Lecture 1

BIOMOLECULES
A. Brief Review of Chemistry Matter-->Element-->Atom-->Subatomic
particles (proton, neutron, electron)
Matter- is anything that occupies space and has mass and weight
Matter is made up of elements (ex. Na and Cl), a substance that cannot be broken down to other
substance chemical reaction.

Molecule is formed when

two or more atoms are
joined together
chemically (ex. H2, O2, N2,
H2O)

Compound is a molecule
composed of two
different elements
combined in a fixed ratio
(ex. NaCl)

Each element is composed of a certain type of atom. Atom is the smallest unit of matter.
Subatomic particles: proton (determines the element, since atomic number depends on the number of
proton), neutron (determines isotopes) and electron (directly involved in chemical bonding)

Isotopes different atomic forms of an element due to difference in the amount of neutrons (thus
different atomic mass)

Radioactive isotope is one in which the nucleus decays spontaneously, giving off particles and energy.
 Application of radioactive isotopes in PET (positron-emmission
tomography) ex. one that can detect an elevated level of
radioactively labeled glucose which indicates high level of
metabolic activity and thus indicates cancer

Electrons are directly involved in chemical bonds. Electrons can be represented in a cloud of negative
charge or electrons within a shell

Electrons occupy specific electron shells with a characteristic energy level. Electrons tend to occupy the
first shell with the lowest energy level.
Each shell also has a maximum amount of electrons that it can cater

Not necessarily that you

have to fill up all the
maximum amount of
electrons that a shell can
have, take note of the
atomic number that
needs to be satisified (see
the case of Argon and
Krypton)

Krypton has total of 36

Argon has total of 18
electrons
electrons
1st shell- 2 electrons
1st shell- 2 electrons
2nd shell- 8 electrons
2nd shell- 8 electrons
3rd shell- 18 electrons
3rd shell- 8 electrons
4th shell- 8 electrons
(though this shell can
(again, though this shell
contain up to 18
can contain up to 32
electrons, since Argon
electrons, since Krypton
only needs 18 in total we
only needs 36 in total we
cannot fill the 3rd shell to
cannot fill the 4th shell to
its maximum, otherwise
its maximum, otherwise it
it will not be Ar
will not be Kr

The chemical behavior of an atom depends mostly on the number of electrons in its outermost shell
called the valence shell. The electrons within on it are called valence electrons

Octet rule – atoms are stable (inert/ chemically unreactive) when their outer shell (valence shell) is full
For many, but not all, types of atoms, their shell is full when it contains eight (8) electrons (if they have
the 2nd to/or 4th shell) (exception is when an atom only has the 1st subshell, it needs 2 instead of 8 valence
electrons to be inert ex. Hydrogen)

Argon and Krypton are inert or chemically unreactive because they have 8 electrons in their valence shell
(3rd shell for Ar and 4th shell for Kr) (see photo above)
Carbon, like Hydrogen, is chemically reactive since its valence shell (2nd shell) contains only 4 electrons,
instead of 8.
For atoms with incomplete valence shells, it can interact with another atom so that each of the their
valence shells can be complete. Such interactions are held by chemical bonds

Covalent Bond is the sharing of a pair of

valence electrons by two atoms.

Polar Covalent Bond

Atom is bonded to a more electronegative atom, and the electrons are not shared equally

Electronegativity is a measure of an atoms ability to attract electrons in a bond with another atom
Shared electrons in a covalent bond are more likely to be closer to the atom with a higher
electronegativity. Due to this, partial positive (see hydrogen) and partial negative (see oxygen) poles
(poles=polar) are formed

Non-Polar Covalent Bond

Electrons are shared equally because the two atoms have the same electronegativity
Two atoms so unequal in their attraction (due to the large difference between the valence electrons of
the two element, ex. Na still needs 7 electron to satisfy the octet rule while Cl only needs 1) for valence
electrons that the more electronegative atom strips an electron completely away from its partner

The resulting oppositely charged

atoms are called ions
(cation-positively charged;
anion-negatively charged) still
attracted together via Ionic Bonds
(due to the opposite charges)

Compounds formed by ionic bonds are called ionic compounds or salts. Most drugs are manufactured as
salts because they are quite stable when dry but can dissociate easily in water (ex. sulfate)

Weak Chemical Interactions

A. Hydrogen Bonds
Attraction between a Hydrogen (such as the partial positive Hydrogen atom in water) and an
electronegative atom (such as the partial negative Nitrogen atom in Ammonia).

