Module 1 Biological Molecules

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Module 1Biological Molecules

• F212 Molecules, biodiversity, food and health

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Module 1 Topics

• Biological molecules
• Water
• Intro to biological molecules
• Proteins
• Carbohydrates
• Lipids
• Practical biochemistry

• Nucleic acids
• Enzymes

3
Learning Outcomes

• describe how hydrogen bonding occurs between
  water molecules, and relate this, and other
  properties of water, to the roles of water in
  living organisms

4
Definitions

• Covalent bond
• Formed when atoms share electrons
• Strong bonds
• Hydrogen bond
• Weak interaction that occurs when a negatively
  charged atom is bonded to a positively charged
  hydrogen

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Water

• 60 70 of mammals
• About 90 of plants
• Life originated in water
• Good solvent
• What else do you know about little old dihydrogen
  monoxide (DHMO)

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Water is a liquid

• A polar molecule
• Made up of two positively charged hydrogen atoms
  and one negatively charged oxygen
• Covalent bonds form between oxygen and hydrogen
  with electrons shared between them.
• Hydrogen bonds form between water molecules
• Up to four may form clusters which break and
  reform all the time

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Water molecule
8
Hydrogen Bonds in water
Hydrogen bonds
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Key features of water

• Key features of water as a constituent of living
  organisms
• Good solvent
• High specific heat capacity
• High latent heat of vaporisation
• High cohesion
• Reactive
• Incompressibility

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Learning Outcomes

• To be able to
• Define metabolism
• State the functions of biological molecules
• Name monomers and polymers of carbohydrates,
  fats, proteins and nucleic acids
• Describe general features of condensation and
  hydrolysis reaction

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Biological Molecules

• Molecular biology
• the study of structure and functioning of
  biological molecules.
• Metabolism
• sum total of all biochemical reactions in the
  body.

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Nutrients and Health

• To maintain a healthy body
• Carbohydrates
• Lipids
• Proteins
• Vitamins and minerals
• Nucleic acid
• Water
• fibre

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Key Biological Molecules

• There are 4 key biological molecules
• Carbohydrates
• lipids
• proteins
• nucleic acids

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Building blocks of life

• 4 most common elements in the living organisms
• hydrogen
• carbon
• oxygen
• nitrogen

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Biochemicals and bonds

• Covalent bonds join atoms together to form
  molecules
• Carbon is able to make 4 covalent bonds
• Carbon can bond to form chains or rings with
  other atoms bonded to the chain
• Carbon can also form double bonds
• E.g. CC or CO

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Polymers

• poly means many polymers
• Macromolecules are made up of repeating subunits
  that are joined end to end, they are easy to make
  as the same reaction is repeated many times.
• Polymerisation is the making of polymers.

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Macromolecules
Macromolecule Subunit (monomer)
polysaccharide monosaccharide
proteins amino acids
nucleic acids nucleotides
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Metabolism

• Metabolism is the sum of all of the reactions
  that take place within organisms
• Anabolism
• Build up of larger, more complex molecules from
  smaller, simpler ones
• This process requires energy
• Catabolism
• The breakdown of complex molecules into simpler
  ones
• This process releases energy

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Condensation reactions

• In a condensation reaction
• A water molecule is released
• A new covalent bond is formed
• A larger molecule is formed by bonding together
  of smaller molecules

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Hydrolysis Reactions

• In hydrolysis reactions
• A water molecule is used
• A covalent bond is broken
• Smaller molecules are formed by the splitting of
  a larger molecule

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Hydrolysis and condensation
OH
HO
CONDENSATION
HYDROLYSIS
O
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Learning Outcomes

• describe, with the aid of diagrams, the structure
  of an amino acids
• describe, with the aid of diagrams, the formation
  and breakage of peptide bonds in the synthesis
  and hydrolysis of dipeptides and polypeptides

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Introduction to protein

• 50 of the dry mass of cells is protein
• Important functions include
• Cell membranes
• Haemoglobin
• Anti-bodies
• Enzymes
• Keratin (hair and skin)
• collagen

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Structure of proteins

• All proteins are made up of the same basic
  components ? amino acids
• There are 20 different amino acids, which alter
  by having different residual groups (R groups)
• A single chain of amino acids makes a polypeptide

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Structure of an amino acid

• Amino acids contain
• Amine group (NH2)
• Carboxylic acid group (COOH)
• Joined at the same C atom

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Structure of an amino acid
R group varies in different amino acids
R
H
O
C
C
N
OH
H
H
Amine group
Carboxyl group
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TEST TIME

• Build an amino acid using the molymod models
• Glycine is an amino acid where the R group is
  hydrogen change you molecule into glycine
• Build a dipeptide using the molymod models

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Different Amino Acids

• Glycine R group H
• Alanine R group CH3
• Valine R group C3H7
• You will be expected to learn how to draw the
  basic structure of an amino acid. Remember that
  each Amino acid has its own specific R group

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Learning Outcomes

• explain, with the aid of diagrams, the term
  primary structure
• explain, with the aid of diagrams, the term
  secondary structure with reference to hydrogen
  bonding

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Peptide bond
R
O
H
R
O
H
N
C
C
N
C
C
H
H
H
OH
Peptide bond
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Building a polypeptide

• Peptide bonds are formed in condensation
  reactions
• Primary structure
• The primary structure of a polypeptide is its
  amino acid sequence
• This is determined by the gene that codes for the
  polypeptide

Peptide Bond
Amino acid
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Secondary Structure

• Polypeptides become twisted or coiled
• They fold into one of two structures
• Alpha helix (right handed helix)
• Beta-pleated sheet
• Hydrogen bonds hold coils in place
• Weak but give stability to the parts of a protein
  molecule.

