BIOLOGICAL MOLECULES (FIRST SEMESTER)

CARBOHYDRATES

What do humans get from food? Heterotrophs, such as human beings, obtain energy and
raw materials from food. These are important for cell growth, cell division, metabolism,
repair, and maintenance of the body. Nutrients can be classified as either organic
nutrients (i.e., those that contain carbon such as carbohydrates, fats, proteins, vitamins,
and nucleic acids) or inorganic nutrients (i.e., those that do not contain carbon such as
water and mineral salts)

What are carbohydrates?

Carbohydrates are organic compounds made up of carbon, hydrogen, and oxygen. These
compounds have a general formula of CnH2mOm. This means that the hydrogen and
oxygen atoms are present in a ratio of 2:1. For example, glucose has a formula of
C6H12O6 and sucrose has a formula of C12H22O11. Carbohydrates are usually good
sources of raw materials for other organic molecules and energy. One gram of
carbohydrates provides four food calories or 16 kJ of energy. In the human diet,
carbohydrates mainly come from plants although they are found in all organisms.

How are carbohydrates formed?

Carbohydrates are examples of macromolecules. These are chainlike molecules called

polymers (mere means part) made from repeating units like monomers. Polymers can be
formed from covalently-bonded monomers much like a single structure can be made out
of repeated building blocks linked to each other.
These monomers, called monosaccharides, form covalent bonds when one monomer
loses a hydroxyl group and the other loses a hydrogen atom in dehydration or
condensation reactions, forming disaccharides. This reaction requires energy to occur. The
bond formed is called a glycosidic linkage.
Longer polysaccharide chains are formed by monomer addition through succeeding
dehydration reactions. These reactions can occur in the human liver as carbohydrates are
stored as polysaccharides called glycogen or in ground tissues of plants where these are
stored as starch.
Polysaccharides are broken down into simpler components through the use of water to
break covalent bonds and release energy. The process, known as hydrolysis (hydro means
water and lysis means split), is the opposite of dehydration reactions and often occurs in
the digestive tract during chemical and mechanical digestion. Here, enzymes break bonds
within polysaccharides. With the aid of water, one –H group attaches to a monosaccharide
while another –OH group attaches to the other.
 on top of plane of
ring)
How are carbohydrates classified? Dissacharides • energy .forms when a • Maltose
source glycosidic linkage (glucose +
Carbohydrates can be classified into three main categories, according to increasing forms between glucose)—malt
complexity: • sweetener two sugar often
and dietary monosaccharides found in
• monosaccharides (monos means single and sacchar means sugar) component sprouting grains,
malt-based
• disaccharides (di means two)
energy
• polysaccharides (poly means many) drinks, or beer
• Lactose
Classification Functions Structures Examples (glucose +
Monossacharide • major cellular • contains a • Ribose—a 5C galactose)—milk
nutrient carbonyl group aldose that sugar that
• often incorporated (C=O) and may be forms part of the is a source of
into more complex classified as an backbone of energy for
carbohydrates aldose or nucleic infants; an
ketose depending acids enzyme
on the • Glucose—a 6C called lactase is
position aldose required to digest
• may have three that is the this. Many
to seven product of adult Filipinos
carbons in the photosynthesis have low levels of
skeleton and the this enzyme
• may be substrate for leading to a
arranged in a respiration condition called
linear form when that provides lactose
solid energy for intolerance.
and is converted cellular activities • Sucrose
into a • Fructose—a 6C (glucose +
ring form in ketose fructose)—found
aqueous that is found in in table
solution (α form many sugar processed
when H is plants and is from sugar cane,
on top of plane of often sweet fruits,
ring bonded to and storage roots
and β form when glucose like carrots
-OH is Polyssacharide • storage • forms when • Storage
material for polysaccharides
important hundreds to are large sheet-like
monosaccharides thousands molecules structure)
of retained in the o Cellulose—
• structural monosaccharides cell and are tough sheet-like
material for the are insoluble in water structures that
cell or the entire joined by (formed from α make up plant
organism glycosidic 1,4 linkage and algal cell
linkages monomers; with walls that may be
a helical processed to
structure) form paper and
o Starch— paper-based
amylase is products;
unbranched humans lack the
starch forming a enzymes to
helical structure digest β 1,4
while linkages so
amylopectin is is passed out of
branched the digestive
starch, these are tract and aids in
present in plant regular bowel
parts like potato movement
tubers, corn, and o Chitin—used
rice and serve as for structural
major sources of support in the
energy. walls
o Glycogen— of fungi and in
found in animals external
and fungi; often skeletons of
found in liver arthropods
cells and muscle o
cells Peptidoglycan—
• Structural used for
polysaccharides structural
(formed from β support in
1,4 bacterial cell
linkage of walls
monomers; What are lipids?
strands associate
to form a Lipids are a class of large biomolecules that are not formed through polymerization. They
have diverse structures but are all non-polar and mix poorly, if at all, with water. They may
have some oxygen atoms in their structure but the bulk is composed of abundant acid) have the cardiovascular
nonpolar C-H bonds. They function for energy storage, providing nine food calories or 37 maximum disease
kJ of energy per gram. They also function for the cushioning of vital organs and for number • Unsaturated
insulation. Furthermore, they play important roles in plasma membrane structure and of hydrogen fat—plant and fish
atoms bonded to oils have
serve as precursors for important reproductive hormones.
each carbon unsaturated fatty
