UNIT 1B: BIOMOLECULES

BIOL2410 D01 Lecture Notes

A) Biomolecules - Overview
Ø All of the structures and functions in the human body can be traced back to the ions and
biomolecules that are essential for life and the interactions between them.
Ø In this unit you will cover:
1. Atoms and Ions Important for the structure and function of the body
2. Types of Molecular Bonds
3. Organic vs Inorganic Molecules
4. Biomolecules
a. Carbohydrates
b. Lipids
c. Nucleotides, Nucleosides and Nucleic Acids.
d. Proteins
5. Solutes and concentration
6. Acids, Bases, & pH
 B) Atoms & Ions in the Body
1. >90% of the body’s mass consists of:
a. Oxygen
b. Carbon
c. Hydrogen Silverthorn 8th edition
inside back cover.
2. <10% of the body’s mass consists of
other major and minor essential elements.
Many of these appear in their ionic forms.
a. Major
Ø Cations (lost an electron, positively charged): Sodium (Na+);
Potassium (K+); Calcium (Ca2+); Magnesium (Mg2+); Hydrogen (H+)
Ø Anions (gained an electron, negatively charged): Chloride (Cl-);
bicarbonate (HCO3-); Phosphate (PO42-), Sulfate (SO42-)
Ø Other major elements: Nitrogen (N); Phosphorus (P); Sulfur (S)
b. Minor
Ø Examples include: Iron (Fe); Iodine (I); Copper (Cu); Zinc (Zn), etc. Figure 2.5
C) Types of Molecular Bonds
Ø Atoms join together to form the molecules involved in the structures and functions
of the human body (and of all living organisms).
Ø Bonds:
1. Covalent Bonds – atoms share electrons
Ø Strong bonds that require energy to make or break
Ø Can form single, double and triple bonds depending on how many
electrons are shared.
Ø Form non-polar and polar covalent bonds. Polarity helps to
determine the solubility of different molecules and in turn how
they will be transported in the body and how they will interact Figure 2.6a&b
with the cell membranes (as we will see in unit 2).
a. Non-Polar Covalent Molecules: shared electrons are distributed evenly amongst
atoms, leading to all regions of the molecule having a neutral charge. Non-polar
molecules are not very soluble in water (i.e. are hydrophobic not hydrophilic).
Ø E.g. O2, CO2, fatty acids, cholesterol (or any molecule composed mostly of
carbon and hydrogen atoms).
C) Types of Molecular Bonds
b. Polar Covalent Molecules: shared electrons are
distributed unevenly (spend more time around a
particular atom or part of the molecule). Result:
one region of the molecule has a partial negative
charge (d-) and another region has a partial
positive charge (d+).
Ø Molecules with polar covalent bonds are Figure 2.6a&b
soluble in water (i.e. are hydrophilic)
Ø E.g. water (H2O), glucose (C6H12O6)

