Download Topic 4: BIOLOGICALLY IMPORTANT ORGANIC MOLECULES

Topic 4: BIOLOGICALLY IMPORTANT ORGANIC MOLECULES (lecture 6)
OBJECTIVES:
1. Know the general formula for carbohydrates. Be able to identify the chemical
structure of simple sugars from those of other low molecular weight organic
compounds.
2. Know the major polysaccharides, how they differ in terms of structure, location and
function.
3. Know the structural components of fats and the major determinants as to whether
the fat is fluid or solid at room temperature.
4. Understand the roles of the various parts of phospholipids in the formation of
micelles.
5. Be able to tell whether a particular amino acid is non-polar, polar or electrically
charged.
6. Understand the four basic levels of protein structure and the importance of weak
bonds in stabilizing secondary through quaternary structure. Be able to describe
what happens during protein denaturation.
7. If you are given the structure of a sugar, amino acid or fat, be able to classify this
molecule as to whether it is a sugar, amino acid or fat.
macromolecule - large molecules often consist of polymers of many subunits
(building blocks); subunits are often referred to as monomers and are assembled
together by condensation reactions which involve the formation of water (Fig. 5.2); the
breakdown of polymers is by hydrolysis reactions in which water is cleaved.
CARBOHYDRATES
Major functions: energy storage and structural
Sugars and their polymers; loosely defined as molecules that contain carbon, hydrogen
and oxygen in a molar ratio of 1:2:1 , [C(H)2O]n. Because they contain many C-H
bonds, which release energy when broken, carbohydrates are used for energy storage
(to be talked about later). Polymers of carbohydrate can be used as structural elements.
Monosaccharides- simple sugars, are classified by the number and arrangement of
carbons; each carbon has a hydroxyl group attached except one which has a carbonyl
group (Fig. 5-3). There are two types of sugars based on the carbonyl group- ketoses (
keto ) and aldoses (aldehyde).
Fig. 5.4- in solution monosaccharides typically form ring structures- either in  or  form
Common monosaccharides include glucose (blood sugar) and fructose (fruit sugar)
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Disaccharides- when two sugars are joined together; the bond is known as an Oglycosidic linkage (fig. 5.5). Disaccharides include maltose (glucose + glucose),
sucrose (glucose + fructose) and lactose (glucose + galactose).
Polysaccharides- large polymers of monosaccharides that are used for energy storage
(glycogen, plant starch) and structural support (cellulose, chitin). These are assembled
by glycosidic linkages but the nature of the bonding determines the polysaccharide.
Fig. 5.6- Starch vs. Glycogen
starch- polymers of glucose accumulated in plant cells as linear polymers
(amylose) or polymers with branches (amylopectin); fuel storage
glycogen- polymers of glucose accumulated in animal cells as large branching
clumps; fuel storage
cellulose- long, linear polymers of glucose accumulated in plant cells; structural
component
fig. 5.7- biosynthesis of starch vs. cellulose in plants; glucose in solution exists as two
ringed form-  and  forms;  glucose polymers form starch and  glucose polymers
form cellulose.
Fig. 5.8- cellulose molecules are long and become wrapped together to form
microfibrils; these are meshed together to form a very strong material (wood).
Another polysaccharide structural material is chitin, the primary constituent of the
exoskeleton of arthropods (insects, crustaceans, spiders etc); is a polymer of a sugar
derivative known as acetylglucosamine.
LIPIDS
Functions: energy storage, thermal insulation, cushion, membranes, hormones
Sugars are often converted to another storage form of energy- lipids. Lipids are a fairly
complex set of organic molecules which generally are not particularly soluble in water.
We will talk about three kinds of lipids- (1) fats, (2) phospholipids and (3) steroids.
Fats- consist of two kinds of molecules, glycerol (a sugar alcohol) and fatty acids. Fig.
5.10 shows how fats are formed. A fatty acid molecule is attached to each of the -OH
groups on the glycerol molecule by a condensation reaction forming an ester (R-O-R)
bond. What is formed is triacylglyerol (a triglyceride or neutral (depot) fat)
Characteristics-
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(1) the molecule is essentially uncharged and each fatty acid has a long hydrocarbon
“tail”; this means that it is not soluble in water, it is hydrophobic.
(2) there are many H-C bonds which means that the molecule has a very high energy
storage content; these are often referred to as “depot” lipids.
(3) the hydrogen tails may have singly C-C (“saturated”) and doubly C=C (“unsaturated’)
bonded carbons. Presence of a double bond introduces a bend in the hydrocarbon
tail (see Fig. 5.11) which disrupts the alignment of the hydrocarbon tails in the
molecule. This means that unsaturated fats are liquid at room temperature whereas
saturated fats are not. Hydrogenation converts liquid fats (corn oil) to solid fats
(margarine).
