(Bio)Chemistry and
Cytology
BIOL241
Introduction or Recap of Cell
Structure & chemistry
INTERCONNECTEDNESS
• Matter and Energy
• Atoms, molecules, and chemical bonds
• Importance of organic and inorganic nutrients
and metabolites
• Structure and function of carbohydrates,
lipids, proteins, and nucleic acids
• Enzymes and ATP help run the metabolic
reactions of the body
Energy
• The capacity to do work (put matter into
motion)
• Types of energy
– Kinetic – energy in action
– Potential – energy of position; stored
(inactive) energy: chemical energy
• Energy is easily converted from one form
to another
• During conversion, some energy is “lost”
as heat
Chemistry
• Chemistry is the science that deals with
matter
• Matter is anything that takes up space and
has mass
• Smallest stable units of mass are atoms
But I thought this was biology?
•
•
•
•
Mathematics (the language of science)
Physics (the structure of matter & energy)
Chemistry (organic and inorganic structure)
Biology: uses them all to understand Life.
Atoms, Elements, Molecules
• Elements are atoms of one particular
type (see the periodic table)
• Molecules are groups of atoms that
(usually) contain more than one
element

Biologically significant elements
• 13 principal elements
–
–
–
–
–
Carbon (C)
Oxygen (O)
Hydrogen (H)
Nitrogen (N)
Calcium (Ca), phosphorus (P), potassium (K),
Sulphur (S), sodium (Na), chlorine (Cl),
magnesium (Mg), iodine (I), and iron (Fe)
• 13 trace elements
– (e.g. zinc, manganese)
Atoms with unfilled electron
shells are reactive
• Octet Rule
• To become stable they form chemical bonds.
• Three main types of chemical bonds
– Intramolecular:
• Ionic bonds (charged atoms resulting from the
gain or loss of electrons)
• Covalent bonds (electrons are shared)
– Intermolecular
• Hydrogen bonds
Covalent & Ionic Bonds
• Molecules: atoms held together by
covalent bonds
• Salts: molecules held together by ionic
bonds
Q: What are the strongest type of bonds?
H2 O
The body is mostly water (~2/3rd of total
body weight) so all chemical reactions in
the body occur in water
Covalent bonds are much stronger than
ionic bonds in water
H2O – “Special” Properties
• Water can dissolve organic and
inorganic molecules making a solution
• Water is needed for chemical reactions
• Water absorbs and retains heat
• Water is an effective lubricant
H2 O
• What is it about water that makes it so
special?
• Water has all these amazing properties due to
its molecule’s ability to form hydrogen bonds
H-bonds b/t + & - charges
Mixtures and Solutions
• Mixtures – two or more components physically
intermixed (not chemically bonded)
– Solutions – homogeneous mixtures of components
– Colloids (emulsions) – heterogeneous mixtures
whose solutes do not settle out
– Suspensions – heterogeneous mixtures with visible
solutes that tend to settle out
Essential Molecules
• Nutrients:
– essential molecules obtained from food (you
have to eat them to get them)
• Metabolites:
– molecules made or broken down in the body
Organic vs. inorganic
Organic molecules:
• Always contain carbon with hydrogen, and
sometimes oxygen
• Often soluble in water
Inorganic: Electrolytes, minerals, and compounds that
do not contain carbon with hydrogen.
• Important examples: oxygen, carbon dioxide, water,
inorganic acids and bases, salts
Vitamins and Minerals
• Vitamins and minerals are essential nutrients
that are required in very small amounts for
healthy growth and development.
Examples?
• They cannot be synthesized by the body and
are essential components of the diet.
Vitamins
• Organic substances necessary for metabolism
• There are 13 known vitamins (e.g. A, B1, D, K)
• Some are fat soluble while others are water
soluble
• Are Coenzymes that help carry out the
reactions of metabolism
Minerals
• Inorganic compound (often salts or elements)
necessary for proper body function
• Can be bulk or trace minerals
• Are Cofactors in metabolic reactions
Electrolytes
• Inorganic ions (usually minerals) that conduct
electricity in solution
• Electrolyte balance is maintained in all body
fluids; imbalance seriously disturbs vital body
functions
Electrolytes
Table 2–3
Biological Macromolecules
• Life depends on four types of organic
macromolecules:
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic acids
Can you think of an example of each?
