ib bio 2015

1. • Essential idea: Living organisms control their
composition by a complex web of chemical reactions.
2.1 Molecules to metabolism

2. Understandings
Statement Guidance
2.1 U.1 Molecular biology explains living processes in
terms of the chemical substances involved.
2.1 U.2 Carbon atoms can form four covalent bonds
allowing a diversity of stable compounds to exist.
2.1 U.3 Life is based on carbon compounds including
carbohydrates, lipids, proteins and nucleic acids.
Sugars include monosaccharides and
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 U.4 Metabolism is the web of all the enzyme-
catalyzed reactions in a cell or organism.
2.1 U.5 Anabolism is the synthesis of complex molecules
from simpler molecules including the formation
of macromolecules from monomers by
condensation reactions.
2.1 U.6 Catabolism is the breakdown of complex
molecules into simpler molecules including the
hydrolysis of macromolecules into monomers.

3. Applications and Skills
Statement Guidance
2.1 A.1 Urea as an example of a compound that is
produced by living organisms but can also be
artificially synthesized.
2.1 S.1 Drawing molecular diagrams of glucose, ribose, a
saturated fatty acid and a generalized amino
acid.
Only the ring forms of D-ribose, alpha–D-
glucose and beta-D-glucose are expected in
drawings.
2.1 S.2 Identification of biochemicals such as sugars,
lipids or amino acids from molecular diagrams.
Students should be able to recognize from
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.

4. Atoms
• Atoms are the smallest forms of matter that
retain the chemical characteristics of a given
element
• Atoms have a nucleus , which:
Contains protons (p)
May contain neutrons (n)
• Clouds of electrons (e) surround the nucleus
2.1 U.1 Molecular biology explains living processes in terms of the
chemical substances involved.

15. • Most common chemical elements (98 % of mass of living organisms
comes from O, C, H, N, Ca, and P ):
•Carbon (C)
•Oxygen (O)
•Hydrogen (H)
– Nitrogen which is found in protein (CHON)
– Calcium which is found in bones / teeth
– Iron which is to be found in hemoglobin (animal)
– Sodium which is needed for a nerve impulse
– Phosphorus found in cell membrane structures
– Sulfur found in several key amino acids
2.1 U.1 Molecular biology explains living processes in terms of the
chemical substances involved.

16. Bonds
• Atoms stick together by linkages we call bonds.
• All biological reactions involve some sort of reorganization of bonds.
• Bond reorganization (breakage or building of bonds) results in the
uptake or release of energy.
• Bond energy is the energy needed to break a given bond.
Types of Bonds
1. Ionic Bonds
 In ionic bonds, electrons are donated by one atom to
another
 An electronegative atom steals an electron from another
atom to fill its valence shell
 That is, one or more electrons LEAVE one atomic center to
‘live’ with another
2.1 U.1 Molecular biology explains living processes in terms of the
chemical substances involved.

17. Ionic Bonds in Salt

18. 2. Covalent Bonds
• In covalent bonds, two electrons are shared per bond
• More than one bond can occur between two atoms

19. • Biochemistry a study of biological processes from the
structures of the molecules and how they interact with
each other
• There are many molecules important to living organisms
including water, carbohydrates, lipids, proteins and nucleic
acids
• Molecular biologists break down biochemical processes
into their component parts (reductionism)
• When they look at the sum of all these reactions as a
whole, they can study the emergent properties of that
system
2.1 U.1 Molecular biology explains living processes in terms of the
chemical substances involved.