B. Van der Waals Interactions

Occur only when atoms and molecules are very close together

Numerous Van der waals interaction between

molecules of the foot and molecules of wall's
surface
Chemical reactions cannot create or destroy atoms but can only rearrange (redistribute) electons among
them. See the figure below, you can see Hydrogen (in the form of H2) in the reactant, you can also see it
in the product (H2O); same case for Oxygen.

B. Water
Water covers three-quarters of the earth's surface.
It can exist in three forms:
-Solid (as ice)
-Liquid (as H20)
-Gas (as water vapor)

A water molecule, composed of one atom of Oxygen and two atoms of Hydrogen are bonded to one
another via polar covalent bond

However, between water molecules, they are bonded to one another via hydrogen bond (specifically
hydrogen bond exists between partial negative Oxygen and partial positive Hydrogen)

Four emergent properties of water:

1. Cohesion of water molecules
Hydrogen bonds holds water molecules close to one another
2. Water's high surface tension
Related to cohesion, surface tension is the measure of how difficult it is to stretch or break the surface of
a liquid. Due to the ordered arrangement of water molecules to one another, but not to the air above

3. Water's high specific heat

Specific heat is the amount of heat that must be absorbed or lost for 1g of that substance to change its
temperature by 10 deg. C. Much of the heat absorbed is used to disrupt Hydrogen bonds before the
water molecules can begin moving faster. Why the need to move faster? Thermal energy- kinetic energy
associated with the random movement of atoms/molecules; Heat- thermal energy in transfer from one
body of matter to another)

4. Water's high heat of vaporization

Heat of vaporization is the quantity of heat a liquid must absorb for 1g of it to be converted from the
liquid to gaseous state. This is again due to hydrogen bond which must first be broken down before
water can change in state.
To evaporate 1g of water at 250C. about 580 calories of heat is needed. Calories- the amount of heat it
takes to raise the temperature of 1g of water by 10C.

Evaporative cooling
As liquid evaporates, the surface of the liquid that remains behind cools down (its temperature
decreases) because the “hottest” molecules, with greatest kinetic energy, most likely leave as gas

Why does ice float in water?

Ice- slow breakage of hydrogen bonds (from 4 to 0 deg. C) keeps molecules at arm's length (hydrogen
bonds should break and re-form easily however this cannot be easily done at lower temperatures thus
hydrogen bonds become kind of longer (since it cannot break easily)). Molecules becomes locked into a
crystalline lattice (0 deg. C)
Liquid water- as ice absorbs heat, Hydrogen bonds are disrupted and molecules have few hydrogen
bonds, allowing them to slip/be closer together
The floating ice insulates the liquid water below preventing it from freezing and allowing life to exist
under the frozen surface

Water as the solvent of life

Solution- homogenous mixture of two or more
substances
Aqueous solution- the solute is dissolved in water
Hydrophilic- any substance that has an affinity for water.
In some cases substances can be hydrophilic without actually dissolving (ex. A towel made up of cotton
can absorb water but will not be dissolved by water)
Hydrophobic- substances that are non-ionic and non-polar (they cannot form Hydrogen bonds) seem to
repel water

In a “normal” setting/ reaction between water molecules, a hydrogen atom participating in a hydrogen
bond between two water molecules shifts from one molecule to another

H+ exists as Hydronium ion

(H3O+)

