Professional Documents
Culture Documents
The information in this document covers the IB syllabus for topics 3.6, 3.7, 3.8, 7.6, 8.1 and 8.2.
Enzymes
Enzyme: a globular protein molecule that accelerates a specific chemical reaction. Enzymes are
biological catalysts.
Active Site: the region of an enzyme surface that binds the substrate during the reaction catalyzed by
the enzyme.
Substrate: the reactant(s) in an enzyme-catalyzed reaction
Denaturation: a structural change in a protein that results in a loss of its biological properties. The
loss of function is usually permanent.
Exergonic & Endergonic Reactions
Exergonic reactions are those in which the free energy of the final state is less than the free energy of
the initial state. (-G) This represents energy that can be used to do biological work.
Endergonic reactions are those in which the free energy of the initial state is less than the free energy
of the final state. (+G)
Image from
http://www.biology.arizona.edu/biochemistry/problem_sets/energy_e
nzymes_catalysis/graphics/8ta.gif
Image from
http://www.biology.arizona.edu/biochemistry/problem_sets/energy_e
nzymes_catalysis/graphics/16t.gif
A. De Jong/TFSS 2009
1 of 25
HL Biology
Enzyme-Substrate Specificity
Part 1 the Lock & Key Model
Most enzymes are specific to a specific biochemical reaction. According to the lock and key model,
this is due to the three-dimensional structure of the active site which is complementary to its substrate
like a lock to its key.
According to the lock and key model, the shape of the active site is so specific that it can only catalyze
one reaction.
Part 2 the Induced Fit Model
Some enzymes are can catalyze several similar reactions. The induced fit model suggests that the
active site can change shape to suit the particular substrate. The active site will interact with the
substrate and adapt to it to make a perfect fit.
Enzyme Activity
The speed of a reaction can be measured in two ways: how fast does the substrate disappear and
how fast does the product form?
Enzyme activity is affected by the following:
Concentration
Substrate: with a fixed amount of enzyme and ample cofactors present, the rate of reaction
increases as substrate concentration increases, up to the point where enzyme saturation is
reached (plateau)
Enzyme: with ample substrate and cofactors present, the rate of reaction increases as enzyme
concentration increases (linear relationship).
A. De Jong/TFSS 2009
2 of 25
HL Biology
http://www.colchsfc.ac.uk/biology/newsite/brian/substrate.gif
http://www.colchsfc.ac.uk/biology/newsite/brian/conc.gif
Temperature: all enzymes have an optimum temperature at which their activity is highest.
High temperatures denature enzymes, and low temperatures limit enzyme activity by reducing
the number of successful collisions. Human enzymes function best at body temperature
(37C). Most enzymes denature above 60C. Thermophilic archaeans have enzymes that can
function at 80C.
pH: all enzymes have an optimum pH at which their activity is highest. Stomach enzymes
function best at acidic pH, but intestinal enzymes function best in slightly basic pH.
A. De Jong/TFSS 2009
3 of 25
HL Biology
Enzyme activity is often influenced by the presence of other chemicals. Some of these can enhance
an enzymes activity, while others inhibit the enzymes action.
Some enzymes require the presence of a non-protein molecule called a cofactor. A cofactor may be
an inorganic ion (e.g. Ca2+, Zn2+, K+) or a small organic molecule called a coenzyme (e.g. NAD).
Sometimes, the coenzyme is permanently attached to the enzyme as a prosthetic group, and other
times it only attaches during the reaction, and detaches after the reaction is completed.
Enzyme inhibitors are molecules that deactivate enzyme activity, either temporarily or permanently.
Reversible enzyme inhibitors are used to control enzyme activity. There is often an interaction
between the substrate or end product and the enzyme controlling the reaction. Build-up of the end
product or lack of substrate may serve to deactivate the enzyme.
Competitive inhibitors deactivate the enzyme by binding to the active site, blocking the substrate.
For example, the antibiotic Prontosil inhibits the synthesis of folic acid in bacteria by binding to the
active site of the enzyme required for folic acid synthesis. Since folic acid is a coenzyme itself, the
bacterium will die if it cannot make folic acid. Animal cells are not affected, because they absorb folic
acid from food.
