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Course Contents
•Building Blocks of Biomolecules-Structure anddynamics
•Structure and functions of macromolecules
•Carbohydrates•Proteins
•Lipids
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Biomolecule
• A biomolecule is any organic molecule thatis produced by a living organism, includinglarge polymeric molecules such as
proteins, polysaccharides, and nucleicacids as well as small molecules such asprimary metabolites, secondary
metabolites, and natural products.
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Building Blocks of Biomolecules
• BUILDING BLOCKS
• Macromolecules form when smallermolecules (building blocks or subunits)
come together
• Monomers are joined by covalent bonds to
form polymers
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Building blocks of proteins
• Amino acids20 common amino acids
• Central carbon with attached hydrogen,amino group, carboxylic acid group, and a
R group
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PROTEINS
Functions• Structural
• EnzymaticCatalyze chemical reactions
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Structure• Proteins are polymers of amino acids
• There are 20 common amino – Each has a central carbon attached to 4 groups
• Hydrogen
• Amine
• Carboxylic acid• An R group
– Amino acids differ by their R groups • There are 20 different R groups.
• 2 amino acids are connected by dehydrationsynthesis – The covalent bond is called a peptide bond
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Levels of organization of Protein
Primary structure
• Sequence of amino acids.
– The 20 different amino acids can be joined inany sequence
– This sequence is determined by the DNAsequence of the gene that encodes for thatparticular protein
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Secondary structure
–Due to interactions of the amino
acids near each other• Hydrogen bonds between amino
hydrogens and carboxyl oxygens
–Results in an a -helix configurationor a b - sheet configuration
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Tertiary structure
• The 3-dimensional folding of thepolypeptide chain
• Due to interaction of R-groups of
amino acids some distance away fromeach other
• These interactions could be hydrogenbonding, ionic bonding, or covalent bonding.
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Quaternary structure
• Interaction between proteins
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Building blocks of lipids
• Fatty acids
• Long hydrophobic hydrocarbons
• Glycerol• A triose
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LIPIDS• FunctionLong term storage of energy
• Also insulates and cushions major organs
• Component of membranes
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Types
• Fats (lard and butter) are solids at room
temperature• Oils (vegetable oils) are liquids at room
temperature
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• Structure
• Lipids are composed of glycerol andthree fatty acids
• Two to three fatty acids are bonded to theglycerol by dehydration synthesis
• Fatty acids can be removed from the
glycerol by hydrolysis
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Fatty acids
• Hydrocarbon chains with a carboxylgroup
• Most have 16 - 18 carbons
• Saturated fatty acids• No double bonds between the carbon
atoms
– The carbons are saturated with hydrogens• These will result in lipids that are less fluid
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Unsaturated fatty acids
– One or more (polyunsaturated) double bondsbetween the carbon atoms
– These will result in lipids that are more fluid
–Fatty acids are non-polar andtherefore hydrophobic
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Phospholipids• Lipids with two fatty acids and a
phosphate group attached to glycerol
• Amphipathic
• Has a hydrophilic head and hydrophobic tail
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Lipid bilayer
• Two layers of phospholipids
• Heads face out into the water
• Tails face towards each
B ildi bl k f l i
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Building blocks of nucleic
acids(DNA & RNA)
• Nucleotides
• Nitrogenous base
• A, T, C, U, and G• Pentose sugar
• Ribose in RNA
• Deoxyribose in DNA
• Phosphate
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NUCLEIC ACIDS
Function• Store genetic information
• Transfer genetic information during
reproduction
• Controls protein synthesis
• Types• DNA compromises the chromosomes
• RNA is used in protein synthesis
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Monomers
• Nucleic acids are polymers ofnucleotides
• Nucleotides are bonded by dehydration
synthesis
• Nucleotide consists of three parts
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• Sugar
– A pentose
• Ribose in RNA
• Deoxyribose in DNA
• Phosphate group
• Base• A, T, C, and G in DNA
• A, U, C, and G in RNA
• The order of these bases controls the aminoacid sequence in proteins
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Structure
• Backbone –Alternating sugars and phosphate
• Bases
–Stick out from the sugars
• DNA is often double stranded,
while RNA can be singlestranded, double stranded, or
both
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Structure and Functions ofCarbohydrates
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• One of the most abundant compounds ofliving cells
• Originally thought to have the formula
(CH2O)n.