C
O
H
N
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Learning Outcomes

• explain, with the aid of diagrams, the term
  tertiary structure with reference to
  hydrophobic and hydrophilic interactions,
  disulphide bonds and ionic interactions

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Tertiary Structure

• Folding of the polypeptide to give a more complex
  3-D shape, the shape is specific to the function
  of the polypeptide.
• Examples
• Hormone must fit into the hormone receptor in a
  target cell
• Enzymes have a complementary active site to its
  substrate

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Tertiary Structure - bonds

• Four types of bond help to hold the folded
  proteins in their precise shape.
• Hydrogen Bonds
• Disulphide bonds
• Ionic bonds
• Hydrophobic interactions

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Hydrogen Bonds

• Between polar groups
• Electronegative oxygen atoms of the CO
• Electropositive H atoms on either the OH or NH
  groups.

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Disulphide bonds

• Between sulfur-containing R groups of the amino
  acid cysteine.
• Covalent bonds
• Form strong links which make the tertiary protein
  structure very stable.
• This bond can be broken by reducing agents

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Ionic Bonds

• Between R groups, which ionise to form positively
  and negatively charged groups that attract each
  other.

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Hydrophobic Interactions

• These are interactions between the non-polar side
  chains of a protein molecule.
• The bond forms between non-polar, hydrophobic R
  groups on the amino acids.
• Once the two hydrophobic molecules are close
  together the interaction is reinforced by Van der
  Waals attractions (which provide the weak bond).

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Van der Waals attractions

• Electrons are always in motion, and are not
  always evenly distributed about a molecule.
• This results in areas of positive and negative
  charge, which are continuously changing, and
  enables molecules to stick to one another.

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Denaturing Protein

• The Polar R groups of proteins interact with
  water forming hydrogen bonds that face outwards,
  This creates a hydrophobic core to the molecule
• When proteins are heated these bonds break, the
  tertiary structure changes and the protein does
  not function.
• The destruction of shape or loss of function is
  denaturation.

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Denaturing Proteins

• Frying an egg

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Learning Outcomes

• explain, with the aid of diagrams, the term
  quaternary structure, with reference to the
  structure of haemoglobin

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Quaternary Structure

• Association of different polypeptide chains
  bonded together to form intricate shapes
• Sometimes contain prosthetic groups, which are a
  permanent part of a protein molecule but not made
  of amino acids

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Quaternary Structure

• Globular protein
• Molecules curl up into a ball shape
• Examples myoglobin, haemoglobin
• Metabolic roles
• Fibrous Proteins
• Form long strands
• Usually insoluble
• Have a structural role
• Examples keratin, collagen

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Haemoglobin

• Function oxygen carrying pigment found in red
  blood cells
• Structure
• 4 polypeptides
• 2 x a-globin
• 2 x ß-globin
• Each polypeptide has a 3o structure stabilised by
  hydrophobic interactions in the centre
• In the middle each polypeptide in a haem group

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OK so lets summarise proteins
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Protein structure and diversity

• It is difficult to describe in a simple sentence
  the role of proteins.
• when there is something to do, it is a protein
  that does it.
• Therefore proteins are
• important
• numerous
• very diverse
• very complex,
• able to perform actions and reactions under some
  circumstances

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Some examples of proteins

• Antibodies
• they recognise molecules of invading organisms.
• Receptors
• part of the cell membrane, they recognise other
  proteins, or chemicals, and inform the cell...
• Enzymes
• assemble or digest.
• Neurotransmitters and some hormones
• Trigger the receptors...
• Channels and pores
• holes in the cell membrane

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Summary of levels of protein structure

• Primary Structure
• Amino acids linked in a linear sequence
• Secondary Structure
• folding or coiling of polypeptide
• Tertiary structure
• Folding of polypeptide by disulphide bonds, ionic
  bonds, hydrogen bonds or hydrophobic interactions
• Quaternary structure
• Two or more polypeptides bonded together

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Learning Outcomes

• describe, with the aid of diagrams, the structure
  of a collagen molecule
• compare the structure and function of haemoglobin
  (and example of a globular protein) and collagen
  (an example of a fibrous protein)

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Collagen (a fibrous protein)

• Collagen is found in skin, teeth, tendons,
  cartilage, bones and the walls of blood vessels,
  making it an important structural protein.

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Structure of collagen

• 3 identical polypeptide chains wound into a
  triple helix this is a left-handed helix.
• Each polypeptide is about 1000 amino acids long
• Primary structure
• Every 3 amino acids glycine

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Collagen

• Sequences of polypeptide chains are staggered so
  that glycine is found at every position along the
  triple helix.
• The three polypeptide chains are held together by
  hydrogen bonds.
• Adjacent molecules of collagen are held together
  by covalent bonds formed between the carboxyl
  group of one amino acid and the amine group of
  another.

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? Pupil Activity ?

