quick notes for IB Biology revisions

2. Introduction
 Biochemistry - is the set of chemical reactions that
happen in the cells of living organisms to sustain life.
 Chemical Elements in Living things: C, H, O, N, S
 Processes:
 Metabolism – the sum total of all biochemical processes
 Catabolism – breaking down of large molecules
 Ex. Cellular respiration, Digestion
 Anabolism – building up of molecules
 Ex. Photosynthesis, carbon fixation, Synthesis of
biomolecules

3. Terms to know
Element - matter composed of atoms that all have the same atomic
number (protons).
Atom - the smallest component of an element that still has properties of
the element, consisting of a positively charged nucleus surrounded by a
charged cloud of electrons."+" and "-" charges strongly attract.
Proton - particle in the nucleus with a positive charge of +1 and an atomic
mass number of 1 Dalton.
Neutron - a non-charged nuclear particle with the same mass as the
proton.
Electron - negatively charged particle (-1) with a mass 1/1837 of that of a
proton.
Isotope - atoms with the same number of protons and electrons, but
different numbers of neutrons.

4. Electrons determine chemical
properties of elements
 Chemical reactions involve sharing
(COVALENT) or exchanging electrons
(IONIC).
 Absorption of energy can cause an electron
to move up to a higher energy level.
 The atom is stable when the outermost
energy level of most atoms has eight
electrons (Octet Rule).
 The H atom can carry electrons for
transferring energy.
 Oxygen has a strong affinity for electrons.
 Redox reaction transfer of electrons from
one molecule (oxidized) to another
(reduced).
 Stability can be achieved by adding, losing,
or sharing electrons.
element
number of
covalent
bonds
H 1
O 2
N 3
C 4
S 5

5. Chemical bonds and Attractive
forces
 Covalent bonds – electrons are shared
 Ionic bonds – electrons are transferred
 Electronegativity - tendency for atoms to bind electrons.
 Oxygen (O) - electronegativity of 3.5 has a strong affinity.
 Hydrogen (H)(2.1) and carbon (C)(2.5) each have lower
affinities.
 A bond between C and H will have nearly equal sharing of
electrons.
 Oxygen and hydrogen form a highly polar bond because of
the much stronger affinity for electrons by O.

6. Non-covalent bonds and other
weak forces
 Electrostatic bonds(ionic)-result from the electrostatic attraction
between two ionized groups of opposite charge, such as carboxyl
(-COO-) and amino (-NH3
+). In water, these bonds are very weak.
 Hydrogen bonds-result from electrostatic attraction between an
electronegative atom (O or N) and a (partially +) hydrogen atom
that is bonded covalently to a second electronegative atom.
 Van der Waals force-are short range attractive forces between
chemical groups in contact. Caused by slight charge
displacements.
 Hydrophobic attractions-cause non-polar groups such as
hydrocarbon chains to associate with each other in an aqueous
environment.

7. Chemistry of Water
 It is composed of one oxygen atom and two
hydrogen atoms, forming a covalent bond.
 H bond – joins 2 molecules of water
 Bond formed between the partially (+) H of one
water molecule and the partially (-) O of
another water molecule
 Water is a "polar" molecule - there is an uneven
distribution of electron density.
 partial negative charge (-) near O and partial
positive charges (+) near H. Oxygen is an
"electronegative" or electron "loving" atom
compared with hydrogen.

8. Water as a universal solvent
 The ability of ions and other molecules to dissolve in
water is due to polarity.
 Positively charged ions are attracted with patially (-) O
in water and negatively charged ions are attracted with
partially (+) H.

9. Surface tension of water
 The molecular polarity of water is responsible for its
surface tension property.
 Partially positive side of
water is attracted to the
partially negative side. The
resulting polarity of charge
causes molecules of water to
be attracted to each other
forming strong molecular
HYDROGEN bonds. – this is
surface tension

10. Water: Surface Tension
 This phenomenon also causes water to stick to the
sides of vertical structures despite gravity's downward
pull. Water's high surface tension allows for the
formation of water droplets and waves, allows plants to
move water (and dissolved nutrients) from their roots
to their leaves, and the movement of blood through
tiny vessels in the bodies of some animals.

11. Water: Cohesion and Adhesion
 Cohesion – attraction between like particles
 Water is attracted to other water.
 Results to surface tension
 Adhesion – attraction between unlike particles
 Water can also be attracted to other materials.
 Rationale of capillary action
 Factors:
 Size of capillary tube – indirect proportion
 Gravity – indirect proportion
 Plants take advantage of capillary action to pull water from the soil
to the roots. From the roots water is drawn through the plant by
another force, transpiration.

