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INTRODUCTION TO BIOTECHNOLOGY

Chapter 2 Macromolecules

Presented by: Engr. Juvyneil E.Cartel

Instructor, ChE Dept., EVSU

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

NONPOLAR COVALENT BONDS

H2 or Cl2

2. Covalent bonds- Two atoms share one or more pairs of outer-shell electrons.

Oxygen Atom

Oxygen Atom

Oxygen Molecule (O2)

POLAR COVALENT BONDS

H2O

Polar Covalent Bonds: Unevenly matched, but willing to share.

- 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

DER WAALS FORCES

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)

Hydrogen Bonding : the attractive force between hydrogen in a polar


bond (particularly H-F, H-O, H-N bond) and an unshared electron pair on a nearby small electronegative atom or ion Very polar bond in H-F. The other hydrogen halides dont form hydrogen bonds, since H-X bond is less polar. As well as that, their lone pairs are at higher energy levels. That makes the lone pairs bigger, and so they don't carry such an intensely concentrated negative charge for the hydrogens to be attracted to.

Hydrogen Bonding & Water

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.

Weaker Intermolecular Forces Ion-Dipole Forces


An ion-dipole force is an attractive force that results from the electrostatic attraction between an ion and a neutral molecule that has a dipole. Most commonly found in solutions. Especially important for solutions of ionic compounds in polar liquids. A positive ion (cation) attracts the partially negative end of a neutral polar molecule. A negative ion (anion) attracts the partially positive end of a neutral polar molecule.
Ion-dipole attractions become stronger as either the charge on the ion increases, or as the magnitude of the dipole of the polar molecule increases.

Dipole-dipole Attractive Forces

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

Prof. Fritz London

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

distribution produces a larger dipole due to larger charge separation)


The number of electrons is greater (higher probability of asymmetric distribution) thus, dispersion forces tend to increase with increasing molecular mass Dispersion forces are also present between polar/non-polar and polar/polar molecules (i.e. between all molecules)

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.

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 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).

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.

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

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

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