2. Why is energy needed?
• To maintain the structural integrity of the cell by repairing damage to its
constituents
• To synthesize new cellular components
• To transport certain substances into the cell from its surroundings
• For the cell to grow and multiply
• For cellular movement
3. METABOLISM
- is the term used to describe all the biochemical reactions that take place inside the
cell.
CATABOLISM
- Is the term used to describe reactions that break down large molecules, usually
coupled to a release of energy.
ANABOLISM
- Is the term used to describe reactions involved in the synthesis of
macromolecules, usually requiring an input of energy.
4. ENZYMES
• An enzyme is a cellular catalyst, specific to a particular reaction or group of
reactions.
• It makes biochemical reactions proceed many times more rapidly than they
would if uncatalyzed.
5. ENZYMES
• Like any other catalyst, an enzyme remains
unchanged at the end of a reaction.
• Enzyme-substrate interaction
An enzyme interacts with its substrate(s) to form an
enzyme-substrate complex, leading to the formation of
a product.
- Substrate: A reactant in a chemical reaction that is
acted upon by an enzyme.
- Active site: It is the region of an enzyme where
substrate molecules bind and undergo a chemical
reaction.
It is the precise formation of the active site that
accounts for one of the major characteristics of
enzymes, their specificity.
6. Certain enzymes have a non-protein component
• Many enzymes require the involvement of an additional, non-protein
component in order to carry out their catalytic reaction.These “extra” parts
are called cofactors.
• Cofactors are usually metal ions or complex organic molecules called
coenzymes.
• The purely protein component of an enzyme is known as the apoenzyme.
• The complex of apoenzyme and cofactor is called holoenzyme.
7. How do enzymes speed up reaction?
• Activation energy - it is the energy needed to convert the molecules at the
start of a reaction into intermediate forms known as transition states, by
the rearrangement of chemical bonds.
• The great gift of enzymes is that they can greatly lower the activation
energy of a reaction, so that it requires a smaller energy input, and may
therefore occur more readily.
8. ENVIRONMENTAL FACTORSTHAT
AFFECT ENZYME ACTIVITY
The rate at which an enzyme converts its substrate into product is called
velocity (v), and is affected by a variety of factors.
9. Temperature
• The rate of any chemical reaction
increases with an increase in
temperature due to the more rapid
movement of molecules, and so it is
with enzyme-catalyzed reactions, until
a peak is reached (optimum
temperature) after which the rate
rapidly falls away.
• Excessive heat results to denaturation.
It alters the three-dimensional protein
structure.
• It leads to changes in configuration of
the active site, and loss of catalytic
properties.
Denaturation – is a process in which the structure of a
protein or nucleic acid is modified by application of some
external stress.
10. pH
• Changes in the pH affect the ionization
of charges ‘R’-groups on amino acids at
the active site and elsewhere, causing
changes in enzyme’s precise shape,
and a reduction in catalytic properties.
• When pH deviates appreciably from
either direction, denaturation occurs,
leading to a reduction of enzyme
activity.
11. Substrate concentration
• Under conditions where the active sites
of an enzyme population are not
saturated, an increase in substrate
concentration will be reflected in a
proportional rise in the rate of reaction.
• A point is reached, however, when the
addition of further substrate has no
effect on the rate.This is because all
the active sites have been occupied and
the enzymes are working flat out; this
is called maximum velocity orVmax
Michaelis constant
(Km) – a measure of
the affinityan enzyme
has for its substrate.
12. Enzyme inhibitors
• Many substances are able to interfere with an enzyme’s
ability to catalyze a reaction.
• Competitive inhibition – the inhibitory substance
competes with the normal substrate for access to the
enzyme’s active site; if the active site is occupied by a
molecule of inhibitor, it can’t bind a molecule of
substrate, thus the reaction will proceed less quickly.
• Non-competitive inhibition – acts by binding to a
different part of the enzyme and in so doing alter its
three-dimensional configuration.Although it will not
affect substrate binding, it will reduce the rate at which
a product is formed.
13. Enzyme inhibitors
• Both competitive and non-competitive forms of
inhibition are reversible, since the inhibitor molecule is
relatively weakly bound and can be displaced.
• Irreversible inhibition – is due to the formation of a
strong covalent linkage between the inhibitor and an
amino acid residue on enzyme. As a result of its binding,
the inhibitor effectively makes a certain percentage of
the enzyme population permanently unavailable to
catalyze substrate conversion.
14. PRINCIPLES OF ENERGY
GENERATION
In this section, we shall consider how enzyme-catalyzed reactions are
involved in the cellular capture and utilization of energy.
15. Principles of energy generation
• Adenosine triphosphate (ATP)
- high-energy transfer compounds, which store the energy from
the breakdown of nutrients (or trapped by photosynthetic
pigments) and release it when required by the cell.
• ATP has a structure similar to the nucleotides found in RNA,
except it has two additional RNA groups.The bond that links the
third phosphate group requires a lot of energy for its formation,
and is often referred to as a “high-energy” phosphate bond. When
this bond is broken, the same large amount of energy is released.
• Thus, when ATP is broken down to ADP and a free phosphate
group, energy is made available to the cell.
