4BBY1013- Biochemistry
L2: Molecules of Life
• Monosaccharides are classed as aldoses (top) or ketoses (bottom) depending on their C=O
location on the linear sugar.
• In aqueous solution, 5 and 6 carbon sugars (such as glucose)
spontaneously form ring structures as the carbonyl group reacts
with a hydroxyl group (can switch between alpha and beta).
• Optical isomers/enantiomers are mirror versions of themselves.
• They are classed as either L- or D-. If the hydroxyl group furthest
from the carbonyl is on the left it is L-, if it is on the right it is D-.
• Most naturally occurring isomers are D- isomers.
• The anomeric carbon (C1) is the carbon that changes between alpha and beta glucose. This
makes alpha and beta glucose anomers. Epimers are where the functional groups of
one chiral centre differ.
• The 1,4 glycosidic bond differs depending on whether the structure is alpha or beta
glucose.
𝛼 vs β glucose
• Lipids are molecules that are water-insoluble (hydrophobic) but
soluble in organic solvents.
• To form triacylglycerols and glycerophospholipids, ester linkages
are formed between the fatty acid and the glycerol/phosphate.
• Fused alkyl rings are the basis or structural template for steroid hormones and cholesterol,
which is a steroid lipid.
• Nucleotides are made up of a nitrogenous base, phosphate and pentose sugar. In DNA the
sugar is deoxyribose sugar. whereas in RNA it is ribose sugar.
• Mono nucleotides can also have other functions such as ATP which carries energy in its
phosphoanhydride bonds.
• There are 20 amino acids common to all living organisms. Amino acids are water soluble and
electrically charged at physiological pH (pH 7).
• When it is at pH 7 it is known as a zwitterion as the amino acid has both a
positive and negative charge.
• Amino acids are linked by peptide bonds. Amino acids with an acidic R group
have a - charge at pH 7 whereas a basic R group indicates a + charge at pH 7.
L3: Energy Considerations in Biochemistry
• The first law of thermodynamics is that energy cannot be created or destroyed however it can
be transferred from one form to another.
• When bonds are made energy is released, the stronger the bond the more energy released.
• When bonds are broken energy is required, the stronger the bond the more energy required.
• The enthalpy changes (ΔH) of a reaction is energy used/created when bonds broken + bonds
made.
• If ΔH is -ve the reaction is exothermic (heat lost) whereas if ΔH is +ve the reaction is
endothermic (heat used).
• Exothermic reactions are more likely to happen as no energy is required.
Page 1 of 16
,• Entropy (S) is the level of disorder in a system. Reactions where entropy increases are
favourable.
• The second law of thermodynamics is that all processes must increase the entropy of the
universe.
• Cells use energy released by the oxidation of foods to maintain organisation but the breakdown
of food also contributes to the entropy of the universe by releasing small molecules such as CO2
and heat into the environment.
ΔG = ΔH - TΔS where T = temperature in Kelvin (K)
• If ΔG is -ve the reaction is exergonic and will occur spontaneously. If not the reaction in
endergonic and will not occur spontaneously.
• Even if a reaction is spontaneous, whether it occurs or not is based on the rate of reaction.
• The value of ΔG changes as a reaction proceeds towards equilibrium:
e.g when [Y]=[X] Y→X is -ve and X→Y is +ve
This means Y→X will occur more often. Eventually there will be a large enough excess of X over Y
due to the rate of reaction of X→Y being too slow.
Eventually the number of Y→X and X→Y reactions will be the same and the reaction has reached
equilibrium, however [Y]≠[X]
• At equilibrium there is no net change in the ratio of products:reactants meaning the ΔG for the
forward and backward reactions is 0.
• ΔG˚ is ΔG under standard conditions: [1M] of reactants and products, 25˚ (298K) and pH 7.
