Transcript File

Biochemistry
Intro to Macro molecules
Molecular Biology
 The study of the structure and functioning of biological molecules
 Closely linked with biochemistry
 Structures of molecules closely linked with function of the molecule
 Metabolism
 The sum of all the biochemical reactions that happen in the body
 The breaking down of molecules in order to obtain ATP that will then be
used to build other molecules needed for life
What were the first molecules?
 Chemical evolution occurred billions of years ago
 Thousands of carbon based molecules emerged from the more
simple molecules that existed on early Earth
 Raw ingredients on earth that were used to create life:
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Carbon dioxide (CO2)
Hydrogen gas (H2)
Water (H2O)
Nitrogen gas (N2)
Ammonia (NH3)
Hydrogen sulfide (sulphide) (H2S)
Energy source (electrical discharge lightning)
 All these led to the first Amino acids…what is the structure of AA?
 AA led to first proteins=LIFE
4 most abundant elements in living
organisms
 Hydrogen
 Carbon
 Oxygen
 Nitrogen
 They account for 99% of all atoms found in living things
 Carbon however, is the most important…why do you think
so?
Carbon
 The element of LIFE!
 Found in all living organisms!
 We are always looking for carbon based life forms
 Organic molecules: molecules that contain carbon
 C6H12O6, CO2, CH4
 Some molecules are made of just CARBON and HYDROGEN…we
call these HYDROCARBONS
 These are important in FUEL (aka GASOLINE!!)
 Many organic molecules, such as fats, have hydrocarbon components
 Hydrocarbons can undergo reactions that release a large amount of energy
 Inorganic molecules: molecules that do not contain carbon
 H2O, NH3, O2
LE 4-4
Hydrogen
(valence = 1)
Oxygen
(valence = 2)
Nitrogen
(valence = 3)
Carbon
(valence = 4)
Structure of Carbon
 Structure
 Valence electrons: 4
 How many bonds can carbon make with other atoms?
 4: single, double, or triple…as long as it has 4 lines touching it
 This makes carbon a versatile atom…it can make long chains of
carbons, branched carbon structures, even ring structures with
itself
Drawing and numbering carbon structures
 Start with the carbon that is in a carboxyl functional group…that is #1
and then follow sequentially
 In ring structures, the C for carbon may be omitted…it is understood that
where ever there are vertices, there is a carbon atom
 H’s for hydrogen are also left off for simplicity
LE 4-5
Ethane
Propane
Butane
2-methylpropane
(commonly called isobutane)
Length
Branching
1-Butene
Double bonds
Cyclohexane
Rings
2-Butene
Benzene
Some important words to know
 Molecule
 Group of covalently bonded atoms
 Macromolecule
 large molecules composed of thousands of covalently connected atoms
 Functional Groups
 Group of atoms within a molecule that interact in PREDICTABLE ways
 Polar, non-polar, acidic, basic, charged (+/-)
 Hydroxyl group
 Carbonyl group
 Carboxyl group
 Amino group
 Sulfhydryl group
 Phosphate group
LE 4-10aa
STRUCTURE
(may be written HO—)
Ethanol, the alcohol present in
alcoholic beverages
NAME OF COMPOUNDS
Alcohols (their specific names
usually end in -ol)
FUNCTIONAL PROPERTIES
Is polar as a result of the
electronegative oxygen atom
drawing electrons toward itself.
Attracts water molecules, helping
dissolve organic compounds such
as sugars (see Figure 5.3).
LE 4-10ac
STRUCTURE
EXAMPLE
Acetic acid, which gives vinegar
its sour taste
NAME OF COMPOUNDS
Carboxylic acids, or organic acids
FUNCTIONAL PROPERTIES
Has acidic properties because it is
a source of hydrogen ions.
The covalent bond between
oxygen and hydrogen is so polar
that hydrogen ions (H+) tend to
dissociate reversibly; for example,
Acetic acid
Acetate ion
In cells, found in the ionic form,
which is called a carboxylate group.
LE 4-10ba
STRUCTURE
EXAMPLE
Glycine
Because it also has a carboxyl
group, glycine is both an amine and
a carboxylic acid; compounds with
both groups are called amino acids.
