Modern Biology Lecture II

CHEMICAL BASIS OF LIFE

WATER: MOLECULE THAT SUPPORTS LIFE

STANDARDS

 Describe how the polarity of water molecules results in the

hydrogen bonding.
 Describe how the chemical properties of water are advantageous
for life. Provide specific examples for water as a temperature
regulator, solvent and lubricant.
 Describe both acids, bases and indicate the importance of pH to
biological systems.
 Show or model how buffers work to regulate pH.

NATURE’S CHEMICAL LANGUAGE

 Chemicals play many more roles in life than signalling.

 Making up our bodies, those of other organisms, and the physical
environment.

 Living organisms are composed of about 25 chemical elements.

 Mostly made up of carbon, hydrogen, oxygen and nitrogen; make up the
bulk of living matter. (96.3%)
 Modern Biology Lecture II

Atoms

 Atoms consist of a nucleus of positively charged protons and neutrally

charged neutrons.
 Negatively charged electrons are arranged outside the nucleus.

2 Protons
Nucleus 6 Protons
2 Neutrons Nucleus
6 Neutrons
2 Electrons 6 Electrons
A. Helium atom B. Carbon atom

Molecules

 Molecules are groups of two or more atoms held together by chemical

bonds.
 Chemical bonds between atoms form because of the interaction of their
electrons.

Electronegativity

The electronegativity of an atom, or the ability of an atom to attract

electrons, plays a large part in determining the kind of bond that forms.

I. IONIC BONDS

 Ionic bonds form between two atoms when one or more electrons are
transferred from one atom to the other. This bond occurs when the
electronegativities of the atoms are very different and one atom has a
much stronger pull on the electrons (high electronegativity) than the other
atom in the bond.
 The atom that gains electrons has an overall negative charge, and the
atom that loses electrons has an overall positive charge.
 Modern Biology Lecture II

–
+

Na Cl Na Cl

Na Cl Na+ Cl–
Sodium atom Chlorine atom Sodium ion Chloride ion

Sodium chloride (NaCl)

The attraction of the positive ion to the negative ion constitutes the ionic
bond.

II. COVALENT BONDS

 Covalent bonds form when electrons between atoms are shared, which
means that neither atom completely retains possession of the electrons
(as happens with atoms that form strong ionic bonds).
 Covalent bonds occur when the electronegativities of the atoms are
similar.

 NONPOLAR COVALENT
 Nonpolar covalent bonds form when electrons are shared equally.
 When the two atoms sharing electrons are identical, such as in
oxygen gas (O2), the electronegativities are identical and both
atoms pull equally on the electrons.
 Modern Biology Lecture II

 POLAR COVALENT
 Polar covalent bonds form when electrons are shared
unequally.
 Atoms in this kind of bond have electronegativities that are
different and an unequal distribution of the electrons results.
 The electrons forming the bond are closer to the atom with
the greater electronegativity and produce a negative
charge, or pole, near that atom.
 The area around the atom with the weaker pull on the
electrons produces a positive pole.
 In a molecule of water (H2O), for example, electrons are
shared between the oxygen atom and each hydrogen atom.
 Oxygen, with a greater electronegativity, exerts a stronger
pull on the shared electrons than does each hydrogen atom.
This unequal distribution of electrons creates a negative pole
near the oxygen and positive poles near each hydrogen
atom.

(–) (–)

H H

(+) (+)

III. HYDROGEN BONDS

 Hydrogen bonds are weak bonds between molecules.
 Modern Biology Lecture II

 They form when a positively charged hydrogen atom in one

covalently bonded molecule is attracted to a negatively
charged area of another covalently bonded molecule.
 In water, the positive pole around a hydrogen atom forms a
hydrogen bond to the negative pole around the oxygen atom
of another water molecule

PROPERTIES OF WATER

The hydrogen bonds among water molecules contribute to some very special
properties for water.

1. Water is an excellent solvent.

 Ionic substances are soluble (they dissolve) in water because the poles of
the polar water molecules interact with the ionic substances and
separate them into ions.
 Substances with polar covalent bonds are similarly soluble because of the
interaction of their poles with those of water.
 Substances that dissolve in water are called hydrophilic (“water loving”).
 Because they lack charged poles, nonpolar covalent substances do not
dissolve in water and are called hydrophobic (“water fearing”).

Na+

– Na+ –

+ Cl– +
Cl–
– + –

+ –

Ions in Salt
solution crystal
 Modern Biology Lecture II

2. Water has a high heat capacity.

 Heat capacity is the degree to which a substance changes

temperature in response to a gain or loss of heat.
 Water has a high heat capacity, changing temperature very slowly
with changes in its heat content.
 Thus, the temperatures of large bodies of water are very stable in
response to the temperature changes of the surrounding air.
 You must add a relatively large amount of energy to warm (and
boil) water or remove a relatively large amount of energy to cool (and
freeze) water.
 When sweat evaporates from your skin, a large amount of heat is
taken with it and you are cooled.