• Using your brains and what you have been taught
• compare the structure and function of haemoglobin
  and collagen
• Try to make a bullet point list of at least 10
  things

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Collagen vs Haemoglobin

• Collagen
• Repeating sequence of amino acids
• Most of molecule has left handed helix structures
• Does not contain prosthetic group
• Insoluble in water
• Metabolically unreactive
• Structural role

• Haemoglobin
• Precise 1o structure
• 2o structure wound into alpha helix
• Contains prosthetic group
• Soluble in water
• Metabolically reactive

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Learning Outcomes

• describe, with the aid of diagrams, the molecular
  structure of alpha-glucose as an example of a
  monosaccharide carbohydrate
• state the structural difference between alpha and
  beta glucose

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Carbohydrates

• contain carbon, hydrogen oxygen
• organic compounds
• general formula Cx(H2O)y
• glucose C6H12O6
• 3 main groups
• monosaccharides
• disaccharides
• polysaccharides

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Monosaccharides

• dissolve easily in water to form sweet solution
• general formula (CH2O)n, where n is the number of
  carbons
• 3 main types
• Trioses (3C)
• Pentoses (5C)
• Hexoses (6C)

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Glucose - a hexose

• Glucose is made of a chain of atoms long enough
  to close up upon itself and form a stable ring
  structure.
• Carbon atom 1 (1C) joins to the O on 5C.
• The six sided structure formed is known as a
  pyranose ring.

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Chain for a glucose
O
H
1C
H
2C
OH
3C
OH
H
4C
OH
H
OH
5C
H
6CH2OH
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a-glucose ring form
6CH2OH
5C
O
H
H
H
4C
1C
OH
H
3C
2C
OH
OH
H
OH
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Making the drawing easier
H
O
OH
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Glucose a hexose

• Isomers
• possess the same molecular formula but differ in
  arrangement of atoms.
• a-glucose and ß-glucose are isomers of glucose.
• Depending on whether the OH of 1C is above or
  below the plane of the ring.

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The Isomers

• a-glucose

• ß-glucose

OH
H
O
O
H
OH
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Learning Outcomes

• describe, with the aid of diagrams, the formation
  and breakage of glycosidic bonds in the synthesis
  and hydrolysis of a disaccharide (maltose) and a
  polysaccharide (amylose)

67
Disaccharides and the Glycosidic Bond

• Monosaccharides combine in pairs to give a
  disaccharide, this involves the loss of a single
  water molecule
• This reaction is called condensation
• The bond formed is known as a glycosidic bond.
• To break a disaccharide the addition of water is
  needed, this reaction is called hydrolysis.

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Formation and breakage of the glycosidic bond
69
Polysaccharides

• Final molecules maybe 1000s of monosaccharides,
  the size of these molecules make them insoluble.
• Polysaccharides are NOT sugars
• The most important polysaccharides are built up
  entirely of glucose molecules.
• These are starch, glycogen and cellulose.

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Learning Outcomes

• describe, with the aid of diagrams, the structure
  of starch
• describe, with the aid of diagrams, the structure
  of glycogen

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Starch

• A mixture of two substances amylose and
  amylopectin.
• Starch granules are insoluble in water.
• The form of carbohydrate used for storage in
  plants.
• Starch grains build up in chloroplasts, or in
  storage organs such as potato tubers.

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Amylose

• Long unbranching chains
• 1-4 glycosidic bonds
• formed by condensation reactions.
• The chains curve and coil into helical structures.

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Amylopectin

• 1,4 linked a-glucose molecules form chains
• shorter
• branch out to the sides.
• The branches form by 1-6 linkages

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Comparison of the structure of amylose and
amylopectin molecules
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Glycogen

• The form in which carbohydrate is stored in the
  animal body.
• Glucose is converted to glycogen in the liver and
  muscles,
• it is kept until required
• then it is broken down again into glucose.
• Formed by a-glucose molecules joining in 1-4 and
  1-6 links
• There are more branches containing a smaller
  number of glucose molecules than amylopectin

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Structure of glycogen
77
Starch and glycogen

• Starch and Glycogen are energy storage molecules
• which take up little space due to their compact
  shapes
• They help to prevent too high concentrations of
  glucose in cells.

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Learning outcomes

• describe, with the aid of diagrams, the structure
  of cellulose

79
Cellulose

• Most abundant organic molecule on the planet due
  to its presence in cell walls.
• Slow rate of breakdown in nature.
• Polymer of about 10,000 ß-glucose molecules in a
  long unbranched chain.
• Many chains run parallel to each other and have
  cross linkages between them, giving increased
  stability.
• hydrogen bonds form these links between chains,
  which collectively give the structure increased
  strength.

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Structure of cellulose
81
Cellulose

• To join together one ß-glucose molecule must be
  rotated at 1800 relative to the other.
• Successive glucose molecules are linked at 1800
  to each other.
• Cellulose molecules become tightly cross-linked
  with each other to form bundles called micro
  fibrils.
• Micro fibrils form cellulose fibres by hydrogen
  bonding giving a high tensile strength similar to
  steel.