12. Physical states of water
 Frozen water molecules arranged in a
particular highly organized rigid
geometric pattern that causes the mass
of water to expand (increase in volume)
and to decrease in density. Expansion
causes ice to float in liquid water.
 Liquid phase - water molecules arranged
into small groups of joined particles. The
fact that these arrangements are small
allows liquid water to move and flow.
 Water vapor are highly charged with
energy. This high energy state causes the
molecules to be always moving reducing
the likelihood of bonds between
individual molecules from forming.

13. Thermal Properties of water – due to H bond
 Has a HIGH specific heat capacity
 is the amount of energy needed to raise the temperature of a given
mass of a substance. Water's specific heat capa
 it can absorb large amounts of heat energy before it begins to get hot.
 releases heat energy slowly when situations cause it to cool.
 Water's high specific heat allows for the moderation of the Earth's
climate and helps organisms regulate their body temperature more
effectively.
 Has a HIGH specific heat of vaporization
 Heat of vaporization is the amount of energy needed to vaporize a
given amount of mass of a substance.
 High Boiling point and High freezing point
 If water will boil at a lower temperature, water inside the living
organism would boil and the organism would not survive.
 Water becomes less dense as it freezes
 Ice first forms on the surface of water – beneficial to aquatic organisms
as it insulates the water underneath and maintains the habitat.

14. Water in a pure state has a
neutral pH
 Acids and Bases, Ionization of Water
 Acid release H+
 Bases accept H+
 The pH of a solution is the negative logarithm of the hydrogen ion
concentration.
 at pH 7.0, a solution is neutral
 at lower pH (1-6), a solution is acidic
 at higher pH (8-14), a solution is basic
 Water in a pure state has a neutral pH. As a result, pure water is
neither acidic nor basic. Water changes its pH when substances
are dissolved in it.
 Rain has a naturally acidic pH of about 5.6 because it contains
natural derived carbon dioxide and sulfur dioxide.

15. Water and metabolism
 Water is the medium for various enzymatic & chemical
reactions in the body. It moves nutrients, hormones,
antibodies and oxygen through the blood stream and
lymphatic system.
 The waste products of metabolism and surplus salts
get removed from your body through urine.
 Water cools body surfaces (sweat) and plant leaves
(transpiration).

16. Other Elements Needed by living
organisms
 Calcium – acts as messenger that binds to calmodulin and a
few other proteins which regulate transcription and other
processes in the cell.
 Stimulates release of neurotransmitters
 Sulfur –for the synthesis of methionine and cysteine
(amino acids)
 Phosphorus – forms part of the nucleic acids and ATP
 Iron – needed for the synthesis of cytochromes needed in
electron transport during cellular respiration and
photosynthesis
 Forms the hemoglobin in red blood cells
 Sodium – major extracellular electrolyte
 Potassium – major intracellular electrolyte

17. Introduction to Organic Molecules
 Organic molecules contain carbon; inorganic
compounds has NO carbon, except oxides of carbon
(CO2 and CO) , carbonates, and hydrogen carbonates
 Organic compounds are classified according to the
functional groups they contain.
 Alcohol - "OH“
 Aldehyde – carbonyl “HC=O”
 Acid - carboxyl "COOH”
 Amine - amine "NH3
+”
 Phosphate - addition of –PO4 =
 Amino Acid - with amino "NH3
+” and carboxyl groups
"COOH”

18. Key Biochemicals
Type of molecule
Name of
monomer forms
Name of polymer
forms
Examples of
polymer forms
Proteins Amino acids Polypeptides
Fibrous and
Globular proteins
Carbohydrate Monosaccharides Polysaccharides
Starch, lycogen,
Cellulose
Nucleic Acid Nucleotides Polunucleotide DNA, RNA
Lipids
Fatty acid and
glycerol
Lipids, triglycerides
Steroid,
cholesterol, wax

19. Carbohydrate – alcoholic
derivatives of aldehydes or ketones
 Function:
 storage of energy – polysaccharides (starch and glycogen)
 structural components (e.g., cellulose in plants
and chitin in arthropods).
 important component of coenzymes (e.g. ribose in
ATP, FAD, and NAD) and the backbone of the genetic
molecule known as RNA. The related deoxyribose is a
component of DNA.
 Saccharides and their derivatives include many other
important biomolecules that play key roles in the immune
system, fertilization, preventing pathogenesis, blood
clotting, and development.