(red circle) Indicates a reversible reaction that reaches a state of equilibrium (water molecules dissociate
at the same rate that they are being reformed from H+ and OH-, or simply that the number of times the
forward reaction occurs is the same as the number of times the reverse reaction occurs)

The reaction above, in a state of equilibrium results into equal concentrations of H+ and OH- in pure
water,however, adding certain kinds of solutes called acids and bases disrupts its balance

Acid- when dissolved in water, donate additional H+ in the

solution. It also removes OH- through formation of water (H+ +
OH- = H2O), thus results in an increase in H+ concentration and
less OH- , a characteristic of acidic solutions

Bases- when dissolved in water, reduces H+ concentration by

accepting H+ or or by dissociating to form OH-, thus results in an
increase in OH concentration and less H+, a characteristic of
basic solutions
(read pg.99 for the different reactions between water and
weak/strong acid, weak/strong base)

*Acidic solutions- higher concentration of H+

Basic solutions- higher OH-

If 0.01 mol of acid is added in water, pH changes from 7.0 to 2.0. If the same amount is added in blood,
pH changes only from 7.4 to 7.3! Why does the addition of acid have so much less effect on the pH of
blood than it does in water?

Buffers- substances that allows biological fluids to maintain a relatively constant pH despite the
addition of acids or bases. Contains a weak acid and its corresponding base
It does so by accepting H+ when it is in excess, and donating H+ when they have been depleted.
C. Carbon

Proteins, DNA, Carbohydrates and other molecules that distinguish living matter from
inanimate material are all composed of Carbon atoms bonded to another atom

There are variations in the structures made up of carbon bonded to another atom that contributes to
molecular diversity…
Hydrocarbons- organic molecules consisting only of carbon and hydogen atoms via covalent bonding.
Hydrocarbons differ in the following:

Isomers- compounds that have the same number of atoms of the same elements but different structures
(for example all the compounds are made up of 6 carbon and 6 hydrogen atoms however their structures
are different or simply you draw their chemical structures in different ways) and hence different
properties (read the book for the description of each type of isomers, pg. 109 and example of
enantiomers, pg.110 )
Chemical groups- specific moieties within molecules with characteristic chemical reaction (see figure in
pg.111 for the description of each chemical groups)

D. Biomolecules
FOUR MAIN CLASSES OF BIOMOLECULES
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic Acids
Of the four biomolecules, only carbohydrates, proteins and nucleic acids are called macromolecules (read
more on page 114)

The macromolecules carbohydrates, proteins and nucleic acids are made up of chain-like molecules
called POLYMERS (Greek polys=many and meris=part).
A polymer is a long molecule consisting of many similar or identical building blocks called MONOMERS
linked together by COVALENT BONDS
Imagine a train, the whole train is the polymer, each car that composes a train is the monomer and the
metal rod that connects each car of the train is the covalent bond

*TRY TO ANSWER CONCEPT CHECK 5.1

1. CARBOHYDRATES
Carbohydrates include:
a. Simple sugars- Monosaccharide and Disaccharides (these are the monomers of carbohydrates)
b. Polymers of sugars- Polysaccharide (this is the polymer of carbohydrates)

Monosaccharides have molecular formulas that are usually multiples of CH2O

Glucose (C6H12O6) is the most common monosaccharide
Function: Monosaccharides serve as a major fuel for cells and as raw material for building molecules

Monosaccharides can be classified based on the number of carbons (triose-made up of 3 Carbons,

pentose- 5 carbons, hexose- 6 carbons) and location of the carbonyl group (see C=O in orange box in the
figure below, if it’s an aldose the carbonyl group is at the end of the structure; if it’s a ketose the carbonyl
group is quite in the middle) (see figure in page 116 for the function of each monosaccharides in the
figure below)