Figure 2.8
C) Types of Molecular Bonds
Ø Bonds:
2. Non-Covalent bonds – facilitate reversible reactions
a. Ionic Bonds – atom to atom transfer of electron(s).
Ø The most polar bond (making them very soluble in
water, i.e. hydrophilic)
Ø Transfer of electrons forms anions & cations.
Ø The two oppositely charged ions are attracted to
one another (electrostatic attraction - like magnets,
opposite charges attract and like charges repel).
Ø E.g. NaCl,
b. Hydrogen Bonds – weak bond between hydrogen atom
and nearby oxygen, nitrogen or fluorine atom.
Ø E.g. attractive forces between individual water
molecules leading to surface tension.
c. Van der Waals Forces – weak bond involving attraction
between electrons of one atom and the nucleus
Figure 2.6
(protons) of another atom.
D) Organic vs Inorganic Molecules
1. Inorganic Molecules: usually lack carbon atoms
Ø E.g. water (H2O), salt (NaCl), hydrochloric acid (HCl)
Ø There are some exceptions. The following are
inorganic molecules that contain carbon: carbonic
acid (H2CO3); Bicarbonate (HCO3-), Carbon dioxide
(CO2), Carbon monoxide (CO).
2. Organic Molecules – molecules that contains
covalently bonded carbon atoms (often combined
with H, O, N, P, or S). Includes all of the
biomolecules:
a. Carbohydrates
b. Lipids
c. Nucleic acids
d. Proteins
“The Person You Love…” (Teagan White, 2010)
 E) Biomolecules
1. Carbohydrates -
a. Consist of C, H, and O
b. General formula of CnH2nOn
Ø E.g.1: glucose (n=6); C6H12O6
Ø E.g.2: ribose found in RNA (n=5); C5H10O5
Ø Some exceptions: E.g.3: deoxyribose found in DNA = C5H10O4
c. Properties:
i. Most are polar and therefore hydrophilic (soluble in water)
ii. Most abundant biomolecule in nature. Found in both plants
(cellulose & starch) and animals (chitin & glycogen)
iii. Monomer (basic unit of structure) called monosaccharides
(glucose, fructose, galactose, ribose, deoxyribose).
iv. Polymers (formed by joining monomers together) include
disaccharides (sucrose, maltose, lactose) and polysaccharides
(starch & glycogen). Figure 2.2
What two monosaccharides form sucrose (table sugar)?
 E) Biomolecules
1. Carbohydrates -
d. Functions:
i. Energy for cells
Ø Glucose metabolism forms ATP (adenosinetriphosphate)
ii. Structural component of other biomolecules (DNA & RNA)
Ø E.g.1: DNA contains deoxyribose
Ø E.g.2: RNA contains ribose
iii. Structural component of cells – e.g. can be bound to lipids and
proteins to form glycolipids and glycoproteins which have
important roles in the structure and function of cell membranes.

Figure 2.2
E) Biomolecules
2. Lipids -
a. Consist of C, H, and O, but in a different ratio than
carbohydrates (less oxygen); some have N and P.
b. Properties:
i. Hydrophobic (insoluble in water)
c. Diverse group of molecules including:
i. Fatty acids
Ø Long hydrocarbon chains with 8-28.carbons
Ø Has a carboxyl (-COOH) functional group (= acidic)
Ø Saturated – no double bonds between carbon atoms so forms
a straight chain. Solid at room temperature. E.g. palmitic acid
(palm oil, butter, animal fats); stearic acid (butter, chocolate,
Figure 2.1
lard); lauric acid (coconut oil).
Ø Unsaturated – has double bonds between carbon atoms. One double bond = monounsaturated. e.g. oleic
acid (most common in nature, part of triglycerides and phospholipids that make cell membranes; olive oil).
Two or more double bonds = polyunsaturated. e.g. linoleic acid (found in canola oil, sunflower oil, nuts,
seeds); arachidonic acid. . The more double bonds, the less likely the fat is to be soluble at room temp
E) Biomolecules Saturated Monounsaturated

2. Lipids -
a. Consist of C, H, and O, but in a different ratio than
carbohydrates (less oxygen); some have N and P.
b. Properties:
i. Hydrophobic (insoluble in water)
c. Diverse group of molecules including:
i. Fatty acids Polyunsaturated
Ø Long hydrocarbon chains with 8-28.carbons
Ø Has a carboxyl (-COOH) functional group (= acidic)
Ø Saturated – no double bonds between carbon atoms so forms
a straight chain. Solid at room temperature. E.g. palmitic acid
(palm oil, butter, animal fats); stearic acid (butter, chocolate,
lard); lauric acid (coconut oil).
Ø Unsaturated – has double bonds between carbon atoms. One double bond = monounsaturated. e.g. oleic
acid (most common in nature, part of triglycerides and phospholipids that make cell membranes; olive oil).
Two or more double bonds = polyunsaturated. e.g. linoleic acid (found in canola oil, sunflower oil, nuts,
seeds); arachidonic acid. . The more double bonds, the less likely the fat is to be soluble at room temp
E) Biomolecules
2. Lipids -
ii. Glycerides
Ø Formed from fatty acids and glycerol via dehydration
synthesis (glycerol gives up the hydrogen atoms from its
hydroxyl group, which combine with the -OH of the fatty
acid carboxyl group to form water).
Ø Glycerol + 1 fatty acid = monoglyceride
Ø Glycerol + 2 fatty acids = diglyceride
Ø Glycerol + 3 fatty acids = triglyceride
Ø Triglycerides are an important form of stored energy in
the body (adipose/fat tissue).