• Carbohydrate- polyhydroxy aldehyde or
ketone or a larger molecule which can behydrolyzed to a polyhydroxy aldehyde orketone.
Carbohydrates
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Occurance of carbohdrates
in plants in animals- First product of photo- - blood sugar : D-
glucose synthesis- milk sugar: lactose
- Stored in foods as starch, - stored as glycogeninulin and hemicelluloses - essentialcomponents of
- Supporting tissue of nucleic acids: riboseplants: cellulose
- Degradation products:gums and mucilages
- Miscellaneous : pectins,glucosides
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• Monosaccharide- one sugar residue. Most wellknown is glucose, C6H12O6
• Oligosaccharide- a few (2-9) sugar residues .Most well known is cane sugar or sucrose,C12H22O11.
• Polysaccharide- many sugar residues. Mostcommon are glycogen, starch and cellulose, fromanimals, plants and plants.
Classification of Carbohydrates
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CARBOHYDRATES
MONOSACCHARIDES(simple sugars)
DISACCHARIDES POLYSACCHARIDES
Structural
support
fructose glucose galactose sucrose maltose lactose starch glycogen cellulose chitin
plants milk sugar beetssugar cane
grains milk storedglucoseİn plants
forms cellwalls inplants
insectsstoredglucose
İn animals
Quick
energy
fruits
Table sugar
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Carbohydrates
Monosaccharides (biological sugars –ose)
Most frequently found in nature: - hexoses (six-carbon sugars) -> glucose and fructose
- pentoses (five-carbon sugars) -> ribose
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Properties
• Differences in structures of sugars areresponsible for variations in properties
• Physical
• Crystalline form; solubility; rotatory power
• Chemical• Reactions (oxidations, reductions, condensations)
• Physiological• Nutritive value (human, bacterial); sweetness;absorption
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1. Energy source for plants and animals
2. Source of carbon in metabolicprocesses
3. Storage form of energy
4. Structural elements of cells andtissues
Functions of Carbohydrates
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Functions of carbohydrates infoods
1. Oxidized to furnish energy (respiration)2. Function as essential components of nucleic acids.
DNA (deoxyribonucleicacid)
3. Function as components of vitamins (ribose,riboflavin are parts of complex B-6 vitamin)
4. Undergo fermentation by yeasts and othermicroorganisms to yield alcohol and various organic
acids such as citric-, acetic-, propionic.5. Impart sweetness to the foods. When dissolved inwater form syrups.
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Functions of carbohydrates infoods
6. At high concentrations the syrups can be usedas preserving media
7. On heating the sugars caramelize producing
desirable taste and flavor compounds.8. In dissolved and colloidal form they bring about
desirable textural effects. Pectins form gels.Pectins and gums are added to food as
thickeners and stabilizers.9. Reducing sugars react with amino acids toproduce dark colors. (browning reactions)
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Proteins
Proteins are organic compoundsmade of amino acids arranged in a
linear chain and joined together by
peptide bonds between the carboxyl
and amino groups of adjacent amino
acid residues.
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The building blocks of proteins
• Like carbohydrate and lipid molecules proteinscontain the elements : Oxygen(O),Carbon(C),and Hydrogen(H)
• In addition they always contain the elementNitrogen(N).
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Characteristics of Proteins
•Contain carbon, hydrogen, oxygen,
nitrogen, and sulfur
•Serve as structural components ofanimals•Serve as control molecules (enzymes)
•Serve as transport and messengermolecules•Basic building block is the amino acid
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Levels of Structure• A polypeptide is one linear chain of amino acids. Each gene produces one
polypeptide. A protein may contain one or more polypeptides. Proteins also
sometimes contain small helper molecules (co-factors) such as heme.
• The primary structure (1o) is just the sequence of amino acids in the polypeptide.
• The secondary structure (2o) is local folding patterns, mostly alpha helix and betasheet.
• The tertiary structure (3o) is the overall folding pattern of the entire polypeptide.
• The quaternary structure (4o) is the joining of individual polypeptides (subunits) into anactive protein. Proteins that are just a single monomeric polypeptide have no
quaternary structure.