[A B]
ΔG = ΔG˚’ + RT ln or ΔG˚’ = -RT ln Kc at equilibrium
[A][B]
• Energetically unfavourable reactions can be achieved by coupling them to a favoured reaction
so the net energy required remains negative. Often the favoured reaction is the hydrolysis of
ATP.
e.g glutamate + NH4+ ⇌ glutamine + H2O ΔG˚’ = +15kJmol-1
ATP + H2O → ADP + Pi + H+ ΔG˚’ = -30kJmol-1
-30 + 15 = -15kJmol-1 = ΔG˚’ for the coupled reaction which is favourable.
L4: Lipids and Membranes
• Triacylglycerols can form fat droplets in aqueous environments.
• Glycerophospholipids have the same structure as triacylglycerols, except the third fatty acid is
replaced by a phosphate group.
• Often a polar head group is attached to the phosphate such as serine,
which is an amino acid and an amino alcohol.
• Other phospholipids are based on sphingosine rather
than glycerol.
• Sphingomyelin is a membrane based on sphingosine
which is found in the myelin sheaths of neurones.
• There are also glycolipids based on sphingosine such as cerebrosides which
are important in brain cell membranes. These have no phosphate and a single
Page 2 of 16
, sugar head group (glucose/galactose).
• Another example are gangliosides which are in ABO blood group determinants, which have no
phosphate and an oligosaccharide head group.
• If a fat is saturated it only has C-C bonds whereas if it is unsaturated it also contains C=C
bonds.
• Naturally occurring C=C bonds are cis which causes a kink in the chain, unlike trans.
• Linoleic acid and Linolenic acid both have 18C however one has 2 C=C bonds and the other
has 3 C=C bonds, meaning the melting point for linolenic acid is lower.
• Arachidonic acid is polyunsaturated and has 4 C=C cis bonds, causing the chain to form a
circle.
• Both bilayer and vesicle formation are energetically favourable. The minimum vesicle size is
25nm.
• Lipids can diffuse laterally at an average of 2µm/s. Movement between the two layers is rare but
can be aided by flippase enzymes.
• Kinks introduced by cis bonds cause looser packing of fatty acid tails. Cholesterol fills this
space.
• Cholesterol acts as a fluidity buffer, stiffening the membrane at high temperatures and
increasing fluidity at low temperatures.
• Cell membranes must stay in liquid crystal form (head groups loosely packs and tails
disordered).
• Cell membranes are selectively permeable, hydrophobic molecules and small uncharged polar
molecules can pass through without help.
L5: Protein Structure I
• All naturally occurring amino acids are the L- isomer (COOH on the left, NH2 on
the right, R on top). This can be remembered by CORN.
• Within the peptide bond the C-N bond is a partial double bond, meaning there
is no rotation about the C-N bond and the peptide unit is planar.
• In a polypeptide chain the α-carbons lie trans, meaning the carbons from two
different amino acids lie on opposite ends of the peptide bond.
• ɸ (phi) and Ѱ (psi) are the two rotatable bonds on either side of the α-carbons (carbons with the
R group attached).
• The α-helix is stabilised by H bonds. All α-helices are right-handed, meaning as the helix forms
the amino acids turn towards the left (like a staircase).
• The β-sheet is also stabilised by H bonds. The 2 chains that make up the sheet are anti-parallel
like DNA as they are more stable, however they can be parallel too.
• The β-turn or reverse turn is when H bonds form between the terminals of 1 polypeptide chain.
• Random coil is the name given to parts of the chain which aren’t in regular secondary structure.
• If both ɸ and Ѱ were 0˚ (cis structure) they would form a steric crash, as would many other
combinations.
• Collagen occurs as a triple helix structure which are all left-handed (not α-helices). Together they
form a right-handed superhelix. H bonds are present between the chains.
L6: Protein Structure II
• There are lots of types of super secondary structure.
• If you look at a β-sheet from the side it has a twist. If a β-sheet has 8 strands, the first will align
with the last forming a β-barrel with H bonds (e.g triose-phosphate isomerase).
