Basic Chemistry and Cell Structure

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Biol 155
Human Physiology
Instructor: Dr. Robert Harris
Office: 1354 Biological Sciences
Phone: 822-5709
Email: [email protected]
Course requirements:

Texts:
Fundamentals of Anatomy and
Physiology 6th ed. Frederic H. Martini
Anatomy & Physiology Coloring Workbook,
7th ed. Elaine Marieb

Read course synopsis!!! Failure to read it, or failure to
listen to what I say does not constitute an excuse

Lecture Notes and synopsis are posted at:
http://www.zoology.ubc.ca/~biomania/biol153/
lecture/main01.htm
Mark Breakdown

Biol 153:

The lecture mark is based on:

Lecture:
Lab:
Course Total:
One mid-term exam in each term:
Winter exam:
Final exam:
Total:
60%
40%
100%
20%
20%
20%
60%
(10% each)
Mark Breakdown cont.

Biol 155:
marks will be based solely on the lecture exams, which
will be weighted as follows:
 One mid-term exam in each term:
30% (15% each)
 Anatomy colouring book
5%
 Winter exam:
30%
 Final exam:
35%
 Total:
100%

Atomic structure and elements

An element is a substance that retains its
chemical and physical characteristics even when
it is broken down into its smallest units.

The smallest practical unit, for our purposes is
the atom.
The chemical characteristics are
determined by the number of
protons

These are the three
forms of hydrogen

All three have one
electron

All three have one
proton
Electron orbits

Number of electrons
generally equals
number of protons.

There are specific
orbits (or shells), that
contain a specific
maximum number of
electrons
Charged atoms

Atoms are most stable when there
are 8 electrons in the outermost
shell.


In order for the outermost shell to be
filled, atoms will either take in or give
off electrons. When this happens
there is a change in net charge.
Charged atoms (ions) can be
electrically attracted (opposite
charges attract)


This is known as ionic bonding
Ionic bonds are fairly weak
Covalent bonds

Another way atoms can fill
their outer shell is to share
electrons with another atom


The electrons orbit around
BOTH nuclei
This is known as a covalent
bond

Covalent bonds are much
stronger than ionic bonds
Molecular dipoles

When covalent bonds are
formed, the electrons may
not be shared equally
between the atoms

This unequal sharing can
result in an uneven
distribution of electrical
charges on the molecule

This is known as a partial
charge, or a dipole
Hydrogen bonding

Water molecules interact
with each other electrically

The partial negative charge
around the oxygen is
attracted to the partial
positive charge around the
hydrogen

These very weak electrical
attractions are called
hydrogen bonds
Ions in aqueous solution




Water molecules can form hydrogen bonds with ions
Ions in solution have a layer of tightly bound water
molecules around them
This layer of water molecules is known as the hydration
sphere
Water can form hydrogen bonds with uncharged
molecules as well (providing there is a partial charge)



pH is the negative log (the small p) of the hydrogen
concentration (the large H)
In pure water, some of the H2O molecules will
dissociate into H+ and OHThe H+ concentration in pure water is 0.1 mM, or
1x10-7 moles/L (hence pH 7)
Molecular Representations


There are several ways or
representing molecular
structures
Here are three
representations of
glucose



Linear model
Structural model
Space-filling model
Synthetic and Lytic Reactions

Smaller organic
molecules can be
linked together


Often this involves
the production of
H2O
Larger organic
molecules can be
broken down into
subunits

This often consumes
H2O, hence the term
“Hydrolysis”
Energetics of chemical reactions



In order for
chemicals to react,
they must first
overcome an energy
barrier
This is known as
the activation
energy
Some bonds are
easily reorganized,
resulting in a lower
activation energy
Enzyme catalyzed reactions

Enzyme has binding sites
for the reactants

The active region will
attack the bonds in the
precursors

Once bonds have been
reorganized, product is
released
Polymers in organic systems

A polymer is a chain made up
of repeating subunits

Useful compounds are often
stored in the form of a
polymer



For example, glycogen is a
branched polymer of glucose
Glycogen molecules can have
different numbers of glucose
subunits
Proteins are also polymers
Fatty acids and lipids
Phospholipids in aqueous solutions

Phospholipids and
glycolipids are
amphipathic


Meaning they have a
hydrophillic region
and a hydrophobic
region
When they are in
solution, they form
micelles
Structure of Amino Acids

All amino acids have the
same basic structure




A carboxylic acid side
An amino group side
A side group on the
central carbon
The side group is
referred to as the Rgroup
Primary protein structure
Secondary protein structure

The chain of amino acids can form folds and coils in
different regions, depending on the amino acid
sequence
Tertiary protein structure

The tertiary structure of a
protein is the 3D shape of a
single subunit.

