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Molecules of Life: Biopolymers
Dr. Dale Hancock
[email protected]
Room 377
Biochemistry building
Housekeeping
• Answers to the practise calculations and a
narration are on WebCT. Access these
through the lab resources link.
• Refresh your browser whenever you go
onto WebCT…I am always adding stuff!
• The advanced lectures start NEXT
week…contrary to your timetable
(confusion with bookings, sorry)
Housekeeping
• There are some concept tests also on
WebCT.
• I would like you all to do the laboratory
calculations, parameters and mole
concept tests.
• Marks don’t count. They are anonymous.
• I will use the results to plan some tutorials.
1
Chemical Bonding
Covalent
The Hydrogen molecule:
the quintessential example of
the perfect couple!
e-
+
+
e-
The Hydrogen molecule:
the quintessential example of
the perfect couple!
0.74 Å
e-
+
+
e-
2
Carbon
e-
ee-
+
ee-
e-
e-
ee-
+
ee-
e-
The electronic configuration of
Carbon
2nd shell
2px
2py
2pz
2s2
1st shell
1s2
3
Carbon as it bonds….
2nd shell
2s
1st shell
2px
2py
2pz
1s2
Carbon as it bonds….
To maximise bonding options
2nd shell
sp3 orbital
hybridisation
1st shell
2s
2px
2py
1s2
4 equivalent bonds…
..tetrahedral
2pz
Tetrahedral Carbon
4
Chemical Bonding
Covalent
H-H
C-C
C-H
Chemical Bonding
Covalent
ionic
H-H
C-C
C-H
NaCl
Na+ ClIn solution
Chemical Bonding
Polar covalent
Covalent
H-H
C-C
C-H
ionic
NaCl
Na+ ClIn solution
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Water
Chemical Bonding
Covalent
Polar covalent
H-H
C-C
C-H
ionic
H-O-H
NaCl
C=O
C-N
CO-NH2
C-OH
Major Biopolymers
Fats or more scientifically lipid has the
general formula (-CH2-)n.
H2
C
H3C
C
H2
H2
C
C
H2
H2
C
C
H2
H2
C
C
H2
H2
C
C
H2
H2
C
C
H2
H2
C
C
H2
COOH
C
H2
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Chemical Bonding
Covalent
Polar covalent
H-H
C-C
C-H
ionic
H-O-H
NaCl
C=O
Hydrophobic
Non-polar
C-N
fat
CO-NH2
C-OH
C-S
Major Biopolymers
Carbohydrate or hydrated
carbon has the general formula
(H-C-OH)n.
H OH
H O
HO
HO
H
H
H
OH
OH
α−D-glucose
Chemical Bonding
Carbohydrate
Covalent
H-H
C-C
C-H
Polar covalent
H-O-H
ionic
NaCl
C=O
C-N
CO-NH2
C-OH
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Information Biopolymers
•
•
•
•
•
•
Nucleic acids: DNA and RNA
Protein
A variety of monomers
The order is important
A template is required
Processes of copying the template
faithfully
Information Biopolymers:
Nucleic Acids
• DNA and RNA
• Nucleic acids have a sugar-phosphate
backbone which makes them hydrophilic.
• The bases, where the variation exists, are
quite hydrophobic and buried in the centre
of the molecule.
• All 4 bases have similar chemical
properties
Information Biopolymers:
Proteins
• Made up of 20 amino acids
• They differ in their side chain
• The amino acid side chains have very
different chemical properties, unlike
nucleic acid bases.
• They can be acidic, basic, polar or
hydrophobic.
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Information Biopolymers:
Proteins
• The amino acid sequence determines the
structure which determines the function.
• Proteins make up over 50% of the cell by
dry weight.
• Proteins give the cell its shape, they form
receptors, enzymes, hormones and growth
factors, toxins, transporters and
antibodies.
How do we get from the DNA to
the protein?
• This is known as the central dogma.
• DNA, a very monotonous biopolymer
codes for a very diverse class of
biopolymers, proteins.
• How?
The Flow of Genetic
Information
Replication
DNA
DNA
Transcription
RNA
Translation
Protein
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Proteins are composed of 20 different
amino acids
alpha carbon
O
+
H3 N
CH
O-
C
Carboxyl group
R
Amino group
Sidechain or R group;
there are 20 different ones!
Two amino acids combine, by condensation
polymerization to form a dipeptide.
O
O
+
H3N
CH
C
+
H3N
+
O-
CH
C
O-
R2
R1
H2O
O
+
H3N
CH
R1
C
O
N
CH
H
R2
C
O-
Peptide bond
Peptide bond resonance
O
O-
N
N+
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The Peptide Bond
• Has 2 resonance structures
• Has a polarity (O is δ-ve and N is
δ+ve) can form H-bonds
• Has a partial double bond character
can’t rotate
Figure 5.2 Anatomy of an amino acid. Except for proline and its derivatives,
all of the amino acids commonly found in proteins possess this type of
structure.
Figure 5.3 The α-COOH and α-
NH3+ groups of two amino acids
can react with the resulting loss
of a water molecule to form a
covalent amide bond.
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The Coplanar Nature of the Peptide Bond
Six atoms of the peptide group lie in a plane!
Figure 5.4
Anatomy of an
amino acid.
Except for proline
and its
derivatives, all of
the amino acids
commonly found
in proteins
possess this type
of structure.
Amino Acid Side Chains
•
•
•
•
Hydrophobic, aliphatic and aromatic
Polar non-ionic
Acidic
Basic
Aliphatic, hydrophobic e.g.
Leucine (leu, L)
O
H2N
CH
C
OH
CH2
CH
CH3
CH3
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Aromatic, hydrophobic e.g.
Phenylalanine (phe, F)
O
H2N
CH
C
OH
CH2
Polar non-ionic amino acids
e.g. Serine (Ser, S).
O
H2N
CH
C
OH
CH2
OH
Acidic amino acids e.g.
Glutamate (Glu, E).
O
H2N
CH
C
OH
CH2
CH2
C
O
OH
13
Figure 4.8 Titration of glutamic
acid.
Basic amino acids e.g.
Lysine (Lys, K)
O
H2N
CH
C
OH
CH2
CH2
CH2
CH2
NH2
Figure 4.8 Titration of lysine.
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Chirality
H
H
COO-
H3N+
R
R
L isomer
CO – R – N spelt in
a clockwise
direction
COO+NH3
D isomer
CO – R – N spelt in
an anti-clockwise
direction
Properties of Amino Acids
• UV absorbance.
– Aromatic amino acids (tyr, phe, trp) absorb
~280 nm
• Charge.
– Acidic side chains (glu, asp) have a negative
charge at pH 7.
– Basic side chains (lys, arg and his) have a
positive charge at pH 7.
Figure 4.15
The ultraviolet
absorption spectra of
the aromatic amino
acids at pH 6. (From
Wetlaufer, D.B.,
1962. Ultraviolet
spectra of proteins
and amino acids.
Advances in Protein
Chemistry 17:303–
390.)
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Charge
•
•
•
•
•
•
Charge is related to pH.
pH is the –log10 [H+] in M
The “p” denotes power
Why use a log measurement?
It was designed before calculators
Because scientific notation is used and the
numbers are ugly!
Charge
• pH 1 is equivalent to 0.1 M [H+] e.g. 0.1 M
HCl.
• The maths:
0.1 = 10-1 log100.1=-1-log = 1
• The lower the pH the more [H+]
• pH 7 10-7 M [H+] = [OH-] neutral
• Kw = [H+]*[OH-] = 10-14
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