20. Classification of Carbohydrate
 Monosaccharide – with one saccharide unit
 Named according to number of C (triose, tetrose, pentose, hexose….)
 Triose – ex. Glyceraldehyde
 Pentose – ex. Ribose and deoxyribose
 Hexose – glucose, fructose, galactose
 Disaccharide – with two monosaccharides joined by covalent glycosidic
linkage
 Lactose  glucose + galactose
 Maltose  glucose + glucose
 Sucrose  fructose + glucose
 Polysaccharide – long chain of saccharide units
 Starch
 Glycogen
 Cellulose

21. Functions of some Carbohydrates
 Energy source
 Glucose – from hydrolysis of polysaccharides
 Fructose – found in fruits
 Lactose – found in milk
 Structural component
 Cellulose – in cell walls

22. Condensation of Carbohydrates

23. Lipids
 The spectrum of lipid functions can be condensed into
the three broad areas of:
1. Storage of energy
2. Structure of cell membranes
3. Signal of chemical biological activities

24. Esterification of lipids

25. Energy: Carbohydrate vs Lipids
Carbohydrate Lipid
Terms of storage Short term Long tern
Water solubility Water solubility allows
easy transport
Insoluble
Digestion Immediate, starts from
the mouth
Latter in the small
intestine
Energy yield 38 ATP per glucose 3-5x more than
carbohydrate

26. Proteins
 Proteins are probably the most important class of
biochemical molecules
 Peptide bonds are formed between the carboxyl
group of one amino acid and the amino group of
the next amino acid. Peptide bond formation occurs
in a condensation reaction involving loss of a molecule
of water.

27. Functions of Proteins
 Enzymes are biological catalysts.
 Pepsin, trypsin chymotrypsin are digestive enzymes, of protein in nature.
 Defense proteins include antibodies which are specific protein
molecules produced by specialized cells of the immune system in
response to foreign antigens.
 Transport proteins carry materials from one place to another in the
body
 Transferrin – carry iron form the liver to the bone marrow
 Hemoglobin and myoglobin – carry oxygen
 Regulatory proteins control many aspects of cell function, including
metabolism and reproduction.
 Hormones such as insulin and glucagon, for the regulation of blood glucose
levels, are proteins.
 Structural proteins provide mechanical support to large animals and
provide them with their outer coverings.
 Keratin – of the hair, nails and skin
 Collagen and elastin

28. Classification of Amino Acids
 With reference to their side chains, amino acids
can be classified into 2 groups:
 Nonpolar amino acids – are hydrophobic. They are
generally buried in the interior of proteins, where
they can associate with each other and remain
isolated from water.
 embedded in membranes
 Polar amino acids – are hydrophilic found on
the surfaces of proteins.
 Protrude out on the surface of membrane

29. Proteins and the Cell membrane
 Functions:
 Hormone binding site
 Electron carriers
 Pumps for active
transport
 Channels for passive
transport – hydrophillic
molecules pass
 Enzymes
 Cell to cell
communication
 Cell adhesion

30. Protein Structure
 Primary structure: the linear arrangement of amino acids in a protein and the
location of covalent peptide linkages between amino acids.
 Ex. mRNA
 Secondary structure: areas of folding or coiling within a polypeptide chain;
examples include alpha helices and pleated sheets, which are stabilized by
hydrogen bonding.
 Tertiary structure: the final three-dimensional structure of a protein; alpha
helix and beta pleated sheets are folded into a compact globule which results
from a large number of non-covalent hydrophobic interactions between amino
acids, such as salt bridges, H-bond, tight packing of side chains and disulfide
bonds.
 Quaternary structure: non-covalent interactions that bind multiple tertiary
proteins into a single, larger protein.
 Ex. Hemoglobin has quaternary structure due to association of two alpha globin
and two beta globin polyproteins.

31. Sickle Cell Anemia
 A variant of HBB (hemoglobin) gene.
 Amino acid Valine substitutes Glutamine at the 6th amino
acid position of the polypeptide.
 This substitution creates a hydrophobic spot on the outside
of the protein that binds with the hydrophobic region of
another beta chain of a Hgb molecule causing clumping
together (polymerization) of Hb molecules into rigid fibers
– sickle cell.
 Polymerization happens after the O2 is detached from the
HBS molecule.
 Oxygenation in the lungs depolymerizes the HBS.
Polymerization and depolymerization patterns cause the
rigidity of the cell resulting to sickled red blood cell

32. Denaturation of Proteins
 Denaturation of proteins involves the disruption and
possible destruction of both the secondary and tertiary
structures, but not strong enough to break the peptide
bonds, the primary structure (sequence of amino
acids) remains the same after a denaturation process.
Denaturation disrupts the normal alpha-helix and
beta sheets in a protein and uncoils it into a random
shape.