UNIT 2: BIOLOGICAL MOLECULES GENERAL BIOLOGY 1

1ST QUARTER
1. CARBOHYDRATES AND LIPIDS

 Biogeochemical cycles such as the carbon-oxygen cycle and the water cycle play important roles in
ensuring that we have access to these important elements. All forms of life, not only that of humans, are
made up of four kinds of important large molecules: carbohydrates, lipids, proteins, and nucleic acids. All of
these have carbon atoms as their backbones since carbon is capable of forming up to four chemical bonds
with atoms of other elements.
 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 CnH 2mOm. 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.

Dehydration synthesis of disaccharides from monosaccharide components.

 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.
 How are carbohydrates classified? Carbohydrates can be classified into three main categories, according to
increasing complexity:
 monosaccharides (monos means single and sacchar means sugar)
 disaccharides (di means two)
 polysaccharides (poly means many)
Classification Functions Structure Examples
Monosaccharide  major cellular nutrient  contains a carbonyl group  Ribose - a 5C aldose that
 often incorporated (C=O) and may be forms part of the backbone
into more complex classified as an aldose or of nucleic acids
carbohydrates ketose depending on the  Glucose - a 6C aldose that
position is the product of
 may have three to seven photosynthesis and the
carbons in the skeleton substrate for respiration that
 may be arranged in a linear provides energy for cellular
form when solid and is activities
converted into a ring form in  Fructose - a 6C ketose that
aqueous solution (α form is found in many plants and
when H is on top of plane of is often bonded to glucose
ring and β form when -OH is
on top of plane of ring)
Disaccharide  energy source  forms when a glycosidic  Maltose (glucose +
 sweetener and dietary linkage forms between two glucose)- malt sugar often
component monosaccharides found in sprouting grains,
malt-based energy drinks, or
beer
 Lactose (glucose +
galactose) - milk sugar that
is a source of energy for
infants; an enzyme called
lactase is required to digest
this. Many adult Filipinos
have low levels of this
enzyme leading to a
condition called lactose
intolerance.
 Sucrose (glucose + fructose)
- found in table sugar
processed from sugar cane,
sweet fruits, and storage
roots like carrots
Polysaccharide  storage material for  forms when hundreds to  Storage polysaccharides
important thousands of are large molecules
monosaccharides monosaccharides are retained in the cell and are
 structural material for joined by glycosidic linkages insoluble in water (formed
the cell or the entire 1,4 linkage
organism monomers; with a helical
structure)
 Starch - amylase is
unbranched starch forming
a helical structure while
amylopectin is branched
starch, these are present in
plant parts like potato
tubers, corn, and rice and
serve as major sources of
energy.
 Glycogen - found in
animals and fungi; often
found in liver cells and
muscle cells
  Structural polysaccharides
(formed from linkage of
monomers; strands
associate to form a sheet-
like structure)
 Cellulose - tough sheet-like
structures that make up
plant and algal cell walls
that may be processed to
form paper and paper-
based products; humans
lack the enzymes to digest
β 1,4 linkages so is passed
out of the digestive tract
and aids in regular bowel
movement
 Chitin - used for structural
support in the walls of fungi
and in external skeletons of
arthropods
 Peptidoglycan - used for
structural support in
bacterial cell walls

LIPIDS
 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 nonpolar C-H bonds. They function for energy storage,
providing nine food calories or 37 kJ of energy per gram. They also function for the cushioning of vital organs
and for insulation. Furthermore, they play important roles in plasma membrane structure and serve as
precursors for important reproductive hormones.
 Lipids can be divided into three main classes according to differences in structure and function.
Classification Functions Structure Examples
Fats  energy storage  formed from dehydration  Saturated fat—animal
(triacylglycerol  cushioning of vital reactions between glycerol products such as butter and
or triglycerides) organs (adipose (an alcohol with three Cs, lard have a lot of saturated
tissue) each with an –OH group) fatty acids. The linear structure
 insulation forming three ester linkages allows for the close packing of
with three fatty acids (16-18 the fat molecules forming
Cs, with the last C as part of a solids at room temperature,
–COOH group) and diets high in these fats may
producing three molecules of increase the risk of
water. developing atherosclerosis, a
 component fatty acids (FA) condition in which fatty
may be either saturated or deposits develop within the
unsaturated walls of blood vessels ,
 Saturated FA (e.g., palmitic increasing the incidence of
acid) have the maximum cardiovascular disease.
number of hydrogen atoms  Unsaturated fat—plant and
bonded to each carbon fish oils have unsaturated fatty
(saturated with hydrogen); acids. The bent structure
there are no double bonds prevents close packing and
between carbon atoms. results in oils or fats that are
 Unsaturated FA (e.g., oleic liquid at room temperature.
acid) have at least one Homemade peanut butter
double bond, H atoms are has oils that separate out of
arranged around the double solution for this reason.
bond in a cis configuration Industries have developed a
(same side) resulting in a process called hydrogenation
bend in the structure. that converts unsaturated fats
into saturated fats to improve
texture spreadability.
 Trans fat—may be produced
artificially through the process
of hydrogenation described
above. The cis double bonds
are converted to trans double
bonds (H atoms on opposite