Figure 2.1
E) Biomolecules
2. Lipids -
iii. Phospholipids & Sphingolipids
Ø Derived from glycerides. Essentially a diglyceride to
which a phosphate group (PO4) and a variable R-
group have been added. Figure 2.1
Ø Glycerol + 2 fatty acids + PO4 + variable R-group
Ø R group – Allows the formation of of different types
of phospholipids. e.g. R-group = serine, forms
phosphatidylserine, if R-group = choline, forms
phosphatidylcholine.
Ø Properties:
Ø Are amphipathic molecules – have both
hydrophilic and hydrophobic regions. Polar heads
(phosphate + R-group) are hydrophilic, and non-
polar fatty acid tails are hydrophobic.
Ø Phospholipids can arrange themselves into
bilayers, micelles and liposomes. Polar heads face Figure 2.8
the ECF or ICF, non-polar tails towards each other.
E) Biomolecules
2. Lipids -
iii. Phospholipids
Ø Derived from glycerides. Essentially a diglyceride to
which a phosphate group (PO4) and a variable R-
group have been added. Figure 2.1
Ø Glycerol + 2 fatty acids + PO4 + variable R-group
Ø R group – Allows the formation of of different types
of phospholipids. e.g. R-group = serine, forms
phosphatidylserine, if R-group = choline, forms
phosphatidylcholine.
Ø Properties:
Ø Are amphipathic molecules – have both
hydrophilic and hydrophobic regions. Polar heads
(phosphate + R-group) are hydrophilic, and non-
polar fatty acid tails are hydrophobic.
Ø Phospholipids can arrange themselves into
bilayers, micelles and liposomes. Polar heads face Figure 3.2
the ECF or ICF, non-polar tails towards each other.
 sphingolipid
E) Biomolecules
2. Lipids -
iv. Sphingolipids, Glycophospholipids, Glycosphingolipids
Ø Modified phospholipids.
Ø Sphingolipids incorporate a sphingosine molecule
instead of glycerol and have only 1 fatty acid.
Ø form lipid rafts on cell membranes that may help glycophospholipid
to protect the cell surface.
Ø Glycophospholipids – a phospholipid with a
carbohydrate group attached (usually a glycosphingolipid
polysaccharide).
Ø Glycosphingolipids – a sphingolipid with a
carbohydrate group attached.
Ø Both glycosphingolipids and glycophospholipids can
be involved in cell recognition and signaling.
E) Biomolecules
2. Lipids -
v. Steroids
Ø Basic structure consists of three 6-carbon rings plus
one 5 carbon ring (17 carbons total).
Ø Many derived from cholesterol.
Ø Different functional groups (R-groups) give steroids
their different functions.
Ø Play roles in communication (hormones) and cell
structure
Ø E.g.1: Cholesterol (stabilizes cell membranes)
Ø E.g.2: Cortisol (stress hormone) Figure 2.1
Ø E.g.3: Testosterone & Estrogen (reproductive
hormones)
E) Biomolecules
2. Lipids -
vi. Eicosanoids
Ø Polyunsaturated fatty acids with a length of 20 carbons (“eicos-” =
Greek for 20) attached to a complete or partial carbon ring. Contains
oxygen atoms.
Ø Many derived from arachidonic acid or other unsaturated fatty acids.
Ø Synthesized as needed (not stored)
Ø Unlike most lipids, eicosanoids do not cross the cell membrane. They
bind to receptors on the cell surface, as opposed to intracellular
receptors.
Ø They Function in communication within and between cells. Figure 2.1
Ø E.g.1: Prostaglandins – help mediate inflammation and pain response
during injury/infection among other roles. Non-steroidal anti-
inflammatory drugs (NSAIDS), like ibuprofen, prevent the production of
prostaglandins, which results in a reduction in pain and inflammation.
Ø E.g.2: thromboxane – important for blood clotting (specifically platelet
aggregation).
E) Biomolecules
2. Lipids -
d. General functions of lipids:
i. Cell structure – important components of cell membranes and
organelles.
ii. Energy source – e.g. triglycerides in adipose tissue of the human
body is a large store of energy.
iii. Communication (within and between cells)

