Ch 3.1.

Chemical elements and water

(taken from assessment statements)

3. 1. 1. State that the most frequently occurring chemical elements in living things are
carbon, hydrogen and nitrogen.
+ 3. 1. 2. State that a variety of other elements are needed by living systems, including
sulfur, calcium, phosphorus, iron and sodium.
+ 3. 1. 3. State the role for each of the elements mentioned in 3. 1. 2.

Symbol
O

Name
Oxygen

Abundance (%) (Wikipedia)

65

C
H

Carbon
Hydrogen

18
10

Ca
Fe

Calcium
Iron

1.5
<0.05

Nitrogen

P
S
K
Na

Phosphorus
Sulfur
Potassium
Sodium

1.2
0.2
0.2
0.1

Mnemonic: SPONCH

Uses
carbohydrates, fats,
water
all organic compounds
water, all organic
compounds
bones, muscle
haem group (in
haemoglobin)
amino acids,
nitrogenous bases
DNA
amino acid side chains
neural synapses
neural synapses

CaFeNaK

3. 1. 4. Draw and label water molecules to show their polarity and hydrogen bond
formation.
Water -> H2O
A hydrogen bond can only form when hydrogen is
to an atom with a very high electronegativity, thus
generating a partial charge (oxygen, nitrogen and

bonded

3. 1. 5. Outline the thermal, cohesive and

properties of water.

solvent

fluorine).

+ 3. 1. 6. Explain the relationship between the properties of water and its uses in living
organisms as a coolant, medium for metabolic reactions and transport medium

Thermal:

because of hydrogen bonds, a lot of energy needs to be invested to increase the kinetic energy of water
molecules => it takes a lot of energy to change the temperature
high thermal capacity / high specific heat (can take in a lot of energy without changing temperature greatly)
=> used in homeostasis
high heat of vaporization (absorbs a lot of energy in vaporization) => used by perspiration

Cohesive:

Cohesion: molecules of the same type are attracted to one another.

Hydrogen bonding holds molecules closer together => used in transpiration
When solid, hydrogen bonds form a crystal structure => ice is less dense than liquid water => stays floating
on top of lakes; turnover effect
Adhesion: molecules of a different kind sticking to one another.

Solvent:

excellent solvent => reactions of polar molecules can occur in it

hydrogen bonds can form with other molecules (ie. ethanol)
polar solvent solves polar solute (many organic molecules, apart from fats are polar)
The fact that water is polar and cytosol etc. is water-based affects the folding of proteins and thus the
functionality of enzymes etc.

Aqueous solution
cytosol

matrix
blood plasma

Location
from the nuclear membrane to
the cellular membrane (apart
from organelles)
inside nuclear membrane
inside chloroplast (outside
grana)
mitochondria cytosol
fluid in blood

xylem fluid
sap

fluid in plant xylem

fluid in plant phloem

nucleoplasm
stroma

Common reactions
glycolysis, translation, many
reactions
transcription, DNA replication
light-independent reactions of
photosynthesis
Krebs cycle of respiration
transport of respiratory gases,
nutrients and antibodies;
clotting
water transport in plants
sugar transport in plants

Ch 3.2 Carbohydrates, lipids and proteins

3. 2. 1. Distinguish between organic and inorganic compounds.
Organic compounds are defined by the presence of carbon.
They often include catenation of carbon. This means that carbon forms long molecules with chains of carbon

3. 2. 2. Identify amino acids, glucose, ribose and fatty acids from diagrams showing their
structures:
Name
Amino acid

Structure

Glucose
Ribose
Fatty acid

see next

3. 2. 3. List three examples each of monosaccharides, disaccharides and polysaccharides

+ 3. 2. 4. State one function of glucose, lactose and glycogen in animals, and of fructose,
sucrose and cellulose in plants.

Monosaccharides
Name
Ribose (D)
/ beta D ribofuranose

Structure

Use
present in RNA

Deoxyribose (beta D)
/ beta-D-ribofuranose

present in DNA

Glucose (D)
/ Alpha-D- glucopyranose

blood sugar, utilized

in glycolysis to
obtain ATP

Fructose (D)
/ Alpha-D-fructofuranose

isomer of glucose,
one of the
monomers of
sucrose

Galactose (D)
/ Beta-D-galactopyranose

monomer of lactose

Disaccharides
Name

Structure

Lactose

Use
Milk sugar (8-10% of milk)

