Molecules of Life: Biopolymers - University of Sydney...1 Molecules of Life: Biopolymers Dr. Dale...
Transcript of Molecules of Life: Biopolymers - University of Sydney...1 Molecules of Life: Biopolymers Dr. Dale...
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Molecules of Life: Biopolymers
Dr. Dale Hancock
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.
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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!
e-
e-
0.74 Å
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Carbon
+ e-
e-
e-
e-
e-
e-
+ e-
e-
e-
e-
e-
e-
The electronic configuration of Carbon
1s2
2s2
2px 2py 2pz
1st shell
2nd shell
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Carbon as it bonds….
1s2
2s 2px 2py 2pz
1st shell
2nd shell
Carbon as it bonds….
1s2
2s 2px 2py 2pz
1st shell
2nd shell
To maximise bonding options
sp3 orbital hybridisation
4 equivalent bonds…..tetrahedral
Tetrahedral Carbon
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Chemical Bonding
Covalent
H-HC-CC-H
Chemical Bonding
Covalent ionic
H-HC-CC-H
NaClNa+ Cl-In solution
Chemical Bonding
Covalent ionic
H-HC-CC-H
NaClNa+ Cl-In solution
Polar covalent
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Water
Chemical Bonding
Covalent ionic
H-HC-CC-H
Polar covalent
NaClH-O-H
C=O
C-N
CO-NH2
C-OH
Major Biopolymers
H3C
CH2
H2C
CH2
H2C
CH2
H2C
CH2
H2C
CH2
H2C
CH2
H2C
CH2
H2C
CH2
COOH
Fats or more scientifically lipid has the
general formula (-CH2-)n.
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Chemical Bonding
Covalent ionic
H-HC-CC-H
Polar covalent
NaClH-O-H
C=O
C-N
CO-NH2
C-OH
C-S
HydrophobicNon-polar
fat
Major Biopolymers
Carbohydrate or hydrated carbon has the general formula
(H-C-OH)n.
O
H
HO
H
HO
H
OH
OHHH
OH
α−D-glucose
Chemical Bonding
Covalent ionic
H-HC-CC-H
Polar covalent
NaClH-O-H
C=O
C-N
CO-NH2
C-OH
Carbohydrate
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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
DNA
RNA
Protein
DNA
Transcription
Translation
Replication
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Proteins are composed of 20 different amino acids
+H3N CH C
R
O-
O
Amino group
alpha carbon
Carboxyl group
Sidechain or R group; there are 20 different ones!
Two amino acids combine, by condensation
polymerization to form a dipeptide.
+H3N CH C
R1
O-
O
+H3N CH C
R2
O-
O
+
+H3N CH C
R1
O
N CH C
R2
O-
O
H
H2O
Peptide bond
Peptide bond resonance
N
O
N+
O-
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The Peptide Bond
• Has 2 resonance structures
• Has a polarity (O is δδδδ-ve and N is δδδδ+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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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.
The Coplanar Nature of the Peptide Bond
Six atoms of the peptide group lie in a plane!
Amino Acid Side Chains
• Hydrophobic, aliphatic and aromatic
• Polar non-ionic
• Acidic
• Basic
Aliphatic, hydrophobic e.g. Leucine (leu, L)
H2N CH C
CH2
OH
O
CH CH3
CH3
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Aromatic, hydrophobic e.g. Phenylalanine (phe, F)
H2N CH C
CH2
OH
O
Polar non-ionic amino acids e.g. Serine (Ser, S).
H2N CH C
CH2
OH
O
OH
Acidic amino acids e.g. Glutamate (Glu, E).
H2N CH C
CH2
OH
O
CH2
C
OH
O
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Figure 4.8 Titration of glutamic
acid.
Basic amino acids e.g. Lysine (Lys, K)
H2N CH C
CH2
OH
O
CH2
CH2
CH2
NH2
Figure 4.8 Titration of lysine.
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Chirality
L isomer CO – R – N spelt in a clockwise
direction
D isomerCO – R – N spelt in an anti-clockwise
direction
H
H3N+COO-
R
H
R+NH3
COO-
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