Figure 2.2
E) Biomolecules
3. Nucleotides, Nucleosides, Nucleic Acids –
Ø Nucleotides and nucleosides have important roles in
energy metabolism and signaling. Nucleic acids (DNA and
RNA) function in information storage and transmission
(genetics), in addition to protein synthesis.
a. Nucleotides – general structure includes:
i. a 5-carbon sugar (ribose, deoxyribose)
ii. a phosphate (PO4) group
iii. A nitrogenous base (carbon-nitrogen ring structure)
Ø Nitrogenous bases are either purines (2 rings) or
pyrimidines (single ring).
Ø Purines = adenine + guanine
Ø Pyrimidines = Cytosine, Thymine, Uracil
b. Nucleosides – are nucleotides minus the phosphate
group. They include:
Figure 2.4
Ø Adenosine, Guanosine, Cytidine, Thymidine, Uridine
E) Biomolecules
3. Nucleotides, Nucleosides, Nucleic Acids -
Ø Examples of important molecules that incorporate nucleosides:
i. Adenosine Triphosphate (ATP) – main molecule for storing and
transferring energy within cells. Powers many cellular processes.
ii. Breaking high energy phosphate bonds in ATP creates,
Adenosine Diphosphate (ADP), Adenosine
Monophosphate (AMP)
iii. Adenosine – a neurotransmitter
iv. Cyclic AMP (cAMP) = important signaling molecule
within cells (often in response to signals from other cells)
v. Guanosine Triphosphate (GTP) – energy source in
many physiological chemical reactions Figure 2.4
vi. Guanosine Monophosphate (GMP), Guanosine Diphosphate (GDP).
vii. Cyclic GMP (cGMP) – important signaling molecule within cells
E) Biomolecules
4. Proteins -
a. Macromolecules that consist of C, H, O, N (and sometimes S)
b. The basic units of protein structure are amino acids.
Ø central carbon atom to which is attached:
Ø Carboxyl group (-COOH)
Ø Amino group (-NH2)
Ø R-group (functional group – determines the structure of the
amino acid).
c. DNA/RNA code for 20 amino acids
Ø 9 are essential and we need to consume them in the foods we eat
(e.g. leucine, tryptophan, valine, etc.)
Ø 11 are non-essential, the body synthesizes them (e.g. tyrosine,
glycine, etc.)
d. Amino acids are joined together by peptide bonds to form:
Ø 9 are essential and we e, glutamine, etc.). Figure 2.2
E) Biomolecules
4. Proteins -
d. Amino acids (aa) are joined together by peptide bonds to
form:
i. Peptides – short chains of amino acids (oligopeptides = 2-9 amino
acids; polypeptides = 10-100 amino acids)
ii. Proteins – long chains of amino acids (>100 aa)
e. Structure of peptides and proteins:
i. Primary – the sequence of amino acids in the chain
ii. Secondary – hydrogen bonds between adjacent amino acid chains
or loops within the same chain create b-sheets and a-helices (helix
= singular) respectively.
iii. Tertiary – a-helices and b-sheets combine to form globular or
fibrous proteins. Globular proteins are usually soluble, while fibrous
proteins are not.
iv. Quaternary – multiple tertiary structures combine to form the
finished protein (e.g. hemoglobin has 4 globular protein subunits).
Figure 2.3
E) Biomolecules
4. Proteins -
d. Protein Functions:
Ø Proteins are used for the structure, function and regulation of cells, tissues and
organs. They are responsible for carrying out many physiological processes.
Ø In any mammalian cell 10,000-15,000 different proteins can be expressed. The
proteins expressed by a cell determine its function.
Ø Soluble proteins are divided into 7 functional groups:
i. Enzymes – control chemical reactions inside of cells and on their outer surface.
ii. Membrane transporters – protein channels or carrier proteins that move
substances into and out of cells (e.g. Na+ channels; glucose transporters like
GLUT4).
iii. Signal molecules – e.g. peptide hormones, like insulin
iv. Receptors – can bind specific molecules (ligands) and start a cellular response.
v. Binding proteins – found mostly in ECF. Bind to and allow transport of other
molecules (especially those that may not be soluble in water). E.g. hemoglobin
is a protein that binds to and transports oxygen (O2 has poor solubility in the
blood plasma).
E) Biomolecules
4. Proteins -
d. Protein Functions:
Ø Proteins are used for the structure, function and regulation of cells, tissues and
organs. They are responsible for carrying out many physiological processes.
Ø In any mammalian cell 10,000-15,000 different proteins can be expressed. The
proteins expressed by a cell determine its function.
Ø Soluble proteins are divided into 7 functional groups:
vi. Regulatory proteins – turn cell processes on/off or up/down. E.g. transcription
factors turn specific genes on/off in response to various genetic or
environmental signals. E.g.2: Tropomyosin and troponin regulate skeletal and
cardiac muscle contraction.
vii. Immunoglobulins – immune proteins (antibodies) found in the ECF that protect
the body from pathogens. E.g. IgG = most common antibody involved in
fighting off bacterial and viral infections. More on these next term when we
look at the immune system

