What have you learned in the previous lectures

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What have you learned in the previous lectures?
What is a cell? What are its main
components? What is a gene? What is DNA
composed of? What is a protein composed
of? What is a lipid? What is a sugar?
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A cell is somewhat self-contained and
self-maintaining it can take in nutrients,
convert these nutrients into energy, carry out
specialized functions, and reproduce as
necessary. Each cell stores its own set of
instructions for carrying out each of these
activities.                                       
       Mouse cells grown in a
culture dish. These cells grow in large clumps,
but each individual cell is about 10 micrometres
across
What is a cell?
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Some organisms, such as bacteria, are unicellular
(consist of a single cell). Other organisms,
such as humans, are multicellular. Humans have
an estimated 100 trillion or 1014 cells a
typical cell size is 10 µm a typical cell mass
is 1 nanogram.
From wikipedia
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• All cells have several different abilities
• Reproduction by cell division (binary
  fission/mitosis or meiosis).
• Use of enzymes and other proteins coded for by
  DNA genes and made via messenger RNA
  intermediates and ribosomes. Metabolism,
  including taking in raw materials, building cell
  components, converting energy, molecules and
  releasing by-products.
• The functioning of a cell depends upon its
  ability to extract and use chemical energy stored
  in organic molecules. This energy is derived from
  metabolic pathways.
• Response to external and internal stimuli such as
  changes in temperature, pH or nutrient levels.
• Cell contents are contained within a cell surface
  membrane that contains proteins and a lipid
  bilayer.
• Some prokaryotic cells contain important internal
  membrane-bound compartments, but eukaryotic cells
  have a highly specialized endomembrane system
  characterized by regulated traffic and transport
  of vesicles.

What is a cell?
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In the highly crowded environment of a cell,
biological macromolecules occur at a
concentration of 300-400 g/l and they physically
occupy a significant fraction of the total volume
(20-30).
Most proteins interact at least transiently with
other proteins, but it is clear that many
essential cellular processes such as signal
transduction, transport, cellular motion and
regulatory mechanisms are mediated by
protein-protein interactions.
What is a cell?
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1 Fibrous protein o 1.1
cytoskeletal proteins o 1.2
Extracellular matrix proteins 2 Globular
proteins o 2.1 Plasma proteins
2.1.1 Coagulation factors
2.1.2 Acute phase proteins o 2.2
Hemoproteins o 2.3 Cell adhesion
o 2.4 Transmembrane transport proteins
2.4.1 Ion channels
2.4.2 synport/antiport proteins o 2.5
Hormones and growth factors o 2.6
Receptors 2.6.1 Transmembrane
receptors 2.6.2 Intracellular
receptors o 2.7 DNA-binding protein
2.7.1 transcription regulation
o 2.8 Immune system proteins o 2.9
Nutrient storage/transport o 2.10
Chaperone proteins o 2.11 enzymes
3 Complexes with multiple components including
proteins
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The primary structure is held together by
covalent peptide bonds, which are made during
the process of translation. The alpha helix and
beta sheet are stabilized primarily by hydrogen
bonds. The tertiary structure is held together
by hydrophobic interactions, van der Waals
forces, and hydrogen bonds, although ionic
interactions, and disulfide bonds are usually
involved too. The two ends of the amino acid
chain are referred to as the carboxy terminus
(C-terminus) and the amino terminus (N-terminus)
based on the nature of the free group.
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Tertiary structure is formed by long distance
interactions of the amino acids side chains.
There are several types of bonds Hydrogen
bonds Ionic bonds Hydrophobic interactions Disulf
ide bonds weak covalent bond between 2 Cys
residues (R-Cys-S-S-Cys-R) But which are the
atomic constituents of such interactions?
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Type of bonds
A COVALENT BOND results when two atoms "share"
valence electrons between them. An IONIC BOND
occurs when one atom gains a valence electron
from a different atom, forming a negative ion
(ANION) and a positive ion (CATION),
respectively. These oppositely charged ions are
attracted to each other, forming an ionic bond.

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Non-covalent bonds and other weak forces are
important in biological structures.

• Electrostatic bonds(ionic) result from the
  electrostatic attraction between two ionized
• groups of opposite charge, such as carboxyl
  (-COO-) and amino (-NH3).
• In water, these bonds are very weak.

• Hydrogen bonds result from electrostatic
  attraction between an electronegative atom
• (O or N) and a hydrogen atom that is bonded
  covalently to a second electronegative
• atom. N-H ----- OC- -O-H----- OC-

• Van der Waals bonds are short range attractive
  forces between chemical groups
• in contact. Caused by slight charge
  displacements.

• Hydrophobic attractions cause non-polar groups
  such as hydrocarbon chains to
• associate with each other in an aqueous
  environment.