1. Carbohydrates
• Contain carbon, hydrogen and oxygen in a
ratio of 1:2:1
• Account for less that 1% of body weight
• Used as energy source
• Called saccharides (sugars, starches)
Glucose is a monosaccharide
Disaccharides
Sucrose
Lactose
Polysaccharides
• Starch
• Glycogen
• Cellulose
All are long strings of glucose molecules
Difference lies in how they are bonded together
Polysaccharides
• Polysaccharides or polymers of simple sugars
PLAY
Polysaccharides
Figure 2.14c
Polymers
• A polymer is any molecule made up of several
repeating units. Starch is a polymer of glucose.
2. Lipids
• Contain carbon, hydrogen, and oxygen but the
ratio of C:H is 1:2 (much less O)
• May also contain other elements,
phosphorous, nitrogen, and sulfur
• Form essential structures in cells
• Are important energy stores
Lipids: Triglycerides (Fats and Oils)
• Consist of 3 fatty acids
and glycerol
– Insulation
– Energy
– protection
Q: What’s the
difference
between
saturated and
unsaturated?
Lipids: Steroids and Cholesterol
• All consist of a
complex ring
structure
Lipids: Phospholipids
Amphipathic
3. Proteins
• Consist of chains of
amino acids liked
together by peptide
bonds
• Enzymes are proteins
Protein Structure
• Proteins are the most abundant and
important organic molecules
• Basic elements:
– carbon (C), hydrogen (H), oxygen (O), and nitrogen
(N)
• Basic building blocks:
– 20 amino acids
Protein Structure – 4 levels
Primary: amino acid sequence
Secondary: Hydrogen bonds form spirals or
pleats (α-helix, β-sheet)
Tertiary: Secondary structure folds into a unique
shape
Quaternary: several tertiary structures together:
again: Shape!!
Figure 2–20a
Protein structure
Shape and Function
• Protein function is based on shape
• Shape is based on sequence of amino acids
• Denaturation:
– loss of shape and function (due to heat, pH
change or other factors)
Protein Functions
– support:
• structural proteins
– movement:
• contractile proteins
– transport:
• transport proteins
– buffering: regulation
of pH
– metabolic regulation:
• enzymes
– coordination and
control:
• hormones
– defense:
• antibodies
Activation Energy
• Chemical reactions in cells cannot start
without help
• Activation energy gets a reaction started
Figure 2–7
Characteristics of Enzymes
Figure 2.20
Energy In, Energy Out
• Exergonic reactions:
– produce more energy than they use
• Endergonic reactions:
– use more energy than they produce
KEY CONCEPT
• Most chemical reactions that sustain life
cannot occur unless the right enzymes are
present
How Enzymes Work
• Substrates:
– reactants in enzymatic reactions
• Active site:
– a location on an enzyme that fits a particular
substrate
Active site
Amino acids
+
How
Enzymes
Work
Enzyme (E)
Substrates (S)
Enzyme-substrate
complex (E-S)
H2O
Free enzyme (E)
Peptide bond
Internal rearrangements
leading to catalysis
Figure 2–21
Dipeptide product (P)
4. Nucleic acids
• Contain C, H, O, N,
and P
• DNA and RNA are
nucleic acids
• Nucleotide consists
of
– Sugar
– Phosphate group
– Nitrogenous base
Structure of
DNA
Figure 2.22b
A nucleotide: ATP
• Energy storage for
cells
• Many enzymes use
ATP
• Provides a way to
run reactions that
are otherwise
endergonic
(require energy)
Membrane
protein
Pi
P
Solute
ATP is the
energy currency
of the cell
Solute transported
(a) Transport work
ADP
+
Pi
ATP
Relaxed smooth
muscle cell
Contracted smooth
muscle cell
(b) Mechanical work
Pi
X
P
+
X
Y
Y
Reactants
Product made
(c) Chemical work
Figure 2.24
Compounds Important
to Physiology
Table 2–8
Summary
• Energy and matter
• Atoms, molecules, and chemical bonds
• Importance of organic and inorganic
nutrients and metabolites
• Structure and function of
carbohydrates, lipids, proteins, and
nucleic acids
• Enzymes and ATP help run the
metabolic reactions of the body