NAME OF COMPOUNDS
Amine
FUNCTIONAL PROPERTIES
Acts as a base; can pick up a
proton from the surrounding
solution:
(nonionized) (ionized)
Ionized, with a charge of 1+,
under cellular conditions
LE 4-10bc
STRUCTURE
EXAMPLE
Glycerol phosphate
NAME OF COMPOUNDS
Organic phosphates
FUNCTIONAL PROPERTIES
Makes the molecule of which it
is a part an anion (negatively
charged ion).
Can transfer energy between
organic molecules.
What are macromolecules made of?
• A polymer is a long molecule consisting of many similar building blocks
called monomers
Poly=many
Mono=one
Think of a beaded bracelet….
Large variety of polymers but there are less than 50 like the alphabet…lots of
words, only 26 letters
• Polymerization: THE PROCESS OF MAKING A LARGER MOLECULE BY
PUTTING TOGETHER SMALLER MOLECULES
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• Three of the four classes of life’s organic molecules are polymers:
 Carbohydrates
 Proteins
 Nucleic acids
***Lipids/fats are not polymers but they are still macromolecules
Brief Overview of 4 Macromolecules
 Carbohydrates
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Monomer: monosaccharaides and disaccharides
Polymer: polysaccharides aka complex carbohydrates (Starches, cellulose)
 Proteins
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Monomer: Amino acids
Polymer: Polypeptide Chain (PROTEINS)
 Nucleic Acids
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Monomer: Nucleotide
Polymer: Nucleic Acids (DNA and RNA)
 Lipids, fats, oils and steroids
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Monomer: NONE
Polymer: NONE
Making and Breaking Polymers
 Polymerization: making polymers
 Dehydration/condensation Reaction
 Dehydrate means water loss
 When a water molecule (H-OH) is released to join a monomer to another monomer
 Hydrolysis
 Hydro- water
 Lysis- to break down
 Def: to break apart or disassemble a polymer by adding water (H-OH)
LE 5-2
Short polymer
Unlinked monomer
Dehydration removes a water
molecule, forming a new bond
Longer polymer
Dehydration reaction in the synthesis of a polymer
Hydrolysis adds a water
molecule, breaking a bond
Hydrolysis of a polymer
Polymerization (polymerisation)
 Process of putting together many monomers to make a larger
polymer
 Examples of common polymers:
 Natural:
 Rubber
 cellulose
 Industrially produced:
 Polyester
 Polythene
 Polyvinyl chloride (PVC)
 Nylon
 All of the above are carbon based subunits containing thousands of
carbon atoms joined end to end
Carbohydrates
 Divided into 3 main groups:
 Monomer: Monosaccharide or Disaccharide
 Polymer: Polysaccharide
 Link between monomers is called: Glycosidic Linkage
 Formed by a dehydration/condensation reaction
 Always have Carbon, Hydrogen, and Oxygen
 Cx(H2O)y
 Common name: sugar
 End with suffix “-ose”
 Function: Energy/fuel, structure, storage
 GLUCOSE!!!!
 What all cells need for energy
Monosaccharides
 Sugars
 Dissolve easily in water to form sweet solutions
 Large carbs (starches and cellulose) do not dissolve
 Think about your towels and clothes, duh!
