This document summarizes key concepts about biomolecules and human physiology. It discusses the four major classes of biomolecules - carbohydrates, lipids, proteins, and nucleotides - including their structures, functions, and examples. It also describes protein structure and interactions, including binding sites, affinity, competition, and modulation of binding. Overall, the document provides a concise overview of fundamental biochemical concepts and biomolecules important for human physiology.
5. Characteristics of Biomolecules
• Most of the molecules of concern have 3
elements in common C, H and O
• Also many biological molecules contain P and N
• Each group has a characteristic composition
and molecular structure
• Many are polymers- large molecules of
repeating units
6. Functional Groups
• Combinations of atoms that tend to move from
molecule to molecule as a single unit
• Several functional groups are found repeatedly in
biomolecules
• E.g.; –OH is a hydroxyl group- tends to be added
and removed from molecules as a group rather than
as single H or O atoms
• Functional Groups tend to attach to molecules via a
single covalent bond
8. Carbohydrates
• Carbohydrates (carbon with water)
• Most abundant biomolecules
• General formula is (CH2O)n (carbon and water)
• n= number of repetitions of the carbohydrate unit
in the molecule
• To write the formula- multiply each subscript by n
• E.g.; glucose has 6 units C6H12O6
9. Carbohydrates
• Mono or disaccharides = simple sugars
– Have suffix –ose at end of names
– The most common monosaccharides are the building
blocks for the complex carbohydrates
• Polysaccharides = complex polymers of glucose
– Glucose is stored in the body for energy as a
polysaccharide called glycogen, plants store it as
starch
10. Carbohydrates
• The major function of carbohydrates in the body
is to provide cells with energy in chemical
reactions (i.e.. as a fuel).
• 1 gram of carbohydrates releases 4.2 kcal of
energy when oxidised in the body.
11.
12. 2. Lipids
• Predominantly Carbon and Hydrogen with some
Oxygen
• Non-polar so not very water soluble
• Fats= lipids solid at room temp, most derived from
animals are fats
• Oils= liquid at room temp, most derived from plants
are oils
• 3 types of lipid-related molecules
– Phospholipids, steroids, eicosanoids
13.
14. 2. Lipids Structure
• Glycerol = 3 carbon molecule
• Fatty acid = long molecule- long chains of C atoms
bound to H with a carboxyl group at one end
(-COOH)
• Saturated = no double bonds between C atoms in
chain
• Monounsaturated= 1 double bond in chain
• Polyunsaturated= 2 or more double bonds in the
molecule
• More double bonds means less hydrogen
• Shape is more ‘kinked’ with double bonds
15.
16. • Glycerol links to 1, 2 or 3 Fatty Acids (FA) to form
mono, di or tri- glycerides
• Triglycerides=triacylglycerol's- most abundant
lipid in body- over 90%
– =1 glycerol linked to 3 FA
Glycerol
17. Steroids
Composed of four interconnected carbon rings with a few
polar hydroxyl groups attached.
Cholesterol is source in human body.
18. Functions:
• Triacylglycerols (fats):
– Major fuel reserve
– Protection and insulation
• Phospholipids:
– Major constituent of cell membrane
• Steroids:
– Cholesterol aids in absorption of fatty acids
– constituent of cell membrane
– Components of some important hormones
• Eicosanoids
– regulate various physiological functions
19.
20. • Polymers of Amino Acids (AA)
• Amino Acids have a carboxyl group, an amine
group and a hydrogen attached to the same
carbon atom. The 4th bond attaches to a variable
group known as the ‘R’ group
3. Proteins
• All AA have a similar core structure
• Amino acid consists of
– a carboxylic acid group (-COOH)
– an amino group (-NH2)
– a side chain (-R)
– a hydrogen atom (-H)
21. 3. Proteins
• R groups vary in size, shape & ability to form
ions or H bonds so make each AA unique
• 20 protein forming AA assemble into polymers
with almost infinite combinations possible
22.
23.
24.
25. • Dehydration reaction- water molecule is
removed and bond is formed
– For peptide bond -OH is removed from carboxyl
group and –H from amine group
• Hydrolysis reaction- water is added to break
the bond
– For peptide bond –OH added to carboxyl gp, -H
added to amine group
26. • Parts of cell structure
• Protein or peptide hormones contribute to
regulation of body function
• Enzymes are proteins that catalyse chemical
reactions in the body
• Antigens, antibodies and receptors in immune
defence system
• Haemoglobin transports O2 and CO2
Functions of Proteins
27.
28. Shape (spatial arrangement)
H bonding between different parts of the
molecule stabilises the shape
Secondary Structure
30. Tertiary Structure
2 large groups
• 1. Fibrous –
– found in pleated sheets or long chains of helices
– insoluble in water
– important structural component of cells and tissues
e.g.; collagen, keratin
• 2. Globular –
– AA chains fold back on selves creating pockets,
channels, knobs etc.