Page 3 of 16
L2: Molecules of Life
• Monosaccharides are classed as aldoses (top) or ketoses (bottom) depending on their C=O
location on the linear sugar.
• In aqueous solution, 5 and 6 carbon sugars (such as glucose)
spontaneously form ring structures as the carbonyl group reacts
with a hydroxyl group (can switch between alpha and beta).
• Optical isomers/enantiomers are mirror versions of themselves.
• They are classed as either L- or D-. If the hydroxyl group furthest
from the carbonyl is on the left it is L-, if it is on the right it is D-.
• Most naturally occurring isomers are D- isomers.
• The anomeric carbon (C1) is the carbon that changes between alpha and beta glucose. This
makes alpha and beta glucose anomers. Epimers are where the functional groups of
one chiral centre differ.
• The 1,4 glycosidic bond differs depending on whether the structure is alpha or beta
glucose.
𝛼 vs β glucose
• Lipids are molecules that are water-insoluble (hydrophobic) but
soluble in organic solvents.
• To form triacylglycerols and glycerophospholipids, ester linkages
are formed between the fatty acid and the glycerol/phosphate.
• Fused alkyl rings are the basis or structural template for steroid hormones and cholesterol,
which is a steroid lipid.
• Nucleotides are made up of a nitrogenous base, phosphate and pentose sugar. In DNA the
sugar is deoxyribose sugar. whereas in RNA it is ribose sugar.
• Mono nucleotides can also have other functions such as ATP which carries energy in its
phosphoanhydride bonds.
• There are 20 amino acids common to all living organisms. Amino acids are water soluble and
electrically charged at physiological pH (pH 7).
• When it is at pH 7 it is known as a zwitterion as the amino acid has both a
positive and negative charge.
• Amino acids are linked by peptide bonds. Amino acids with an acidic R group
have a - charge at pH 7 whereas a basic R group indicates a + charge at pH 7.
L3: Energy Considerations in Biochemistry
• The first law of thermodynamics is that energy cannot be created or destroyed however it can
be transferred from one form to another.
• When bonds are made energy is released, the stronger the bond the more energy released.
• When bonds are broken energy is required, the stronger the bond the more energy required.
• The enthalpy changes (ΔH) of a reaction is energy used/created when bonds broken + bonds
made.
• If ΔH is -ve the reaction is exothermic (heat lost) whereas if ΔH is +ve the reaction is
endothermic (heat used).
• Exothermic reactions are more likely to happen as no energy is required.
Page 1 of 16
,• Entropy (S) is the level of disorder in a system. Reactions where entropy increases are
favourable.
• The second law of thermodynamics is that all processes must increase the entropy of the
universe.
• Cells use energy released by the oxidation of foods to maintain organisation but the breakdown
of food also contributes to the entropy of the universe by releasing small molecules such as CO2
and heat into the environment.
ΔG = ΔH - TΔS where T = temperature in Kelvin (K)
• If ΔG is -ve the reaction is exergonic and will occur spontaneously. If not the reaction in
endergonic and will not occur spontaneously.
• Even if a reaction is spontaneous, whether it occurs or not is based on the rate of reaction.
• The value of ΔG changes as a reaction proceeds towards equilibrium:
e.g when [Y]=[X] Y→X is -ve and X→Y is +ve
This means Y→X will occur more often. Eventually there will be a large enough excess of X over Y
due to the rate of reaction of X→Y being too slow.
Eventually the number of Y→X and X→Y reactions will be the same and the reaction has reached
equilibrium, however [Y]≠[X]
• At equilibrium there is no net change in the ratio of products:reactants meaning the ΔG for the
forward and backward reactions is 0.
• ΔG˚ is ΔG under standard conditions: [1M] of reactants and products, 25˚ (298K) and pH 7.