82
Learning Outcomes

• compare and contrast the structure and functions
  of starch (amylose) and cellulose
• explain how the structures of glucose, starch
  (amylose), glycogen and cellulose molecules
  relate to their functions in living organisms

83
Comparing polysaccharides
Characteristic amylose amylopectin glycogen cellulose
Found in
Found as
Function
Monomer
Bonds
chain
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Homework Question

• Discuss the structures of glucose, starch,
  glycogen and cellulose in relation to their
  functions include diagrams to illustrate your
  answer

85
Learning outcomes

• compare, with the aid of diagrams, the structure
  of a triglyceride and a phospholipids
• explain how the structure of a triglyceride,
  phospholipids and cholesterol molecules relate to
  their functions in living organisms

86
Lipids are not polymers

• Large molecules
• few oxygen atoms
• many carbon and hydrogen atoms
• hydrophobic
• Less dense than water

87
Lipids

• Two important groups
• Triglycerides
• Fats solid at room temperature
• Oils liquid at room temperature
• phospholipids

88
Lipids - functions

• A source of energy
• Store of energy (adipose tissues)
• Biological membranes
• Thermal insulators / insulation
• Buoyancy
• Protection
• Cuticle of a leaf
• Internal organs
• Metabolic source of water
• hormones

89
Glycerol and fatty acids

• glycerol

• Fatty acid

O
C
H
HO
90
Fatty Acids

• Fatty acids have
• an acid group at one end (COOH)
• Hydrocarbon chain (2 ? 20 carbons long)
• Fatty acids can be
• Saturated
• Unsaturated

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Saturated fatty acid

• All possible bonds are made with hydrogen

O
C
H
HO
92
Unsaturated fatty acid

• One or more double bond between carbon atoms

O
C
C
C
H
HO
H
H
93
Saturated and unsaturated fatty acids

• Polyunsaturated
• more than one double bond
• Monounsaturated
• only one double bond
• Animal lipids are often saturated and occur as
  fats
• plant lipids are often unsaturated and occur as
  oils

94
Triglycerides

• Most common form of lipid
• Combination of 3 fatty acid molecules and one
  glycerol molecule.
• Glycerol is a type of alcohol
• Fatty acids are organic molecules with a COOH
  group attached to a hydrocarbon tail.

95
Triglycerides

• Each of the glycerol molecules 3 -OH groups
  reacts with the carboxyl group of a fatty acid.
• This is a condensation reaction, and an ester
  bond is established.

96
Structure of a triglyceride

• Glycerol 3 fatty acids

O
H
H
HO
C
C
OH
O
C
C
H
OH
HO
O
C
C
H
OH
HO
H
97
Condensation reaction and formation of an ester
bond
Ester bond
O
H
H
C
C
O
O
C
C
H
O
O
C
C
H
O
H
98
Triglycerides

• Triglycerides are
• insoluble in water,
• soluble in some organic solvents, e.g. ether or
  ethanol.
• non-polar
• hydrophobic.

99
Roles of triglycerides

• Energy reserve
• Insulator against heat loss
• Buoyancy
• Protection (vital organs)
• Metabolic source of water.

100
Phospholipids

• Special type of lipid
• one of the fatty acid groups is replaced by
  phosphoric acid.
• phosphoric acid is hydrophilic (attracts water)
• Biological significance of this molecule is its
  role in the cell membrane.

101
Simplified structure of phospholipid
102
Structure of a phopholipid
O
Phosphate group
O
P
H
OH
H
C
O
C
C
H
O
O
C
C
H
O
H
103
Structure of a phospholipid
104
Cholesterol - structure

• Small molecule
• -OH group is polar
• 4 carbon rings and hydrocarbon tail are non polar

105
Cholesterol - Structure
106
Cholesterol - function

• Found in biological membranes
• Steroids e.g. testosterone, oestrogen and
  progesterone are made from cholesterol
• Excess cholesterol
• Form gallstones in bile
• Cause atherosclerosis in blood vessels

107
Learning Outcomes

• describe how to carry out chemical tests to
  identify the presence of the following molecules
  protein (Biuret test), reducing and non-reducing
  sugars (Benedicts test), Starch (iodine
  solution) and lipids (emulsion test)

108
Chemical Tests

• Chemical tests can be done to confirm the
  presence of various biological molecules within a
  sample
• These tests are qualitative tests
• They indicate presence of a molecule not how much
  is present

109
Testing for presence of a carbohydrate

• Starch
• Reducing sugar
• Non reducing sugar

110
starch

• Iodine solution
• iodine in potassium iodide
• Add to solution will turn blue-black quickly if
  comes into contact with starch.

111
Starch

• Starch molecules curl up into long spirals, with
  a hole down the middle of the spiral, just the
  right size for an iodine molecule.
• The starch-iodine complex forms a strong
  blue-black colour.

112
Reducing sugar

• Benedicts Reagent (copper II sulphate in
  alkaline solution)
• Add benedicts reagent to the solution testing
• Heat in a water bath (80oC) for 3 minutes

113
Reducing sugars

• If added to a reducing agent Cu2 ions are
  reduced to Cu, and the change in colour to red
  of Copper (I) sulphate.
• All monosaccharides are reducing sugars
• Reducing sugars have an aldehyde group (H-C0)
  somewhere in their molecule, which contribute an
  electron to the copper.
• Reducing sugars become oxidised.
• Reducing sugar Cu2 oxidised sugar Cu

114
Non reducing sugar

• Heat sugar solution with acid to hydrolyse any
  glycosidic bonds present
• Neutralise solution by adding sodium hydroxide
• Add benedicts reagent
• Heat in a water bath
• If it goes orange/red a non-reducing sugar is
  present.