20. 2.1 A.1 Urea as an example of a compound that is produced by living
organisms but can also be artificially synthesized.
Source: http://www.biog1445.org/demo/08/nitrogenouswastes.html
Nature of Science: Falsification of theories—
the artificial synthesis of urea helped to falsify
vitalism. (1.9)
Wöhler accidentally synthesized urea in 1828, while
attempting to prepare ammonium cyanate. In a letter to a
colleague he says “I can no longer, so to speak, hold my
chemical water and must tell you that I can make urea
without needing a kidney, whether of man or dog". This is
supposed to undermine vitalism as organic chemicals were
previously thought to be synthesized only by organisms.
Source: http://en.wikipedia.org/wiki/File:Friedrich_woehler.jpg

21. Vitalism nowadays has no credit
as a theory, but the statement
from the previous page is seen
by many from a historical
perspective to be untrue. For an
outline on vitalism read this
article by William Betchel. The
application statement above
implies that the central tenet
Vitalism is ‘only organisms can
synthesize organic compounds’.
This is not accurate, in essence
vitalism proposes that an
unknowable factor is essential
in explaining life. Vitalism on
this premise is both unscientific
and and unfalsifiable.

22. 2.1 U.2 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.
• Carbon atoms contain four
electrons in their outer shell
allowing them to form four
covalent bonds with potential
four other different atoms, e.g.
methane (CH4).
• Covalent bonds are the
strongest type of bond between
atoms. Stable molecules can be
formed.
• The result of these properties
is an almost infinite number
of different possible
molecules involving carbon. http://commons.wikimedia.org/wiki/File:Carbon-atom.jpg
http://upload.wikimedia.org/wikipedia/commons/3/3e/Methane-2D-dot-cross.png

23. 2.1 U.3 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
http://www.doctortee.com/dsu/tiftickjian/cse-img/biology/chemistry/polysaccharides.jpg
pentose (5 carbon) monomers

24. 2.1 U.3 Life is based on carbon compounds including carbohydrates,
lipids, proteins and nucleic acids.
Lipids
• Lipids are a group of organic molecules that are insoluble in water but
soluble in non-polar organic solvents
• Common lipids include triglycerides (fats – solid at room temperature
and oils – liquid at room temperature), phospholipids and steroids
http://hyperphysics.phy-astr.gsu.edu/hbase/organic/imgorg/lipid.gif

25. 2.1 U.3 Life is based on carbon compounds including carbohydrates,
lipids, proteins and nucleic acids.
Leucine – an amino acid
Proteins
• Contain carbon, hydrogen, oxygen and nitrogen (additionally sulfur 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

26. 2.1 U.3 Life is based on carbon compounds including carbohydrates,
lipids, proteins and nucleic acids.
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
http://www.nature.com/scitable/topicpage/Chemical-Structure-of-RNA-348

27. To the right is the structure of alpha Glucose.
•C6H12O6
•Carbon 5 is connected to Carbon 1
•Each Carbon has an -OH group
•Each Carbon has an -H (C6 has 2)
To the right is the structure of alpha beta Glucose.
•C6H12O6
•Carbon 5 is connected to Carbon 1
•Each Carbon has an -OH group
•Each Carbon has an -H (C6 has 2)
2.1 S.2 Identification of biochemicals such as sugars, lipids or amino
acids from molecular diagrams.

28. Galactose
• To the right is the structure of Galactose
• Sugar which is less sweet than glucose.
• It is found in dairy products, in sugar
beets and gums. When combined with
glucose, through a dehydration reaction,
the result is the disaccharide lactose
found in most milks.
Ribose
To the right is the structure of Ribose
•C5H10O5
•Carbon 1 is attached to Carbon 4
•Each Carbon has a -H group (C5 has 2)
•Each Carbon has a -OH group
2.1 S.2 Identification of biochemicals such as sugars, lipids or amino
acids from molecular diagrams.

29. Lipid Molecule Structure
Glycerol
• 3 carbons
• each has a -OH group
• others are single C bonds
Fatty Acid This is a long chain of CH2 with an carboxyl group (COOH)
at the end . The other end is methyl group CH3
2.1 S.2 Identification of biochemicals such as sugars, lipids or amino
acids from molecular diagrams.