Disaccharides consists of two monosaccharides linked together by glycosidic linkage, a covalent bond.
Example: Maltose made up of 2 glucose monomers and Sucrose made up of glucose and fructose
monomers (glucose and fructose are monosaccharides, thus are monomers of sugars)
(see page 117 for the figure on dehydration reaction for the synthesis of disaccharides)

Polysaccharides, the polymers of sugars, have storage and structural roles. They are made up of
monosaccharides
a. Storage polysaccharide
b. Structural polysaccharide

Storage polysaccharides
Starch, a storage polysaccharide of plants, consists entirely of glucose monomers. Plants store surplus
starch as granules within chloroplasts and other plastids
Glycogen is a storage polysaccharide in animals. Humans and other vertebrates store glycogen mainly in
liver and muscle cells
(see figure in page 118 so that you can see the difference between the two forms of starch (amylose
and amylopectin) and glycogen in terms of structure and source)
Structural polysaccharide
Cellulose is a major component of the tough cell wall of plants. Like starch, glucose is the monomer of
cellulose
Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods
Chitin also provides structural support for the cell walls of many fungi

The structure and function of a polysaccharide is determined by its

(a) sugar monomers (for example, the monomer of cellulose and starch, is the monosaccharide glucose)
(b) positions of glycosidic linkages (for cellulose it is 1,4 linkage between two α glucose monomers, one
in which the OH is below Carbon no. 1; for starch it is 1,4 linkage between two β glucose monomers, one
in which the OH is above Carbon no. 1)
(see figure in page 119)

Enzymes that digest starch by hydrolyzing α linkages can’t hydrolyze β linkages in cellulose

Cellulose in human food passes through the digestive

tract as insoluble fiber

Some microbes use enzymes to digest cellulose

Many herbivores, from cows to termites, have symbiotic
relationships with these microbes

2. LIPIDS
The unifying feature of lipids is having little or no affinity for water
Lipids are hydrophobic because they consist mostly of hydrocarbons, which form non-polar covalent
bonds
The most biologically important lipids are (a) fats, (b) phospholipids, and (c) steroids

Fats:
are constructed from two types of smaller molecules: (a) 1 molecule of glycerol and (b) 3 molecules of
fatty acids (ex. palmitic acid) linked together by ester linkage.
Saturated vs. Unsaturated fats

So that you can remember it easily, imagine that the double bond in the structure of unsaturated fat acts
as a spring, that no matter how you try to coil it into a solid structure, that spring will prevent you from
doing so, thus, unsaturated fat remains liquid at room temperature. Since saturated fat lacks this
“spring” they can be coiled into a solid structure, thus, are solid at room temperature.

Hydrogenation is the process of converting unsaturated fats to saturated fats by adding hydrogen
Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds or trans fat (you
can read more about trans fat in page 122 of the book)

These trans unsaturated fats are like

saturated fats that though they have
double bonds (that should have acted as a
“spring” preventing them from coiling into
a solid structure) the trans arrangement
between the two hydrogen molecule
around the Carbon makes it kind of
“straighter/without a bend ” similar to
saturated fat. Trans fat may contribute
more than saturated fats to cardiovascular
disease

Phospholipids
Steroids
These are lipids characterized by a carbon skeleton consisting of four fused rings (see red box).

*TRY TO ANSWER CONCEPT CHECK 5.3

3. PROTEINS
Proteins are constructed from the same set of amino acids

Amino acids are organic molecules with carboxyl and amino groups
Amino acids differ in their properties due to differing side chains, called R
groups

The 20 amino acids:

Peptide - a short chain of amino acids linked together by peptide bonds
Polypeptide- the polymer of proteins, are long chains of peptides

A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique
shape (see page 127 of the book so that you can see the different models used in visualizing proteins)

To achieve a functional protein there are 4 steps that has to be done or what we call the 4 levels of
protein structure (go to page 128 and 129 of the book so that you can see the differences in the 4 levels
of the structure of the protein transthyretin, a globular protein that transports Vitamin A and one of
the thyroid hormones in the body)
1. Primary structure- the sequence of amino acids in a protein, is like the order of letters in a long word.
2. Secondary structure- are coils and folds resulting from hydrogen bonds between repeating
constituents of the polypeptide backbone.Typical secondary structures are a coil called an α helix and a
folded structure called a β pleated sheet

Imagine a ribbon at one end I coiled it in the

other end I folded the ribbon.