 General formula: (CH2O)n
 Consist of single sugar molecule (hence mono)
 Classified according to # of carbon atoms in each molecule
 Trioses (3C)
 Pentoses (5C)
 Ribose & deoxyribose
 Hexoses (6C)
 Glucose, fructose, galactose
 Ex: Glucose, Fructose, Galactose
 2 major Functions:
 1. Energy source in respiration (b/c of large # of C-H bonds that can be broken to
release ATP)
 2. Important building blocks for larger molecules
Molecular and structural formulas
 Molecular formulas show the # of each atom in a molecule
but not how they are arranged
 Molecular Formula for hexoses: C6H12O6
 Both glucose and fructose have the same molecular
formula… C6H12O6
 Structural formulas are used to show the arrangements of
the atoms
 Ring structures
 Pentoses and hexoses are a chain of carbon atoms that are long
enough to close up on each other and form rings (occurs
in AQUEOUS environment)
 This ring structure is more stable than a chain, therefore atoms in
these molecules stay inn rings not chains
 Glucose: carbon #1 joins the oxygen attached to carbon
#5…carbon #6 is not part of the ring
 C6H12O6
Glucose
 Hydroxyl groups on carbon #1 can either
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be above the plane or below the plane
Different spatial arrangement of atoms in the
same molecule are called ISOMERS
These isomers of glucose are important in
the formation of polysaccharides: starch,
cellulose and glycogen
Hydroxyl group on C-2 is always below
the plane, and the following carbon atoms
alternate
Alpha Glucose
 hydroxyl group is BELOW the ring plane
 Beta Glucose
 Hydroxyl group is ABOVE the ring plane
Alpha vs
Beta
glucose
Dissaccharides
 formed by glycosidic linkage
 join together two hydroxyl groups by a process called
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CONDENSATION (dehydration)
literally lose a water molecule
HYDROLYSIS is the opposite of condensation rxn…it
causes the breaking of a glycosidic linkage…occurs during
the digestion of disaccharides and polysaccharides
Both reactions controlled by enzymes
Common disaccharides: Maltose and Sucrose
Lactose, Maltose and Sucrose
Functions of Monosaccharides &
Disaccharides
Good sources of energy for living things
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Used in respiration  ATP
Due to solubility, this is the form carbohydrates are
transported through an organisms body
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Animals  glucose is dissolved in blood plasma for transport
Plants  sucrose is transported in phloem sap
Reducing vs.Non-reducing Sugars
Reducing sugars
Non-reducing sugars
 All monosaccharides
 Disaccharide SUCROSE
(glucose)
 Some disaccharides
(maltose)
 Carry our reduction
reaction (donates
electrons) and thus become
oxidised
 Do NOT carry our
reduction reactions
Reducing Sugar Test
 Benedicts Solution/Reagent
 Blue colored solution
 Copper (II) sulfate in an alkaline solution
 In the presence of reducing sugars, copper (II) sulfate (contains
copper II ions…Cu2+ ) becomes reduced to insoluble redbrown copper-oxide (contains copper I…Cu1+ )
 it loses 1+ charge because it has gained an electron from the reducing
sugar
 Red-brown copper oxide is visible as a brick red precipitate
 Reducing sugar + Cu2+  oxidized sugar + Cu1+
BLUE
RED/BROWN
Reducing Sugar Test Continued
 Reducing sugar + Cu2+  oxidized sugar + Cu1+
BLUE
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RED/BROWN
Intensity of red color is related to concentration of reducing sugar
Benedicts solution is added to solution being tested
Mixture is heated in warm water bath
In presence of reducing sugar, gradual color change occurs…
 Green  yellow  orange  red/brown
 Must use EXCESS of benedicts solution to ensure relationship between color
intensity on concentration of reducing sugar
 2 ways to measure concentrations:
 Compare to set of colour standards previously made with known reducing sugar concentrations
 Use a colorimeter to measure concentrations more precisely
Test for non-reducing sugar (sucrose)
 Benedicts test would yield NEGATIVE result (no color change, solution
remains blue)
 Testing a non-reducing sugar
 First break disaccharide a into monosaccharides using ACID HYDROLYSIS
(use hydrochloric acid and a warm water bath)
 Benedicts requires ALKALINE environment, so after heating sugar/HCL
mixture, add sodium hydroxide in excess to NEUTRALIZE
 THEN, add Benedicts reagent to neutralized solution and heat
 Results:
 Blue to brick red precipitate = non-reducing sugar present
 No color change for either test = no sugars present at all
 Mixture of reducing and non-reducing sugars will yield a heavier
precipitate in the non-reducing sugar test than in the reducing sugar test
previously described
Reducing Sugar Test
 Safety
 Equipment
 How to read syringe
 Range of Solutions
of different
concentrations
 0% water
 20%solution
 50% solution
 100% solution
Practice Question Set 2 (6 questions)