• Phosphorylation – the process of adding a phosphate
group
• Dephosphorylation – the process of removing a
phosphate group.
16. Oxidation-reduction reactions
• Many metabolic reactions involve the transfer of electrons from one molecule to
another; these are called oxidation-reduction or redox reactions.
• When a molecule loses an electron, it is said to be oxidized.
• When a molecule gains an electron, it is said to be reduced.
NAD /NADH are generally involved in
catabolic reactions and
NADP/NADPH in anabolic reactions.
17. Oxidation-reduction reactions
• Redox potential – or oxidation-reduction potential, is the tendency of a
compound to lose or gain electrons.
• Electrons are donated to carriers with a more positive redox potential.
18. Biochemical pathway
Also known as metabolic pathway, is a series of chemical
reactions in a cell that build and breakdown molecules for cellular
processes.
19. Glycolysis
• The initial sequence of reactions, in which a molecule of glucose is converted to
two molecules of pyruvate.
• It is common to both aerobic and anaerobic organisms.
• The pathway, which takes place in the cytoplasm, comprises a series of 10 linked
reaction, in which each molecule of the six-carbon glucose is converted to two
molecules of the three carbon pyruvate, with a net gain of two molecules of ATP.
• The overall energy balance in glycolysis is therefore a gain of two molecules of
ATP for each molecule of glucose oxidized to pyruvate.
20. Glycolysis is not the only way to metabolize glucose
• Entner-Doudoroff pathway
- This pathway produces a mixture of pyruvate and glyceraldehyde-3-phosphate
(G3P).The net result of catabolism by the Entner-Doudoroff pathway is the
production of one molecule each of ATP, NADH and NADPH per molecule of
glucose degraded.
• Pentose phosphate pathway
- also known as the hexose monophosphate shunt. It can operate in tandem
with glycolysis or the Entner-Doudoroff pathway.This pathway has a mainly
anabolic (biosynthetic) function, acting as a source or precursor molecules for other
metabolic pathways.
21. Tricarboxylic acid (TCA) cycle or Krebs cycle
• It is also simply known as citric acid cycle.
• During this cycle, a series of redox reactions result in the gradual transfer of the
energy contained in the pyruvate to coenzymes (mostly NADH).This energy is
finally conserved in the form of ATP by a process of oxidative phosphorylation.
• For each “turn” of the citric acid cycle, 1 molecule of ATP, 3 molecules of NADH,
and 1 molecule of FADH2 are produced. Overall, two molecules of ATP are
produced in the Krebs cycle.
22. Oxidative phosphorylation and the Electron
transport chain
• The electron transport chain is a series of donor/acceptor molecules that transfer
electrons from donors (e.g. NADH) to a terminal electron acceptor (e.g. Oxygen).
• The energy originally stored in the glucose molecule is now held in the form of the
reduced coenzymes (NADH and FADH2) produced during glycolysis and theTCA
cycle.This will be converted to no less than 34 molecules of ATP per glucose
molecule by oxidative phosphorylation.
25. Fermentation
• Fermentation is the microbial process by which an organic substrate (usually a
carbohydrate) is broken down without the involvement of oxygen or an electron
transport chain, generating energy by substrate level phosphorylation.
• There are two common fermentation pathways: Alcoholic fermentation and
Lactic acid fermentation.
26. Alcoholic Fermentation
• Alcoholic fermentation which is more common in yeasts than in bacteria, results
in pyruvate being oxidized via the intermediate compound acetaldehyde to
ethanol.
• There is no further ATP generated during these reactions, so the only ATP
generated in the fermentation of a molecule such as glucose is that produced by
the glycolysis steps.
27. Lactic Acid Fermentation
• Some organisms, such as Streptococcus and Lactobacillus, produce lactic acid as
the only end product; this is referred to as homolactic fermentation.
• Other microorganisms, such as Leuconostoc, generate additional products such as
alcohols and acids in a process called heterolactic fermentation.
• In both alcohol and lactic acid fermentation, the two NADH molecules produced
per molecule of glucose have been reoxidised to NAD.
28. Other types of fermentation
• Mixed acid fermentation
- pyruvate is reduced by the NADH to give succinic, formic and acetic acids,
together with ethanol.
- Enteric bacteria that carry out this type of fermentation are: Escherichia,
Shigella, and Salmonella
• 2,3-butanediol fermentation
- the products are not acidic, and include an intermediate called acetoin. Much
more carbon dioxide is produced than in mixed acid fermentation.
- Enteric bacteria: Klebsiella and Enterobacter
29. Metabolism of lipids and proteins
• LIPIDS: Beta-oxidation pathway
- is the catabolic process by which fatty acid molecules are broken down in the
cytosol in prokaryotes and in the mitochondria in eukaryotes to generate acetyl-
CoA, which enters the citric acid cycle, and NADH and FADH2, which are coenzymes
used in the electron transport chain.
• PROTEINS: Deamination
- proteins are initially hydrolyzed to their constituent ‘building blocks’, amino
acids. It will then undergo the loss of an amino group (deamination), resulting in a
compound that is able to enter, either directly or indirectly, theTCA cycle.
