The Biological Molecular

PRESENTED BY : RINA RESTANTI

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

 Cemist component
• Biological molecules are made by the
relatively simple process of joining
together many small repeating subunits
 Organic Molecules
• Composed primarily of H, C, O, & N.
• Look at the common functional groups.
 Carbohydrates

Copyright © 1999-2008 by Joyce J.

Diwan.
All rights reserved.
 General characteristics
• the term carbohydrate is derived from the
french: hydrate de carbone
• compounds composed of C, H, and O
• (CH2O)n when n = 5 then C5H10O5
• not all carbohydrates have this empirical
formula: deoxysugars, aminosugars
• carbohydrates are the most abundant
compounds found in nature (cellulose: 100
billion tons annually)
 General characteristics
• Most carbohydrates are found naturally in
bound form rather than as simple sugars
• Polysaccharides (starch, cellulose, inulin, gums)
• Glycoproteins and proteoglycans (hormones, blood group
substances, antibodies)
• Glycolipids (cerebrosides, gangliosides)
• Glycosides
• Mucopolysaccharides (hyaluronic acid)
• Nucleic acids
Carbohydrates (glycans) have the
following basic composition: I
(CH2O)n or H - C - OH
I
 Monosaccharides - simple sugars with multiple OH
groups. Based on number of carbons (3, 4, 5, 6), a
monosaccharide is a triose, tetrose, pentose or hexose.
 Disaccharides - 2 monosaccharides covalently linked.
 Oligosaccharides - a few monosaccharides covalently
linked.
 Polysaccharides - polymers consisting of chains of
monosaccharide or disaccharide units.
 Monosaccharides
Aldoses (e.g., glucose) have Ketoses (e.g., fructose)
an aldehyde group at one end. have a keto group, usually
at C2.
H O
C CH2OH

H C OH C O

HO C H HO C H

H C OH H C OH

H C OH H C OH

CH2OH CH2OH

D-glucose D-fructose
 Sugar Nomenclature

For sugars with more O H O H

than one chiral center, C C
D or L refers to the H – C – OH HO – C – H
asymmetric C farthest HO – C – H H – C – OH
from the aldehyde or
H – C – OH HO – C – H
keto group.
H – C – OH HO – C – H
Most naturally occurring CH2OH CH2OH
sugars are D isomers. D-glucose L-glucose
 1
CH2OH

2C O

HO C H
1 CH2OH
3 HOH2C 6 O
H C OH
4 5 H HO 2

H C OH H 4 3 OH
5
OH H
6
CH2OH

D-fructose (linear) -D-fructofuranose

Fructose forms either

 a 6-member pyranose ring, by reaction of the C2
keto group with the OH on C6, or
 a 5-member furanose ring, by reaction of the C2
keto group with the OH on C5.
 6 CH 2 OH 6 CH 2 OH
5 O 5 O
H H H OH
H H
4 H 1 4 H 1
OH OH
OH OH OH H
3 2 3 2
H OH H OH
-D -glucose -D -glucose

Cyclization of glucose produces a new asymmetric center at

C1. The 2 stereoisomers are called anomers,  & .
Haworth projections represent the cyclic sugars as having
essentially planar rings, with the OH at the anomeric C1:
 (OH below the ring)
  (OH above the ring).
 Carbohydrates
• Organic molecules
that contain carbon,
hydrogen and
oxygen.
– CnH2n0n.
• Monosaccharides =
simple sugars.
– Structural isomers:
• Glucose, fructose,
galactose.
• Disaccharide:
– 2 monosaccharides joined covalently.
• Sucrose (glucose and fructose), lactose (glucose and
galactose), maltose (2 glucose).
• Polysaccharide:
– Numerous monosaccharides joined covalently.
• Starch (thousands of glucose joined), glycogen
(repeating glucose joined that are highly branched)..
• Organic molecules are built by dehydration
synthesis:
C6H12O6 + C6H12O6 C12H22O11 + H2O
• Organic Molecules are broken down by
hydrolysis
C12H22O11 + H2O C6H12O6 + C6H12O6
 Lipids
• Insoluble in water because of nonpolar
molecules
– Triglycerides = 3 fatty acids + glycerol
• Saturated = joined by only single bonds
• Unsaturated = joined by at least one double bond
• Hydrolysis of triglycerides in adipose tissue
releases free fatty acids.
– Free fatty acids can be converted in the liver
to ketone bodies.
– Excess ketone bodies can lower blood pH..
– Phospholipids = phosphate + fatty acid
• phosphate end is polar = hydrophilic
• fatty acid end is nonpolar = hydrophobic
– Steroids = aromatic rings = three 6-carbon
rings joined to a 5-carbon ring
• Steroid hormones are cholesterol derivitaves..
 Proteins
• Large molecules composed of long chains
of amino acids.
– 20 different amino acids can be used in
constructing a given protein.
– Each amino acid contains an amino group
(NH2) at one end and carboxyl group (COOH)
at the other end.
• Differences between amino acids are due
to differences in functional groups (“R”).
• Amino acids are joined by peptide bonds..
 Protein Structure Levels