Red box indicates that hydrogen bond exists

between the amino group (one with N) of an
amino acid in one polypeptide chain and the
carboxyl group (one with C=O) of an amino acid
of another polypeptide chain

3. Tertiary structure- the overall shape of a polypeptide resulting

from interaction between R groups (see parts of an amino acid in
pg.14 for you to remember what an R group is) of polypeptides in a
secondary structure (either alpha helix or beta pleated sheet).
These interactions between R groups include hydrogen bonds, ionic
bonds, hydrophobic interactions, and van der Waals interactions.
Strong covalent bonds called disulfide (S-S) bridges may reinforce
the protein’s structure.

Imagine the ribbon *The nature of amino acid whether non-polar, polar, acidic or basic is
earlier this time I determined by the nature of its functional R group. Thus, the R group also
crumpled it in a ball-like determines the type of bonds that will be formed for a tertiary structure. Ex.
structure charged R group can form ionic, polar can form hydrogen bond etc.
4. Quaternary structure- results when two or more polypeptide chains (in tertiary structure) form one
macromolecule. It can result into a fibrous or globular protein. Collagen is a fibrous protein consisting of
three polypeptides coiled like a rope. Hemoglobin is a globular protein consisting of four polypeptides:
two alpha and two beta chains.

After the quaternary structure there are still finishing touches that needs to be done such as attachment
of sugars (ex. Glycoprotein) or lipids (ex. Lipoproteins)

Recap…

*Tertiary structure- made up of polypeptides in their

secondary structure
*Quaternary structure- made up of polypeptides in their
tertiatry structure
Where does protein folding occur within the cell?
It occurs in/facilitated by proteins called chaperonins.

What determines protein structure?

1. Sequence of amino acids- any changes in the sequence of amino acids such as what occurs in the
disease sickle cell anemia, can cause damages to the protein structure (ex. The natural sequence of
amino acids is Val-His-Leu-Thr-Pro-Glu however, the last amino acid “Glu” was replace by “Val”)
(see figure in page 130 which shows how sickle-cell anemia develops due to change in the amino acid
sequence)
2. Physical and chemical conditions- Alterations in pH, salt concentration, temperature, or other
environmental factors can cause a protein to unravel. This loss of a protein’s native structure is called
denaturation. A denatured protein is biologically inactive.

Misfolded proteins- could turn into infectious and deadly proteins. Misfolding of the glycoprotein PrPC
causes a prion (infectious protein that can cause diseases! ex. Kuru, Creutzfeldt-Jakob’s disease) to form.

Proteins can be of different functions they can be hormonal, receptor, contractile & motor, structural,
defensive, storage and transport proteins and even enzymes (see figure in page 124 for the description
and example of each protein functions)

*TRY TO ANSWER CONCEPT CHECK 5.4

Enzymes:
During chemical reactions, either energy is “absorbed” or released back to the environment. This energy
is what we call the free energy…
Free energy- is the portion of a system's energy (from the environment) that can perform work when
temperature and pressure are uniform throughout the system, as in a living cell.

Exergonic reactions- proceeds with a net release of

free energy. It is spontaneous which means that is
energetically favorable because it increases the
entropy of the universe.
This is an accordance to the 2nd law of
thermodynamics which states that every energy
transfer or transformation increases the entropy of the
universe
entropy- a measure of molecular disorderliness and
randomness, why is an increase in entropy energetically
favorable such as in the case of exergonic reactions?
spontaneity is favorable because there is an
unstoppable trend towards disorderliness of the
universe as a whole.