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Amino Acid
„ Amine group acts like a base, tends to be positive.
„ Carboxyl group acts like an acid, tends to be negative.
„ “R” group is variable, from 1 atom to 20.
„ Two amino acids join together to form a dipeptide.
„ Adjacent carboxyl and amino groups bond together.
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• 20 Different Amino Acids arerequired by body (Found in
plants & animals)
–Essential : (9) Can not be
synthesized
–Non-Essential : (14) Can be
manufactured by the body
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Amino acidsessential (9) nonessential (14)
methionine alanine, argininethreonine aspartic acid,tryptophan cysteine, cystineisoleucine glutamic acid
leucine glycinelysine hydroxyprolinevaline proline, serinephenylalanine tyrosine
histidine asparagineglutaminehydroxylysine
A h i f A i A id i
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Another View of Amino Acid Properties
O L
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One LetterAmino Acid
Codes
P tid Ch i
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Peptide Chain
• The amino acids are linked
together by peptide bonds,which are the same asamide bonds.
• The peptide backbone is
made up of the C and Ninvolved in the peptidebond, plus the Cα that linksthem.
• The beginning of every
protein is the N-terminusand the end is the C-terminus. – This means that there is a
free amino group at the Nterminus and a free acid
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Formation of a Dipeptide Bond
Dehydration synthesis
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Tertiary protein structure
• This is when a polypeptide is folded intoa precise shape.
• The polypeptide is held in ‘bends’ and
‘tucks’ in a permanent shape by a rangeof bonds including:
• Disulphide bridges [sulphur-sulphurbonds]
• Hydrogen bonds• Ionic bonds.
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Tertiary protein structure
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Quaternary protein structure
• Some proteins consist of different polypeptidesbonded together to form extremely intricateshapes.
• A haemoglobin molecule is formed for separatepolypeptide chains.
• It also has a haem group, which contains iron.
• The inorganic group is known as the prosthetic
group.• In haemoglobin it aids oxygen transport.
Q i
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Quaternary protein structure
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Functions of Proteins
• Structural component of bodytissues
–Average cell is 16% protein –Varies from 10% (Brain) to 20%
(RBC, muscle, heart, glands, & liver)
–Skeletal muscle protein = 65% ofbody’s total protein content. • Can be increased with resistance
training
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• Regulate acid – base quality ofbody fluids.
–Buffers the large quantities ofacidic metabolic byproducts.
• Assist with fluid balance –Globulins & albumins in blood
plasma maintain osmotic gradient
to prevent blood plasma loss fromcapillaries.
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How useful are proteins?
• Cell membrane proteins: Transportsubstances across the membrane forprocesses such as facilitated diffusion and
active transport.• Enzymes: Catalyse biochemical reactions,
e.g. pepsin breaks down protein in to
polypeptides.
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• Hormones: are passed through the bloodand trigger reactions in other parts of the
body e.g. insulin regulates blood sugar.
• Immuno-proteins: e.g. antibodies aremade by lymphocytes and act against
antigenic sites on microbes.• Structural proteins: give strength to
organs, e.g. collagen makes tendons
tough.
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• Transport proteins: e.g. haemoglobin transportsoxygen in the blood.
• Contractile proteins: e.g. actin and myosin helpmuscles shorten during contraction
• Storage proteins: e.g. aleurone in seeds helpsgermination, and casein in milk helps supply
valuable protein to babies.
• Buffer proteins: e.g. blood proteins, due to theirhigh charge, help maintain the pH of plasma.
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Lipids
Lipids are• biomolecules that contain fatty acids or a
steroid nucleus.
• soluble in organic solvents, but not in
water.
•named for the Greek word lipos, whichmeans “fat.”
• extracted from cells using organic solvents.
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Characteristics of Lipids
•Composed of Carbon, Hydrogen, andOxygen•Greater than 2:1 ratio of H:O
•Includes fats, oils, phospholipids, andcholesterol•Building blocks are fatty acids andglycerol.
•Energy storage molecules•Phospholipids part of cell membrane
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Major Categories of Lipids
• Fats and Oils
– Biosynthesis of fatty acids
• Phospholipids
• Waxes
• Terpenes
• Steroids
• Prostaglandins
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Fats
• Esters of fatty (long chain carboxylic) acids
• Common are triacyl glycerols, which can behydrolyzed (saponified) into soaps:
CH2O2C
CHO2C
CH2O2C
NaOHaq.
