BIOLOGY 1A03 Chapter Notes -Hemoglobin, Chemical Formula, Thiol

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Biology 1AA3 - Textbook Notes - Chapter 3
INTRODUCTION
Idea of Chemical Evolution first introduced by Alexander Oparin in 1923 and then again by JBS Haldane.
o Can now be considered as an official scientific theory.
o The theory consists of two components:
Pattern: Increasingly complex carbon-containing molecules formed in the atmosphere and ocean of
ancient Earth.
Process responsible for Pattern: Conversion of energy, from sunlight and other sources , into chemical
energy in the bonds of large, complex molecules.
This theory has been modified as well since more research has been conducted and new information has been
recovered.
It can be broken down into four parts essentially:
o Chemical evolution: Started with the production of small organic compounds such as formaldehyde and
hydrogen cyanide -> REACTANTS WERE H2, CO3, CH4 and NH3.
o Small organic compounds combined to form mid sized molecular compounds such as AMINO ACIDS, SUGARS
AND NITROGENOUS BASES.
o These molecules accumulated in shallow waters of ancient ocean --> complex solution formed called
PREBIOTIC SOUP.
o MID SIZED MOLECULES joined to form large molecules found in cells today such as PROTEINS, NUCLEIC
ACIDS AND COMPLEX CARBOHYDRATES.
o These large molecules are made up of distinctive chemical subunits (monomers).
Proteins - Made up of Amino Acids
Nucleic Acids - Made up of Nucleotides
Complex Carbs - Made up of Sugars
o Origin of life was possible when one of these large molecules gained the ability to replicate itself.
Self replicating molecule began to multiply by means of chemical reactions that it controlled.
Chemical evolution led to Biological Evolution.
PROTEINS: STRUCTURE, FUNCTION AND SIGNIFICANCE
Structure Proteins are basically made up of Amino acids
o As Miller proposed later research also found that amino acids and other compounds of the prebiotic soup
are formed readily under conditions that accurately simulate the atmosphere and the oceans ancient Earth.
o Amino acids are basically building blocks of proteins Most of the proteins in the humans body are
composed of just 21 amino acids.
o All amino acids have similar backbone structure
o It contains carbon atoms that 3 similar bonds:
The first bond is with NH2 which is known as an amine or amino group.
The second group is COOH which is the carboxyl group this group is acidic due to the high
electronegativity of the two oxygen atoms.
They pull electrons away from the hydrogen and hence the molecule is able to lose the
H+ quite easily.
Third bond is with a hydrogen atom.
These are the bonds which are present in every amino acid.
The fourth group is what makes each amino acid unique R-group or side chains
Side chains can be one single H atom or a large group of atoms
Different amino acids in the body can have:
Polar Side Chains
Non-Polar Side Chains
Electrically Charged Side Chains
o R-groups also influence the reactivity of the amino acids.
There can either be R-groups that are made up entirely of C and H.
Or they can be made up of hydroxyl, carboxyl, sulfhydryl groups.
o Isomers molecules of the same molecular formula may not have the same molecular structure.
Structural Isomers same atoms but differ in order that the covalently bonded atoms are
attached in.
Geometric Isomers same atoms but differ in the arrangement of atoms or groups on either
side of a double bond or ring structure.
Optical Isomers same atoms but differ in the arrangement of atoms or groups around a carbon
atom that has four different groups attached to it. Eg refer to DOPA in lecture notes
Amino acids mostly have Optical Isomers these isomers cannot be super imposed on one
another they are mirror images and are not in a plane cannot be bisected to produce
identical halves.
All amino acids have optical isomers except for Glycine.
Cells have “left-handed” version of amino acid and if the other is introduced into the cell it will
not function properly.
Once again the structure of the amino acid determines the function.
o How are amino acids linked to form proteins?
Amino acid = molecular subunit that joins to form a larger molecule = MONOMER
Protein = large molecules made up of numerous subunits of the same kind = POLYMER
Process of forming Polymers = POLYMERIZATION
A MACROMOLECULE = large molecules made up of smaller molecules joined together
Chemical evolution states that the monomers in the prebiotic soup polymerized to form
proteins and other types of macromolecules found in organisms.
