Biology 1103 – Week 3

Biochemistry II
Cell Biology
Osmosis and Diffusion Lab
 Osmosis and Diffusion Lab
• Understanding the processes of diffusion and
osmosis using an “intestine”

• Test tubes and additions

– Keep track of your test tubes (label them)
– Stay focused when adding chemicals to the tubes
 Learning outcomes
• Organic molecules in the body – part 2
– Proteins
– Nucleic acids
• Structure of the plasma membrane (fluid
mosaic model)
• Transport mechanisms across the plasma
membrane
Proteins and Nucleic Acids

BIOCHEMISTRY III
Building blocks and macromolecules

Monosaccharides are the building blocks of polysaccharides.

Amino acids are the building blocks of proteins.

Nucleotides are the building blocks of nucleic acids.

 “Proteins do everything”
Structural Regulatory
Proteins Proteins

Contractile Proteins Transport

Proteins Proteins

Catalytic Immunological
Proteins Proteins
 Proteins
• 20 different type of amino acids, each with
different chemical properties
• All amino acids contain the elements:
• carbon (C)
• hydrogen (H)
• oxygen (O)
• nitrogen (N)
• two of the 20 amino acids contain sulphur (S)
 Amino acids
• Basic structure of an amino acid (ionized form
shown):
Do not need to
memorize any of
these structures
 Formation of proteins
• Amino acids can be linked together via
peptide bonds to form proteins
• Different proteins can be made by linking
different combinations of amino acids
together
Peptide bond
 Protein structure
• Proteins are not found as long loose chains in
the body
• After proteins are made, they tend to fold up
into specific structures which are important
for its function

Be able to list and describe the functions of proteins

 Functions of proteins
Structural proteins : form the framework for
different parts of the body
Collagen
Keratin
 Functions of proteins
Regulatory proteins: used to control various
processes in the body (e.g., insulin helps
regulate blood sugar levels)
Reproduction

Blood pressure
Calcium levels
Milk
production

Reproduction
Glucose levels

Growth and metabolism

Stress response NOTE: not all hormones are proteins

 Functions of proteins
Contractile
proteins: allows
for movement
within and of the
body (e.g., actin
and myosin are
proteins found in
substantial
amounts in muscle
cells and cause
muscle
contraction)
 Functions of proteins
Immunological proteins: involved in the
protection of the body from foreign
substances (e.g., antibodies, also called
immunoglobulins, are specialized proteins that
recognize and inactivate foreign substances)
Examples of Immunoglobulins

IgM IgG IgA

First antibody to appear after exposure to Most abundant in circulation, able to pass Found in mucosal linings and secretions
an antigen through the placenta
 Functions of proteins
Transport proteins: carry vital substances
throughout the body (e.g., hemoglobin which
transports O2 from lungs to all of the various
tissues in body)
Hemoglobin transports oxygen
 Functions of proteins
Catalytic proteins: also called enzymes; used
to speed up chemical reactions in the body.
Enzymes are essential to almost every single
metabolic reaction in the body. They increase
the rate of reactions by at least a millionfold.
(e.g., salivary amylase found in your saliva,
catalyzes the breakdown of starch)
 Mechanism of enzyme action
Product (P)
Substrates (S) Energy is Water is e.g., dipeptide
e.g., amino acids absorbed; released.
bond is Peptide
+ formed. bond

Active site

Enzyme-substrate
complex (E-S)
Enzyme (E) 1 Substrates bind at active
site, temporarily forming an
enzyme-substrate complex.
Figure 2.21 Mechanism of enzyme action.
2 The E-S complex Enzyme (E)
undergoes internal 3 The enzyme releases
rearrangements that
form the product. the product of the
reaction.