How are lipids classified? (saturated with acids. The bent
hydrogen); there structure prevents
Lipids can be divided into three main classes according to differences in structure and are no double close packing and
function. Some notes on their structures and functions are found in the following table: bonds between results in oils or
carbon atoms fats that are liquid
Classifications Functions Structure Example o Unsaturated FA at room
Fats energy f o r m e d f ro m Saturated fat— (e.g., oleic temperature.
(triacylglycerols storage dehydration animal products acid) have at Homemade peanut
or triglycerides) • reactions such as least one double butter has
cushioning of between glycerol butter and lard bond, H atoms oils that separate
vital organs (an have a lot of are arranged out of solution for
(adipose alcohol with saturated fatty around the this reason.
tissue) three Cs, each acids. double bond in a Industries have
• with The linear cis developed a
insulation an –OH group) structure allows for configuration process called
forming three the close packing (same side) hydrogenation that
ester linkages of resulting in a converts
with three fatty the fat molecules bend in the unsaturated fats
acids (16-18 Cs, forming solids at structure into
with the last C as room saturated fats to
part of a –COOH temperature, diets improve texture
group) and high in these fats spreadability.
producing three may increase • Trans fat—may
molecules of the risk of be produced
water developing artificially
• component atherosclerosis, a through the
fatty acids (FA) condition in process of
may which fatty hydrogenation
beeithersat deposits develop described
uratedor within the walls of above. The cis
unsaturated blood vessels, double bonds are
o Saturated FA increasing the converted to trans
(e.g., palmitic incidence of
 double bonds (H the ‘head’ of the
atoms on opposite molecule
sides) resulting • fatty acids are
in fats that behave hydrophobic
like saturated fats. and form the
Studies show ‘tails’ of the
that trans fat are molecule
even more Steroids and • regulate • characterized • Cholesterol
dangerous to sterols fluidity of cell by a Cskeleton found in
health membranes with four fused cell membranes
than saturated fats • base of sex rings regulates
to the extent that hormones • functional the rigidity of the
they have been • group cell
banned from emulsification of attached to the membrane and are
restaurants in fats during rings vary (if – the base
some countries digestion OH is attached to material for the
Phospholipids major formed from Phospholipids self- the 4th C, then production
component dehydration assemble it is called a of sex hormones
of cell reactions into bilayers when cholesterol) like
membranes between glycerol surrounded by estradiol and
(an alcohol with water and progesterone
three Cs, form the Benedict’s solution, a blue solution with CuSO4(aq), can detect the presence of reducing
each with a –OH characteristic sugars (i.e.,any sugar with a free aldehyde or ketone group such as all monosaccharides
group), structure of plasma and the disaccharides lactose and maltose). When boiled, these sugars reduce Cu2+ in
forming two membranes Benedict’s solution to produce a brickred precipitate of Cu2O(s). Iodine test can be used
ester linkages to detect the presence of starch.
with two fatty
acids (16-18 Emulsion test can be used to identify fats
Cs, with the last C
as part of Amino Acids and Proteins
a –COOH group)
and a last • DNA—is the repository of genetic information
linkage with a
phosphate • RNA—serve as the transcripts and regulators of expressed genetic information
group
• phosphate • Proteins—are the functional products and executors of cellular functions
group is
Table 1: Important Physical Properties of Biomolecules
hydrophilic and is
called Biomolecule Physical Property Functional Relevance
DNA Complementary Base Allows each strand to Addition point for new
Pairs serve as a template for amino acids during
replication and polypeptide
transcription growth
Phosphodiester bonds Essential for Peptide Bond Links Amino Acids
polynucleotide chain Planar character
elongation Phi Angle Angle between:
Deoxyribose 5’OH Start of the Ci-1-Ni-Cαi-Ci
polynucleotide chain Ci-1 : Carbonyl C of
Deoxyribose 3’OH “End” of the previous AA
polynucleotide chain Ni : Amide Nitrogen of
Connection point for current AA
extending the chain Cαi: Alpha Carbon of
Deoxyribose 2’H Difference between the current AA
sugar residues of DNA Ci : Carbonyl C of
(deoxyribose) current AA
and RNA (ribose) Angle is observed by
RNA Complementary Base Allows RNA to serve as looking down the bond
Pairing transcripts (mRNA) and between Ni
translators and Cαi; coming from
(tRNA) of genetic the N-terminus of the
information from DNA polypeptide
Uracil Nitrogenous base Psi Angle Angle between
equivalent to T in RNA. Ni+1-Ci-Cαi-Ni
Ribose 2’OH Difference between the Ni+1 : Amide Nitrogen of
sugar residues of DNA succeeding AA
(deoxyribose) Ci : Carbonyl C of
and RNA (ribose) current AA
Limits the compaction of Cαi: Alpha Carbon of
RNA molecules. current AA
Double stranded RNA Ni : Amide Nitrogen of
molecules are similar in current AA
structure as Angle is observed by
the A-form of DNA looking down the bond
N-Terminus Start of the polypeptide between Ci
chain and Cαi; coming from
C-Terminus End of the polypeptide the C-terminus of the
chain polypeptide
Amino Acid R-Groups Defines Amino Acid
Character
 a. non-polar investment of energy in order to start a reaction is called the activation energy. It is often
i. aliphatic supplied as thermal energy or heat absorbed by reactants from their surroundings.
(G,A,V, L, I, M) Reactant molecules absorb heat which causes them to collide more frequently and more
ii. aromatic forcefully. This agitates the atoms within the molecules that results in the likely breaking
(Y,W,F) of bonds.
b. polar, uncharged
(S,T,C,P,Q) • When the new bonds of the products form, energy is released as heat and the molecules
return to stable shapes with lower energy. This results in an overall decrease of free
Enzymes energy.

