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MBLG1001 Lecture 2
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COURSE: MBLG1001
Lecturer: Dale Hancock
Title of Lecture: Molecules of Life: Proteins
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MBLG1001 Lecture 2
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MBLG Lecture 2: Molecules of Life: Proteins
I am also assuming that you are all well versed in the nature of chemical bonding so I won’t bore
you by going over it too much. Let’s consider the extremes:
At one end of the spectrum you have the perfect coupling where each atom shares its
electron with the other. This perfectly equal, harmonious relationship is, like couples in real life,
quite rare. The quintessential example given is H2. Both atoms are equal and very small. They both
share their only electron equally so the charge is evenly distributed. The other examples of even
sharing are the carbon – carbon bond and the carbon-hydrogen bond. Note that both carbon and
hydrogen have a half-full (or half-empty depending on your state of mind) outer or valence shell of
electrons.
At the other end of the spectrum is the completely ionic bond, characterized by NaCl.
This pair of atoms is such a dysfunctional couple that one atom (Cl) grabs the electron from the
other atom (Na) and hogs it. There is no sharing in this relationship; one partner completely takes
the electron from the other. Note that the Cl has a full outer shell bar one electron and the Na has
only one electron in its outer shell. This makes both these atoms incredibly reactive; one wants to
lose its only valence electron and the other wants to take it. In relationship terms it is completely
one sided but the analogy falls down here because both atoms are satisfied with the arrangement;
two very reactive elements form a compound, common table salt, which is very stable. In solution
this compound exists as Na+ and Cl- ions. These two ions are in atom heaven; they have full outer
shells!
It is the in-between coupling (sometimes termed polar covalent) that is often interesting to
molecular biologists and biochemists; bonds which show some covalent and some ionic character.
The two atoms in the partnership share the bonding electron(s), but not evenly. One of the atoms
involved in the coupling has a stronger affinity for the electron(s), hence we generate a partial
charge or dipole, denoted as delta positive (δ+) or delta negative (δ-). It is not a complete swap and
no true ion forms. But it gives the compound a polar character. The best and most important
example from a life scientist’s point of view is water. The oxygen is very electronegative (that
means it has a great affinity for electrons in any bonding. It has 6 electrons in its outer shell; of
which 2 pairs never participate in bonding. It only needs another 2 for a complete outer shell:
nirvana or heaven for atoms). The hydrogen-oxygen bond has a dipole so the water has a delta
negative charge at the oxygen and a delta positive charge at the hydrogen. Water is a very polar
solvent and this property has immense significance for the workings of the cell. Molecules which
also have a dipole will be attracted to the water and will be soluble in it. They are termed
hydrophilic (or water loving) or polar. Molecules with no dipole are not attracted to the water and
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are much less soluble in aqueous solutions. They are termed hydrophobic (or water hating) or
non-polar.
Two common compounds found in everyday life display these properties; fat (hydrophobic) and
polysaccharides (hydrophilic). Both these compounds are very important polymers (VIPs) for life.
Let’s briefly consider these two polymers to see what gives them their different solubility
properties.
Fats or more scientifically lipid has the general formula (-CH2-)n. Examples are fatty acids such
as palmitic acid (where n=15) with a –COOH group attached at one end. Three of these fatty acids
esterify to a glycerol molecule to form triglycerides. Lipids are very hydrophobic, the long
carbon chains are very non-polar. They consist of C-C and C-H bonds; both of which are evenly
sharing covalent bonds. The long chains are known as aliphatic chains; the longer this chain the
more hydrophobic.
This polymer is made up of the same monomer, it has repeating units and hence we can give a
general formula.
Carbohydrate or hydrated carbon has the general formula (H-C-OH)n. Polymer examples are
cellulose, starch and glycogen (fuel for your body). The polymer has the general name
polysaccharide (many saccharides), the monomer is a saccharide or “sugar”. Sugars with 5 or 6
carbons readily cyclise forming ring structures, the most common being glucose C6H12O6 . Sugars
are also components of nucleic acids, hence I would like to mention one property of sugars that
impacts on the properties of DNA and RNA. Sugars are very water soluble or hydrophilic. The –
OH groups (remember the O-H bond in water) are responsible for this property.
Carbohydrate polymers are also made up of repeating units.