• Primary structure is the sequence of the

amino acids in the protein.
• Secondary structure is produced by
weak hydrogen bonds between
hydrogen of one amino acid and the
and oxygen of a different amino acid
nearby.
 -helix or -sheet..
• Tertiary structure is formed when
polypeptide chains bend and fold to
produce 3 -dimensional shape.
– Formed and stabilized by weak chemical
bonds between functional groups.
• Each type of protein has its own own
characteristic tertiary structure.
• Quaternary structure is produced when
a number of polypeptide chains
covalently linked together..
 Nucleic Acids
• Include DNA and RNA.
• Nucleic acids are composed of
nucleotides to form long polynucleotide
chains.
– Each nucleotide is composed of 3 smaller
units:
• 5-carbon sugar (deoxyribose or ribose).
• Phosphate group attached to one end of sugar.
• Nitrogenous base attached to other end of
sugar..
• The “backbone” of the nucleic acid is
formed by the sugar and phosphate
pairs.
• The “rungs” are formed by paired
nitrogenous bases.
– Nitrogenous bases complementary pair
• A + T (U)
• C + G..
 Overview: Types of Bonds
• There are 2 bond types : ionic and covalent
• In ionic bonding one atom has a stronger
attraction for electrons than the other, and
“steals” an electron from a second atom
• In covalent bonding the attraction for
electrons is similar for two atoms. They
share their electrons to obtain an octet

• MgO (ionic), CaCl2 (ionic), SO2 (covalent),

PbCl2 (ionic), CCl4 (covalent), CH4 (covalent)
• Bonding is accomplished by interactions
between two atom’s valence e-.
– If e- are shared between two atoms that
forms a covalent bond.
• Single bonds = one shared pair
• Double bonds = two shared pairs
• Triple bonds = three shared pairs
– If e- are transferred from one atom (ion)
to another that forms an ionic bond.
• Hydrogen bonds are special (polar)
covalent bonds that are very important
to physiology.
Covalent Animation
Ionic Animation..
02_06_stable arrangement.jpg
 Ionic bonding
• Ionic bonding involves 3 steps (3 energies)
• 1) loss of an electron(s) by one element, 2)
gain of electron(s) by a second element, 3)
attraction between positive and negative

1) e– 2)
Na Cl
3)
Na+ Na+ Cl–
 Ionic bonding: Al + Cl

Al + 3Cl [Al]3+[Cl]3–

Cl

Al Cl [Al]3+ [ Cl ]3–

Cl
 Covalent bonding
CCl4 - Covalent HCl - Covalent MgF2 - Ionic

Cl H Cl [Mg]2+ [ F ]2–

Cl C Cl
NH3 - Covalent NaCl - Ionic
Cl
H N H [Na] + [ Cl ]–
H2O - Covalent
H H2 - Covalent
H O H OH– - Covalent
H H
O H
For more lessons, visit
www.chalkbored.com
Multiple Build models of molecules, O3 as
challenge (can’t build it or ionic)
bonds
HCl - Covalent CO2 - Covalent Na2O - Ionic

H Cl H Cl O C O [Na]2+ [ O ]2–
O C O
NH3 - Covalent O2 - Covalent I2 - Covalent
H N H H N H O O I I

H H O O I I
Al2O3 - Ionic O3 - Covalent H H
O O O H C H H C H
[Al]2 3+
[ O ] 3
2–

O O O H H
• Electronegativity is the property that
describes an atom’s attraction for a
shared pair of e-.
• If two atoms with different electro-
negativity values share e-, i.e. form a
covalent bond, one of the atoms will have
a “larger share” of the e-.
• This produces a molecule with differently
charged ends (poles). This type of
molecule is called polar..
• Bonds formed between the hydrogen
end (+ charged) of a polar molecule
and the – end of any other polar
molecule or highly electronegative atom
(e.g. P, N, O) are called hydrogen
bonds.
• These hydrogen bonds are very
important because they alter the
physical and chemical properties of
many molecules (especially water)..
• Molecules that are formed by polar
covalent bonds have a tendency to
break apart when the electron from the
hydrogen is transferred to the more
electronegative atom. This is called
dissociation or ionization.
• Water ionizes to form equal amounts of
hydroxyl (OH-) and hydrogen (hydro-
nium, H+) ions..
• An acid is a molecule that can release
protons (H+).
–Proton donor.
• A base is a molecule that can combine
with H+ and remove it from solution.
Bases are also defined as releasing OH-.
–Proton acceptor..
 Water

Life on earth evolved in water,and all life still depends

on water.
At least 80% of the mass of living organisms is water
and almost all chemical reactions of life take place in
aqueous solution.

.
02_12_polar covalent.jpg
 Polarity
• Polarity of water molecules allows them to
form hydrogen bonds with each other
– Contributes to four properties of water critical
to life processes
–
+ Hydrogen
H bonds

+ – H
– +
+ –

Figure 3.2
 Cohesion
– The bonding of a high percentage of molecules to
neighboring molecules
– Helps pull water up through the microscopic vessels of
plants

Water conducting cells

Figure 3.3 100 µm

 Cohesion
Surface tension (related to cohesion) is measure of
how hard it is to break the surface of a liquid

Figure 3.4
 A universal solvent
• Is polar
– Can dissolves salts
 Water as a solvent
• The different regions of the polar water
molecule can interact with ionic compounds
called solutes and dissolve them
Negative
oxygen regions
–
of polar water molecules Na+
are attracted to sodium + –
+
cations (Na+). –
+ –

Positive
Na+ –

hydrogen regions + +
Cl – Cl – +
of water molecules –
–

cling to chloride anions (Cl –). + –

+ –
–

Figure 3.6
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