[A B]
ΔG = ΔG˚’ + RT ln or ΔG˚’ = -RT ln Kc at equilibrium
[A][B]
• Energetically unfavourable reactions can be achieved by coupling them to a favoured reaction
so the net energy required remains negative. Often the favoured reaction is the hydrolysis of
ATP.
e.g glutamate + NH4+ ⇌ glutamine + H2O ΔG˚’ = +15kJmol-1
ATP + H2O → ADP + Pi + H+ ΔG˚’ = -30kJmol-1
-30 + 15 = -15kJmol-1 = ΔG˚’ for the coupled reaction which is favourable.
L4: Lipids and Membranes
• Triacylglycerols can form fat droplets in aqueous environments.
• Glycerophospholipids have the same structure as triacylglycerols, except the third fatty acid is
replaced by a phosphate group.
• Often a polar head group is attached to the phosphate such as serine,
which is an amino acid and an amino alcohol.
• Other phospholipids are based on sphingosine rather
than glycerol.
• Sphingomyelin is a membrane based on sphingosine
which is found in the myelin sheaths of neurones.
• There are also glycolipids based on sphingosine such as cerebrosides which
are important in brain cell membranes. These have no phosphate and a single
Page 2 of 16
, sugar head group (glucose/galactose).
• Another example are gangliosides which are in ABO blood group determinants, which have no
phosphate and an oligosaccharide head group.
• If a fat is saturated it only has C-C bonds whereas if it is unsaturated it also contains C=C
bonds.
• Naturally occurring C=C bonds are cis which causes a kink in the chain, unlike trans.
• Linoleic acid and Linolenic acid both have 18C however one has 2 C=C bonds and the other
has 3 C=C bonds, meaning the melting point for linolenic acid is lower.
• Arachidonic acid is polyunsaturated and has 4 C=C cis bonds, causing the chain to form a
circle.
• Both bilayer and vesicle formation are energetically favourable. The minimum vesicle size is
25nm.
• Lipids can diffuse laterally at an average of 2µm/s. Movement between the two layers is rare but
can be aided by flippase enzymes.
• Kinks introduced by cis bonds cause looser packing of fatty acid tails. Cholesterol fills this
space.
• Cholesterol acts as a fluidity buffer, stiffening the membrane at high temperatures and
increasing fluidity at low temperatures.
• Cell membranes must stay in liquid crystal form (head groups loosely packs and tails
disordered).
• Cell membranes are selectively permeable, hydrophobic molecules and small uncharged polar
molecules can pass through without help.
L5: Protein Structure I
• All naturally occurring amino acids are the L- isomer (COOH on the left, NH2 on
the right, R on top). This can be remembered by CORN.
• Within the peptide bond the C-N bond is a partial double bond, meaning there
is no rotation about the C-N bond and the peptide unit is planar.
• In a polypeptide chain the α-carbons lie trans, meaning the carbons from two
different amino acids lie on opposite ends of the peptide bond.
• ɸ (phi) and Ѱ (psi) are the two rotatable bonds on either side of the α-carbons (carbons with the
R group attached).
• The α-helix is stabilised by H bonds. All α-helices are right-handed, meaning as the helix forms
the amino acids turn towards the left (like a staircase).
• The β-sheet is also stabilised by H bonds. The 2 chains that make up the sheet are anti-parallel
like DNA as they are more stable, however they can be parallel too.
• The β-turn or reverse turn is when H bonds form between the terminals of 1 polypeptide chain.
• Random coil is the name given to parts of the chain which aren’t in regular secondary structure.
• If both ɸ and Ѱ were 0˚ (cis structure) they would form a steric crash, as would many other
combinations.
• Collagen occurs as a triple helix structure which are all left-handed (not α-helices). Together they
form a right-handed superhelix. H bonds are present between the chains.
L6: Protein Structure II
• There are lots of types of super secondary structure.
• If you look at a β-sheet from the side it has a twist. If a β-sheet has 8 strands, the first will align
with the last forming a β-barrel with H bonds (e.g triose-phosphate isomerase).
Page 3 of 16