Other examples of
enzymes [substrates]

• Amylase [starch]
• Lactase [lactose]
• Lipase [lipids]
Nucleic acids
 DNA

Function
of Nucleic Acids: Synthesis of

How Genetic mRNA in the nucleus

mRNA

Information Flows
NUCLEUS
CYTOPLASM

DNA
mRNA

transcription Movement of
mRNA into cytoplasm
Ribosome
via nuclear pore

RNA
Synthesis
translation of protein

Proteins Amino
acids
Polypeptide
 Nucleic acids
• Nucleic acids contain the elements:
• carbon (C)
• hydrogen (H)
• oxygen (O)
• nitrogen (N)
• phosphorus (P)
 5 end

Nucleotide structure
• Nitrogen base:
Nucleoside – Purines
(double ring
Nitrogenous structures);
base adenine and
guanine
– Pyrimidines
(single ring
structures);
Phosphate
cytosine,
group Pentose thymine, and
sugar uracil
Nucleotide
• Pentose sugar:
– Ribose
3 end – Deoxyribose
Polynucleotide, or • Phosphate
nucleic acid group
 Figure 2.22b Structure of DNA.
Hydrogen
bond
DNA double helix
• Double strands form a
helical ladder-like
structure with the
nucleotides forming the
Deoxyribose
Sugar-
phosphate
sugar rungs of the ladder and
Phosphate
backbone
the phosphate and
sugar groups form the
sides of the ladder
• Specific nucleotide
Adenine (A)
Thymine (T) pairing:
Cytosine (C)
Guanine (G) A pairs with T
G pairs with C
 DNA (deoxyribonucleic acid)

• Stores genetic information of cell in the nucleus

• Contains the sugar, deoxyribose
• Contains the nucleotides: adenine, guanine, cytosine,
and thymine
• Double stranded (two strands of DNA held together by
hydrogen bonds)
Do not need to memorize structures
 RNA (ribonucleic acid)
• Carries genetic information from
nucleus to cytoplasm
• Several different types
• Contains the pentose sugar,
ribose
• Contains the nucleotides:
adenine, guanine, cytosine and
uracil
• Typically single stranded
Be able to describe and contrast DNA versus RNA
ATP (adenosine triphosphate)
other uses of nucleotides
High-energy phosphate
bonds can be hydrolyzed
to release energy.

Adenine

Phosphate groups

Ribose Figure 2.23

Structure of
ATP
Adenosine (adenosine
triphosphate).

Adenosine monophosphate (AMP)

Adenosine diphosphate (ADP)

Adenosine triphosphate (ATP)

NAD (nicotinamide adenine dinucleotide)
other uses of nucleotides

• NAD+ is a co-enzyme
derived from the B
vitamin (niacin)
• NAD+ is used to carry
electrons during
chemical reactions
that occur during the
synthesis of ATP
Biology 1103 – Week 3

Biochemistry II
Cell Biology
Osmosis and Diffusion Lab
Structure of the cell membrane and movement across the cell membrane

CELL BIOLOGY
Is the plasma membrane solid or fluid?
 What are the components of the cell
membrane?
Extracellular
fluid

Lipid
bilayer
Glycoprotein

Peripheral protein

Glycolipid
Cytosol

Integral (transmembrane)
proteins
Phospholipids
Peripheral protein

Cholesterol
Components of the cell membrane
1. Phospholipids form the main structure of a membrane.
They form a bilayer in which polar heads face outwards
towards extracellular environment and intracellular
environment, nonpolar tails face each other
2. Integral proteins (also have other names): span the entire
lipid bilayer; functions to transport specific molecules across
membrane
– NOTE: Peripheral proteins: touch the membrane or another
protein superficially; functions to support the plasma membrane,
anchor integral proteins, participate in metabolic activities
3. Cholesterol is embedded in the lipid bilayer to influence the
fluidity of the membrane
4. Sugar groups: found attached to the proteins (glycoproteins)
or to phospholipids (glycolipids)
– Have a variety of functions. Example: glycocalyx located on the
outside of the cell membrane functions in cell-cell recognition
 The many names of transport
proteins….
• Transport proteins
• Integral proteins
• Membrane proteins
• Transmembrane proteins
• Carriers
• Protein pumps (eg. sodium/potassium pump)
• Ion channels (for ions only)
 How does the plasma membrane
regulate what goes in/out of the cell?
• The membrane is described as being
selectively permeable (i.e., some molecules
can easily pass through, other cannot)
• With respect to what type of molecules will
easily pass through a membrane:
– Size matters!
– But more importantly, chemical
properties matter!
Practice Question 1
 Definition of solvent and solute
• In biology, water is always the solvent (the
material in which substances are dissolved
into)
• Example: if sodium chloride is dissolved into
water, water is the solvent, sodium and
chloride are the solutes
 Transport across a membrane
• When comparing the concentration of a solute on
two sides of a membrane, if there is a higher
concentration of the solute on one side versus the
other side, there is a concentration gradient
• Molecules moving down a concentration gradient
are going from an area of high concentration to low
concentration
• Molecules moving against a concentration gradient
are going from an area of low concentration to high
concentration
 Figure 3.7a Diffusion through the plasma membrane.