– Structure results partly from angles of covalent bonds
between AA, hydrogen bonds, van der Waals forces
and ionic bonds.
31. –Also the AA cysteine has sulphur as part of a
sulfhydryl group.
–2 cysteines can bond covalently forming a
disulphide bond pulling different parts of the
chain together.
–Water soluble- act as carriers for water insoluble
lipids in blood (bind to lipids and make them
soluble)
–Enzymes, hormones, neurotransmitters, defence
molecules
Tertiary Structure -Globular Proteins
33. Combined Molecules
Biomolecules can be combinations of Carbohydrate,
Lipid and Protein
• Conjugated protein= protein molecule combined
with another kind of biomolecule
– E.g.; lipoprotein= lipid and protein (found in cell
membranes, transport hydrophobic molecules in
blood eg; cholesterol
• Glycosylated molecule- a carbohydrate has been
attached
– E.g.; glycoprotein, glycolipid= both important parts of
cell membranes
35. 4. Nucleotides
• Store and transmit genetic info and energy
• A single nucleotide consists of 3 parts
–a sugar (2 possibilities)
–1 or more phosphate groups
–1 of 5 nitrogenous bases
37. 4. Nucleotides
• Sugars = ribose or deoxyribose(=ribose
minus 1 Oxygen)
• 2 types of Nitrogenous bases
–1. Purines- have a double ring structure-
adenine (A), guanine(G)
–2. Pyrimidines-single ring structure-
cytosine (C), thymine (T), uracil (U)
38. Single Nucleotide
• Smallest nucleotides include- Adenosine
triphosphate (ATP), Adenosine diphosphate
(ADP)= energy transferring compounds
• cAMP- (cyclic Adenosine monophosphate)
transfer of signals between ECF and cell
• Nicotinamide adenine dinucleotide (NAD) and
Flavin adenine dinucleotide (FAD)- energy
transferring nucleotides
39. Nucleic Acids
• Nucleotide polymers
• nucleotides linked into long chains
–Sugar of one links to phosphate group of
next
– nitrogenous bases extend to the side of the
chain
–DNA and RNA- store and transmit genetic
info
• DNA=deoxyribonucleic acid
• RNA=ribonucleic acid
42. Deoxyribonucleic Acid(DNA)
– Bases: Adenine, Guanine, Cytosine, Thymine
(Pairing: A-T, G-C)
– Two chains of nucleotides in a double helix molecules
– Hydrogen bonds between complementary base pairs
hold molecule together
– Function: storage of genetic information
43. Ribonucleic acid (RNA)
– Bases: Adenine, Guanine, Cytosine, Uracil
(Pairing: A-U, G-C)
– One chain of nucleotides
– Types: ribosomal RNA (rRNA), messenger RNA
(mRNA), transfer RNA (tRNA)
– Function: translate genetic information into protein
synthesis.
44.
45. • Most soluble proteins fall into one of 7 broad
categories
• 1. Enzymes
– speed up chemical reactions
• 2. Membrane Transporters
– move substances in and out of cells via channels in membrane
or binding molecules and carrying them thru
• 3. Signal Molecules
– hormones etc
Protein Interactions
• 4. Receptors-
– bind signal molecules and initiate cellular responses
46. • 5. Binding proteins
• mostly in ECF bind and transport molecules through body e.g.;
Hb, LDL- cholesterol transport
• 6. Regulatory proteins
• turn cell processes on/off or up/down e.g.; transcription
factors- bind DNA for gene expression and protein synthesis
• 7. Immunoglobulins
• extracellular immune proteins = antibodies- immune protection
Protein Interactions
47. • All bind to other molecules non-covalently
• Binding site = location on protein molecule where
binding takes place
• Binding of a molecule to a protein binding site can
initiate a process
• Ligand = any molecule that binds to another
molecule
• Substrate = ligand that binds to an enzyme or
membrane transporter
• Protein signal molecules and transcription factors
are ligands
Common Features of Soluble Proteins
48. • For binding to occur the binding site and the
ligand must be compatible.
• In protein binding, when ligand and binding site
come close, non-covalent interactions allow the 2
molecules to bind.
• The binding site and ligand don’t have to fit
exactly, they interact via H-bonds and van der
Waals forces, then the binding site changes
shape(conformational change) to fit more closely
to the ligand
Induced Fit-Model
49. Binding sites exhibit the following 4 properties
1. Specificity
2. Affinity
3. Competition
4. Saturation
Binding site properties
50. • Ability of protein to bind a certain ligand or
groups of ligands
– Some are very specific, some will bind whole groups
– E.g.; Enzymes- peptidases will break apart any
polypeptides peptide bonds regardless of AA ( not very
specific)
– Amino peptidases will only bind to the terminal end of
a peptide chain (specific)
1. Protein Specificity
51. Degree to which protein is attracted to ligand
Higher affinity = more likely to bind
Binding can be reversible
P + L ↔ PL
Reversible reactions reach a state of equilibrium
where rate of binding = rate of
unbinding(dissociation)
A + B ↔ C + D
2. Affinity
52. • In the body, concentrations of ligands or proteins
are constantly changing
• Protein–ligand binding reactions are often
reversible
• Law of Mass Action states- when a reaction is at
equilibrium, the ratio of the concentration of
products to substrates is always the same. If the
ratio is disturbed by adding or removing a product
or substrate, the reaction will shift in the direction
that restores equilibrium.
