Chap 2 Macromolecules 120711

7/30/2019 Chap 2 Macromolecules 120711

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INTRODUCTION TO BIOTECHNOLOGY

Chapter 2Macromolecules

Presented by: Engr. Juvyneil E.CartelInstructor, ChE Dept., EVSU


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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


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Between nonmetallic elements of similarelectronegativity.

Formed by sharing electron pairs

Stable non-ionizing particles, they are notconductors at any state

Examples; O2, CO2, C2H6, H2O, SiC


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Bonds in all thepolyatomic ions anddiatomics are allcovalent bonds


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NONPOLAR

COVALENT BONDS

H2 or Cl2

l b d


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

Oxygen Atom Oxygen Atom

Oxygen Molecule (O2)
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POLAR COVALENT

BONDS

H2O


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Polar Covalent Bonds: Unevenly

matched, but willing to share.


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- water is a polarmolecule because oxygen is more electronegative

than hydrogen, and therefore electrons are pulled closer to oxygen.


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Covalent bonds (Figure 3.1) are strongbonds that bind elements in macromolecules.


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Covalent Bonding


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Weak bondssuch as hydrogen bonds(Figure 3.2), van der Waals forces, andhydrophobic interactionsalso affect

macromolecular structure, but through moresubtle atomic interactions.


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HYDROGEN BONDING


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Hydrogen Bonding


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VAN DER WAALS FORCES


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Group 4A hydrides

Groups 4, 5, 6A hydrides

Van der Waals forces are made of dipole-dipole and London dispersion forces


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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 polarbond (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 carrysuch an intensely concentrated negative

charge for the hydrogens to be attracted

to.


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Hydrogen Bonding & Water


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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.
http://www.its.caltech.edu/~atomic/snowcrystals/ice/iceIh.gifhttp://www.its.caltech.edu/~atomic/snowcrystals/photos/photos.htm


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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 thepartially positive end of a neutral polar

molecule.

I on-dipole attractions become stronger as either the charge on the ion increases,

or as the magni tude of the dipole of the polar molecule increases.


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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 forcesDipole-dipole forces increase with an increase in the polarity of the molecule


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Boil ing points increase for polar molecules of simi lar mass, but

increasing dipole:

SubstanceMolecular Mass

(amu)Dipole moment,

u (D)Boiling Point

(K)

Propane 44 0.1 231

Dimethyl ether 46 1.3 248

Methyl chloride 50 2.0 249

Acetaldehyde 44 2.7 294

Acetonitrile 41 3.9 355


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London Dispersion Forces

significant only when molecules are close to each other

Prof. Fritz London

Due to electron repulsion, a temporary dipole on one

atom can induce a similar dipole on a neighbor ingatom


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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)


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A variety of functional groups containingcarbon atoms are common in biomolecules(Table 3.1) and in the folding of complexbiomolecules.


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Understanding the relative composition of abacterial cell (Table 3.2) helps us tounderstand the metabolic needs of the

organism.


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The bacterial cell is about 70% water, withover one-half of the dry portion being madeup of protein and one-quarter being made up

of nucleic acids.


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Proteins (Figure 3.3a) are polymers ofmonomers called amino acids. Nucleic acids(Figure 3.3b) are polymers of nucleotides andare found in the cell in two forms, ribonucleicacid (RNA) and deoxyribonucleic acid (DNA).


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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.


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The cohesive and polar properties of waterpromote chemical interaction and help shapemacromolecules into functional units.


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Sugars combine into long polymers calledpolysaccharides.


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The relatively simple yet eloquent structureof the polysaccharides (Figure 3.4) and theirderivatives (Figure 3.5) makes them the mostabundant natural polymer on Earth andallows them to be used for metabolism, as acomponent of information transfer molecules(Figure 3.8), and for cellular structure.


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Nucleotides


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Glycosidic bonds (Figure 3.6) combinemonomeric units (monosaccharides) intopolymers (polysaccharides), all with a carbon-

water (carbohydrate) chemical compositionapproaching (CH2O)n.


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The two different orientations of theglycosidic bonds that link sugar residuesimpart different properties to the resultant

molecules. Polysaccharides can also containother molecules such as proteins or lipids,forming complex polysaccharides.


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Lipids are amphipathicthey have bothhydrophilic and hydrophobic components.

This property makes them ideal structuralcomponents for cytoplasmic membranes.


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Simple lipids (triglycerides) are composed ofa glycerol molecule with fatty acids (Figure3.7) covalently linked in ester (Bacteria) orether (

Archaea) bonds.


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Many lipids draw their polar characteristicsfrom complex, nonfatty acid groupsconnected to carbon 1 or 3 of glycerol (Figure3.7).


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The nucleic acids deoxyribonucleic acid(DNA) and ribonucleic acid (RNA) aremacromolecules composed of monomerscalled nucleotides. Therefore, DNA and RNAare polynucleotides. Without a phosphate, abase bonded to its sugar is referred to as anucleoside.


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All nucleotides have a phosphate group anda five-carbon sugar, with the sugar beingribose (OH at carbon 2) in RNA ordeoxyribose (H at carbon 2) in DNA (Figure3.10).


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It is the primary structure, or order, ofpyrimidine and purine bases (Figure 3.9)connected by the phosphodiester bond(Figure 3.11) that gives nucleic acids theirinformation-storing capacity.


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Both RNA and DNA are informationalmacromolecules. RNA can fold into variousconfigurations to obtain secondary structure.


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Although the -carbon of an amino acidcan form four covalent bonds like other

carbon atoms, the groups bonding to the -carbon are very specific.


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Hydrogen, an amino functional group(NH2), and a carboxylic acid functional group(COOH) are a part of each amino acid (Figure3.12a).


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The fourth bond can be one of 21 commonside groups, which may be ionic, polar, ornonpolar (Figure 3.12b). It is theheterogeneity of these side groups thatdefines the properties of a peptide or protein.


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Through a dehydration synthesis reaction,amino acids can bond covalently by forming apeptide bond between the amino andcarboxylic acid groups.


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Isomers are molecules that have the samemolecular composition but have differentstructural form (Figure 3.15a).

Isomers Ball and Stick Model


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IsomersBall and Stick Model


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Enantiomers contain the same molecularand structural formulas, except that one is a"mirror image" of the other; these are giventhe designations d and l (Figure 3.15b).

Enantiomers


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These different structural forms can greatlyaffect metabolism; for example, whereassugars are typically d enantiomer, aminoacids typically exist in the l form.


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The sequence of covalently linked aminoacids in a polypeptide is the primarystructure. When many amino acids arecovalently linked via peptide bonds, theyform a polypeptide.


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Secondary structure results from hydrogenbonding that produces an -helix("corkscrew") or -sheet ("washboard")formation, or domain (Figure 3.16). Proteinsmay have an assortment of either or bothdomains.

Secondary structure of proteins- alpha-helix


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Secondary structure of proteins- beta sheets


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The polar, ionic, and nonpolar properties ofamino acid side "R" chains cause regions of

attraction and repulsion in the amino acidchain, thus creating the folding of thepolypeptide (i.e., tertiary structure) (Figure3.17).

Tertiary structure of polypeptides


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Similarly, association of severalpolypeptides results in a unique, predictablefinal structure (quaternary structure) (Figure3.18).

Quaternary structure of human hemoglobin


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It is this final orientation and folding thatdictate the usefulness of a protein as acatalyst (enzyme) or its structural integrity inthe cell. Destruction of the folded structureby chemicals or environmental conditions iscalled denaturation (Figure 3.19).

Denaturation and renaturation of ribonuclease


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Chap 2 Macromolecules 120711

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