Introduce the list of important terms that the learners will encounter:
• enzyme
• catalyst How do enzymes affect reactions?
• activation energy Heat speeds up reactions. This is inappropriate for biological systems because it denatures
• substrate
proteins, kills cells, and speeds up all reactions, not just those that are needed. Enzymes
• enzyme-substrate complex
catalyze specific reactions by lowering the activation energy barrier and allowing the
• active site
• induced fit reactant molecules to absorb enough energy at moderate temperatures. Enzymes cannot
• cofactor change the !G for a reaction and can only hasten reactions that would eventually occur
• coenzyme anyway.
• competitive inhibitor
• noncompetitive inhibitor The active site and functional groups of its amino acids may lower activation energy by:
Enzymes—are organic substances that accelerate the rate of chemical reaction. Enzymatic
• acting as a template for substrate orientation
browning can be a significant problem because it limits the shelf life of fruits and • stressing the substrates and stabilizing the transition state
vegetables. However, enzymatic browning is not always unwanted. The browning reaction • providing a favorable microenvironment
contributes to the desirable color and flavor of raisins, prunes, coffee, tea, and cocoa. • participating directly in the catalytic reaction
Although enzymatic browning causes changes in flavor and taste (i.e., bitter, astringent)
and may reduce quality, the browning agents formed are not toxic. Brown fruits are safe What is the difference between a competitive and noncompetitive inhibitor?
to eat up to a few hours after cutting. The presence of non-protein helpers called co-factors and of organic molecules like co-
enzymes may activate apoenzymes to produce
• Enzymes are organic or biological catalysts. Catalysts are substances that speed up a holoenzymes by binding to their active sites. Common examples may be found in popular
reaction without being used up, destroyed, or incorporated into the end product. They are supplements such as ions of iron, copper, zinc, or in
vital to the regulation of the metabolic processes of the cell. Many enzymes are proteins. vitamins like vitamins A, C, and B-complex.

• What keeps spontaneous reactions from occurring more rapidly?

• All chemical reactions between molecules involve the breaking and forming of bonds.
Converting starch into glucose involves contorting starch into a highly unstable state
before the reaction can proceed. This unstable state is called the transition state that
happens when reactants absorb energy from their surroundings and. This initial