A non-competitive inhibitor deactivates the enzyme by binding to another part of the enzyme, which
still allows the substrate to bind to the active site, but slows down the rate of reaction. For example,
cyanide (CN-) attaches itself to the SH groups in an enzyme. This destroys disulfide bridges, altering
tertiary structure of the enzyme. This alters the shape of the active site, and disrupts cellular
respiration, which relies heavily on enzymes. If this happens to a large number of cells, the organism
dies.
Allosteric enzyme inhibitors block the active site altogether, and prevent its function. This may
occur when a non-competitive inhibitor binds to a part of the enzyme, and causes the shape of the
active site to change. The binding of end products to an allosteric site can alter the shape of allosteric
enzymes. This decreases their activity. Certain products of metabolism can act as allosteric inhibitors
to enzymes that occur earlier in a metabolic pathway. This regulates metabolism according to the
requirements of the organism. This is a form of negative feedback. ATP acts as an allosteric inhibitor
to the enzyme phosphofructokinase (PFK), which is involved in an early stage of glycolysis.
Some enzymes require the binding of an allosteric activator in order for the substrate to bind.
A. De Jong/TFSS 2009
4 of 25
HL Biology
A. De Jong/TFSS 2009
5 of 25
HL Biology
Energy in Cells
Redox Reactions
Oxidation: the loss of electrons from a substance
Reduction: the gain of electrons by a substance
Many chemical reactions involve the oxidation of one substance and the reduction of another. These
reactions are called redox reactions, and the oxidation and reduction occur simultaneously. The
electrons lost by a substance are taken up by another.
Biological redox reactions often involve hydrogen or oxygen atoms. Since a hydrogen atom is
essentially a hydrogen ion plus an electron, gaining a hydrogen atom is considered to be a reduction.
Losing an oxygen atom is also a reduction. Conversely, losing a hydrogen atom is an oxidation, as is
gaining oxygen.
During cellular respiration, the coenzyme NAD accepts hydrogen ions and electrons, becoming
reduced:
NAD+ + H+ + 2e- NADH
(oxidized NAD)
(reduced NAD)
NADH is oxidized when the hydrogen ions (protons) and electrons are released.
Oxidizing Agents
A substance with a strong tendency to take electrons from another substance is called an oxidizing
agent. NAD+ is an oxidizing agent. Oxidizing agents become reduced as they oxidize other
substances.
The net result of cellular respiration is the oxidation of glucose to carbon dioxide. The main oxidizing
agent in cellular respiration is NAD+.
Reducing Agents
A substance with a strong tendency to lose electrons to other substances is called a reducing agent.
NADH is a reducing agent. Reducing agents become oxidized as they reduce other substances.
The net result of photosynthesis is the reduction of carbon dioxide to carbohydrate, (CH 2O)n, as
hydrogen is added to carbon dioxide. The main reducing agent in photosynthesis is NADP.
Oxidation
addition of oxygen
removal of hydrogen
loss of electrons
release of energy
Reduction
removal of oxygen
addition of hydrogen
gain of electrons
uptake of energy
6 of 25
HL Biology
A. De Jong/TFSS 2009
7 of 25
HL Biology
In the diagram above, the bonds between the first and second, and second and third phosphates are
considered to be high energy, and are indicated with a heavy line to distinguish them from the
others. When the third phosphate group of ATP is removed by hydrolysis, a substantial amount of free
energy is released. This also occurs when the second phosphate is removed from ADP.
ATP Production in Cells
There are two methods of ATP production in cells:
1. Substrate-Level Phosphorylation involves the transfer of a phosphate from a high-energy (i.e.
food) molecule to ADP with the assistance of an enzyme.
2. Chemiosmosis requires a phospholipid bilayer, a proton pump (intrinsic protein), protons (H +),
and ATPase (ATP synthase). Energy from food molecules is used to pump protons out,
creating a high concentration of protons outside the membrane. Protons come back through
the membrane by facilitated diffusion through a channel in ATPase, activating the enzyme.