Endergonic reactions- is one that absorbs free energy

from the environment. This is not energetically
favorable and thus is non-spontaneous

Using figure above, in an exergonic reaction you have a release of free energy because the reactant has a
higher free energy compared to the product. In an endergonic reaction since the product have a higher
free energy than that of the reactant, energy must be “absorbed”.

A spontaneous chemical reaction (such as exergonic reactions) occurs without any requirement for
outside energy, but it may occur so slowly that it becomes imperceptible that’s why in chemical
reactions in biological systems, enzymes are used (ex.sucrase)

How does enzymes work?

During chemical reaction we have what we call the

activation energy (EA)- The initial investment of energy,
the energy required to contort the reactant molecules so
the bonds can break (in what we call the transition state)

After bonds (of the reactants) have been broken, then, new
bonds for the product can be formed and energy can be
released.
In order to reach the transition state where bonds of the reactants can break, the activation energy
needed must be attained. One way of doing so is to use heat or a high temperature…

Biomolecules are rich in free energy, that is they can decompose spontaneously, however, the
temperature within cells is not high enough if we use heat so that we can attain the needed EA and
reach the transition state, proteins and enzymes will denature and all reactions, even those not
needed, will speed up!
Thus, enzymes are used in a process called catalysis, a process by which a catalyst (ex. Enzyme) speeds
up a reaction without itself being consumed

How does enzymes work?

Through the use of enzymes the activation energy needed to reach the transition state become lower
because the enzyme itself can already stretch the substrate (reactants) to its transition state form. This
also speeds up the reaction (see figure about catalysis below)

Initial interaction between the enzyme and the substrate (reactant)

Enzymes are very specific in their substrate
Catalysis in the active site

An enzyme is “saturated” if there is high substrate concentration and all the active site of enzymes are
occupied. Thus the rate of reaction is determined by how fast and enzyme converts the substrate to its
product.

Effects of pH and temperature

An enzyme has an optimal pH and temperature that favor the most active shape of the enzyme (see
figure 156 of the book for examples)

Cofactors
-are non-protein helpers that binds tightly or loosely and reversibly in an enzyme (ex. ionorganic such as
metal ions)
Coenzymes- are organic cofactors (ex. vitamins)

Enzyme inhibitors
(see figure 6.18, page 157 of the book)
 Allosteric regulation of enzymes
Any case in which a protein's function in one site is affected by the binding of a regulatory molecule (see
red box) at one site. This can result to inhibition or stimulation

This is a multisubunit
enzyme (see yellow
box) with four active
site and four regulatory
site where regulators
bind

Activators- stabilizes
the active form In a multisubunit enzyme,
Inhibitors- stabilizes cooperativity works when one
the inactive form substrate binds to one of the four
active site (activator in image in
the left is not a substrate, only an
activator), resulting to the
activation of the rest of the active
site.
Ex. Although hemoglobin is not an
enzyme, when one oxygen molecule
binds to it, it kind of promotes more
Oxygen molecule to bind, increasing
hemoglobin’s efficiency in

In glycolysis, ADP acts as an

activator to the enzyme which
converts/breaks down 1,3-
bisphosphoglycerate to
3-phosphoglycerate. By doing so,
1,3 bisphosphoglycerate losses
one phosphate group (that’s why
we lose the word bis in its name
and it becomes
3-phosphoglycerate) the lost
phoshate group goes to/adds to
ADP (adenosine diphosphate)
reforming ATP (adenosine
triphosphate) (ADP + P= ATP)
Feedback inhibition
Metabolic pathway is halted by the inhibitory binding of its end product to an enzyme that acts early in
the pathway (technically if product is too much like in the image below, which is isoleucine, the product
will also act as an inhibitor)

Ex. Threonine binds to the enzyme threonine deaminase, the end

product of the whole process is isoleucine, now if isoleucine levels
in the body is already high, isoleucine (the product formed by
converting threonine) will act as an inhibitor to the enzyme
threonine deaminase, blocking further conversion of threonine to
isoleucine.