Extracellular fluid
1. Simple diffusion Lipid-
soluble
solutes
• Passive movement of solute
molecules from an area of
high solute concentration to
an area of low solute
concentration
• No energy required
• Molecules such as oxygen,
Cytoplasm
carbon dioxide, fatty acids
Simple diffusion of
fat-soluble molecules
directly through the
phospholipid bilayer
 Figure 3.7b and c Diffusion through the plasma membrane.

2. Facilitated diffusion
Lipid-insoluble solutes Small lipid-
insoluble
• Movement of (such as sugars or
amino acids)
solutes
molecules
down a
concentration
gradient using
transport
protein
• No energy
required
• Used in the
cell to
transport
glucose,
Channel-mediated
sodium ions, Carrier-mediated facilitated
facilitated diffusion
potassium Diffusion via protein carrier specific
through a channel
for one chemical; binding of substrate
ions causes transport protein to change
protein; mostly ions
selected on basis of
shape size and charge
 Figure 3.7d Diffusion through the plasma membrane.

Special type of simple Water

diffusion: Osmosis molecules

• Refers to the movement of

water through a membrane
• Movement is:
Lipid
– From the side with low solute bilayer
concentration to the side with
high solute concentration

OR Aquaporin

Osmosis, diffusion of a
– From the side with high water solvent such as water
concentration to the side with through a specific
channel protein
low water concentration (aquaporin) or through
the lipid bilayer
 NOTE: Movement of water
• In the plasma membrane of a cell, water can
move through either osmosis (simple
diffusion) or through the use of aquaporins
(integral membrane proteins that act as water
channels – facilitated diffusion) (NOTE: not all
cells have aquaporins)
 Osmosis
• The movement of water can affect the
integrity of a cell

• A classic experiment is placing red blood cells

in solutions containing different
concentrations of solutes that are
impermeable to the membrane
Red blood cells in different solutions

Isotonic Hypotonic Hypertonic

(“same”) (“low”) (“high”)
 Red blood cells in an isotonic solution

Salt solution
(physiological
concentrations)

Red
Blood cell
Result:
__________
Red blood cells in a hypotonic solution

Distilled
water

Red
Blood cell
Result:
__________
Red blood cells in a hypertonic solution

Salt
solution

Red
Blood cell
Result:
__________
 3. Active transport
• Movement of molecules across a membrane
with the use of cellular energy (ATP)
• Molecules can be moved against a
concentration gradient (from low concentration
to high concentration)
• A transport protein is required
• Often used to maintain high concentrations of
specific molecules for proper cell functioning
 Example of Active Transport: sodium
potassium pump
Na+ Extracellular fluid 2K+
3 Na+ expelled
gradient Na+/K+ ATPase

P
Cytosol 3 Na+
K+ ATP 2 K+
1 2 ADP 3 P 4 imported
gradient

• Sodium is maintained at high levels outside of

cells, potassium at high levels inside cells
 Phagocytosis
• An active process by which a cell
can take in large pieces of solid
material
• Also referred to as endocytosis
• Done by specialized cells
• Cellular membrane wraps around
the material and engulfs it
• A vesicle is formed and the
material inside is digested by
lysosomes
• Important for destroying cellular
debris or to kill pathogens
 Pinocytosis
• Small molecules or
droplets of fluid are
taken up by the cell
• Also referred to as
endocytosis
• Done by most cells to
uptake fluid and
nutrients
 Exocytosis
• The reverse of endocytosis
• Molecules contained in vesicles in the cell are
pushed out of the cell
• Controlled process to release molecules
• Examples: release of neurotransmitters or
enzymes from a cell
Practice Question 2