Laws of Mass Action
53. • So- if you add extra protein or ligand, the reaction
will go in the direction of increased binding of
protein to ligand, until equilibrium is restored
• If you take away protein or ligand, the reaction
will go in the reverse direction where the protein-
ligand complex will unbind until equilibrium is
restored
Laws of Mass Action
54. Related ligands compete for binding sites
Agonist= a ligand that mimics another ligands
action.
–E.g.; nicotine mimics activity of ACh by binding
to same receptor
–Drugs can be designed to be agonists
A competitive antagonist = an inhibitor- will
bind to a protein and decrease its activity
Competition
55. • A protein’s affinity for a ligand is not always
constant as chemical and physical factors can
alter or modulate binding affinity. Binding affinity
can be removed altogether.
• Some proteins require activation before they have
a functioning binding site
• Modulator = a factor that influences either
protein binding or protein activity
Modulation of Binding Affinity
56.
57. • Can be chemical or physical
• Isoforms = closely related proteins with similar
functions but different affinities for ligand
Factors that Alter Protein Binding
58. • Some proteins are inactive when synthesised in
the cell.
• Proteolytic Activation = In order for these
proteins to become active, enzymes must chop
off certain parts of the protein molecule
• Inactive forms of proteins often have the prefix
‘pro’ or suffix ‘ogen’ e.g.; proinsulin is activated
to form insulin, trypsinogen is activated to form
trypsin
Activation
59. • Some proteins require the presence of cofactors to
activate binding sites
• Cofactors are ions or small functional groups that
must attach to binding site before the ligand will
bind
Activation by Cofactors
60. • E.g.; Mg2+ ,Ca2+ , Fe2+
• Many enzymes can’t function without cofactors
Activation by Cofactors
61. • 2 Basic Mechanisms- Modulator either
–1. Changes ability of ligand to bind to
binding site, or
–2. Changes protein’s activity or ability to
create a response
• Factors including temperature, pH and
molecules that interact with the protein,
can all modulate protein activity
Modulation
62. • Molecules that bind covalently or non covalently
to proteins and alter their binding ability
• Can activate or enhance ligand binding, decrease
binding ability, or completely inactivate protein
binding ability (inactivation may be reversible or
irreversible)
• Antagonists= inhibitors- bind to a protein and
decrease its activity
Chemical Modulators
63. • Competitive inhibitors= reversible antagonists
– They compete with the usual ligand for that binding
site
– The degree of inhibition depends on the relative
concentrations of the ligand and inhibitor as well as
the different affinities of ligand and inhibitor for the
binding site.
– Competitive inhibitors can be displaced from the
binding site by increasing the concentration of the
usual ligand
Competitive inhibitors
64. • Irreversible Antagonists= bind tightly to the
protein and can’t be displaced
– Some powerful drugs act in this way
Competitive inhibitors
65. • Can be activators or antagonists
• Bind reversibly to protein at a regulatory site
away from the binding site and this causes a
change in shape of the binding site
• Allosteric inhibitors- decrease affinity of binding
site for ligand and decrease protein activity
• Allosteric activators- increase protein ligand
binding and enhance protein activity
Allosteric inhibitors
66. • Atoms or functional groups bind covalently to
protein and alter its properties
• Can activate or inhibit
• E.g.; Phosphorylation- very common
– Phosphate group binds to protein
– Can activate or inactivate
Covalent Modulators
67. • pH or Temperature
• Small changes act as modulators to increase or
decrease activity
• BUT- a critical point is reached at which non-
covalent bonds are disrupted and tertiary
conformation is lost = denatured (protein loses
shape and activity e.g.; cooked egg white. This is
usually not reversible hence body closely
regulates pH and Temp
Physical Modulators
68.
69. • The body regulates the amount of proteins in cells
• Up-regulation = complex signalling pathways
direct cells to make new proteins
• Down-regulation = proteins are removed
[ ] = concentration
• Cells regulate protein [ ] to control physiological
processes. Increased protein [ ] means increased
reaction rate and vice versa
Regulation of Protein
70. • If protein [ ] is constant then ligand [ ] determines
reaction rate.
• At low ligand [ ] response rate is directly
proportional to [ ]
• BUT once the ligand molecules reach a certain
level the protein will have no more free binding
sites so reaction rate reaches its maximal value =
saturation
Saturation