ATPase catalyzes the formation of ATP from ADP.
A. De Jong/TFSS 2009
8 of 25
HL Biology
Glycolysis
All cells use glycolysis to produce ATP:
efficiency of the process is 2%, because there is still a lot of energy stored in the bonds of
pyruvate
Overall, the process of glycolysis can be broken down into four stages:
1. Glucose mobilization (phosphorylation): Glucose is converted to fructose-1,6-diphosphate by
substrate-level phosphorylation, with the expenditure of 2 ATP.
Net Reaction:
glucose + 2 ATP fructose-1,6-diphosphate + 2 ADP
2. Cleavage (lysis): Fructose-1,6-diphosphate is cleaved into two 3-carbon molecules. One is
glyceraldehyde-phosphate (G3P). The other is converted into G3P. (G3P is also called PGAL,
for phosphoglyceraldehyde.)
Net Reaction:
fructose-1,6-diphosphate 2 glyceraldehyde-3-phosphate (G3P)
3. Oxidation of G3P: Removal of a hydrogen atom carrying two electrons results in the reduction
of NAD+ to NADH.
4. Production of ATP: Each molecule of G3P is converted into pyruvate (3-carbons), with a total
of 4 ATP produced.
Net Reaction:
2 glyceraldehyde-3-phosphate + 2 Pi + 4 ADP 2 pyruvate + 4 ATP
A. De Jong/TFSS 2009
9 of 25
HL Biology
Mitochondria
Mitochondria are self-replicating organelles found in most eukaryotic cells. They are enclosed by a
double membrane, and because of this, they are thought to have originated as symbiotic aerobic
bacteria which were engulfed by prehistoric cells. This theory is called the Endosymbiotic theory, and
includes the chloroplasts of plant cells.
A. De Jong/TFSS 2009
10 of 25
HL Biology
The outer membrane encloses the entire structure. It is thought to have been derived from the host
cells plasma membrane. It contains many complexes of integral membrane proteins, which serve as
channels for many ions and molecules.
The inner membrane encloses a fluid-filled matrix, and is thought to have been derived from the
bacterial membrane. It is folded into cristae, in a similar fashion to bacterial membranes. Folding the
membrane into cristae helps to increase the surface area for the electron transport chain.
The matrix contains a mixture of enzymes that catalyze the catabolism of pyruvate and other small
molecules. It is the site of the Citric Acid Cycle (a.k.a. Krebs Cycle).
What Happens to Pyruvate?
No Oxygen?? Fermentation!
Fermentation is a form of anaerobic respiration, which occurs when there is insufficient oxygen for the
Krebs cycle to occur. In animals, this may be a result of oxygen debt caused by exercise. In animal
muscle tissue, pyruvate may be converted into lactic acid, by fermentation. In plants, pyruvate may be
converted into ethyl alcohol, with the release of CO2. The elimination of pyruvate allows glycolysis to
continue, and further production of ATP. Fermentation produces no ATP.
A. De Jong/TFSS 2009
11 of 25
HL Biology
A. De Jong/TFSS 2009
12 of 25
HL Biology
The Krebs cycle oxidizes Acetyl-CoA. The first step in this process is the binding of acetyl-CoA to
oxaloacetate, a four-carbon molecule. The resulting six-carbon molecule is citrate (citric acid). Citrate
is passed through a series of electron-yielding oxidation reactions, during which two CO2 are split off.
This regenerates oxaloacetate, which may continue the series of reactions with another acetyl-CoA.
The nine reactions of the Krebs cycle may be grouped into two stages:
1. Preparation: Acetyl-CoA joins the cycle, and two reactions cause rearrangement of
chemical groups.
2. Energy Extraction: Four of the six remaining reactions are oxidations in which electrons
are removed. One generates an ATP by substrate-level phosphorylation.
Together, these reactions make up a cycle that begins and ends with oxaloacetate. For each molecule
of glucose that is metabolized, the Krebs cycle runs twice, oxidizing acetyl-CoA to CO2 and H2O,
releasing electrons, which will eventually drive the proton pumps that generate ATP in the electron
transport chain. These electrons are temporarily housed within NADH and FADH2 molecules.