115
Non-reducing sugars

• Not all disaccharides are reducing sugars.
• To check for the presence of a reducing sugar,
  the disaccharide needs to be broken down into its
  constituent monosaccharides,
• monosaccharides are reducing sugars and will
  react with benedicts solution.

116
Testing for the presence of proteins
117
Proteins

• Biuret reagent
• copper sulphate and potassium or sodium hydroxide
• Add Biuret solution to the substance
• If protein present get a purple colour

118
proteins

• All proteins have several amine, NH2, groups
  within their molecules.
• These groups react with copper ions to form a
  complex that has a strong purple colour.

119
Testing for the presence of lipids
120
lipids

• Emulsion test
• Shake substance (lipid) with absolute ethanol
• Pour ethanol into a tube containing water
• If no lipid is present mixture looks transparent
• If lipids are present looks white and cloudy.

121
lipids

• Lipids are insoluble in water, but soluble in
  ethanol.
• As the ethanol mixture is poured into water,
  lipid molecules cannot remain mixed in water and
  clump together to form little groups.
• The lipid molecules impede light and we see an
  emulsion (white cloudiness).

122
Learning Outcomes

• describe how the concentration of glucose in a
  solution may be determined by using colorimetry

123
Banana Qualitative

• Bananas, at each of five different stages of
  ripeness.
• The stages must range from very green (inedible)
  to very ripe (brown skin).
• Each student will require an approximately 5 cm
  length of each banana.
• The bananas must be labelled or presented on
  labelled watch glasses.
• 50cm3 fresh iodine in potassium iodide solution
  in a beaker labelled iodine solution.
• 50cm3 fresh Benedicts solution in a beaker
  labelled Benedicts solution.

124
Nucleic Acids

• Module 1 Biological Molecules
• Unit 2 Molecules, Biodiversity, food and health

125
Learning Outcomes

• state that deoxyribonucleic acid (DNA) is a
  polynucleotide, usually double stranded and made
  up of the nucleotides adenine (A), thymine (T),
  cytosine (C) and guanine (G)
• state that ribonucleic acid (RNA) is a
  polynucleotide usually single-stranded and made
  up of the nucleotides adenine (A), uracil (U),
  cytosine (C) and guanine (G)

126
Nucleic Acids DNA and RNA

• The nucleic acids have
• The ability to carry instructions
• The ability to be copied
• DNA and RNA are polymers the individual
  nucleotides are the monomers that build up the
  polynucleotides.
• DNA deoxyribonucleic acid
• RNA ribonucleic acid

127
Nucleotides

• Nucleotides are made up of three smaller
  components
• Nitrogen containing base
• Pentose sugar (5 carbon atoms)
• Phosphate group

Phosphate
sugar
base
128
Bases

• There are 5 different nitrogen-containing bases
• A Adenine
• T Thymine (DNA only)
• U Uracil (RNA only)
• G Guanine
• C Cytosine
• DNA A, G, C and T
• RNA - A, G, C and U

129
Bases

• Purines (larger)
• These have double rings of carbon and nitrogen
  atoms
• adenine
• Guanine
• Pyrimidines (smaller)
• These have a single ring of carbon and nitrogen
  atoms
• Thymine
• uracil
• cytosine

130
Polynucleotides

• Polynucleotides strands are formed of alternating
  sugars and phosphates

131
DNA

• Cut and paste activity
• Cut out the nucleotides and stick them down to
  form a double stranded DNA molecule

132
Learning Outcomes

• describe, with the aid of diagrams,
• how hydrogen bonding between complementary base
  pairs (A-T, G-C) on two anti-parallel DNA
  polynucleotide leads to the formation of a DNA
  molecule,
• how the twisting of DNA produces its
  double-helix shape outline, with the aid of
  diagrams,

133
DNA

• 2 strands side-by-side running in opposite
  directions (antiparallel)
• The two strands are held together by hydrogen
  bonds.

134
Complementary base pairs

• A purine in one strand is always opposite a
  pyramidine in the other strand.
• Adenine thymine
• Guanine - cytosine
• DNA forms a double helix, the strands are held in
  place by hydrogen bonds.
• These bonds can be broken relatively easily, this
  is important for protein synthesis and DNA
  replication.

135
Pupil Activity

• Build your own DNA molecule
• Equipment needed
• 2 purple pipe cleaners
• 2 white pipe cleaners
• 6 red beads
• 6 yellow beads
• 12 aqua beads
• 12 purple beads
• Follow the instructions on the handout

136
DNA a double helix

• Two polynucleotides held together by hydrogen
  bonds
• Complementary base pairs
• A?T (2 hydrogen bonds)
• G?C (3 hydrogen bonds)
• Polynucleotides are anti-parallel
• Parallel but with chains running in opposite
  directions
• 3 to 5direction
• 5 to 3direction

137
Structure to function

• Information storage
• Long molecules
• replication
• Base-paring rules
• Hydrogen bonds
• Stable

138
Learning Outcomes

• how DNA replicates semi-conservatively, with
  reference to the role of DNA polymerase

139
DNA Replication

• Each polynucleotide acts as a template for making
  a new polynucleotide
• This is known as semi-conservative replication

140
Experimental Evidence for the semi-conservative
replication of DNA

• Three ways were suggested for DNA replication
• Conservative replication
• Semi-conservative replication
• Dispersive replication

141

• Scientists thought that semi-conservative
  replication was most likely but there was no
  evidence to support this theory.
• 1958 Matthew Meselsohn and Franklin Stahl
  demonstrated that DNA replication was
  semi-conservative following experiments with E.
  Coli.