(Galactose must be beta-D, glucose can be

beta-D or alpha-D)
linked through beta1->4 glycosidic linkage
Sucrose

energy source

alpha-D-glucopyranose and beta-Dfructofuranose with alpha 1->2 glycosidic

linkage
Maltose

Malt sugar
Constituent of starch

(Two alpha D glucopyranoses linked through

alpha 1->4 glycosidic linkage

Polysaccharides
Name
Amylose

Structure

Use
~20% of starch, soluble in
water, plant energy
storage

(alpha D glucopyranoses with alpha 1->4 glycosidic

linkages)
Amylopectin

~80& of starch, insoluble

in water, plant energy
storage

(like amylose, but additional alpha 1->6 bonds linking

individual chains)
Glycogen

Cellulose
Chitin

storage in animals

(very similar to amylopectin, but it is impossible to tell,

what chain is main)
(hydrogen bonds between chains provide more stability)
You do not need to know this!

Cell walls, structural

Structural, cell walls of
fungi, exoskeletons of
insects

3. 2. 5. Outline the role of condensation and hydrolysis in the relationships between fatty
acids, glycerol and triglycerides; and between amino acids and polypeptides.

Condensation reaction in triglycerides

3. 2. 6. State three functions of lipids:

1.
2.
3.
4.

Thermoregulation
Energy storage
Protection
Membranes

3. 2. 7. Compare the use of carbohydrates and lipids in energy storage.

Carbohydrates
better for short-term
faster utilization (breaking up by enzymes)
undergo glycolysis and acetyl CoA step
same mass can result in of the energy a lipid
could provide

Lipids

better for long-term

slower utilization
go straight into Krebs cycle
same mass can result in 2x much energy as
carbohydrate

Ch 3.3 DNA structure

3. 3. 1. Outline DNA nucleotide structure in terms of sugar, base and phosphate.
+ 3. 3. 2. State the names of the four bases in DNA.

In RNA, theres uracil:

3. 3. 3. Outline how DNA nucleotides are linked together by covalent bonds into a single
strand.
+ 3. 3. 4. Explain how a DNA double helix is formed using complementary base pairing and
hydrogen bonds.
+ 3. 3. 5. Draw and label a simple
diagram of the molecular structure of
DNA.

Ch 3.4 DNA replication

3. 4. 1. Explain DNA replication in terms of unwinding the double helix and separation of
the strands by helicase, followed by formation of the new complementary strands by DNA
polymerase.

3. 4. 2. Explain the significance of complementary base pairing in the conservation of the

base sequence of DNA.
Because base pairing is complementary, the DNA strands are also fully complementary. This means that since DNA
replication is semi-conservative, the daughter strands (newly synthesised) will be complementary to the original.
Why? Well, if base pairing is complementary, only one base can hydrogen bond to any other base of the parent
strand, and only the one that bonds can then be polymerized into the newly synthesised DNA strand. So, the DNA
sequence will be conserved. (Of course, mutations can occur)

3. 4. 3. State that DNA replication is semiconservative.

DNA replication is semiconservative. This means, that after replication, the two DNA molecules will each contain a
new DNA strand and an old one.

Ch 3.5 Transcription and translation

3. 5. 1. Compare the structure of RNA and DNA.
sugar
nucleotides
3D structure

DNA
2-deoxyribose
thymine
usually double helix

RNA
ribose
uracil
usually single stranded

3. 5. 2. Outline DNA transcription in terms of the formation of an RNA strand

complementary to the DNA strand by RNA polymerase.
This occurs in the nucleus.
1. The sequence to be transcribed is recognized by
TRANSCRIPTION FACTORS, which bind to it, changing
conformation.
2. RNA polymerase binds to the promoter
sequence with the help of the already bound
transcription factor.
3. RNA polymerase breaks the hydrogen bonds
holding the two strands together.
4. RNA polymerase synthesises pre-mRNA
(direction 5->3).
5. Upon recognition of the terminator, RNA
synthesis is terminated.
6. The RNA transcript is released and travels out of
the nucleus through nuclear pores.
The DNA strand read is the antisense strand and the
mRNA sequence corresponds to that of the sense strand.

3. 5. 3. Describe the genetic code in terms of codons composed of triplets of bases.

The DNA, and thus mRNA, triplets can be
translated into amino-acids. These triplets are
called codons.
The genetic code is specific, but degenerate.
Specific: one codon can only be translated to
one amino acid only.
Degenerate: Multiple codons can be translated
into the same amino acid.
It is also conserved throughout evolution
(there can be some exceptions , but the vast
majority is the same).

3. 5. 4. Explain the process of translation, leading to polypeptide formation.