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Now let’s introduce the next 2 classes of biopolymer: nucleic acids and protein. These polymers
differ from the others in that a number of different types of the monomer are joined to make
them up AND THE ORDER IS IMPORTANT. When we refer to genetic information transfer
this is the information that is transferred; the order of the monomer. To have a sequence dependent
polymer you must have a template. There must be some way of copying that template and
ensuring that the template copy is accurate. The cell goes to extraordinary lengths to ensure the
accuracy of the synthesis of DNA, RNA and protein, particularly DNA.
Let’s see why we need to be so fussy about order or is the cell just anal!!
I will briefly consider DNA and RNA now and return to these polymers later. Both DNA and
RNA are nucleic acids, named thus as they were first isolated from the nucleus and they were
acidic. They are composed of four monomers (I am sure you know this from high school
biology!!). These monomers, however, are made up of more than just the base. Each monomer
contains a sugar moiety, either ribose or deoxyribose, and a phosphate. These groups confer on
nucleic acids some of their familiar chemical properties; water solubility and acidity. Both nucleic
acids are composed of a repeating sugar phosphate backbone. The variation, and hence
information, comes about from the order of the 4 bases. These bases are attached to the sugar and
‘hang off’ the backbone.
Proteins are polymers made up of amino acids. There are 20 different amino acids; they differ in
the side chain. We have side chains that are hydrophobic, aromatic, polar, acidic and basic. The
type of side chains and their sequence determines many of the properties of the protein. Some side
chains are attracted to each other; some are repelled. Some form weak bonds with each other.
Proteins are found everywhere in your cell. They function to hold the shape of the cell
(cytoskeleton), receptors, transporters carrying molecules in and out of the cell and most
importantly enzymes. They make up whole classes of hormones and growth factors, toxins and
antibodies. These molecules are the doing molecules, definitely the molecules of life. Some
proteins are hydrophobic and are synthesized embedded in membranes; some are water soluble,
located in the cytosol. The incredible diversity of protein structures and hence their function is
made possible by having 20 different amino acids and by maintaining the order of these amino
acids each time a new protein molecule is synthesized.
How is the order determined and maintained?
In eukaryotic cells transcription and replication are carried out in the nucleus and translation is
carried out in the cytoplasm. In prokaryotes, which have no organelles to compartmentalize the
processes, transcription is tightly coupled to translation. One follows the other almost
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simultaneously. Replication is carried out by DNA polymerases, transcription by RNA
polymerases and translation is performed on ribosomes.
How do amino acids combine to form proteins?
To understand what’s going on lets look at your typical amino acid. It has the following general
structure:
alpha carbon
O
+
H3N
CH
C
O-
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
The peptide bond is a strong covalent bond with some unique properties. Amino acids are added in
a sequential process to the growing peptide chain, at the carboxyl (or C-terminal) end. The
incorporated portion of the amino acid is termed an amino acid residue (some of the monomer has
been lost in the polymerization). The mRNA is the template for translation; this is copied from the
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DNA. Notice as the polypeptide grows that you have a “common” backbone, irrespective of the
sequence; it is only the side chain “hanging off” the backbone where the variation occurs. It has a
defined beginning, termed the N terminal and a chemically different end, the C terminal. The
protein then must be folded, often modified (glycosylated, phosphorylated etc) then transported to
the correct location before we have a fully functional protein. All the enzymes you will meet in the
up-coming lectures will have undergone this process.
The peptide bond: The double bond between the oxygen and the carbon resonates between the
C=O and the C=N. This resonance gives the C-N bond a partial double bond character. It is
considered to exist as C=O for 60% of the time and C=N for the remaining 40%. Once the peptide
bond is formed the carboxyl group of amino acid 1 loses its charge as does the amino group of the
second amino acid. The bond formed is an amide bond, having the dipole properties of an amide
ie. the N has a net positive charge (δ+ve) and the carbonyl C (C=O) has a net negative charge (δve). The partial double bond character of the peptide bond restricts rotation and has a big impact
on the 3-D conformations the protein can exist as. The partial charge or dipole of the peptide bond
allows for H-bonding between different portions of the backbone.
O
O-
N
N+
Let’s now consider the different side chains available for protein synthesis.
Recapping…..There are 20 amino acids found in all naturally occurring proteins. These vary in the
side chain or R group attached. We will divide them up by their chemical properties.
alpha carbon
O
+
H3N
Amino group
CH
R
C
O-
Carboxyl group
Sidechain or R group;
there are 20 different ones!