142
Stage 1

• E. Coli were grown in a medium containing a heavy
  isotope nitrogen (15N).
• The bacteria used 15N to make the purine and
  pyrimidine bases in its DNA.

143
Stage 2

• After many generations, they were then
  transferred to light isotope nitrogen (14N)

144
Stage 3

• Bacteria were taken from the new medium after one
  generation, two generations and later
  generations.
• DNA was extracted from each group of bacteria,
• samples were placed in a solution of caesium
  chloride and spun in a centrifuge.

145
Results
Generation 1 2 3
146
Conclusions

1. Explain why the band of DNA in the first
   generation is higher than that in the parental
   generation.
2. If replication were conservative what results
   would you expect in the first generation?
3. If the DNA had replicated dispersively what
   results would you expect in the first generation?
4. Explain how the second generation provides
   evidence that the DNA has reproduced
   semi-conservatively and not dispersively
5. What results would you expect to see from a third
   generation, draw a diagram of the results?

147
Explanation of results

• Parental generation - both strands made with 15N
• First generation DNA made of one strand 15N and
  one strand 14N
• Second generation some DNA made of 2 strands of
  14N and some made of 15N and 14N.

148
DNA Replication

• Double helix unwinds and the DNA unzips as
  hydrogen bonds break
• Existing polynucleotides acts as a template for
  assembly of nucleotides
• Free nucleotides move towards exposed bases of
  DNA
• Base pairing occurs between free nucleotides and
  exposed bases
• Enzyme DNA polymerase forms covalent bonds
  between free nucleotides
• Two daughter DNA molecules form separate double
  helices.

149
Learning Outcomes

• state that a gene is a sequence of DNA
  nucleotides that codes for a polypeptide
• outline the roles of DNA and RNA in living
  organisms (the concept of protein synthesis must
  be considered in outline only)

150
RNA

• single strand, containing
• uracil not thymine
• Ribose sugar
• There are 3 forms of RNA
• Messenger RNA mRNA
• Transfer RNA tRNA
• Ribosomal RNA rRNA

151
DNA and Protein Synthesis

• All chemical reactions are controlled by enzymes,
  all enzymes are proteins, DNA codes for proteins,
  therefore DNA controls all the activities of a
  cell.
• The shape and behaviour of a protein depends on
  the exact sequence of amino acids in the primary
  structure (polypeptide).

152
The Genetic Code

• DNA determines the exact order in which amino
  acids join together.
• The genetic code
• sequence of bases along the DNA molecule,
• There are 20 different amino acids, only 4 bases,
  
• a sequence of 3 bases codes for an amino acid.
• This is called the triplet code.
• A gene is the part of a DNA molecule, which codes
  for just one polypeptide.

153
Protein Synthesis

• The process of protein synthesis occurs in four
  stages
• transcription of DNA to make messenger RNA (mRNA)
• movement of mRNA from the nucleus to the
  cytoplasm
• amino acid activation
• translation of mRNA to make a polypeptide

154
Transcription

• This is the process by which mRNA is built up
  against one side of an opened up piece of DNA.
• The relevant section of DNA unwinds, the hydrogen
  bonds between base pairs are broken and the two
  strands split apart.
• Free nucleotides then assemble against one strand
  of DNA.
• The enzyme RNA polymerase moves along the DNA
  adding on RNA nucleotide at a time.

155
Movement of mRNA to ribosomes

• mRNA leaves the nucleus through a nuclear pore
  into the cytoplasm, and attaches to a ribosome.

156
Amino Acid Activation

• Enzymes attach amino acids to their specific tRNA
  molecule.
• This needs energy supplied by ATP.
• An anti-codon is a triplet of bases forming part
  of a tRNA molecule and it is complementary to a
  codon.

157
Translation

• Amino acid attaches to the ribosome
• Adjacent amino acids are joined together by
  peptide bonds and a polypeptide chain is built
  up.
• This carries on until the ribosome reaches a stop
  codon, the polypeptide breaks loose from the
  ribosome and translation is complete.

158
Enzymes
159
Learning Outcomes

• state that enzymes are globular proteins, with a
  specific tertiary structure, which catalyse
  metabolic reactions in living organisms

160
Recap

• What is metabolism?
• sum total of all biochemical reactions in the
  body.

161
Enzymes

• All enzymes are
• globular proteins
• catalysts
• Specific
• affected by temperature and pH

162
More about enzymes

• Two basic functions within cells
• Act as biological catalysts
• Provide a mechanism whereby individual chemical
  reactions can be controlled
• Enzyme molecules have a specific 3D shape and all
  possess an active site.

163
Learning Outcomes

• Follow the progress of an enzyme-catalysed
  reaction

164
Catalase

• The enzyme catalase breaks down hydrogen peroxide
  into water and oxygen.
• 2H2O2 gt 2H2O O2
• Hydrogen peroxide is formed continually as a
  bi-product of various chemical reactions in
  living cells.
• It is toxic and if the cells did not immediately
  break it down it would kill them.

