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Introduction to
Molecular Biology
z Molecular biology is interdisciplinary
(biochemistry, genetics, cell biology)
z Impact of genome projects (human, bacteria,
fungi, plants, etc.)….”postgenomics era”
z Integration with other fields (e.g. computer
science) leading to interdisciplinary career
paths (Bioinformatics)
Molecular Biology syllabus web site
Model Organisms
Central Dogma
zDNA is transcribed to
mRNA
zmRNA is translated to
protein
Proteins play many roles
Lecture 1
Protein Structure and Function
Reading: Chapters 1-3
Protein Structure & Function
- protein structure
- protein purification &
analysis
- protein structure
determination
Protein structure determines function
z Proteins are single, unbranched chains
of amino acid monomers
z There are 20 different amino acids
z A protein’s amino acid sequence
determines its three-dimensional
structure (conformation)
z In turn, a protein’s structure determines
the function of that protein
All amino acids have the same general structure but the
side chain (R group) of each is different
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Hydrophilic amino acids
Figure 2-13
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Hydrophobic & “special” amino acids
Figure 2-13
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Peptide bonds connect amino acids into linear
chains
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Fig 3-2
Amino acids are the repeating units in proteins, but it
is the 3-D protein structure that underlies function.
How is 3-D structure obtained?
Four levels of structure determine the shape of
proteins
z Primary: the linear sequence of amino acids
z Secondary: the localized organization of parts
of a polypeptide chain (e.g., the  helix or 
sheet)
z Tertiary: the overall, three-dimensional
arrangement of the polypeptide chain
z Quaternary: the association of two or more
polypeptides into a multi-subunit complex
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Secondary structure:
the  helix
The spiral is held by hydrogen bonds
between nearly adjucent
backbone O and H atoms
Figure 3-4
Secondary
structure:
the beta sheet
Hydrogen bonds
occur between
backbone O and H
of separate ajucent
strands
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Motifs are regular combinations of secondary
structures
A coiled coil motif is
formed by two or more helices
wound around one another
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Other examples of motifs
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Tertiary structure // quaternary structure
Regions of proteins
form domains:
functional, topological
or structural
(like in case of HA)
The structure is
stabilized by
Interactions
between domains
Hydrophobic,
hydrophylic
interactions and
disulfide bonds
help to keep
the structure
hemagglutinin
Sequence homology suggests functional and evolutionary
relationships between proteins
Figure 3-10
Folding, modification, &
degradation of proteins
z A newly synthesized polypeptide chain must
undergo folding and often chemical modification to
generate the final protein
z All molecules of any protein species adopt a single
conformation (the native state), which is the most
stably folded form of the molecule
The information for protein folding is encoded in the
sequence
Folding of proteins in vivo is promoted by
chaperones
Aberrantly folded proteins are implicated is slowly developing
diseases
An amyloid plaque in
Alzheimer’s disease is
a tangle of protein
filaments
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Chemical modifications and processing alter the biological
activity of proteins
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Protein degradation via the ubiquitin-mediated
pathway
Cells contain several other pathways for
protein degradation in addition to this
pathway
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Functional design of proteins
z Protein function generally involves conformational
changes
z Proteins are designed to bind a range of molecules
(ligands)
y Binding is characterized by two properties: affinity
and specificity
z Antibodies exhibit precise ligand-binding specificity
z Enzymes are highly efficient and specific catalysts
y An enzyme’s active site binds substrates and
carries out catalysis
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Kinetics of an enzymatic reaction are described by
Vmax and Km
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Mechanisms that regulate protein function
z Allosteric transitions
y Release of catalytic subunits, active / inactive
states, cooperative binding of ligands
z Phosphorylation / dephosphorylation
z Proteolytic activation
z Compartmentalization
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Purifying, detecting, and characterizing proteins
z A protein must be purified to determine its
structure and mechanism of action
z Molecules, including proteins, can be
separated from other molecules based on
differences in physical and chemical
properties
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Centrifugation can separate molecules that differ in
mass or density
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Electrophoresis separates molecules according to their
charge:mass ratio
SDS-polyacrylamide
gel electrophoresis
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Two-dimensional electrophoresis separates molecules according
to their charge and their mass
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Separation of proteins by size: gel filtration
chromatography
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Separation of proteins by charge: ion exchange
chromatography
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Separation of proteins by specific binding to another molecule:
affinity chromatography
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Highly specific enzymes and antibody assays can detect
individual proteins
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Time-of-flight mass spectrometry measures the mass of proteins
and peptides
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X-ray crystallography is used to determine protein
structure
Other techniques such as cryoelectron microscopy and NMR
spectroscopy may be used to solve the structures of certain types of
proteins
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