• Multiple weak bonds or forces can cause strong
  interactions.
• Biological recognition results from a three
  dimensional structure that allows multiple
• weak forces between molecules

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dipoles (Hellènic di(s)- twi- and pòla
pivot, hinge). An electric dipole is a
separation of positive and negative charge. The
simplest example of this is a pair of electric
charges of equal magnitude but opposite sign,
separated by a small distance.
Many molecules have such dipole moments due to
non-uniform distributions of positive and
negative charges on the various atoms.
HCl molecules, for example, have a dipole moment
because the hydrogen atom has a slight positive
charge and the chlorine atom has a slight
negative charge. Because of the force of
attraction between oppositely charged particles,
there is a small dipole-dipole force of
attraction between adjacent HCl molecules.
                                                  
                                              
The dipole-dipole interaction in HCl is
relatively weak only 3.3 kJ/mol. (The covalent
bonds between the hydrogen and chlorine atoms in
HCl are 130 times as strong.) The force of
attraction between HCl molecules is so small that
hydrogen chloride boils at -85.0oC.
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Many of the atoms in proteins carry partial
charges due to their electronegativity.
Since the CO and N-H groups are aligned by
hydrogen bonds in an alpha helix, the dipole
moments of each peptide bond tend to align almost
linearly, which has the effect of an isolated
positive half unit charge at the N-terminal end
of the helix, with the compensatory charge
separated from it by the full length of the
helix.
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In the left-hand diagram, the bonds are
proton-ordered hydrogen atoms are bonded to
oxygen atoms in a regular pattern. In the
right-hand diagram, the bonds are
proton-disordered hydrogen atoms are bonded to
oxygen atoms in a random fashion, although there
is a hydrogen atom between every pair of
adjacent oxygen atoms. It doesn't take a lot of
energy to break up proton ordering, so it tends
to appear mostly at very low temperatures. Many
of the polymorphs of ice have proton-ordered
forms at temperatures below -80 to -100 C.
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Dynamically changing clusters of Hydrogen Bonds
in liquid water
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Nucleic acids interactions
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Model structure of DNA Francis Crick, James
Watson
At that time Maurice Wilkins and Rosalind
Franklin, both working at King's College, London,
were using X-ray diffraction to study DNA. Crick
and Watson used their findings in their own
research. In April 1953, they published the news
of their discovery, a molecular structure of DNA
based on all its known features - the double
helix. Their model served to explain how DNA
replicates and how hereditary information is
coded on it. This set the stage for the rapid
advances in molecular biology that continue to
this day. Watson, Crick and Wilkins shared the
Nobel Prize in Medicine in 1962. Franklin had
died in 1958 and, despite her key experimental
work, the prize could not be received
posthumously. Crick and Watson both received
numerous other awards and prizes for their work.
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Salt bridges

• Salt bridges or ion-pairs are a special form of
  particularly strong hydrogen bonds made up of the
  interaction between two charged residues.
• The contribution of salt bridges to protein
  stability is a somewhat contentious issue in the
  literature. On the one hand is the observation
  that thermophilic and hyper-thermophilic
  analogues of mesophilic proteins tend to have
  increased numbers of salt-bridges (Tanner et al.,
  1996 Perutz Raidt, 1975 Perutz, 1978 Dekker
  et al., 1991). On the other hand are mutational
  studies showing that the contribution of salt
  bridges to stability is small. Perhaps at higher
  temperatures salt bridges make more of a
  contribution to stability.
• Horovitz et al . (1990) measured the stability of
  a surface salt bridge triad between Asp8, Asp12
  and Arg110 on the surface of barnase by
  construction of a thermodynamic cycle of all
  possible combinations of 1, 2, or 3 alanine
  mutants. The free energy contribution to the
  stability of the protein is only 1.25 kcal/mol
  for the Asp12/Arg110 pair and 0.98 kcal/mol for
  the Asp8/Arg110 pair. Removal of Arg 110 has no
  effect on stability!

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Amino acids classification

• small glycine, alanine,cysteine
• Hydrophobic valine, leucine, isoleucine,
  methionine, proline
• aromatics (hydrophobic) phenylalanine,
  tyrosine, histidine, tryptophan
• Hydrophilic serine, threonine, asparagine,
  glutamine, (tyrosine)
• . Positively charged lysine, arginine,
  (histidine)
• . Negatively charged aspartic acid, glutamic
  acid

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Of course things are not so easy....
The classification of amino acid
conservation. Taylor WR. J Theor Biol. 1986
119(2)205-18.
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Formation of a peptide bond between two amino
acids by the condensation (dehydration) of the
amino end of one amino acid and the acid end of
the other amino acid. The above image is from
http//zebu.uoregon.edu/internet/images/peptide.gi
f.
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small glycine, alanine,cysteine
Glycine Gly G
Alanine Ala A
Cysteine Cys C
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• Hydrophobic valine, leucine, isoleucine,
  methionine, proline