Translation involves the reading of an mRNA template and the synthesis of a polypeptide strand based on the
genetic code.
INITIATION
1. Small ribosomal
subunit scans the mRNA
strand.
2. First tRNA with the
anticodon to AUG becomes
activated with Methionine.
(Met-tRNA-Met).
3. Small ribosomal
subunit (40S) recognizes
mRNA binding site.
4. Met-tRNA-Met
recognizes start codon
(AUG) on mRNA and binds
(with hydrogen bonds.
5. Large ribosomal subunit (60S) arrives and ribosome assembles.
ELONGATION / PROPAGATION and TRANSLOCATION
6. Met-tRNA-Met is currently at the P site of the ribosome.
7. Another activated tRNA arrives at the A site (the one with the appropriate anti-codon) and binds via hbonds.
8. A peptide bond is formed between the Methionine and the next amino acid.
9. Ribosome translocates along mRNA and the Met-tRNA is currently at the E site, stops bonding and leaves the
ribosome. A new activated tRNA arrives at the A site.

TERMINATION
10. Stop codon is not matched to any tRNA, but to the termination factor.
11. Peptide is released.
12. Ribosome disassembles.

3. 5. 5. Discuss the relationship between one gene and one polypeptide.

One polypeptide is coded for by one gene.
Note that it is not true, that one protein = one gene. This is because one protein can be composed of multiple
subunits.

Ch 3.6 Enzymes
3. 6. 1. Define enzyme and active site.
Enzymes are globular proteins acting as biological catalysts (a catalyst decreases the activation energy of a reaction
and is not used up in the reaction).
There are 3 main types of enzymes:

catabolic -> catalyse the breaking up of polymers and large molecules (ie. AMYLASE -> amylose into maltose,
LACTASE -> lactose into glucose and galactose)
anabolic -> catalyse the synthesis of polymers and large molecules (ie. RUBISCO in photosynthesis)
isomerases -> catalyse isomerization ( ie. from fructose to glucose)

The active site is an area within the 3D structure of the protein that will match the shape of the substrate and where
reactions occur.

3. 6. 2. Explain enzyme-substrate specificity.

Enzymes are generally specific for substrates and reactions. This is because of the 3D shape of the enzymes active
site, into which only the specific substrate(s) will fit.
Lock and key model
This model describes that an enzyme is like a lock and the substrate is the key. That is, their shapes fit completely
and no other substrate will click no other reaction can occur. It also states that the shape of the active site is
complementary to the shape of the substrate at all times, even when no reactions are occurring.
This is an older and too simplified model, though.
Induced fit model
Unlike the lock and key model, the induced fit model does not say that the active site is perfectly fitting the substrate
at all times. Rather, it proposes that the active site changes shape to acquire complementary to the substrate due to
electrostatic forces etc. upon contact with the substrate. Of course, the specificity still applies.
This model expresses reality significantly better and is presently used.

3. 6. 3. Explain the effects of temperature, pH and substrate concentration on enzyme

activity.
The factor which results in lower enzyme activity (and when removed, the enzyme activity grows) is called the
limited factor.
Temperature
An increase in energy means an increase in kinetic energy of the molecules.

The kinetic energy is so high

that the enzyme is shaken so
much, that its 3D structure
gets distrupted.

The kinetic energy makes all

the molecules move more
and thus it will be more likely
for an enzyme and substrate
to collide and meet.
pH
(Negative logarithm of H+)
Thus, pH is indirectly proportional to the concentration of H+ ions (in acids, there are many H+ ions and thus the pH is
very low).
The enzyme will be more acidic than its
environment and will therefore start
losing hydrogens. This will break it up.

With falling pH, there will be many

hydrogen ions in the environment. These
will interact with the enzyme via their
charge (electrostatic interactions) and
change its conformation.
Substrate concentration

With growing substrate concentration, the reaction can occur

faster (more product over same time), because the enzymes
available will be able to catalyse the reaction of more substrates
at the same time.

In this graph, enzyme concentration is the limiting factor, because at a certain substrate concentration, not enough
active sites will be available for catalysis of the reaction.

3. 6. 4. Define denaturation.
In denaturation, the 3D structure of an enzyme is permanently disrupted to the extent that it cannot function at all.

3. 6. 5. Explain the use of lactase in the production of lactose -free milk.

Lactose is a disaccharide naturally occurring in milk. Most adults on Earth (mostly of other races than Caucasian) are
not able to digest it. Lactase is an enzyme that can digest lactose into glucose and galactose, its two constituents. If
lactose is pre-digested by lactase prior to consumption, even lactose-intolerant people will be able to drink milk,
because no lactose (only glucose and galactose) will be present.

