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2.1 Molecules To Metabolism
2.1 Molecules To Metabolism
1 Molecules to metabolism
By Chris Paine
http://www.bioknowledgy.info/
Understandings
Statement Guidance
2.1.U1 Molecular biology explains living processes in
terms of the chemical substances involved.
2.1.U2 Carbon atoms can form four covalent bonds
allowing a diversity of stable compounds to exist.
2.1.U3 Life is based on carbon compounds including Sugars include monosaccharides and
carbohydrates, lipids, proteins and nucleic acids. disaccharides. Only one saturated fat is
expected and its specific name is not
necessary. The variable radical of amino acids
can be shown as R. The structure of individual
R-groups does not need to be memorized.
2.1.U4 Metabolism is the web of all the enzyme-catalysed
reactions in a cell or organism.
2.1.U5 Anabolism is the synthesis of complex molecules
from simpler molecules including the formation of
macromolecules from monomers by condensation
reactions.
2.1.U6 Catabolism is the breakdown of complex molecules
into simpler molecules including the hydrolysis of
macromolecules into monomers.
Applications and Skills
Statement Guidance
2.1.A1 Urea as an example of a compound that is
produced by living organisms but can also be
artificially synthesized.
2.1.S1 Drawing molecular diagrams of glucose, ribose, a Only the ring forms of D-ribose, alpha–D-
saturated fatty acid and a generalized amino acid. glucose and beta-D-glucose are expected in
drawings.
2.1.S2 Identification of biochemicals such as sugars, lipids Students should be able to recognize from
or amino acids from molecular diagrams. molecular diagrams that triglycerides,
phospholipids and steroids are lipids.
Drawings of steroids are not expected.
Proteins or parts of polypeptides should be
recognized from molecular diagrams showing
amino acids linked by peptide bonds.
2.1.U1 Molecular biology explains living processes in terms of the chemical substances involved.
https://en.wikipedia.org/wiki/File:DNA_chemical_structure.svg
2.1.U1 Molecular biology explains living processes in terms of the chemical substances involved.
https://en.wikipedia.org/wiki/File:DNA_chemical_structure.svg
2.1.U2 Carbon atoms can form four covalent bonds allowing a diversity of stable compounds to exist.
Despite only being the 15th most abundant element on the planet carbon
forms the backbone of every single organic molecule.
Covalent bonds are the strongest Carbon atoms contain four electrons
type of bond between atoms. in their outer shell allowing them to
Stable molecules can be formed. form four covalent bonds with
potential four other different atoms,
e.g. methane (CH4).
http://commons.wikimedia.org/wiki/File:Carbon-atom.jpg
http://www.ks.uiuc.edu/images/ofmonth/2002-11/titin.jpg
http://upload.wikimedia.org/wikipedia/commons/3/3e/Methane-2D-dot-cross.png
2.1.U3 Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.
Carbohydrates
• Contain carbon, hydrogen and oxygen
• Organic compounds consisting of one or more simple sugars
• Monomers follow the general basic formula of (CH2O)x
• Monomers are commonly ring shaped molecules
Glucose – a hexose
(6 carbon) monomer
Lipids
Lipids The common lipids triglycerides, phospholipids and steroids can be distinguished in
molecular diagrams use the annotated features.
http://www.ib.bioninja.com.au/_Media/lipid-types_med.jpeg
2.1.U3 Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.
Proteins
• Contain carbon, hydrogen, oxygen and nitrogen (additionally sulphur is common
component, but it is not present in all proteins)
• Proteins are large organic compounds made of amino acids arranged into one or more
linear chains
Nucleic acids
• Contain carbon, hydrogen,
oxygen, nitrogen and
phosphorus
• Chains of sub-units called
nucleotides
• Nucleotides consist of base,
sugar and phosphate groups
covalently bonded together
• If the sugar is ribose then the
nucleic acid formed is RNA if the
sugar is deoxyribose then DNA is
formed
phosphate
base
sugar
http://www.nature.com/scitable/topicpage/Chemical-Structure-of-RNA-348
2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.
http://commons.wikimedia.org/wiki/File:Alanine.png
http://commons.wikimedia.org/wiki/File:Arginine.png
http://commons.wikimedia.org/wiki/File:Leucine.png
2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.
http://commons.wikimedia.org/wiki/File:AminoAcidball.svg
2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.
The amine
group (NH2)
The carboxyl
group (COOH)
n.b. this is an
acidic group
What shall we
call this class
of molecule?
http://commons.wikimedia.org/wiki/File:Filos_tercer_logo.JPG
2.1.S2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.
Explore the IUBMB-Sigma-Nicholson Metabolic Pathways Chart and realise that most
cells use the majority of the pathways and that every path is controlled by a different
enzyme. The metabolism as a concept is the sum of all the pathways used in a
particular cell.
http://commons.wikimedia.org/wiki/File:Peptidformationball.svg
2.1.U5 Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of
macromolecules into monomers.
A protease hydrolyses a
dipeptide into two amino
acids breaking the peptide
bond
http://commons.wikimedia.org/wiki/File:Lactose_hydrolysis.svg
http://commons.wikimedia.org/wiki/File:Amino_acid4.png
Condensation & Hydrolysis – IB Style Qns
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answers
A condensation reaction is when two molecules are combined to form one single
larger molecule, with the loss of a water molecule
Condensation makes larger molecules from smaller sub-units whereas Hydrolysis breaks
larger molecules into their smaller sub-units.
When drawing molecular diagrams which show all the atoms which make up a molecule and
the way in which they are bonded together it is first important to know how many bonds each
molecule has.
When drawing the biological molecules checking that each atom has the right number of
bonds, will avoid mistakes.
A good way to remember the structures is to draw each diagram in three steps
Hints:
Hints:
Drawing ribose
Hints:
2
Drawing a saturated fatty acid
Hints:
Hints:
This molecule is similar to a fatty acid because of the carboxyl group (C=O & -OH)
Remember N has just 3 bonds
The R group represents the part of the molecule which is different in each amino acid.
Reading Activity: How was vitalism disproved buy the synthesis of urea?
Read one or more of the following articles and make notes to explain how the synthesis of
urea helped to disprove the theory of vitalism - the idea that there is a 'vital force' in living
organisms as well as in organic molecules.
Web links:
http://youtu.be/YNmfSHSq_HY
http://humantouchofchemistry.com/urea-and-the-beginnings-of-organic-chemistry.htm
You might see the term “dehydration reaction”
mentioned interchangeably with condensation reaction.
http://www.flickr.com/photos/zachd1_618/5738829330/
2.1.A1 Urea as an example of a compound that is produced by living organisms but can also be artificially synthesized.
AND Nature of Science: Falsification of theories - the artificial synthesis of urea helped to falsify vitalism. (1.9)
Vitalism was a doctrine that dictated that organic molecules could only be synthesised by living systems
It was believed that living things possessed a certain “vital force” needed to make organic molecules
Hence organic compounds were thought to possess a non-physical element lacking from inorganic
molecules
In 1828, Frederick Woehler heated an inorganic salt (ammonium cyanate) and produced urea
Urea is a waste product of nitrogen metabolism and is eliminated by the kidneys in mammals
The artificial synthesis of urea demonstrates that organic molecules are not fundamentally different to
inorganic molecules
Bibliography / Acknowledgments
Jason de Nys