Maya Dian Rakhmawatie

curlymaya_muah@yahoo.co
m

Object learning of biology molecular

To understand molecular basic for
determining phenomena biologist

a. Chemical reaction in organism

biochemistry,
Biomolecular gene expression that encode
enzyme in chemical reaction
b. Human response cause stimulant
physiology
physiologist aspect in biomolecular antibody
formation, molecule transport ,
hormone/neurotransmitter action

Special biological aspect in biology

molecular are :
a. Genetic

materials
b. Synthesis protein process

Maya Dian Rakhmawatie

curlymaya_muah@yahoo.com

Protein can be function as structurally or

functionally :
as catalysts
as transport and store other molecules
such as oxygen
provide mechanical support and immune
protection
generate movement
transmit nerve impulses
control growth and differentiation.
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Most living organism single cells, which :

1. Store their hereditary in DNA
2. Replicate their hereditary information by
template polymerization
3. Transcript portions of their hereditary
information into RNA
4. Use protein as catalysts
5. Translate RNA into protein

Fragment of genetic information

corresponding to one protein GENE
Gene DNA segment coding protein
Genome total genetic information in DNA
sequence
Protein subsequent fate depends on their
amino acid sequences (signal sequences),
which can contain sorting signals that direct
their delivery to locations outside the cytosol

Presence of a sorting signal sequences in each of

the proteins directs them to a particular
compartment

Signal sequences direct proteins to the correct

destination compartment
15-60 amino acids long
Usually on the N-terminal end of the protein
Signal sequence is removed once the protein
transported

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Protein folding
Delivery to different cell
compartments

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 Disulfide bond formation

proteins becomes more

stable
resistant to pH
changes or enzymes
Glycosylation is a covalent
attachment of
oligosaccharides; function:
Protects from
degradation
Transport signal for
packaging into
appropriate vesicle

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The different property of Amino Acids side chains are

nonpolar and hydrophobic (water-fearing)
negatively or positively charged
reactive, and so on.

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A few of the amino acids have functional

groups and the rest are hydrophobic.

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CHARGED POLAR

Acidic (COO) and basic (NH3) amino acid side

chains have a charge at neutral pH and strongly

prefer to be on the exterior, exposed to water,
rather than in the interior of the protein.

Charged groups are usually found on the surface of

proteins.

On the surface of the protein, a charged residue can

be solvated by water, and it is easy to separate

oppositely charged ions.

If a charged group is found in the interior of the

protein, it is usually paired with a residue of the

opposite charge. This is termed a salt bridge.
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These side chains are uncharged, but

they have groups (OH, SH, NH, C=O)
that can hydrogen-bond to water.

In an unfolded protein, these residues are

hydrogen-bonded to water.

They prefer to be exposed to water, but if

they are found in the protein interior they
are hydrogen-bonded to other polar groups.

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Hydrocarbons (both aromatic and aliphatic)

do not have many groups that can
participate in the hydrogen-bonding
network of water.
Theyre greasy and prefer to be on the
interior of proteins.

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The folding of a
protein chain is :
constrained by many

different noncovalent
bonds
hydrogen bonds
ionic bonds
van der Waals
attractions

involve atoms in

polypeptide
backbone and in side
chains.
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Proteins fold in order to put as much of the greasy

stuff out of contact with water as possible.
This provides much of the driving force for
protein folding, proteinprotein interactions, and
proteinligand interactions (Figure).

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These are very short-range interactions

between atoms that occur when atoms are
packed very closely to each other.

When the hydrophobic effect brings atoms

very close together, van der Waals
interactions and London dispersion forces,
which work only over very short distances,
come into play.
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Hydrogen bonding means sharing a

hydrogen atom between one atom that has
a hydrogen atom (donor) and another
atom that has a lone pair of electrons
(acceptor):

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The one-dimensional
information contained in the
primary amino acid sequence of
cellular proteins is enough to
guide a protein into its threedimensional structure, to
determine
its specificity for interaction with

other molecules
its ability to function as an enzyme
to set its stability and lifetime.

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Four levels of organization in structure of a

protein:
1. primary structure: amino acid sequence
2. secondary structure is formed by helices
and sheets
3. tertiary structure: full three-dimensional
organization of a polypeptide chain
4. quaternary structure: is formed as a complex
of more than one polypeptide chain
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Proteins can be grouped into protein families,

each family member having an amino acid
sequence and a three-dimensional conformation
that resemble those of other family members.

E.g. the serine proteases, a large family of

proteolytic enzymes that includes the digestive
enzymes chymotrypsin, trypsin, and elastase, and
several proteases involved in blood clotting.

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Noncovalent bonds fold a protein chain into a

specific.

Any region of a protein's surface that can interact

with another molecule through sets of
noncovalent bonds is called a binding site.

Many of proteins in cells contain two or more

types of polypeptide chains.
Hemoglobin: contains two identical -globin
subunits and two identical -globin subunits,
symmetrically arranged.

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The biological properties of a protein

molecule depend on its physical interaction
with other molecules.

Substance that is bound by the protein is

referred to as a ligand for that protein
specific binding

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Antibodies, or immunoglobulins:

are proteins produced by immune system in

response to foreign molecules

recognizes antigen with remarkable specificity.
Each antibody binds to antigen extremely
tightly (inactivate target directly or marking it
for destruction).

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Basic enzymatic reaction path is

E + S ES EP E + P
If concentration of substrate is increased, rate at
which product is formed also increases, up to a
maximum value (enzyme molecule is saturated with
substrate)

Km is concentration of substrate that cause rate

reaction is 0.5 its maximum rate (0.5 Vmax)

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Lysozyme catalyzes cutting of polysaccharide chains

in cell walls of bacteria.

Product chains are then quickly released, freeing

enzyme for further cycles of reaction.

Reaction catalyzed by lysozyme

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Proteins often use small nonprotein to perform

functions:
iron atom is a nonprotein portion is hemoglobin.

By binding reversibly to oxygen gas through its

iron atom, heme of hemoglobin pick up oxygen in
lungs and release it in tissues.

Coenzymes (derivate of vitamins) are needed by

some enzymes for their activity

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Points where different enzymes compete for the

same substrate so it requires regulation when
and how rapidly each reaction occurs at many
levels.
1. cell controls how many molecules of each

enzyme it makes by regulating expression of

gene that encodes that enzyme.
2. regulates rate of protein destruction by
targeted proteolysis

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Most control occurs when a molecule other than

one of substrates binds to an enzyme at a
special regulatory site outside active site
alters rate at which the enzyme converts its
substrates to products.

Feedback inhibition:
an enzyme acting early in a reaction pathway
is inhibited by a late product of that pathway.
can work almost instantaneously and is
rapidly reversed when the level of the
product falls.
is negative regulation: it prevents an enzyme
from acting.
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Many enzymes must have at least two different

binding sites on their surface

an active site that recognizes the substrates

a regulatory site that recognizes a regulatory molecule.

These two sites must communicate to allows catalytic

events at active site to be influenced by binding of
regulatory molecule at its separate site on protein's
surface.

During feedback inhibition, the binding of an

inhibitor at one site on protein causes protein to
shift to a conformation in which its active site
becomes incapacitated.

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