Transcript 1-Lec1- 2014

Molecules, Gene and disease
Session 1
Introduction to the cell and
biological molecules
Dr. Mona Abdel Ridha Rasheed
Learning Outcomes
At the end of this session you should be able to:
1. Identify the main organelles in a mammalian cell and list their
functions.
2.List the principal differences between a prokaryotic and an
eukaryotic cell.
3. Discuss the bonds important for macromolecular structure and
interaction.
4.Explain the differences between hydrophobic and hydrophilic
molecules in water.
Learning Outcomes
5. Explain the concept of pH, pK and buffers.
6. Recognise and draw the generalised structure of an amino acid.
7. Classify amino acids according to the properties of their side
chains.
8. Explain how the charges on amino acids are affected by pH.
9. Show how a peptide bond is formed and list its key features.
10. Explain how amino acid charge can influence the isoelectric
point of a protein.
Structure of the session 1
Lecture 1: Introduction to the cell
Lecture 2: Amino acids and protein
(8.00-8.50)
(8.50-9.40)
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Lecture 1
Introduction to the cell
The Cell-Basic Unit of Life
Cells
are the structural and functional units of
all living organisms.
Cells are capable of carrying out all the
activities necessary for life.
Cells are small, membrane enclosed units filled
with a concentrated aqueous solution of
chemicals and provide with the surprising
ability to create copies of themselves by
growing and dividing in two.
Cell Components
1- Plasma membrane: It is a phospholipid bilayer that
responsible for the cell morphology and movement, and
transport of ions and small molecules.
2- Cytosol: liquid portion of cytoplasm
(cytoplasm composed of all materials contained within
cytosol).
3- Organelles: complex intracellular locations where
processes necessary for eukaryotic cellular life occur. Most
organelles are membrane enclosed structures, each organelle
carries out a specific function.
Mammalian cell: Organelles
Mammalian Cell: Organelles functions
Organelles
Functions
Nucleus/nucleolus
RNA synthesis
RNA processing and ribosome assembly( nucleolus)
DNA synthesis and repair
Ribosome
Protein synthesis
Endoplasmic
reticulum
Export of proteins, Membrane synthesis, Lipid and
steroid synthesis, Detoxification reactions
(Protein synthesis)
Golgi complex
Export of proteins, Detoxification reactions
Mitochondrion
ATP synthesis
Lysosome
Cellular digestion
peroxisomes
Fatty acids and purine brake down, Detoxification of
hydrogen peroxide, and synthesis of cholesterol, bile
acids and myelin
Cell
Eukaryotic
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Eu =well or truly
Karyon = nucleus
Organisms whose cells
have a nucleus are called
eukaryotic
Ex: mammalian cells
Prokaryotic
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•
•
•
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Pro = before
Lack a nucleus but have
nucleoid which has a
large DNA molecule.
Lack intracellular
organelles.
Have a cell wall
Ex: bacterial cell
Cell component
Macromolecules
Subunits of Macromolecules
Bonds important for macromolecular
structure and interaction
Covalent bond:
A covalent bond forms when two atoms come very close
together and share one or more of their electrons. Each atom
forms a fixed number of covalent bonds.
Bonds important for macromolecular structure and
interaction
Bonds important for macromolecular
structure and interaction
Ionic bond: A bond formed between two atoms where there
is a complete transfer of an electron resulting in the
formation of two ions (one positive and one negative).
e.g. NaCl
It should be differentiate between ionic bond and ionic
interaction which may be attraction ( between two groups
with different charges), or Repulsion (between two groups
with the same charges)
Bonds important for macromolecular
structure and interaction
Hydrogen bond: A weak electrostatic interaction
between a hydrogen atom bound to an electronegative
atom (N, O) and another electronegative atom.
Bonds important for macromolecular
structure and interaction
Hydrophobic interaction: A weak electrostatic
interaction between two hydrophobic groups.
Van der Waals interaction: A weak interaction
between any two atoms in close proximity
Bonding
Bond length and strength
Water
The principal fluid medium of the cell is water,
which is present in most cells, except for fat
cells, in a concentration of 70 to 85 per cent.
Many cellular chemicals are dissolved in the
water.
Water
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WATER is the solvent of choice for biological
systems
Helps regulate temperature since it is able to
absorb large amounts of heat
Helps regulate intracellular pH
Used for transport – delivers nutrients and removes
waste from cells
In water, the hydrogen atoms have a partial positive
charge, and the oxygen atoms have a partial negative
charge, so water is polar solvent
Water as a solvent
Water as a solvent
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Water is a polar molecule. It can readily dissolve
biomolecules that are charged or polar. Molecules that
can interact with water via hydrogen bonds are said to
be hydrophilic.
Non-polar molecules are insoluble in water and
interact with other non-polar compounds; they are said
to be hydrophobic.
Molecules that have both hydrophilic and hydrophobic
properties are said to be amphipathic.

Some examples of polar, non-polar and amphipathic
biological molecules are shown below:
pH and buffer
Ionization of Water
Water dissociates into hydronium (H3O+) and hydroxyl
(OH-) ions. For simplicity, we refer to the hydronium ion as
a hydrogen ion (H+) and write the equilibrium as:
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K w is the ion product of water. At 25°C, K w is 1.0 × 10-14.
Note that the concentrations of H+ and OH- are
reciprocally related.
If the concentration of H+ is high, then the concentration of
OH- must be low, and vice versa.
For example, if [H+] = 10 -2 M, then [OH-] = 10-12 M.
Definition of Acid and Base
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An acid is a proton donor.
A base is a proton acceptor.
The species formed by the ionization of an acid is its
conjugate base. Conversely, protonation of a base yields
its conjugate acid. Acetic acid and acetate ion are a
conjugate acid-base pair.
Definition of pH and pK
The pH of a solution is a measure of its concentration of H+. The pH is defined as:
The ionization equilibrium of a weak acid is given by:
The apparent equilibrium constant K a for this ionization is:
The pK a of an acid is defined as:
The pK a of an acid is the pH at which it is half dissociated, when [A-]=[HA].
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Henderson-Hasselbalch Equation
What is the relation between pH and the ratio of acid to base?
Therefore
And
This equation is commonly known as the HendersonHasselbalch equation.
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The pH of a solution can be calculated from this equation
if the molar proportion of A- to HA and the pK a of HA
are known.
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Conversely, the pK a of an acid can be calculated if the
molar proportion of A- to HA and the pH of the solution
are known.
Buffers

An acid-base conjugate pair (such as acetic acid and
acetate ion) has an important property: it resists
changes in the pH of a solution. In other words, it
acts as a buffer. Consider the addition of OH- to a
solution of acetic acid (HA):
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A plot of the dependence of the pH of this solution
on the amount of OH- added is called a titration curve.
there is an inflection point in the curve at pH 4.8,
which is the pK a of acetic acid.
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Titration curve of acetic acid
Application of Henderson equation
Application of Henderson equation
Thank you