3. Ice Floats

 Unlike most substances that contract and become more dense

when they freeze, water expands as it freezes, becomes less dense
than its liquid form, and, as a result, floats in liquid water.
 Hydrogen bonds are typically weak, constantly breaking and
reforming, allowing molecules to periodically approach one
another.
 Modern Biology Lecture II

 In the solid state of water, the weak hydrogen bonds between

water molecules become rigid and form a crystal that keeps the
molecules separated and less dense than its liquid form.
 If ice did not float, it would sink and remain frozen due to the
insulating protection of the overlaying water.

Hydrogen bond

ICE LIQUID WATER

Hydrogen bonds are stable Hydrogen bonds constantly
break and re-form

4. Water has strong cohesion and high surface tension

 Cohesion, or the attraction between like substances, occurs in

water because of the hydrogen bonding between water
molecules.
 The strong cohesion between water molecules produces a high
surface tension, creating a water surface that is firm enough to
allow many insects to walk upon without sinking.
 Modern Biology Lecture II

5. Water adheres to other molecules

 Adhesion is the attraction of unlike substances. When water adheres to

the walls of narrow tubing or to absorbent solids like paper, it
demonstrates capillary action by rising up the tubing or creeping through
the paper.

BIOMOLECULES

A biomolecule or biological molecule is a loosely used term for molecules

and ions that are present in organisms, essential to some typically biological
process such as cell division, morphogenesis, or development.

Biomolecules include large macromolecules (or polyanions) such as

proteins, carbohydrates, lipids, and nucleic acids, as well as small molecules
such as primary metabolites, secondary metabolites, and natural products. A
more general name for this class of material is biological materials. Biomolecules
are usually endogenous but may also be exogenous. For example,
pharmaceutical drugs may be natural products or semisynthetic
(biopharmaceuticals) or they may be totally synthetic.

Biology and its subsets of biochemistry and molecular biology study

biomolecules and their reactions. Most biomolecules are organic compounds,
and just four elements—oxygen, carbon, hydrogen, and nitrogen—make up 96%
of the human body's mass. But many other elements, such as the various
biometals, are present in small amounts.

The uniformity of specific types of molecules (the biomolecules) and of

some metabolic pathways as invariant features between the diversity of life
forms is called "biochemical universals" or "theory of material unity of the living
beings", a unifying concept in biology, along with cell theory and evolution
theory.
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Types of Biomolecules

A diverse range of biomolecules exist, including:

Small molecules:

 Lipids, fatty acids, glycolipids, sterols, monosaccharides

 Vitamins
 Hormones, neurotransmitters
 Metabolites

Monomers, oligomers and polymers:

Biomonomers Bio-oligo Biopolymers Polymerization Covalent bond

Process name between
monomers

Amino acids Oligopeptides Polypeptides, Polycondensation Peptide bond

proteins
(hemoglobin...)

Monosaccharides Oligosaccharides Polysaccharides Polycondensation Glycosidic

(cellulose...) bond

Isoprene Terpenes Polyterpenes: Polyaddition

cis-1,4-
polyisoprene
natural rubber
and trans-1,4-
polyisoprene
gutta-percha

Nucleotides Oligonucleotides Polynucleotides, Phosphodiester

nucleic acids bond
(DNA, RNA)

Nucleosides and Nucleotides

Nucleosides are molecules formed by attaching a nucleobase to a ribose

or deoxyribose ring. Examples of these include cytidine (C), uridine (U),
adenosine (A), guanosine (G), and thymidine (T).

Nucleosides can be phosphorylated by specific kinases in the cell,

producing nucleotides. Both DNA and RNA are polymers, consisting of long,
linear molecules assembled by polymerase enzymes from repeating structural
units, or monomers, of mononucleotides. DNA uses the deoxynucleotides C, G,
A, and T, while RNA uses the ribonucleotides (which have an extra hydroxyl(OH)
group on the pentose ring) C, G, A, and U. Modified bases are fairly common
(such as with methyl groups on the base ring), as found in ribosomal RNA or
 Modern Biology Lecture II

transfer RNAs or for discriminating the new from old strands of DNA after
replication.

Each nucleotide is made of an acyclic nitrogenous base, a pentose and

one to three phosphate groups. They contain carbon, nitrogen, oxygen,
hydrogen and phosphorus. They serve as sources of chemical energy
(adenosine triphosphate and guanosine triphosphate), participate in cellular
signaling (cyclic guanosine monophosphate and cyclic adenosine
monophosphate), and are incorporated into important cofactors of enzymatic
reactions (coenzyme A, flavin adenine dinucleotide, flavin mononucleotide,
and nicotinamide adenine dinucleotide phosphate).