165
Investigation 1

• Catalase is the fastest enzyme known.
• In this investigation you will be able to watch
  the action of catalase and compare it with an
  inorganic catalyst that catalyses the same
  reaction.
• Pour hydrogen peroxide into two test tubes to a
  depth of about 2cm.
• Into one test tube sprinkle about 0.1g of
  manganese dioxide.
• Into the 2nd test tube put in a 1cm2 piece of
  potato.
• Observe the two test tubes and record what
  happens.

166
Results

• Describe the difference in reaction with the
  inorganic catalyst and the organic catalyst

167
Investigation 2
Graduated measuring cylinder
15ml Hydrogen peroxide
water
168
Method

• Design a results table to record the oxygen
  produced every 10 seconds.
• cut up 4cm3 piece of potato into this slices into
  the conical flask, and start recording results
  immediately.
• Take a reading for the amount of oxygen produced
  every 10 seconds, until the oxygen is no longer
  being produced.

169
Extension

• If you have time, you could repeat the above
  experiment, but this time grind up the 4cm3 of
  potato with some fine sand. How do the results
  compare?

170
Results

• Draw a graph of oxygen produced against time.
• Describe the graph in terms of interaction
  between the molecules of catalase and hydrogen
  peroxide.
• How could you adapt this experiment to
  investigate the effect of the following on the
  rate of the reaction.
• temperature
• pH
• substrate concentration
• enzyme concentration

171
Learning Outcomes

• state that enzyme action may be intracellular or
  extra cellular
• describe, with the aid of diagrams, the mechanism
  of action of enzyme molecules, with reference to
• specificity,
• active site,
• lock and key hypothesis,
• induced-fit hypothesis,
• enzyme-substrate complex,
• enzyme-product complex
• lowering of activation energy

172
Active Site

• The Active site is the region to which another
  molecule or molecules can bind. This molecule is
  the substrate of the enzyme.
• The enzyme and substrate form an enzyme-substrate
  complex.
• When enzyme and substrate collide in the correct
  orientation, the substrate becomes attached and
  held temporarily in position at the active site.

173
Substrate ? end products

• Enzyme and substrate molecules then interact so
  that a chemical reaction involving the substrates
  takes place and the appropriate products are
  formed.
• When the reaction is complete, the product or
  products leave the active site.

174
Enzyme Specificity

• Active sites are specific for one type of
  molecule
• Examples of specificity
• Amylase breaks down glycosidic bonds in starch to
  form maltose
• Catalase breaks down hydrogen peroxide into water
  and oxygen
• Trypsin is a protease that only breaks peptide
  bonds next to the amino acids arginine and lysine

175
Lock and Key Theory

• Some part of the enzyme has an active site, which
  is exactly the correct shape to fit the
  substrate.
• Active site lock
• Substrate key

176
Induced fit Theory

• Active site is a cavity of a particular shape
• initially the active site is not the correct
  shape in which to fit the substrate.
• As the substrate approaches the active site, the
  site changes and results in being a perfect fit.
• After the reaction has taken place and the
  products have gone.
• The active site returns to its normal shape.

177
Metabolism

• A catabolic reaction
• substrate has been broken down
• An anabolic reaction
• substrate used to build a new molecule

178
Lowering of Activation Energy

• Activation energy is the energy given temporarily
  to a substrate to convert it into a product.
• The higher the activation energy the slower the
  reaction.
• Enzymes help to decrease activation energy by
  providing an active site where reactions can
  occur more easily than elsewhere.

179
Lowering Activation Energy
Activation energy without enzyme Activation
energy with enzyme
180
Learning Outcomes

• To follow the progress of an enzyme-catalysed
  reaction

181
Experiments with enzymes

• Follow the time course of an enzyme-catalysed
  reaction by measuring
• rates of formation of products (for example using
  catalase),
• rate of disappearance of substrate (for example
  using amylase).
• When an enzyme and a substrate are mixed
  together, a reaction begins. Substrate molecules
  collide with the enzyme and bind to its active
  site product molecules are formed.

182
Experiments with enzymes

• As the reaction proceeds the number of substrate
  molecules decreases and the number of product
  molecules increase. The number of enzyme
  molecules remains constant.
• We can measure the rate of a reaction by
  measuring either
• Increasing product
• Decreasing substrate

183
Increasing ProductExample catalase breaks down
hydrogen peroxide into water and oxygen
184
Decreasing SubstrateExample amylase breaks down
starch into maltose
185
Explanations for the course of reaction

• As the reaction proceeds there is less substrate
  available, therefore less product gets released.
• Rate of reaction is quickest at the beginning
  when there is a high concentration of substrate.
• Later the substrate becomes the limiting factor
  and the reaction slows down.
• Eventually all substrate is used up, so the
  reaction stops

186
Learning Outcomes

• describe and explain the effects of pH,
  temperature, enzyme concentration and substrate
  concentration on enzyme activity
• describe how the effects of pH, temperature,
  enzyme concentration and substrate concentration
  on enzyme activity can be investigated
  experimentally

187
Factors Affecting enzyme Activity

• Enzyme Concentration
• Substrate concentration
• Temperature
• pH

188
Enzyme Concentration

• The rate of reaction is directly proportional to
  the enzyme concentration
• assuming that there are plenty of substrate
  molecules and enzymes are the only limiting
  factors.