13 of 25
HL Biology
The final step of the ETC, the cytochrome c oxidase complex, uses four electrons to reduce a
molecule of oxygen gas to water. The reaction is:
O 2 + 4 H + + 4 e - 2 H 2O
Since oxygen is the final acceptor of electrons in the ETC, a lack of oxygen halts the entire process.
When this occurs, each acceptor molecule in the chain is stuck with its electrons until there is more
oxygen available. Since most aerobic organisms cannot survive on the ATP produced by glycolysis
alone, lack of oxygen causes death. Some poisons, such as cyanide, also halt the ETC, by binding to
a cytochrome, inhibiting it from passing its electrons on to oxygen.
14 of 25
HL Biology
Much of the protein we consume is ultimately converted into glucose (a process called
gluconeogenesis) to provide fuel for the brain and other tissues.
Although all our foods are interconvertible to some extent, they are not completely so. In other words,
no single food can supply all our anabolic needs. We can indeed synthesize many fats from glucose,
but certain unsaturated fats cannot be synthesized and must be taken in directly in our diet.
Although we can synthesize 11 of the amino acids from carbohydrate precursors, we must obtain 9
others (the "essential amino acids") directly.
Many of the points that connect carbohydrate metabolism to the catabolism of fats and proteins serve
as two-way valves. They provide points of entry not only for the catabolism (cellular respiration) of fatty
acids, glycerol, and amino acids, but for their synthesis (anabolism) as well. Thus the catabolic
breakdown of starches can lead (through acetyl-CoA and PGAL) to the synthesis of fat (as so many of
us know!).
Overview of Cellular Respiration
A. De Jong/TFSS 2009
15 of 25
HL Biology
Photosynthesis
Structure of the Chloroplast
Image from
http://www.agri.huji.ac.il/~zacha/images/chloroplast.jpg
Image from
http://www.daviddarling.info/images/chloroplast.jpg
Introduction to Photosynthesis
plant are autotrophs, organisms that convert sunlight energy into chemical energy
the process used is called photosynthesis, and converts carbon dioxide from the
atmosphere into carbohydrates and other organic compounds
carbon dioxide + water glucose + oxygen
products of photosynthesis are used by organisms for cellular respiration (this includes
autotrophs and heterotrophs)
actually consists of many biochemical reactions, which occur in two stages:
light-dependent reactions which capture energy
light-independent reactions which turn carbon dioxide into carbohydrates
sunlight, which is perceived as white light, is actually made up of many colours (ROYGBIV),
and is just a small portion of the electromagnetic (EM) spectrum
a spectrophotometer is an instrument that is used to analyze light specifically, the wavelength
() or colour being absorbed
plants use light in the 450 nm (indigo-blue) and 700 nm (orange-red) range
the reason they appear green is because green light is being reflected, not absorbed like
the blue and red
plants are able to absorb light energy because of the presence of pigments, primarily
chlorophyll a and b, located in the chloroplast
A. De Jong/TFSS 2009
16 of 25
HL Biology
Photosynthetic Pigments
1. Chlorophyll a
absorbs violet-blue and red light strongly
absorbs only small amounts of green, yellow and orange light
only pigment that can transfer light energy to carbon fixation reactions
blue-green chlorophyll
2. Chlorophyll b
absorbs blue light very strongly and violet and orange lights moderately
absorbs only small amounts of green, yellow and red light
accessory pigment, absorbing only those wavelengths that chlorophyll a cannot
yellow-green chlorophyll
Both chlorophylls absorb green light poorly, giving plants their characteristic green colour.
3. Carotenoids
absorb violet and blue-green light strongly
transmit shades of yellow, orange and red
energy-absorbing role protecting chlorophyll from damage (caused by absorbing a lot of
light)
e.g. -carotene
Absorption Spectra vs. Action Spectrum
Action spectra display the effectiveness of different wavelengths of light on photosynthesis, plotting
rate of photosynthesis versus wavelength. The absorption and action spectra are similar for
chlorophyll a but are not identical due to the presence of accessory pigments.