This is a combination of all
the folds, coils and sheets.

This is usually dictated by
hydrophobic and hydrophilic
interactions with water
Tertiary and Quaternary protein
structure

The quaternary structure
of a protein is the
interactions between the
different subunits

If a protein is only
composed of a single
subunit, there is no
quaternary structure
DNA and RNA structure
Adenosine triphosphate (ATP)

Adenosine
backbone

Three phosphate
groups attached in
a chain

Last two have high
energy bonds
Characteristics of a lipid bilayer:

At normal temperatures, a lipid bilayer is liquid.

This means that the phospho- and glycolipids which
make it up can move freely, within the bilayer.

Because of the hydrophobic layer in the centre,
a bilayer is impermeable to water.

Because of the hydrophilic and hydrophobic
interactions, a bilayer is structurally quite strong.
Membrane fluidity
Membrane proteins:
Diffusion
Effect of osmotic concentration on cells


Cell membranes are semipermeable, and thus subject to osmotic
forces.
Animal cell membranes are flexible, and allow for inflation and
deflation depending on the movement of water
Transport of solutes through cell
membranes

Cell membranes are made up of phospholipids
arranged in a bilayer.
The centre of the bilayer is hydrophobic, which
means that hydrophilic molecules cant penetrate.
 Hydrophobic and lipid-soluble molecules can
penetrate cell membranes.


In order for hydrophilic molecules to be taken
up, a transport mechanism is needed.

These transport mechanisms are integral membrane
proteins.
Ion channels






Ions are fairly small
molecules.
Specialized proteins in the
membrane form aqueous
pores, which allow ions
through.
The driving force is the
chemical gradient
These pores can be quite
selective.
Most of these pores are
regulated
Example: CFTR
Facilitated diffusion



Molecules that are slightly larger need more help in
getting into or out of cells.
Rather than a pore, molecules are actually bound to
carrier protein, which translocates molecule.
Driving force is still the chemical gradient
Active transport



In order to move ions
against a concentration
gradient, energy must be
used.
Energy is supplied by the
hydrolysis of the
terminal high-energy
bond of ATP.
Example: Na-K-ATPase
Active secondary transport




ATPases only pump ions, nothing bigger.
Larger molecules are transported by coupling them to
movement of an ion down its concentration gradient.
Ions can also be transported in this way.
Example: Na-coupled glucose uptake.
Membrane transport and cycling


Molecules can bind to cell surface receptors and then
be internalized.
This same mechanism can be used to recycle
membrane.
Phagocytosis



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
Phagocytosis also involves membrane
invagination.
This process does not involve clathrin.
Pseudopods extend around a particle,
forming a phagosome.
Phagosome will fuse with a lysosome,
containing digestive enzymes.
There are smaller transport mechanisms
in the wall of the secondary lysosome.
Cellular organelles



Most intracellular organelles are membranebound.
Since membranes are barriers to diffusion of
aqueous solutes, they allow for partitioning of
cellular components
Such partitioning allows for the generation of
gradients and/or the segregation of specific
compounds inside the cell, a process that is
essential for life.
Endoplasmic reticulum



The endoplasmic reticulum consists of a series of
interconnected membrane-bound tubes and lamina that
are all continuous.
It is essential in the production of membrane proteins.
It also serves as a Ca2+ storage organelle.
Ribosomes



Ribosomes are
enzymes made up of
two subunits.
Ribosomes are the
enzyme that synthesize
proteins, based on an
mRNA template
Some ribosomes are
attached to the ER and
some a free in the
cytoplasm.
Translation
Golgi apparatus


The Golgi apparatus is a contiguous system of lamellae
and cisternae.
It is responsible for post-translation modifications of
proteins, formation of secretory vesicles and
membrane formation and trafficking.
Membrane flow



Transport vesicles bud off the ER and are transported to the
forming face of the Golgi.
Membrane-bound proteins and secretory proteins then move
through the Golgi, where they are modified, usually by
glycosylation.
The proteins and membranes are then packaged into specific
vesicles, which are targeted.
Mitochondria



Mitochondria actually have two membranes, separated
by a small space.
Mitochondria also have their own DNA.
Mitochondria are essential for oxidative
phosphorylation.
Nucleus



Nucleus also has two membranes.
Nucleus protects the DNA and maintains a specific
environment for the DNA.
Nuclear pores allow for transport into and out of
nucleus.
Library tutorial
http://toby.library.ubc.ca/ereserve/er-coursepage.
cfm?id=1416
For the Biol 153 students: Lee Ann Bryant (from
the library) will be here at the end of the lecture
to give a short talk about the library assignment.
Cell cycle
DNA condensation
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