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Molecules of Life: Biopolymers

Dr. Dale Hancock

D.Hancock@mmb.usyd.edu.au

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