Download Biophysics II Key points to be covered

Biophysics II
Life: based on materials
By
A/Prof. Xiang Yang Liu
Biophysics & Micro/nanostructures Lab
Department of Physics,
NUS
„
Organelle, formed by a variety
of molecules: protein, DNA,
RNA, polysaccharides…
Even elephants are
molecules…
Molecule and chemical bonding
„
Molecules:
clusters
that
consist
of
a
chemical combination (of one, two or
more atoms are called molecules.
„
Key points to be covered
„
C
molecules-basic units display the chemical and
physical properties of a compound.
ica
h em
nd s
l bo
Molecule and chemical bonding
Bio Molecules and structures-bio
functions: determined by
„
„
Chemical bonds-covalent bonds (primary
structure)
Non-bond interactions (secondary, tertiary
structures).
Primary structure
Strong Bond
Covalent bond
Weak interactions
Weak interactions
3D structure
2nd , tertiary
structures
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Molecule and chemical bonding
„
„
What is the Bond
force to bind
different atoms
together
to
form
a
molecule?
Chemical
bond:
an
attractive
force
linking two or
more atoms is
called a chemical
bond.
Molecule and chemical bonding:
chemical bonding
„
„
„
More electrons will
go to the next shelllike a “party” shell.
They like a party in
a group of “8”.
If there are less
than 8 electron, the
atom will find
another atom to
bond to.
Molecule and chemical bonding:
chemical bonding
„
…or it finds a
relationship with O
by sharing its
election with O,
creating a covalent
bond.
Molecule and chemical bonding:
chemical bonding
„
„
Electrons follow a
certain rule of
behavior: The first two
always hand out on
the orbit close to the
nucleus.
And only 2 electrons
(↑↓) on the first shell
because they like have
their privacy.
Molecule and chemical bonding:
chemical bonding
„
„
„
H atom has only one
e – it really feels
“lonely”, likes
company…
… find a relationship
with another atom.
Example H → H2
Molecule and chemical bonding:
chemical bonding
„
„
O has 8 electrons-6
in the outer shell.
To keep the O
happy, “he” needs 8
electrons in the
outer shell…
2
Molecule and chemical bonding:
chemical bonding
„
„
„
„
… the O atom finds
another H.
He has 8 in his outer
shell.
Two covalent bonds
have been formed.
A molecule of water
H2O.
Molecule and chemical bonding:
chemical bonding
„
„
„
„
A rule: 2 electrons in the
inner and 8 in the outer.
To achieve the most stable
electronic structure of
atom, the outer shell
should be completely
empty or filled.
Sharing electrons forms
covalent bonds, then forms
molecules, like H2O
H shares 1, O → 2, N→ 3,
C → 4.
Molecule and chemical bonding:
chemical bonding
Molecule and chemical bonding:
chemical bonding
A covalent bond is a pare of
electrons shared by two atoms
Molecule and chemical bonding:
chemical bonding
Why do you need
covalent bond?
1. Strength
„
„
Covalent bonds are
strong…
Strength =
togetherness
2. Energy…
Molecule and chemical bonding:
chemical bonding
„
„
Some key points about covalent bond:
…
3
Life: based on materials (cont’d)
Biologically important molecules:
DNA-
RNA-Protein
DNA
„
(deoxyribonucleic
acid) – to control
Carbohydrate, lipids, proteins and nucleic
acids –utmost important organic molecules
in the structure and function of living
things.
the way a organism
looks and performs
„
„
Biologically important molecules:
DNA-
RNA-Protein
„
RNA (ribonucleic acid)massager
„
„
single-stranded
enables information in
DNA to be expressed
double-stranded
helix held together
by hydrogen bonds
is the genetic
material
Biologically important molecules:
DNA-RNA-Protein
„
„
„
Cells synthesize proteins; proteins to perform cellular
functions, maintain inner stability, grow, and reproduce.
Genes control life activities by controlling protein
synthesis.
The genetic codes in DNA are copied to RNA molecules,
and the codes in the RNA molecules are translated by
ribosomes to certain sequences of amino acids.
Copy
Biologically important molecules:
DNA-RNA-Protein
„
Protein:
„
„
„
contain C, H, O, N,
(S)
Amino Acid: Protein
build Blocks (~20
found)
Protein: polypeptide
Biologically important
molecules: Carbohydrates
nC+mH2O
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Biologically important molecules:
Carbohydrates- storage of energy,
building materials
Biologically important molecules: Lipids
(1)Storage of
energy
(2) Building
materials
Biologically important molecules:
Lipids
Biologically important molecules:
Lipids
H
C
Oils: unsaturated fatty acids.
Triglycerides: fat and oils
Fat: straight-chain fatty
acids with no double
bonds. These fatty acids
are
saturated
with
hydrogen.
At some positions in
these
fatty
acid
molecules, adjacent
carbon atoms are
joined
by
two
covalent bonds (a
double bond).
A diet high in saturated
fats appears to contribute
to diseases of the heart and
blood vessels.
H
C
Biologically important molecules:
Bio-macromolecule - 4 level
Lipids
structure
H
2N
KAA
folding
HD
P
Phospholipids as
Waterproof
barriers in living
Organisms.
CWL
H
WY
Phospholipids
KLM
CTH
DEW
WN
…
Primary structure
Secondary
structure
CO
OH
folding
Assembly
Aggregation
quaternary structure
Tertiary structure
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Bio-macromolecule - 4 level
Bio-macromolecule – structure &
functionality
structure
„
Biological functions of biological
molecules are not only determined
by the primary structure, but also to
a large extent by the secondary,
tertiary, quaternary structures
• Myoglobin-monomer-
responsible for oxygen
storage in muscle cell
• Hemoglobin-tetramer: 4
polypeptide assembly α2β2:
a transport protein to carry
oxygen from thelung to the
various tissues.
• The geometric shape (3D
structure) will determine the
functionalities
Molecular Interactions &
Macromolecular Structures
„
Bio-macromoleculeConfigurations and conformations
Covalent Bond – the formation of molecules
(the primary structure of molecules)
„
„
H
The arrangement of atoms or groups of atoms in
a molecule is described by configuration and
conformation.
Molecular configuration, and molecular steric
configuration
H
H
H
H
H
C
C
C
C
C
H
H
H
H
H
H
H
H
H
H
C
C
C
C
H
H
H
C
H
H
H
H
n-Pentane
H
iso-Pentane
Bio-macromolecule-
Bio-macromolecule-
Configurations and conformations
Configurations and conformations
„
H
COOH
CH3
Conformations: describing the spatial arrangement of
groups about one or more freely rotating bonds.
(Torsional angle)
H
COOH
H
CH3
H
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Bio-macromolecule-
Molecular Interactions &
Macromolecular Structures
Configurations and conformations
„
„
The secondary, tertiary, and
quaternary structures of
macromolecules correspond
to different conformations.
Non-bonding interactions
stabilize the conformation of
macro molecules, and lead
to the aggregation/assembly
of molecules
„
Why does different biomacromolecules appear as different
three-dimensional structures?
„
How do macromolecules fold into
secondary, tertiary, and quaternary
structures?
Hemoglobin
Cytochrome C
Key Message
„
„
„
„
„
The properties of life are based on atoms and
molecules.
Atoms are bounded together by chemical bonds
to form more stable clusters-molecules.
Covalent Bond-sharing electrons. Strength,
energy storage.
Bio-molecules: DNA-RNA-Proteins,
carbohydrate, lipid, … Conformation and
configuration.
And 3D (4o) structure of biomolecules
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