Engelmann's Experiment
Engelmann used a prism to illuminate a filament of algae with different wavelengths of light
added aerobic bacteria (attracted to O2) to detect regions producing the most oxygen and
therefore would have the highest rates of photosynthesis
bacteria congregated where violet-blue or red light was illuminated
A. De Jong/TFSS 2009
17 of 25
HL Biology
Photosystems
Photosystems are protein complexes involved in photosynthesis. They are located in the thylakoid
membranes of the chloroplast. Photosystems use light to reduce molecules. Light energy is absorbed
by a reaction centre, and used to excite electrons, which are passed through an electron transport
system, eventually reducing NADP+.
A. De Jong/TFSS 2009
18 of 25
HL Biology
19 of 25
HL Biology
8. Sometimes, electrons take an alternative path that uses PSI only. Electrons cycle back from
ferrodoxin to the cytochrome complex and continue back to the PSI complex. This cycle drives
translocation of protons across the membrane, further increasing the concentration gradient.
This increases ATP production.
A. De Jong/TFSS 2009
20 of 25
HL Biology
A. De Jong/TFSS 2009
21 of 25
HL Biology
Used for cellular metabolism to produce glucose (in cytoplasm, then used for glycolysis).
When glucose is in excess, polymerization occurs to form amylose, amylopectin, and stored as
starch (in the stroma)
Glucose can be converted to sucrose in the cytosol of plant cells and exported via
translocation to other parts of the plant (via the phloem).
G3P is formed after cleavage of fructose-1,6-bisphosphate in the glycolytic pathway further
proof of the interconversion of fuels.
**this doubles when you consider that it takes two G3P to make one glucose!
More ATP is required than NADPH (9:6), which is why there is cyclic and non-cyclic electron
flow in the light dependent reaction.
photorespiration occurs when light is present during hot, dry days in C-3 plants
heat causes stomata openings to decrease in size to prevent transpiration
CO2 absorption and [CO2] in leaves' air spaces
[O2] compared to CO2
(cellular respiration continues during this time)
Effect on RUBISCO:
CO2 and O2 compete for the active site of RUBISCO
[CO2]>[O2]: RUBISCO catalyzes CO2 fixation to RuBP
[CO2]<[O2]: RUBISCO oxidizes RuBP
RuBP oxidation
(C5)
3PG + glycolate
(C3)
(C2)
The 3PG produced by oxidation of RuBP continues to Calvin cycle, but the glycolate does not. It may
result in the production of some CO2.
A. De Jong/TFSS 2009
22 of 25
HL Biology
The C4 Pathway
C4 plants include sugar cane, corn, and members of the grass family. C4 plants utilize an additional
carbon fixation step that precedes the Calvin cycle, where CO2 is first fixed into a 4-carbon compound.
This process reduced the amount of photorespiration that takes place and continuously pumps CO 2
molecules back into Calvin cycle, preventing RUBISCO from binding O2.
Steps:
1. PEP carboxylase converts CO2 and PEP (phosphoenolpyruvate) (C-3) to form oxaloacetate
(C-4).
2. Oxaloacetate is converted to malate.
**These two steps occur in the cytoplasm of a mesophyll cell.
3. The malate then diffuses into bundle sheath cells through a cell to cell connection called
plasmodesmata.
4. The malate is then broken down through a decarboxylation reaction into pyruvate and CO 2.
5. The pyruvate then diffuses back into the mesophyll cell and is converted back into PEP. In the
process, one ATP is dephosphorylated into ADP.
6. The CO2 undergoes a second fixation that is catalyzed by RUBISCO in the Calvin cycle.
**Note this is a more energy-consuming process, since an additional ATP is used.
A. De Jong/TFSS 2009
23 of 25
HL Biology
A. De Jong/TFSS 2009
24 of 25
HL Biology
Temperature
Carbon dioxide
A. De Jong/TFSS 2009
25 of 25