30. H3C (CH2)n C
O
OH
General structural formula for a fatty* acid
*I prefer “big boned”
Carboxylic group
Chain (or ring) of carbon
and hydrogen atoms
http://www.eufic.org/article/pt/nutricao/gorduras/expid/23/
2.1 S.2 Identification of biochemicals such as sugars, lipids or amino
acids from molecular diagrams.

31. • Amino acids are the
building blocks of
proteins.
• AA + AA + AA … =
protein
• Every amino acid has:
– Terminal Hydrogen
– Carboxyl Group
– Amino group
– Variable group
(R group)
2.1 S.2 Identification of biochemicals such as sugars, lipids or amino
acids from molecular diagrams.

32. 2.1 S.2 Identification of biochemicals such as sugars, lipids or amino
acids from molecular diagrams.

33. 2.1 S.2 Identification of biochemicals such as sugars, lipids or amino
acids from molecular diagrams.

34. 2.1 S.2 Identification of biochemicals such as sugars, lipids or amino
acids from molecular diagrams.

35. 2.1.S1 Drawing molecular diagrams of glucose, ribose, a saturated fatty acid
and a generalized amino acid.
Try drawing by hand (or on
eMolecules) the following
molecules:
• Glucose
• Ribose
• A generalized saturated
fatty acid
• A generalized amino acid
• An example amino acid
e.g. Alanine (the simplest)
n.b. you also need to test
yourself 15 mins, 1 day and
one week later to make sure
you remember
eMolecules online drawing tool
http://www.emolecules.com/

36. Metabolism is divided into two
components;
 Anabolism (building large molecules
from smaller ones)
 Catabolism (breaking down of large
molecules into their component
parts)
• Anabolic reactions require
energy as you are building large
molecules from small ones (takes energy
to build things)
• Some anabolic processes are protein
synthesis, DNA synthesis and replication,
photosynthesis, and building complex
carbohydrates, such as cellulose, starch
and glycogen
• If you can’t remember which one is
which, think anabolic steroids are used
to build muscles in athletes and body
builders and catapults are used to break
down walls in wars
2.1 U.5 Anabolism is the synthesis of complex molecules from simpler
molecules including the formation of macromolecules from monomers
by condensation reactions.
http://fc02.deviantart.net/fs70/f/2013/014/1/
9/bodybuilder_159_by_stonepiler-d5rhr6l.jpg

37. Maltose synthase condenses
two molecules of glucose
into maltose forming a
glycosidic bond
A ribosome condenses two
amino acids into a dipeptide
forming a peptide bond
Examples of anabolism by condensation
http://commons.wikimedia.org/wiki/File:Peptidformationball.svg
The bonds formed are types of covalent bonds.
Bonding monomers together creates a polymer
(mono = one, poly = many)

38. 2.1 U.6 Catabolism is the breakdown of complex molecules into simpler
molecules including the hydrolysis of macromolecules into monomers.
• Catabolism are reactions
that break down larger
molecules into smaller ones
or their component parts
• Catabolic reactions release
energy (sometimes captured
in the form of ATP)
• Some examples of catabolic
reactions are digestion of
food, cellular respiration, and
break down of carbon
compounds by decomposers
• Think of "catapults" used to
break down enemy walls
during wars
http://www.ancient.eu/uploads/images/2286.jpg?v=1391417170

39. 2.1 U.5 Catabolism is the breakdown of complex molecules into simpler
molecules including the hydrolysis of macromolecules into monomers.
Lactase hydrolyses Lactose
into Glucose and Galactose
breaking the glycosidic bond
http://commons.wikimedia.org/wiki/File:Amino_acid4.png
http://commons.wikimedia.org/wiki/File:Lactose_hydrolysis.svg
A protease hydrolyses a
dipeptide into two amino
acids breaking the peptide
bond
Examples of catabolism by hydrolysis

40. 2.1 U.5 Anabolism is the synthesis of complex molecules from simpler molecules including the formation of
macromolecules from monomers by condensation reactions.
2.1 U.5 Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of
macromolecules into monomers.

41. Bibliography / Acknowledgments
Jason de Nys