Figure 2.3
E) Biomolecules
4. Proteins -
e. Protein Interactions:
Ø In order for a protein to do something, it must interact with or bind to other
proteins, molecules or ions.
Ø Binding take place at the binding site on the protein.
Ø Properties of the binding site:
i. Specificity - the binding site can only bind to specific ligands.
Ø Ligands = Molecules that bind to protein binding sites. Ligands naturally present in
body (e.g. hormones and neurotransmitters) are endogenous ligands. Non-
endogenous ligands enter the body from the external environment and include
drugs/toxins.
Ø Agonist = a ligand that binds to a protein binding site and alters the state of the
protein resulting in a biological response. E.g. a hormone, neurotransmitter, or drug.
Ø Antagonist = a ligand that reduces the action of an agonist (i.e. binds to the protein
but causes no biological responses). Also called inhibitors, blockers.
Ø Antagonists may be competitive: bind to the same binding site as the agonist.
Ø Antagonists may be allosteric: bind to to a different site than the agonist, but this
interaction inactivates the binding site.
E) Biomolecules
4. Proteins -
e. Protein Interactions:
Ø In order for a protein to do something, it must interact with or bind to other
proteins, molecules or ions.
Ø Binding take place at the binding site on the protein.
Ø Properties of the binding site:
ii. Affinity – refers to strength of the binding between the protein and the ligand.
Ø High affinity = protein binds the ligand strongly
Ø Low affinity = protein binds the ligand weakly
E) Biomolecules
4. Proteins -
f. Factors that affect protein binding or alter the rate of
protein binding/activity:
i. Isoforms – proteins whose structure and functions are
similar, but that have different affinities for the same
ligand. E.g. fetal hemoglobin has a higher affinity for
oxygen than adult hemoglobin.
ii. Activation/protein processing – protein must be
converted into its active form before any binding/activity
can take place. Proteolytic activation
Ø E.g. Pepsinogen in the stomach undergoes proteolytic
activation by HCl, which converts it into its active form pepsin
(pepsin is an enzyme involved in protein digestion).
iii. Cofactors – ions (e.g. Ca++) or molecules that must
attach to the protein in order for the binding site to
become active. If no cofactor is present, binding/activity
Figure 2.12
stops.
E) Biomolecules
4. Proteins -
f. Factors that alter the rate of protein
binding/activity:
iv.Modulation
Ø Changes ability of protein to bind to the ligand or
changes the response of the protein to the binding of
the ligand.
Ø Types of Modulation:
1) Irreversible inhibition – antagonist binds to
binding site and cannot be removed (even if the
concentration of agonist increases).
2) Competitive inhibition – antagonist binds
reversibly to binding site. Level of activity/binding
of agonist depends on relative concentrations of
agonist and antagonist. More antagonist = more
inhibition, less activity. More agonist = less
inhibition, more activity