(4) function as energy storage materials, insulation and cushioning agent; accumulated
in specialized cells called adipocytes
Phospholipids- consist of glycerol, esters of two fatty acids plus some highly charged
molecule or group ( in the case of Fig. 5.12 it is choline and phosphate). One part of the
molecule is very polar and hydrophilic while the other part of the molecule is non-polar
and very hydrophobic. Phospholipids when added to water and mixed vigorously form
small spheres known as micelles (see Fig. 5.13). Under appropriate circumstances they
will form bilayers (as we will discuss later).
Steroids- complex ringed structures which are typically not water soluble ( see Fig.
5.14);
components of cell membranes and important hormones (chemical messengers).
AMINO ACIDS, PEPTIDES and PROTEINS
peptides- polymers of a few amino acids ( approx. < 20 or so)
polypeptides (proteins) -very large polymers of amino acids (>20)
Proteins are an extremely diverse group of macromolecules; a given cell may express
104 different kinds of proteins- function in structure, support, catalysis, chemical
communication (hormones, neurotransmitters) , membrane transport.
Table 5.1- Overview of protein functions
Amino acids- there are 20 commonly used L-amino acids which differ in terms of
chemical properties.
Fig. 5.15- 3 classes of amino acids based on charge or lack there of
non-polar vs. polar vs. electrically charged amino acids
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1. non-polar- have functional groups which lack charge; in fact these groups are so
hydrophobic that they do not like to interact with water but prefer to interact with each
other.
H- Gly
methyl, hydrocarbon chains- Ala,, Val, Leu, Ile, Met, Pro
phenyl ring- Phe
indole ring- Trp
2. polar- are slightly charged and therefore hydrophilic; Ser, Thr, Cys, Tyr, Asn, Gln
3. electrically chargedacidic- negatively charged due to carboxyl group; Asp, Glu
basic- positively charged due to N; Lys, Arg, His
Fig. 5.16- peptide bond formation; condensation reaction takes place during cellular
biosynthesis of proteins.
There are four orders of structure in proteins- (1) primary, (2) secondary, (3) tertiary and
(4) quaternary
Fig. 5.18
Primary structure- proteins are a linear polymer of amino acids; the primary structure
is the sequence of amino acids. There is a defined N- (amino) terminus and C(carboxy) terminus. Amino acid sequence is coded for by structural genes.
+H N-Lys-Gly-Glu-Glu-Ala-Ala-Arg-……..Leu-COO3
N-terminus
C-terminus
Secondary structure- repeated coiling of the polypeptide chain (Fig. 5.20); two very
common types of coiling both stabilized by hydrogen bonding:
(1)  helix- hydrogen bonding between every fourth peptide bond leads to a
straight coil
(2)  pleated sheet- hydrogen bonding between parallel arrays of polypeptide
chains
Tertiary structure- complicated and irregular folding of the polypeptide chain so that
the protein assumes a unique 3 dimensional structure (Fig. 5.22). Tertiary structure is
stabilized by convalent (dissulfide bonds) and weak bonding (hydrogen bonds, ionic
bonds and hydrophobic interactions).
Protein conformation- a jargon term that refers to the 3-dimensional structure of a
protein in its biological (“active”) state. Proteins can exist in a number of conformations
some of which may differ in biological activity.
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Fig. 5.24
Quaternary structure- some proteins exist as single polypeptides ( known as
monomeric proteins); other exist as polymers on two or more polypeptides or sununitsdimeric (2 polypeptides), tetrameric (4), octameric (8) and so on (see Fig. 5.23).
Subunits usually adhere to each other by weak bonding (hydrogen, ionic).
Folding- Fig. 5.25
The biological activity of proteins depends on its unique 3-D structure; when proteins
are synthesized the amino acids are attached in a linear chain.
Chaperonins- After assembly, the protein assumes its 3-D structure by self-assembly;
sometimes a class of proteins known as chaperonins (molecular chaperone proteins)
helps with this assembly.
Fig. 5.26-chaperonins
The local environment my influence protein structure and solubility:
(1) heat denaturation- high temperatures break H- and ionic bonds causing folding to
change. Hydrophobic amino acids normally buried in the interior may be forced to
the surface causing the protein to denature (lose its structure) and go out of solution
(coagulate). Egg proteins denature when you poach an egg.
(2) acid or base denaturation- adding acid or base to a protein solution will cause
changes in the ionization state of the electrically charged amino acids which will
disrupt polar interactions. Adding acid to milk causes it to “curdle”.
(3) salt precipitation- proteins stay in solution because charged groups on the surface
interact with water. If you add large amounts of salt to a protein solution the salt
competes with the protein for binding with water and the protein may go out of
solution.
NUCLEIC ACIDS will be discussed later….
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