected by the phosphodiester bond
(Figure 3.11) that gives nucleic acids their
information-storing capacity.
• Both RNA and DNA are informational
macromolecules. RNA can fold into various
configurations to obtain secondary structure.
Amino Acids and the Peptide
Bond
• Although the -carbon of an amino acid can
form four covalent bonds like other carbon
atoms, the groups bonding to the -carbon
are very specific.
• Hydrogen, an amino functional group
(–NH2), and a carboxylic acid functional group
(–COOH) are a part of each amino acid
(Figure 3.12a).
• The fourth bond can be one of 21 common
side groups, which may be ionic, polar, or
nonpolar (Figure 3.12b). It is the
heterogeneity of these side groups that defines
the properties of a peptide or protein.
• Through a dehydration synthesis reaction,
amino acids can bond covalently by forming a
peptide bond between the amino and
carboxylic acid groups.
• Isomers are molecules that have the same
molecular composition but have different
structural form (Figure 3.15a).
Isomers – Ball and Stick Model
• Enantiomers contain the same molecular
and structural formulas, except that one is a
"mirror image" of the other; these are given
the designations d and l (Figure 3.15b).
Enantiomers
• These different structural forms can greatly
affect metabolism; for example, whereas
sugars are typically d enantiomer, amino acids
typically exist in the l form.
Proteins: Primary and
Secondary Structure
• The sequence of covalently linked amino
acids in a polypeptide is the primary
structure. When many amino acids are
covalently linked via peptide bonds, they
form a polypeptide.
• Secondary structure results from hydrogen
bonding that produces an -helix
("corkscrew") or -sheet ("washboard")
formation, or domain (Figure 3.16). Proteins
may have an assortment of either or both
domains.
Secondary structure of proteins- alpha-helix
Secondary structure of proteins- beta sheets
Proteins: Higher Order Structure
and Denaturation
• The polar, ionic, and nonpolar properties of
amino acid side "R" chains cause regions of
attraction and repulsion in the amino acid
chain, thus creating the folding of the
polypeptide (i.e., tertiary structure) (Figure
3.17).
Tertiary structure of polypeptides
• Similarly, association of several
polypeptides results in a unique, predictable
final structure (quaternary structure)
(Figure 3.18).
Quaternary structure of human hemoglobin
• It is this final orientation and folding that
dictate the usefulness of a protein as a catalyst
(enzyme) or its structural integrity in the cell.
Destruction of the folded structure by
chemicals or environmental conditions is
called denaturation (Figure 3.19).
Denaturation and renaturation of ribonuclease