DNA and RNA structure

DNA structure is dominated by the well-known double helix formed by

Watson-Crick base-pairing of C with G and A with T. This is known as B-form DNA,
and is overwhelmingly the most favorable and common state of DNA; its highly
specific and stable base-pairing is the basis of reliable genetic information
storage. DNA can sometimes occur as single strands (often needing to be
stabilized by single-strand binding proteins) or as A-form or Z-form helices, and
occasionally in more complex 3D structures such as the crossover at Holliday
junctions during DNA replication.

RNA, in contrast, forms large and complex 3D tertiary structures

reminiscent of proteins, as well as the loose single strands with locally folded
regions that constitute messenger RNA molecules. Those RNA structures contain
many stretches of A-form double helix, connected into definite 3D
arrangements by single-stranded loops, bulges, and junctions.

Examples are tRNA, ribosomes, ribozymes, and riboswitches. These

complex structures are facilitated by the fact that RNA backbone has less local
flexibility than DNA but a large set of distinct conformations, apparently
because of both positive and negative interactions of the extra OH on the
ribose. Structured RNA molecules can do highly specific binding of other
molecules and can themselves be recognized specifically; in addition, they can
perform enzymatic catalysis (when they are known as "ribozymes", as initially
discovered by Tom Cech and colleagues).

Saccharides

Monosaccharides are the simplest form of carbohydrates with only one

simple sugar. They essentially contain an aldehyde or ketone group in their
structure. The presence of an aldehyde group in a monosaccharide is indicated
by the prefix aldo-. Similarly, a ketone group is denoted by the prefix keto-.
Examples of monosaccharides are the hexoses, glucose, fructose, Trioses,
Tetroses, Heptoses, galactose, pentoses, ribose, and deoxyribose. Consumed
fructose and glucose have different rates of gastric emptying, are differentially
absorbed and have different metabolic fates, providing multiple opportunities
 Modern Biology Lecture II

for 2 different saccharides to differentially affect food intake. Most saccharides

eventually provide fuel for cellular respiration.

Disaccharides are formed when two monosaccharides, or two single

simple sugars, form a bond with removal of water. They can be hydrolyzed to
yield their saccharin building blocks by boiling with dilute acid or reacting them
with appropriate enzymes. Examples of disaccharides include sucrose, maltose,
and lactose.

Polysaccharides are polymerized monosaccharides, or complex

carbohydrates. They have multiple simple sugars. Examples are starch, cellulose,
and glycogen. They are generally large and often have a complex branched
connectivity. Because of their size, polysaccharides are not water-soluble, but
their many hydroxy groups become hydrated individually when exposed to
water, and some polysaccharides form thick colloidal dispersions when heated
in water. Shorter polysaccharides, with 3 - 10 monomers, are called
oligosaccharides. A fluorescent indicator-displacement molecular imprinting
sensor was developed for discriminating saccharides. It successfully
discriminated three brands of orange juice beverage. The change in
fluorescence intensity of the sensing films resulting is directly related to the
saccharide concentration.

Lignin

Lignin is a complex polyphenolic macromolecule composed mainly of

beta-O4-aryl linkages. After cellulose, lignin is the second most abundant
biopolymer and is one of the primary structural components of most plants. It
contains subunits derived from p-coumaryl alcohol, coniferyl alcohol, and
sinapyl alcohol and is unusual among biomolecules in that it is racemic. The lack
of optical activity is due to the polymerization of lignin which occurs via free
radical coupling reactions in which there is no preference for either
configuration at a chiral center.

Lipids

Lipids (oleaginous) are chiefly fatty acid esters, and are the basic building
blocks of biological membranes. Another biological role is energy storage (e.g.,
triglycerides). Most lipids consist of a polar or hydrophilic head (typically
glycerol) and one to three nonpolar or hydrophobic fatty acid tails, and
therefore they are amphiphilic. Fatty acids consist of unbranched chains of
carbon atoms that are connected by single bonds alone (saturated fatty acids)
or by both single and double bonds (unsaturated fatty acids). The chains are
usually 14-24 carbon groups long, but it is always an even number.
 Modern Biology Lecture II

For lipids present in biological membranes, the hydrophilic head is from one of
three classes:

 Glycolipids, whose heads contain an oligosaccharide with 1-15

saccharide residues.
 Phospholipids, whose heads contain a positively charged group that is
linked to the tail by a negatively charged phosphate group.
 Sterols, whose heads contain a planar steroid ring, for example,
cholesterol.

Other lipids include prostaglandins and leukotrienes which are both 20-carbon
fatty acyl units synthesized from arachidonic acid. They are also known as fatty
acids.