Valine Val V
Leucine Leu L
Isoleucine Ile I
Methionine Met M
Proline Pro P
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hydrophilic serine, threonine, asparagine,
glutamine
Serine Ser S
Threonine Thr T
Asparagine Asn N
Glutamine Gln Q
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aromatics (idrophobic) phenylalanine, tyrosine,
histidine, tryptophan
Phenylalanine Phe F
Tyrosine Tyr Y
ThryptophanTrp W
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positively charged lysine, arginine, (histidine)
Lysine Lys K
Arginine Arg R
Histidine His H
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negatively charged aspartic acid, glutamic acid
Aspartic acid Asp D
Glutamic acid Glu E
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When you add some drops of oil to water, the
drops combine to form a larger drop. This comes
about because water molecules are attracted to
each other and are cohesive because they are
polar molecules. Oil molecules are non polar
and thus have no charged regions on them. This
means that they are neither repelled or attracted
to each other. The attractiveness of the water
molecules for each other then has the effect of
squeezing the oil drops together to form a
larger drop. Since it looks like the oil
molecules are avoiding the water, this type of
interaction is called a hydrophobic interaction.
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Interactions between water and other molecules
such that the other molecules are attracted to
water are called hydrophilic interactions.
Molecules that have charged parts to them are
attracted to the charges within the water
molecule. This is an important reason why water
is such a good solvent. So for instance the
picture below shows a glucose molecule in
solution. Water molecules surrounding the
glucose molecule are shown in blue for clarity. 
Glucose molecules have polar hydroxyl(OH) groups
in them and these attract the water to them.
Once in solution the molecules stay in solution
at least in part because they become surrounded
by water molecules. This layer of water molecules
surrounding another molecule is called a
hydration shell. 
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Hydrophobic interactions along with hydrophilic
interactions help to determine the
three-dimensional shape of biologically important
molecules and structures such as proteins and
cell membranes.
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movie.
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Torsional angles
Dihedrals are often represented by a periodic
function, with V(dihedral) K (1 cos(nF - ?))
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Consider ethane (CH3-CH3) Kf (total for 9
paths) 1.4 kcal/mol n 3 - ? 0 V(dihedral)
K (1 cos(nF - ?))
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A Ramachandran plot (also known as a Ramachandran
map or a Ramachandran diagram), is a way to
visualize dihedral angles f against ? of amino
acid residues in protein structure. It shows the
possible conformations of f and ? angles for a
polypeptide. Mathematically, the Ramachandran
plot is the visualization of a function (torus).
Hence, the conventional Ramachandran plot is a
projection of the torus on the plane, resulting
in a distorted view and the presence of
discontinuities. One would expect that larger
side chains would result in more restrictions and
consequently a smaller allowable region in the
Ramachandran plot. In practice this does not
appear to be the case only the methylene group
at the ß position has an influence. Glycine has
a hydrogen atom, with a smaller van der Waals
radius, instead of a methyl group at the ß
position. Hence it is least restricted and this
is apparent in the Ramachandran plot for Glycine
for which the allowable area is considerably
larger. In contrast, the Ramachandran plot for
proline shows only a very limited number of
possible combinations of ? and f.
A Ramachandran plot generated from the protein
PCNA, a human DNA clamp protein that is composed
of both beta sheets and alpha helices (PDB ID
1AXC). Points that lie on the axes indicate N-
and C-terminal residues for each subunit. The
green regions show possible angle formations that
include Glycine, while the blue areas are for
formations that don't include Glycine.

• From Wikipedia

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Ramachandran plot
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Residues in ß sheet typically adopt backbone
(f, ?) dihedral angles around (180,180).
The ß sheet (also ß-pleated sheet) is consisting
of beta strands connected laterally by three or
more hydrogen bonds A beta strand (also
ß-strand) is a stretch of amino acids typically
5-10 amino acids long whose peptide backbones are
almost fully extended. The association of beta
sheets has been implicated in the formation of
protein aggregates and fibrils observed in many
human diseases, including Alzheimer's disease
and mad cow disease.
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Conformational propensities
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Levitt conformational preferences of aa in
globular proteins Biochemistry (1978) 17, 427
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and now...lets have a tutorial....
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Tutorial amino acids You should learn to
draw the chemical structures of the following
amino acids. It is also useful to learn the
three-letter and single letter codes for these
amino acids. Glycine Gly G Alanine Ala A
Phenylalanine Phe F Tyrosine Tyr
Y Cysteine Cys C Proline Pro P Lysine
Lys K Arginine Arg R Histidine
His H Aspartic acid Asp D Glutamic acid
Glu E Serine Ser S Asparagine
Asp N Name an amino acid in which the R group
(side chain) contains the following a hydroxyl
group. a sulphur atom. an amino
group. an amide group. an aromatic
ring. an acid group.
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In the following peptide Glu-Thr-Val-Asp-Ile-S
er-Ala identify the hydrophobic amino
acids and the acidic amino acids.
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peptide
Glu- Thr -Val- Asp -Ile -Ser -Ala