Ch 3.7 Cell respiration

3. 7. 1. Define cell respiration.
Respiration is the controlled and slow series of catabolic redox reactions through which organisms extract the energy
stored in complex molecules and use it to generate ATP (adenosine triphosphate).
A slow and controlled oxidation of glucose occurs.

3. 7. 2. State that, in cell respiration, glucose in the cytopla sm is broken down by glycolysis
into pyruvate with a small yield of ATP.
The first step of respiration is called glycolysis. This does not require oxygen and is universal in nature.
ATP
ADP
ATP
ADP
PREPARATORY
PHASE
kinase
kinase
glucose (6C)
glucose -6-phosphate(6C) isomerase fructose -6-phosphate(6C)
NAD+

fructose -1,6-bisphosphate(6C)

NADH+H+

glyceraldehyde-3-phosphate (3C)
dihydroxyacetone
phosphate (3C)

2 1,3-bisphosphoglycerate
(3C)
2Pi

2 pyruvate (3D)
4ADP

4ATP

PAY-OFF PHASE

FEEBACK INHIBITION (occurs when a high concentration of a product inhibits one of the previous steps in the
metabolic pathway):
glucose-6-phosphate inhibits glucoseglucose-6-phosphate
ATP inhibits fructose-6-phosphatefructose-1,6-bisphosphate

YIELD:
-2ATP+4ATP = 2ATP
2NADH+H+
2 pyruvate

3. 7. 3. Explain that, during anaerobic cell respiration, pyruvate can be converted in the
cytoplasm with no further yield of ATP.
Anaerobic respiration occurs when the cell lacks oxygen or the organism is anaerobic. No oxygen is needed for it.

The first step is glycolysis, the second step is fermentation. There are 2 types of fermentation:
ETHANOLIC FERMENTATION

Occurs in yeast

( http://upload.wikimedia.org/wikipedia/commons/thumb/0/08/Ethanol_fermentation-1.svg/495pxEthanol_fermentation-1.svg.png )

LACTIC FERMENTATION

Occurs in bacteria and animal cells deprived of

oxygen
(http://chsweb.lr.k12.nj.us/mstanley/outlines/respiration/image
156.gif)

3. 7. 4. Explain that, during aerobic cell respiration, pyruvate can be broken down in the
mitochondrion into carbon dioxide and water with a large yield of ATP.
In aerobic organisms, aerobic respiration can occur when there is enough oxygen in the environment. This also
begins with glycolysis, but continues with the link reaction (acetyl-CoA step), the Krebs cycle and the electron
transport chain.
In the presence of oxygen, pyruvate produced in glycolysis may enter the mitochondrion, where the rest occurs.
Note that for 1 molecule of glucose, all of the following steps must be doubled (because a pyruvate has the
carbons of a glucose).
LINK REACTION: (in matrix)
CoA
pyruvate 3C

CO2
acetyl-CoA

NAD+

NADH+H

Yield for 1 pyruvate:

1 NADH+H+
1 acetyl-CoA
KREBS CYCLE/CITRIC ACID CYCLE: (in matrix)

CoA

acetyl-CoA

citrate (6C)
oxaloacetate (4C)

NADH+H+

CO2

FADH2

NADH+H

NAD

NAD+

FAD+

(5C)

NAD

ATP

ADP

NADH+H
several compounds (4C)
CO2

Yield for 1 pyruvate:

1 ATP
1 FADH2
3 NADH+H+
2 CO2

ELECTRON TRANSPORT CHAIN: (on

cristae)
Oxidative phosphorylation is the
process of ATP synthesis via redox
processes in the electron transport
chain.
Remember, that NADH+H+ means
that only one H is bound covalently;
the other is floating in the cytosol.
The electron transport chain is a
series of membrane proteins
including proton (H+) channels. The
first membrane protein is
energetically highest and each
following is lower in energy.
Reduced coenzymes produced in
previous steps have their electron
and proton removed by the first
membrane protein. As the electrons are then passed between the membrane proteins (gradually to a lower energy
each time), the energy released can be used to pump proteins of the coenzymes and from the cytosol across the

membrane. This results in more protons in the intermembrane space and thus a negative charge of the matrix
relative to the intermembrane space (an electrical potential, like in a battery). On the last protein (cytochrome c
oxidase), the electrons are passed to the final electron acceptor oxygen (this is the only reason oxygen is needed
in aerobic respiration!), along with two protons from the cytosol:
(

()

The water produced becomes a part of the matrix. The energy released in this reaction is enough to pump 1 more
proton across the membrane.
The electrical potential can be used as a source of energy. The membrane protein ATP synthase is capable of
utilizing this energy for ATP synthesis. Chemiosmosis is the movement of ions across a semipermeable membrane
down their electrochemical gradient. Chemiosmosis of protons through the ATP synthase results in a loss of
potential energy of these ions; this energy is used for ATP synthesis.