4. NUCLEIC ACIDS
Nucleic acids are macromolecules made up of polymers called polynucleotides
Each polynucleotide is made of monomers called nucleotides linked together by 3,5 phosphodiester
bond
Each nucleotide consists of a nitrogenous base, a pentose (5-Carbon) sugar, and a phosphate group

- The sugar can be ribose (such as that in ribonucleic

acid, RNA) or deoxyribose (such as that in
deoxyribonucleic acid, DNA)

The difference is that ribose sugar has hydroxyl (-OH)

in its carbon no.2 while deoxyribose has no OH in its
carbon no.2 (see red box in figure below)

-The nitrogenous base bonded in carbon no. 1 of the

5-C sugar, can be purines (such as adenine and
guanine) and/or pyrimidines (such as thymine,
cytosine and uracil)
 In order to connect one nucleotide to another and eventually form a polynucleotide (or nucleic acid),
a 3, 5 phosphodiester bond is formed between -OH of thecarbon no. 3 of the sugar of one nucleotide and
the phosphate group (PO3-) of the carbon no. 5 of another nucleotide

Ex. In this figure, the 3,5 phosphodiester bond

exists between the -OH of carbon no. 3 of the
nucleotide CMP and the phosphate group of
carbon no. 5 of nucleotide AMP. Together they
form a dinucleotide (di=two nucleotides)

There are two types of nucleic acids:

 Deoxyribonucleic acid (DNA)
 Ribonucleic acid (RNA)
Compared to RNA, DNA is double stranded. The question is that how will you connect this two strands
together?

The two strands of DNA, in order

to form a double helix structure is
connected to one another via
hydrogen bond between the
nitrogenous bases.

The pairing between the

nitrogenous bases is strictly
purines-pyrimidines only.
Ex. A-T (connected by 2 hydrogen
bonds), G-C (connected by 3
hydrogen bonds) (see yellow box)

5-C sugar and phosphate group of one

nucleotide (I’ll name it “nucleotide 2” for
the purpose of teaching, you can’t name
a nucleotide just any name you like)
bonded to other nucleotides through 3,5
phosphodiester bond
Nitrogenous base of “nucleotide 2”
hydrogen bonded to the nitrogenous
base (G) of a nucleotide from the
other strand
Perhaps one of the most important nucleotide in a biological system is ATP (Adenosine triphosphate)

ATP is the energy currency of the cell

The energy released from the hydrolysis or breakdown of ATP to ADP and P does not come from the
bonds between the phosphate groups but rather from the high energy of the reactant (ATP and water)
compared to the products
High energy of the ATP is contributed by the negatively charged triphosphate that acts as “compressed
energy spring”

How ATP works?

1. ATP can phosphorylate the reactant or that simply it will kind of “donate” one of its phosphate group
to the reactant making it less stable with more free energy (remember that exergonic reactions one
where reactant has higher free energy and therefore energy is released, is more favorable (go back to
2nd law of thermodynamics and concept on entropy). Simply, ATP phosphorylated something so that
the reaction becomes favorable. On the other hand, since ATP kind of “donated” its phosphate group it
will become ADP. Eventually, as the product is formed, the donated phosphate group will be
removed/displaced.

2. Similar to no.1 ATP can also phosphorylate transport proteins

3. ATP can also noncovalently bind to motor proteins. The
hydrolysis or break down of ATP to ADP and P causes a shape
change in the protein and thus the protein “moves forward”

(See figure 6.12, pg. 151 of the book for the ATP cycle)
Macromolecule Polymer Monomer Covalent bond
Carbohydrates Polysaccharide Monosaccharide & Glycosidic linkage
Disaccharide
Proteins Polypeptide Amino acids Peptide bond
Nucleic acids Polynucleotide Nucleotides 3,5 phosphodiester
bond