Académique Documents
Professionnel Documents
Culture Documents
Chapter 2 Macromolecules
TOPICS
A. Water in Living Systems 1. Chemical Bonding: Strong and Weak Chemical Bonds 2. Overview of macromolecules and water as the Solvent of Life
B. Molecular Structure of Living Matter 1. Polysaccharides 2. Lipids 3. Nucleic Acids 4. Amino Acids and the Peptide Bonds 5. Proteins: Structure and Function
Between nonmetallic elements of similar electronegativity. Formed by sharing electron pairs Stable non-ionizing particles, they are not conductors at any state Examples; O2, CO2, C2H6, H2O, SiC
Bonds in all the polyatomic ions and diatomics are all covalent bonds
H2 or Cl2
2. Covalent bonds- Two atoms share one or more pairs of outer-shell electrons.
Oxygen Atom
Oxygen Atom
H2O
- water is a polar molecule because oxygen is more electronegative than hydrogen, and therefore electrons are pulled closer to oxygen.
Covalent bonds (Figure 3.1) are strong bonds that bind elements in macromolecules.
Covalent Bonding
Weak bondssuch as hydrogen bonds (Figure 3.2), van der Waals forces, and hydrophobic interactionsalso affect macromolecular structure, but through more subtle atomic interactions.
HYDROGEN
BONDING
Hydrogen Bonding
VAN
Van der Waals forces are made of dipole-dipole and London dispersion forces
Group 4A hydrides
Groups 4, 5, 6A hydrides
Intermolecular Forces: are generally much weaker than covalent or ionic bonds. Less energy is thus required to vaporize a liquid or melt a solid. Boiling points can be used to reflect the strengths of intermolecular forces (the higher the Bpt, the stronger the forces)
One of the most remarkable consequences of H-bonding is found in the lower density of ice in comparison to liquid water, so ice floats on water. In most substances the molecules in the solid are more densely packed than in the liquid. A given mass of ice occupies a greater volume than that of liquid water. This is because of an ordered open H-bonding arrangement in the solid (ice) in comparison to continual forming & breaking H-bonds as a liquid.
A dipole-dipole force exists between neutral polar molecules Polar molecules attract one another when the partial positive charge on one molecule is near the partial negative charge on the other molecule The polar molecules must be in close proximity for the dipole-dipole forces to be significant Dipole-dipole forces are characteristically weaker than ion-dipole forces Dipole-dipole forces increase with an increase in the polarity of the molecule
Boiling points increase for polar molecules of similar mass, but increasing dipole:
Molecular Mass Dipole moment, (amu) u (D) Boiling Point (K)
Substance
Propane
Dimethyl ether Methyl chloride Acetaldehyde Acetonitrile
44
46 50 44 41
0.1
1.3 2.0 2.7 3.9
231
248 249 294 355
London Dispersion Forces significant only when molecules are close to each other
Due to electron repulsion, a temporary dipole on one atom can induce a similar dipole on a neighboring atom
The ease with which an external electric field can induce a dipole (alter the electron distribution) with a molecule is referred to as the "polarizability" of that molecule The greater the polarizability of a molecule the easier it is to induce a momentary dipole and the stronger the dispersion forces Larger molecules tend to have greater polarizability Their electrons are further away from the nucleus (any asymmetric
A variety of functional groups containing carbon atoms are common in biomolecules (Table 3.1) and in the folding of complex biomolecules.
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.
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 are amphipathicthey 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, nonfatty acid groups connected to carbon 1 or 3 of glycerol (Figure 3.7).
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.
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).
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.
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.
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).
Similarly, association of several polypeptides results in a unique, predictable final structure (quaternary structure) (Figure 3.18).
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).