Phospholipids  major component  formed from dehydration
of cell membranes reactions between glycerol
(an alcohol with three Cs,
each with a –OH group),
forming two ester linkages
with two fatty acids (16-18 Cs,
with the last C as part of a –
COOH group) and a last
linkage with a phosphate
group
 phosphate group is
hydrophilic and is called the
‘head’ of the molecule
 fatty acids are hydrophobic
and form the ‘tails’ of the
molecule
Steroids and  regulate fluidity of  characterized by a C-
sterols cell membranes skeleton with four fused rings
 base of sex  functional group attached to
hormones the rings vary (if – OH is
 emulsification of attached to the 4th C, then it
fats during digestion is called a cholesterol
sides) resulting in fats that
behave like saturated fats.
Studies show that trans-fat are
even more dangerous to
health than saturated fats to
the extent that they have
been banned from
restaurants in some countries.
 Phospholipids self-assemble
into bilayers when surrounded
by water and form the
characteristic structure of
plasma membranes
 Cholesterol found in cell
membranes regulates the
rigidity of the cell membrane
and are the base material for
the production of sex
hormones like estradiol and
progesterone

2. AMINO ACIDS AND PROTEINS

 DNA—is the repository of genetic information RNA—serve as the transcripts and regulators of expressed
genetic information Proteins—are the functional products and executors of cellular functions.
Biomolecule Physical Property Functional Relevance
DNA  Complementary Base  Allows each strand to serve as a template for replication and
Pairs transcription
 Phosphodiester bonds  Essential for polynucleotide chain elongation
 Deoxyribose 5’OH  Start of the polynucleotide chain
 Deoxyribose 3’OH  “End” of the polynucleotide chain Connection point for
extending the chain
 Deoxyribose 2’H  Difference between the sugar residues of DNA (deoxyribose)
and RNA (ribose)
RNA  Complementary Base  Allows RNA to serve as transcripts (mRNA) and translators
Pairing (tRNA) of genetic information from DNA.
 Uracil  Nitrogenous base equivalent to T in RNA.
 Ribose 2’OH  Difference between the sugar residues of DNA (deoxyribose)
and RNA (ribose)
 Limits the compaction of RNA molecules. Double stranded
RNA molecules are similar in structure as the A-form of DNA
Protein  N-Terminus  Start of the polypeptide chain
 C-Terminus  End of the polypeptide chain
 Peptide Bond  Addition point for new amino acids during polypeptide growth
 Links Amino Acids
 Planar character
 Phi Angle  Angle between:
Ci-1-Ni- i-Ci
 Ci-1: Carbonyl C of previous AA
 Ni: Amide Nitrogen of current AA
 i: Alpha Carbon of current AA
 Ci: Carbonyl C of current AA
 Angle is observed by looking down the bond between Ni and
Cαi; coming from the N-terminus of the polypeptide
 Psi Angle  Angle between:
Ni+1-Ci- i-Ni
 Ni+1: Amide Nitrogen of succeeding AA
 C i: Alpha Carbon of current AA
 Ni: Amide Nitrogen of current AA
  Angle is observed by looking down the bond between Ci and
 Amino Acid R-Groups i; coming from the C-terminus of the polypeptide
 Defines Amino Acid Character
a. non-polar
i. aliphatic (G,A,V, L, I, M)
ii. aromatic (Y,W,F)
b. polar, uncharged (S,T,C,P,Q)

3. ENZYMES
 Enzymes - are organic substances that accelerate the rate of chemical reaction. Enzymatic browning can be
a significant problem because it limits the shelf life of fruits and vegetables. However, enzymatic browning is
not always unwanted. The browning reaction contributes to the desirable color and flavor of raisins, prunes,
coffee, tea, and cocoa. 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 to eat up
to a few hours after cutting. Enzymes are organic or biological catalysts. Catalysts are substances that speed
up a reaction without being used up, destroyed, or incorporated into the end product. They are vital to the
regulation of the metabolic processes of the cell. Many enzymes are proteins. We will focus on this type of
enzymes in this discussion.
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 investment of energy in order to start a reaction is called the activation energy. It is often supplied
as thermal energy or heat absorbed by reactants from their surroundings. Reactant molecules absorb heat
which causes them to collide more frequently and more forcefully. This agitates the atoms within the
molecules that results in the likely breaking of bonds.
 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 energy.

 The reaction shown in the Figure is spontaneous but the activation energy provides a barrier that determines
the rate of the reaction. Reactants have to absorb enough energy from their environment to surmount this
barrier before the reaction can proceed.
How do enzymes affect reactions?
 Heat speeds up reactions. This is inappropriate for biological systems because it denatures proteins, kills cells,
and speeds up all reactions, not just those that are needed. Enzymes catalyze specific reactions by lowering
the activation energy barrier and allowing the reactant molecules to absorb enough energy at moderate
temperatures. Enzymes cannot change the G for a reaction and can only hasten reactions that would
eventually occur anyway.
The active site and functional groups of its amino acids may lower activation energy by:
 acting as a template for substrate orientation
 stressing the substrates and stabilizing the transition state
 providing a favorable microenvironment
 participating directly in the catalytic reaction
Factors that affect enzyme action
 Enzyme concentration
 Substrate concentration
 Inhibitor concentration
 Temperature
 pH
What is the difference between a competitive and noncompetitive inhibitor?
 The presence of non-protein helpers called co-factors and of organic molecules like co-enzymes may
activate apoenzymes to produce holoenzymes by binding to their active sites. Common examples may be
found in popular supplements such as ions of iron, copper, zinc, or in vitamins like vitamins A, C, and B-
complex.