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Water
Alanine
Diam. DNA
Hemoglobin
Ribosome
Polio Virus
Mitochondrion
E. coli
Liver cell
0.28 nm
0.5 nm
2.5 nm
7.0 nm
20 nm
30 nm
1500 nm
2000 nm
20,000 nm
0.28 mm
0.5 mm
2.5 mm
7 mm
2 cm
3 cm
1.5 m
2m
20 m
pH
pH is a measure of the acidity or basicity of an
aqueous solution
pH ~ -log[H+]
pH>7 is basic
pH<7 is acidic
pH influences most biological processes and is
usually near 7 (neutral) in living cells
Reflection
Can you think of an
example in your body
where the pH is not
neutral (i.e., near pH
7)??
Non-covalent bonding
in biological systems
Hydrogen bonds
Shared hydrogen between two molecules or parts
of a molecule
Non-covalent bonding
in biological systems
Ionic/electrostatic interactions
Non-covalent bonding
in biological systems
Hydrophobic interactions/forces
Non-covalent bonding
in biological systems
van der Waals Interactions
IMPORTANT:
Approximate Bond Strengths
Promotes assembly
Occurs spontaneously
Driven by interaction energy
Large number of small forces creates flexibility of
structures
Example: Membranes/lipid bilayer
Reflection
Why are the
properties of
water so
essential to life
as we know it?
Amino
Acid
Structures
Proline
Only imino acid:
Amino
Acid
Structures
Annotated
Reflection
Why are the
properties of the
amino acid side
chains
important?
PROTEIN STRUCTURE
PROTEIN STRUCTURE
Proteins are written from N-terminus to Cterminus aa sequence is PRIMARY STRUCTURE
Actually synthesized in that orientation
Always written in this orientation
Often written as a sequence of 1- or 3-letter
abbreviations: GKPEESWEG
GlyLysProGluGluSerTrpGluGly
Beta-Sheet Structure
Backbone hydrogen bonding
between strands
Beta-Sheet Structure
Backbone hydrogen bonding
between strands
Note interaction between R
groups (does this limit R size?)
b-Sheet Structure
Orientation can be
anti-parallel
or
parallel
BetaSheet
Structure
Reflection
Why do you think that
the a-helix and b-sheet
are each referenced as
secondary structure?
How does the energy of
these structures compare
to the energy of the
peptide bond?
Reflection
What contribution does
the side chain of each
amino acid make to
secondary structure?
Would you expect all
amino acids participate
in secondary structure?
Tertiary Structure:
Folding into 3-dimensions
Quaternary Structure:
Assembly into higher oligomers
PROTEIN FOLDING
Amino acid sequence of a protein
not functional without folding
3-D structure is the active form of a protein
Non-covalent bonds between side chains (and
peptide backbone interactions) create the
folded form of the protein (IMPORTANT)
Folded form exhibits a biological activity
Folding of amino acid sequence based on
DNA sequence is path to FUNCTION!
Disulfide
bond
formation
(covalent
bond) can
stabilize
protein fold
AND
Structure is dynamic
Large energy penalty for loss of entropy think of it as loss of options for
different states so that the overall difference in energy between
folded/unfolded is small!
Reflection
Can you imagine why
most living organisms
are sensitive to
elevated
temperature?