Figure 2.12
E) Biomolecules
3) Allosteric modulation – modulator binds to site
other than agonist binding site. May cause
inhibition or activation of agonist binding site.
4) Covalent modulation – atoms or functional
groups (like phosphates) bond covalently to the
protein altering its structure and changing its
activity (increase or decrease)
a) Phosphorylation and Dephosphorylation –
addition or removal of a phosphate group
changes the protein’s activity. Common action
of protein kinases.
b) Addition of a lipid or carbohydrate
v. Physical factors, like pH and temperature
Ø Can increase or decrease activity.
Ø At extremes, can denature (cause structural changes)
the protein and make the binding site inactive (loss of
activity)

Figure 2.12
E) Biomolecules
3) Allosteric modulation – modulator binds to site
other than agonist binding site. May cause
inhibition or activation of agonist binding site.
4) Covalent modulation – atoms or functional
groups (like phosphates) bond covalently to the
protein altering its structure and changing its
activity (increase or decrease)
a) Phosphorylation and Dephosphorylation –
addition or removal of a phosphate group
changes the protein’s activity. Common action
of protein kinases.
b) Addition of a lipid or carbohydrate
v. Physical factors, like pH and temperature
Ø Can increase or decrease activity.
Ø At extremes, can denature (cause structural changes) Figure 2.13
the protein and make the binding site inactive (loss of
activity)
E) Biomolecules
vi. Saturation
Ø Protein/enzyme activity depends on the amount of ligand present and
the amount of protein present.
Ø When concentration of ligand is higher than available protein binding
sites can handle, binding sites are completely filled and saturation is
reached.
Ø Enzymes, membrane transporters, receptors, binding proteins, etc can
all reach a saturation point (the point where addition of more ligand
will not make any difference in activity because all binding sites on the
proteins involved in the process are occupied).

Figure 2.13
F) Solutes and Concentration
Ø Solutions
ØSolutes dissolved in a solvent
ØBiological solutions (ECF and ICF) are water-based =
aqueous. For example in the body many ions (solute)
are dissolved in water (solvent).
Ø Solubility
ØAbility of a solute to dissolve a solvent
ØHydrophilic molecules are soluble in water
ØIncludes polar molecules and ionic molecules
ØHydrophobic molecules are not soluble in water
ØIncludes nonpolar molecules

ØConcentration = solute amount/volume of solution

Figure 2.7
G) Acids, Bases, & pH
1. Acids
Ø dissociate in water releasing H+
ØHigher [H+] = lower pH
ØE.g. hydrochloric acid (as produced by the stomach) has
a pH of 2.
2. Bases
Ø substances that bind free H+ ions in solution and so
decrese [H+] in solution..
Ø Lower [H+] = higher pH
Ø E.g. HCO3- + H+ à H2CO3
(bicarbonate) (carbonic acid)

Figure 2.9
G) Acids, Bases, & pH
3. pH scale
Ø measure of the free H+ ion concentration in a solution.
Ø pH = -log [H+] or pH = log (1/[H+])
ØpH >7 = alkaline (basic); pH < 7 = acidic
Ø Log scale, so every time the pH sacel goes up or down
by 1, this represents a 10X increase or decrease in the
[H+]. A pH of 2 has 100X (10x10) more [H+] than a pH of
4. A pH of 1 has 1000X (10x10x10) more [H+] than a pH
of 4.

According to figure 2.9, how many times more

acidic is stomach acid compared to saliva?

Figure 2.9