FADH2 has electrons with a lower energy than NADH+H+ and so it enters the ETC later (at an energetically lower
membrane protein) than the latter.

ATP Yield from ETC:

http://upload.wikimedia.org/wikipedia/commons/thumb/8/89/Mitochondrial_electron_transport_chain%E2%80%94Etc4.svg/600px-Mitochondrial_electron_transport_chain%E2%80%94Etc4.svg.png

Note: you do not need to know other names than ATP synthase and cytochrome c oxidase (IV on picture).

OVERALL ENERGY YIELD OF RESPIRATION

watch this: https://www.youtube.com/watch?v=OXgOsy8yQuk

for 1 glucose molecule

glycolysis
link reaction
Krebs cycle
total

ATP
2
2
4

NADH+H+
2
2
6
10

FADH2

2
2

4 protons are necessary to form 1 molecule of ATP:

1 NADH+H+ 10H+ pumped 2.5ATP
1 FADH2 6H+ pumped 1.5ATP

(Note that the result 36 is acquired when ATP yield in ETC are rounded up)
However, remember that pyruvate is transported into the mitochondrion via active transport (ATP is used up) etc.

Ch 3.8 Photosynthesis
3. 8. 1. State that photosynthesis involves the conversion of light energy into chemical
energy
Photosynthesis an anabolic process in which inorganic molecules (CO2, H2O) in combination with energy from
photons and photosynthesizing pigments create organic molecules (glucose) and excrete O2.
(Electrons are excited by photons of the appropriate wavelength and the energy released when the electrons are
returning to their ground state is then captured in chemical bonds.)

3. 8. 2. State that light from the Sun is composed of a range of wavelengths.

https://steve.files.wordpress.com/2006/03/Elcetromagnetic%20spectrum.jpg

3. 8. 3. State that chlorophyll is the main photosynthetic pigment .

Chlorophyll is a green pigment (reflects the green light and absorbs as follows in 3. 8. 4.) active in photosynthesis. It
is embedded in the thylakoid membrane.

3. 8. 4. Outline the differences in absorption of red, blue and green light by chlorophyll.

http://www.au stincc.edu/bio cr/1406/labm/ex7/im ages/chlorophyll_a_b_spectrum_3.jpg

3. 8. 5. State that light energy is used to produce ATP, and to split water molecules
(photolysis) to form oxygen and hydrogen.
The enzyme catalysis the photolysis of water is called the oxygen evolving complex (OEC).

3. 8. 6. State that ATP and hydrogen (derived from the photolysis of water) are used to fix
carbon dioxide to make organic molecules.
Photosynthesis can be divided into the light-dependent and light-independent reactions.
LIGHT-DEPENDENT REACTIONS:
products framed in pink
The light dependent reactions are also an electron transport chain.

cyclic
electron carriers

Ferredoxin

acyclic

excitation
of 2e

cytochrome
complex

Plastoquinone

excitation
-

of 2e

NADP

Photosystem I
(P700)
Photosystem II
(P680)

pumps H+

ATP synthase

NADP reductase

electron
acceptor

electron
acceptor

NADPH+H

AT
P

PHOTOLYSIS OF WATER:

, ()

LIGHT-INDEPENDENT REACTIONS (Calvin cycle):

from primary phase framed in pink

6 CO2 (1C)
6 (6C) unstable
intermediate
6 ribulose
bisphosphate
(RuBP) (5C)

12 glycerate-3phosphate (3C)

12ATP

12ADP
6ADP
12NADPH+H+
6ATP

10 triose
phosphate (3C)

12NADP+

4Pi
12 triose
phosphate (3C)
2 triose
phosphate (3C)

Pi

sugar phosphates
(6C)

complex carbohydrates

3. 8. 7. Explain that the rate of photosynthesis can be measured directly by the production
of oxygen or the uptake of carbon dioxide, or indirectly by an increase in biomass.
The simplified equation for photosynthesis is:

Since CO2 is a reactant, its amount will decrease as the reaction proceeds.
Since O2 and C6H12O6 are products of the reaction, their amount will increase as the reaction proceeds.

3. 8. 8. Outline the effects of temperature, light intensity and carbon dioxide concentration
on the rate of photosynthesis.
(See enzymes)
Carbon dioxide is a substrate.
Light intensity:

(http://www2.geog.ucl.ac.uk/~plewis/geogg124/_images/chapin1.png)