Amino acids

Amino acids contain both amino and carboxylic acid functional groups.
(In biochemistry, the term amino acid is used when referring to those amino
acids in which the amino and carboxylate functionalities are attached to the
same carbon, plus proline which is not actually an amino acid).

Modified amino acids are sometimes observed in proteins; this is usually

the result of enzymatic modification after translation (protein synthesis). For
example, phosphorylation of serine by kinases and dephosphorylation by
phosphatases is an important control mechanism in the cell cycle. Only two
amino acids other than the standard twenty are known to be incorporated into
proteins during translation, in certain organisms:

 Selenocysteine is incorporated into some proteins at a UGA codon,

which is normally a stop codon.
 Pyrrolysine is incorporated into some proteins at a UAG codon. For
instance, in some methanogens in enzymes that are used to
produce methane.

Besides those used in protein synthesis, other biologically important amino

acids include carnitine (used in lipid transport within a cell), ornithine, GABA and
taurine.

Protein structure

The particular series of amino acids that form a protein is known as that
protein's primary structure. This sequence is determined by the genetic makeup
of the individual. It specifies the order of side-chain groups along the linear
polypeptide "backbone".

Proteins have two types of well-classified, frequently occurring elements of local

structure defined by a particular pattern of hydrogen bonds along the
backbone: alpha helix and beta sheet. Their number and arrangement is called
the secondary structure of the protein.
 Modern Biology Lecture II

Alpha helices are regular spirals stabilized by hydrogen bonds between

the backbone CO group (carbonyl) of one amino acid residue and the
backbone NH group (amide) of the i+4 residue. The spiral has about 3.6 amino
acids per turn, and the amino acid side chains stick out from the cylinder of the
helix.

Beta pleated sheets are formed by backbone hydrogen bonds between

individual beta strands each of which is in an "extended", or fully stretched-out,
conformation. The strands may lie parallel or antiparallel to each other, and the
side-chain direction alternates above and below the sheet. Hemoglobin
contains only helices, natural silk is formed of beta pleated sheets, and many
enzymes have a pattern of alternating helices and beta-strands. The secondary-
structure elements are connected by "loop" or "coil" regions of non-repetitive
conformation, which are sometimes quite mobile or disordered but usually
adopt a well-defined, stable arrangement.

Enzymes

Enzymes are macromolecular biological catalysts. Enzymes accelerate

chemical reactions. The molecules upon which enzymes may act are called
substrates and the enzyme converts the substrates into different molecules
known as products.

Apoenzymes

An apoenzyme (or, generally, an apoprotein) is the protein without any

small-molecule cofactors, substrates, or inhibitors bound. It is often important as
an inactive storage, transport, or secretory form of a protein. This is required, for
instance, to protect the secretory cell from the activity of that protein.
Apoenzymes become active enzymes on addition of a cofactor. Cofactors can
be either inorganic (e.g., metal ions and iron-sulfur clusters) or organic
compounds, (e.g., [Flavin group|flavin] and heme). Organic cofactors can be
either prosthetic groups, which are tightly bound to an enzyme, or coenzymes,
which are released from the enzyme's active site during the reaction.

Isoenzymes

Isoenzymes, or isozymes, are multiple forms of an enzyme, with slightly

different protein sequence and closely similar but usually not identical functions.
They are either products of different genes, or else different products of
alternative splicing. They may either be produced in different organs or cell
types to perform the same function, or several isoenzymes may be produced in
the same cell type under differential regulation to suit the needs of changing
development or environment. LDH (lactate dehydrogenase) has multiple
isozymes, while fetal hemoglobin is an example of a developmentally regulated
isoform of a non-enzymatic protein. The relative levels of isoenzymes in blood
can be used to diagnose problems in the organ of secretion.
 Modern Biology Lecture II

How do Enzymes work?

Enzymes are biological molecules (typically proteins) that significantly

speed up the rate of virtually all of the chemical reactions that take place within
cells.

They are vital for life and serve a wide range of important functions in the
body, such as aiding in digestion and metabolism.

Some enzymes help break large molecules into smaller pieces that are
more easily absorbed by the body. Other enzymes help bind two molecules
together to produce a new molecule. Enzymes are highly selective catalysts,
meaning that each enzyme only speeds up a specific reaction.

The molecules that an enzyme works with are called substrates. The
substrates bind to a region on the enzyme called the active site.

There are two theories explaining the enzyme-substrate interaction.

In the lock-and-key model, the active site of an enzyme is precisely

shaped to hold specific substrates. In the induced-fit model, the active site and
substrate don't fit perfectly together; instead, they both alter their shape to
connect.

Whatever the case, the reactions that occur accelerate greatly — over a
millionfold — once the substrates bind to the active site of the enzyme. The
chemical reactions result in a new product or molecule that then separates
from the enzyme, which goes on to catalyze other reactions.