30. Anaerobic respiration
• In the process of anaerobic respiration, carbohydrate can be metabolized by a
process that utilizes oxidative phosphorylation via the electron transport chain,
but instead of oxygen serving as the terminal acceptor an inorganic molecule such
as nitrate and sulphate is used.These processes are referred to, respectively, as
dissimilatory nitrate or sulphate reduction.
• Obligate anaerobes carry out this process, as they are unable to utilize oxygen.
• Anaerobic respiration is not as productive as its aerobic counterpart in terms of
ATP production.
31. Photosynthesis
• A number of different microbial types are able to carry out photosynthesis, which
we can regard as having two distinct forms:
- Oxygenic photosynthesis: In which oxygen is produced; found in algae,
cyanobacteria (blue-green), and green plants
- Anoxygenic photosynthesis: in which oxygen is not generated; found in the
purple and green photosynthetic bacteria.
32. Oxygenic photosynthesis
• It takes place in the chloroplasts.
• The reactions that make up photosynthesis fall into two distinct phases: light
reactions and dark reactions.
- Light reactions: It takes place in the thylakoid. In this phase, the light energy
is trapped and some of it conserved as ATP.
- Dark reactions: It takes place in the stroma. In this phase, the energy in the
ATP is used to drive the synthesis of carbohydrate by the reduction of caron
dioxide.
34. Anoxygenic photosynthesis
• Anoxygenic photosynthesis is the phototropic process where light energy is
captured and converted to ATP, without the production of oxygen.Water is
therefore not used as an electron donor.
• Anoxygenic organisms rely on bacteriochlorophylls for photosynthesis.
• The electron transport chain of anoxygenic phototrophs is cyclic, meaning the
electrons used during photosynthesis are fed back into the system, therefore no
electrons are left over to oxidize water into oxygen.
35. Anoxygenic photosynthesis
Main differences of anoxygenic photosynthesis:
• No oxygen is generated during this type of photosynthesis
• Bacteriochlophylls absorb light maximally at longer wavelengths, allowing them
more effectively to utilize the light available in their own particular habitat.
• Purple and green bacteria are not able to utilize water as donor electrons, and
must use a compound that is oxidized more easily, such as hydrogen sulphide or
succinate
• Only a single photosystem is involved in the light reaction
• Light reactions take place in lamellar invaginations of the cytoplasmic membrane
in the purples and in vesicles called chlorosomes in the greens.
36. Anabolic reactions
• Biosynthesis – is used to describe those reactions by which nutrients are
incorporated first into small molecules such as amino acids and sugars and
subsequently into biomacromolecules such as proteins and polysaccharides.
• Biosynthesis of carbohydrates
• Biosynthesis of lipids
• Biosynthesis of nucleic acids
• Biosynthesis of amino acids
37. Biosynthesis of carbohydrates
• In carbohydrate anabolism, simple organic acids can be converted into
monosaccharides (e.g. glucose) and then used to assemble polysaccharides (e.g.
starch).
• Gluconeogenesis – is the generation of glucose from compounds like pyruvate,
lactate, glycerol, glycerate 3-phosphate and amino acids. It converts pyruvate to
glucose-6-phosphate through a series of steps, many of which are shared with
glycolysis.
38. Biosynthesis of lipids
• The basic building blocks in the synthesis of fatty acids are acetyl-CoA (two-carbon) and
malonyl-CoA (three-carbon).
• Fatty acids are synthesized by a stepwise process that involves the addition of two-carbon
units to form a chain, most commonly of 16-18 carbons.
• Once fatty acids are formed, it may be incorporated into phospholipids, the major form of
lipid found in microbial cells.
• Phospholipid molecule has three parts: fatty acid, glycerol and phosphate.
• Glycerol and phosphate are provided in the form of glycerol phosphate, which derives
from the dihydroxyacetone phosphate of glycolysis.
39. Biosynthesis of nucleic acids
• Nucleic acids are polymers of nucleotides.
• Nucleotide synthesis is an anabolic mechanism generally involving the chemical
reaction of phosphate, pentose sugar, and a nitrogenous base.
• Nucleic acids involves the formation of the purine and pyrimidine ribonucleotides.
40. Biosynthesis of amino acids
• All amino acids are derived from
intermediated in glycolysis, the citric
acid cycle, or the pentose phosphate
pathway. Nitrogen enters this
pathways by way of glutamate and
glutamine.
• A useful way to organize the amino
acid biosynthetic pathways is to group
them into families corresponding to
the metabolic precursor of each amino
acid.
41. The regulation of metabolism
• Regulation involves controlling the activity of enzymes which direct the many biochemical
reactions occurring in each cell.This can be done by:
- directly affecting enzyme activity by the mechanism of feedback inhibition.
Feedback inhibition – the final product of a metabolic pathway acts as inhibitor to the enzyme that
catalyzes the early step (usually the first) in the pathway. It thus prevents more of its own formation.
- indirectly, at the genetic level, by controlling the level at which enzymes are synthesized.
This is done by induction and repression, which respectively ‘switch on’ and ‘switch off’ the
machinery of protein synthesis.