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Some of the amino acid side chains can be modified post translationally. The types of
modification which can occur include: phosphorylation, hydroxylation, glycosylation, addition of
lipid moiety. These modifications can be carried out for regulation, solubility, anchoring or for
structural reasons.
Amino acid side chains are grouped by their chemical properties as follows:
•
•
•
•
Hydrophobic, including aliphatic and aromatic side chains
Polar non-ionic
Acidic
Basic
Rather than go through all 20 side chains I will show you a representative from each group. The
structures of each of the 20 side chains are presented in the lecture supplement in the front of your
resource manual. The 3 letter and 1 letter code is also quoted. You need to be familiar with the 3
letter code.
O
Hydrophobic aliphatic amino acids e.g. Leucine, (Leu, L).
Leucine has a branched aliphatic (-CH2-) chain which has no dipole
(C-C and C-H bonds share their electrons very evenly) making it quite
hydrophobic (insoluble in water). It does not participate in H-bonding
or ionic interactions. It does, however, interact with other hydrophobic
side chains and is often found buried in the interior of water soluble
proteins or exposed on the outside of membrane embedded portions of
proteins.
H2N
CH
C
OH
CH2
CH
CH3
CH3
O
H2N
CH
CH2
C
Aromatic amino acids e.g. Phenylalanine (Phe, F).
OH Phenylalanine contains an aromatic ring in its side chain which makes
it, not only hydrophobic but also confers UV absorption properties on
the side chain. Proteins absorb UV light at ~280 nm as a result of the
aromatic side chains: tyrosine, tryptophan and phenylalanine (as well as
cysteine and histidine to a lesser extent). Phenylalanine and tryptophan
are quite hydrophobic. Tyrosine, although it contains the aromatic ring,
has a hydroxyl attached. This –OH is polar and actually dissociates at
high pHs.
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O
Polar non-ionic amino acids e.g. Serine (Ser, S). The side
chain of serine contains an –OH which gives the side chain its polar
properties. Except in very rare circumstances (active site of serine
proteases) the proton does not dissociate from O but its polarity
facilitates H-bonding. The serine side chain acts as an H-bond donor.
H2N
H2N
CH
C
CH2
OH
OH
Acidic amino acids e.g. Glutamate (Glu, E). These side chains
contain a carboxylic acid which dissociates with a pKa of ~4. At neutral
OH
pH these side chains carry a negative charge, enabling ionic interactions
with basic (positively charged) side chains. They are hydrophilic and
often found on the outside of water soluble proteins. The dissociation
follows the general formula: HA ↔ H+ + A-
CH2
C
C
CH2
It can also be phosphorylated post translationally; a common
mechanism for enzyme regulation.
O
CH
O
OH
O
H2N
CH
C
OH
Basic amino acids e.g. Lysine (Lys, K). This group is
characterized by side chains with a group containing a protonated N.
The dissociation follows the general formula: BH+ ↔ B + H+. At
physiological pH these side chains carry a positive charge and are often
found on DNA binding proteins, interacting with the sugar phosphate
backbone.
CH2
CH2
CH2
CH2
NH2
Amino acids (19 of the 20) have a chiral carbon (the alpha carbon), having both a D and an L
isomer. Some have more than one chiral carbon. Which amino acid has no chiral carbon? Which
have 2 chiral carbons? Check the structures in the supplement.
All naturally occurring proteins contain only L amino acids, except for a few nasty toxins e.g.
actinomycin D. How to distinguish L from D?
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H
C
+
H3N
COO-
H
R
R
L isomer
CO – R – N spelt in
a clockwise
COO-
C
+
NH3
D isomer
CO – R – N spelt in
an anti-clockwise
Important properties of amino acids.
UV absorption.
Certain side chains containing aromatic rings eg tyrosine, tryptophan and to a lesser extent
phenylalanine absorb UV light strongly, with an absorption maximum of ~280 nm. This property
is often exploited when detecting proteins experimentally, providing a quick and relatively
inexpensive detection method which doesn’t destroy the sample.
Charge.
All amino acids contain charged groups as part of their basic structure. The amino group and the
carboxyl group attached to the alpha carbon are charged at certain pHs. Let’s consider the charge
pattern of a standard simple amino acid, glycine.