Function - Proteins have numerous functions related to them:
o Carbonic Anhydrase: Helps to transport CO2 from cells to lungs where it can be breathed out.
o Hemoglobin is important in transporting oxygen to cells.
o Some of the functions of proteins include:
Defence - Antibodies and Complement Proteins --> destruction of disease causing agents such as
bacteria.
Movement - Motor Proteins and Contractile Proteins --> movement of the cell itself and large
molecules as well as other components inside cell.
Catalysis - Proteins specialized to catalyze or speed up chemical reactions --> these are called
Enzymes.
Amylase is a good example of an enzyme present in the saliva that can break down carbs into
sugars when mastication occurs.
Signalling - Proteins are responsible for performing cell to cell communication via carrying and
receiving of signals.
Peptide hormones bind to receptor proteins on particular cells and the activity of cell in
response changes.
Structure - Provide mechanical support to cells and create structures such as fingernails and hair
(keratin).
Blood cell walls have structural proteins that connect to structural proteins inside the cell itself.
These proteins help to keep the cells flexible and in their regular disc-like shape.
Transport - Responsible for allowing particular molecules to enter and exit a cell and for carrying
specific compounds throughout the body.
Transthyretin - Cerebrospinal fluid carrier of Thyroxine (hormone released by Thyroid gland) and
it also binds to retinol in the eyes (very important for vision).
Hemoglobin is another transport protein which helps with the transportation of oxygen
throughout the body.
Significance
o Presence of amine group and carboxyl group is very important to an amino acid water pH 7 amino
acid acts as base due to concentration of H+
o Leads to NH2 part attracting proton and becoming NH3
+ while the COOH part loses a proton and become
COO-.
o This helps to allow amino acid to stay in solution and interact with each other and with other solutions
o Also adds to their chemical reactivity.
o Amino acids that are NON POLAR do not have charged or electronegative atoms to form hydrogen
bonds with water.
This makes these side chains HYDROPHOBIC unable to interact with water.
They coalesce in aqueous solutions these side chains tend to bind together in aqueous
solutions
o Polar or electrically charged side chains interact readily with water and hence are HYDROPHILIC.
Dissolve in water or aqueous solutions.
TABLE 3.2 IMP!!!!!! AND FIGURE 3.3!!!
o R-groups of C and H hardly react while other functional groups are very reactive such as hydroxyl.
o R-groups affect the properties and functions of amino acids.
EARLY ORIGIN OF LIFE EXPERIMENTS
Stanley Miller Experiment 1953
o Question Can complex organic compounds be synthesized from the simple molecules present in
Earth’s early atmosphere and ocean? Is it possible to recreate the first steps in chemical evolution by
stimulating ancient Earth conditions in laboratory?
o Experiment designed to produce a microcosm of ancient earth.
Large glass flask represented the atmosphere and contained the gases CH4, NH3 and H2 they
all have high free energy
This flask connects to a smaller flask which held 200mL of liquid water
This water was boiled such that the water vapour mixed with the gases in the large flask.
Condensation leads the mixture of gases to transfer back into the small flask where it boiled
again and hence the water vapour constantly keeps circulating through the system.
IMP: molecules stimulated in atmosphere react with one another rain carries them into the
stimulated ocean and forms a stimulated version of the prebiotic soup.
Miller started to send electrical discharges across electrodes he’d inserted into the atmosphere
these added intense electrical energy to the reaction mix.
o Results
After about a day or so the mixture began to turn pink and soon it turned red and cloudy
Solution now contained complex carbon-containing compounds some of which had carbon-
carbon bonds.
Recreation of the start of a chemical evolution
Large quantities of HCN, H2CO (formaldehyde) were found
This was important as these compounds are required for formation of more complex organic
molecules some of which were present in the mixture.
o Conclusion the experiment had produced compounds that were fundamental to life: AMINO ACIDS