CH2OH
CHOH
CH2OH
+ C13H27CO2 C15H31CO2 C17H35CO2Na Na Na+ +
Soap (mixture of salts of fatty acids):
O
CH2OC
CHOC
CH2OC
O
O
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Micelles: mode of action of soap
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
Na O
O
P
Soap (above) can be represented as:
Soap (and detergents) form spherical clusters(right) called micelles; micelles surroundand dissolve non-polar substances (oilystains) and render them “soluble.”
Oil
H2O
H2O
H2O
H2OH2O
H2O
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Oils (polyunsaturated fats)
CH2OCO
CH
O
CH2OC
CO
O
Presence of cis double bonds in oils makes it difficultfor the molecules to pack regularly in a solid structure;oils have lower melting points than fats, and are liquids at RT.
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Biosynthesis of Fatty Acids
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Polyunsaturated Fatty Acids
Polyunsaturated fatty acids (PUFAs) include those havingtwo and three double bonds.
A common omega-3 fatty acid found in fish oil is linolenicacid:
Omega-3 fatty acids are considered beneficial for brain
function.
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Composition of Fats and Oils
lauric myristic palmitic stearic oleic linoleic
C12 C14 C16 C18 C18(1) C18(2)
Animal Fats
Lard - 1 25 8 50 10
Beef Fat - - 27 14 50 3
Butter Fat 2 10 29 10 27 5
Human Fat 1 3 25 8 46 10
Whale Blubber - 8 12 3 35 10
Vegetable Oils
Coconut oil 48 18 11 2 7 1Corn oil - 1 10 3 45 35
Olive oil - 1 7 3 82 6
Peanut oil - - 7 5 58 24
Soybean oil - - 10 2 29 51
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Lipid Bilayer of Cell Membranes
P P P P P P P
P P P P P P P
Cell membrane
Outside the cell (aqueous)
Inside the cell (aqueous)
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Steroids
• Involved in regulatory processes and in sexualcharacteristics and functions
• Common steroids include cholesterol, estradiol,testosterone, estrone and progesterone
Major Functions of Lipids
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Major Functions of Lipids
• Fats and oils – used as energy storage inmany organisms.
• Phospholipids and Sterols – majorstructural elements of biologicalmembranes.
• Others can serve as enzyme cofactorsand messenger molecules.
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Enzymes
Enzymes are a group of biologicalcatalysts responsible for supporting almost all of the chemical reactions
that maintain animal homeostasis.
The macromolecular component of
almost all enzymes are composed ofProtein except for ribozymes
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Enzyme Nomenclature&
Classifications • Traditionally, enzymes were simplyassigned names by the investigator who
discovered the enzyme.
• Currently enzymes are grouped into six
functional classes by the InternationalUnion of Biochemistry & Molecular Biology(I.U.B.M.B)
Nomenclature of enzymes
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Recommended name1.adding – ase to the substrate of the
reaction e.g .glucosidase, urease.
2.Description of action of the enzyme + ase
e.g. lactate dehydrogenase.
• Old names not related to function :e.g .
pepsin, trypsin.
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Systematic Name
• In this system of nomenclature,enzymes are divided into classesand subclasses
• The suffix-ase is attached tocomplete description of thechemical reaction
• E.g.,D-glyceraldehyde3-phosphate:NADoxidoreductase
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•
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Sources of enzymes -•Animal tissues
•Plants
•Microorganisms•Culture media
•Subcellular fractions (e.g. mitochondria,
membranes) etc.
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Comparison of chemical and enzyme catalysis
• Enzymes are biomolecules that catalyze (i.e., increase the rates of)
chemical reactions.
But Enzymes are different from chemical catalysts
• Enzymes work at specific temperature range (called optimum
temperature , 25-45 o C).
• Enzymes are usually very specific as to which reactions they
catalyze and the substrates that are involved in these
reactions.
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• Enzymes are proteins, while chemical catalysts may be organic or
metal.
•Enzymes have short life span comparatively chemical catalysts.
•