189
Enzyme Concentration
190
Substrate concentration

• For a given amount of enzyme, the rate of an
  enzyme controlled reaction increases with
  substrate concentration, up to a certain point.
• This point is Vmax, which is the maximum rate of
  reaction the amount of enzyme becomes the
  limiting factor.

191
Substrate concentration
192
Temperature

• An increase in temperature affects the rate of
  reaction in two ways
• Factor 1
• As the temperature increase the kinetic energy of
  the substrate and enzyme molecules increases and
  they move faster.
• The faster the molecules move the more often they
  collide and the greater the rate of reaction.

193
Temperature

• Factor 2
• As temperature increases, more atoms which make
  up the enzyme molecules vibrate.
• This breaks down the bonds which hold the
  molecules in the precise shape.
• The enzyme becomes denatured and loses catalytic
  properties.

194
Temperature

• OPTIMUM TEMPERATURE
• temperature at which an enzyme catalyses a
  reaction at a maximum rate.

195
Temperature
196
pH

• The precise 3-D shape of an enzyme is partly a
  result of hydrogen bonding.
• These bonds maybe broken down by high
  concentrations of H ions.
• When pH changes from the optimum
• shape of enzyme changes
• affinity of substrate for the active site
  decreases

197
pH
198
Online resources

• Online simulation of practical available at
• http//mvhs.mbhs.edu/coresims/enzyme/index.php
• Good simulation of the theory of temp/pH
  available at AS guru
• www.bbc.co.uk
• Chemistry for biologists
• www.chemsoc.org/networks/learnnet/cfb/

199
Learning Outcomes

• explain the effects of competitive and
  non-competitive inhibitors on the rate of
  enzyme-controlled reactions,
• with reference to both reversible and
  non-reversible inhibitors

200
Enzyme Inhibitors

• Inhibitors prevent enzymes from working
• There are two types of inhibitor
• competitive
• non-competitive.

201
Competitive Inhibitors

• Have a similar shape to the normal substrate and
  are able to bind to the active site.
• Do not react with the active site but leave after
  a time without any product forming.
• The rate of reaction decreases because the
  substrate molecules have to compete with the
  inhibitor for the active site.
• It is possible to reduce the effect of the
  inhibitor by adding more substrate

202
Competitive inhibitor
203
Effect of concentrations of inhibitor and
substrate on the rate of an enzyme controlled
reaction
Rate of reaction
Substrate concentration
204
Examples

• Competitive inhibitor
• Reversible
• Statins compete with a liver enzyme which helps
  to make cholesterol
• Non-reversible
• Penicillin inhibits an enzyme that makes cell
  walls in some bacteria

205
Non-competitive inhibitors

• Molecules bind to some part of an enzyme other
  than the active site.
• This changes the active site so that the
  substrate can no longer fit.
• If the concentration of this type of inhibitor is
  high enough, all enzymes maybe inhibited and the
  reaction slows to nothing.
• Increasing the concentration of the substrate has
  no effect on this type of inhibition.

206
Non competitive inhibitor
207
Rate of an enzyme controlled reaction with and
without a non-competitive inhibitor
Rate of reaction
Substrate concentration
208
Examples

• Non-competitive inhibitor
• Potassium cyanide bind to haem, which is part of
  cytochrome oxidase
• This is non-reversible

209
End product inhibition

• Metabolic reactions must be finely controlled and
  balanced
• end product inhibition regulates certain
  enzyme-catalysed processes in organisms.

210
End product inhibition
211
End product inhibition

• This is an example of non-competitive inhibition
• product 3 binds to another part of the enzyme
  other than the active site.
• It is also an example of a feedback mechanism.

212
Learning Outcomes

• explain the importance of cofactors and coenzymes
  in enzyme-controlled reactions
• state that metabolic poisons may be enzyme
  inhibitors, and describe the action of one named
  poison
• state that some medicinal drugs work by
  inhibiting the activity of enzyme

213
Co-factor

• A non-protein component
• Required by enzymes to carry out reactions
• Examples
• Metal ions in carbonic anhydrase
• Haem in catalase
• Chloride ions and amylase

214
Co-enzyme

• Organic, non protein molecules
• Role is to carry chemical groups between enzymes,
  linking together enzyme controlled reactions
• Examples
• NAD, FAD and coenzyme A involved in respiration
• NADP involved in photosythesis

215
Prosthetic groups

• A coenzyme that is a permanent part of the enzyme
• Example
• Carbonic anhydrase contains a zinc-based
  prosthetic group

216
Metabolic poisons

• Metabolic poisons can be enzyme inhibitors
• Example
• Potassium cyanide
• inhibits cell respiration
• Non-competitive inhibitor for the enzyme
  cytochrome oxidase
• Decreases the use of oxygen so that ATP can not
  be made
• The organism respires anaerobically and lactic
  acid builds up in the blood

217
Medicines and enzymes

• Infection by viruses are treated by using
  chemicals that act as protease inhibitors which
  the virus needs to build new viral coats.
• Antibiotics
• Penicillin inhibits a bacterial enzyme which
  makes bacterial cell walls

218
Learning Outcomes

• Measure the effect of different independent
  variables and independent variable ranges on an
  enzyme-catalysed reaction
• Measure the effect of an inhibitor on an
  enzyme-catalysed reaction.