METABOLISM: Chemical reaction in cells

Countless chemical reactions take place in cells and are responsible for all the actions of organisms.
Together, these reactions make up an organism's metabolism. The chemicals taking part in these
reactions are called metabolites.

In all reactions:

 chemical bonds in the reacting molecules are broken; this takes in energy
 new chemical bonds form to make the products; this gives out energy

When a chemical reaction takes place energy is either taken in or released. This depends on the relative
strengths of bonds being broken and bonds being formed.

In an exergonic reaction, energy is released to the surroundings. The bonds being formed are stronger
than the bonds being broken.

In an endergonic reaction, energy is absorbed from the surroundings. The bonds being formed are
weaker than the bonds being broken

I. Catabolic Process

Catabolic reactions give out energy. They are exergonic. In a catabolic reaction large molecules
are broken down into smaller ones and energy is released in the form of ATP or heat – instead of
consuming energy as in anabolism

Catabolic processes act to break down many different polysaccharides, such as glycogen, starches
and cellulose. These are converted into monosaccharides, which include glucose, fructose and
ribose, used by organisms as a form of energy. Proteins that are created by anabolism, are
converted to amino acids through catabolism, for further anabolic processes

1. Fermentation

In the process of glycolysis, a net profit of two ATP was produced, two NAD+ were
reduced to two NADH + H+, and glucose was split into two pyruvate molecules.
When oxygen is not present, pyruvate will undergo a process called fermentation. In
the process of fermentation the NADH + H+ from glycolysis will be recycled back to
NAD+ so that glycolysis can continue.

a. Alcoholic fermentation
- One type of fermentation is alcohol fermentation. First, pyruvate is
decarboxylated (CO2 leaves) to form acetaldehyde. Hydrogen atoms
from NADH + H+ are then used to help convert acetaldehyde to ethanol.
NAD+ results. Facultative anaerobes are organisms that can undergo
fermentation when deprived of oxygen. Yeast is one example of a
facultative anaerobe that will undergo alcoholic fermentation

b. Lactate Fermentation
 - Some organisms, such as some bacteria, will undergo lactate
fermentation. Two pyruvates are converted to two lactic acid
molecules, which ionize to form lactate. In this process two NADH + H+
are converted to two NAD+. Our muscle cells can undergo this process
when they are in oxygen debt. If enough oxygen is not present to
undergo aerobic respiration, pyruvate will undergo lactic acid
fermentation

RESPIRATION
Respiration is a set of metabolic processes that take place in the cells of organisms to convert
biochemical energy from nutrients into adenosine triphosphate (ATP). Involved in this process are the
so-called catabolic reactions, where large molecules are broken down into smaller one, which releases
energy. In general, there are two types of respiration, the aerobic and anaerobic respiration.

A. Aerobic Respiration
This type of respiration requires oxygen in order to create ATP. Carbohydrates, fats, and
proteins are consumed as reactants in order to produce carbon dioxide and water, but the
energy transferred is used to break bonds in ADP as the third phosphate group is added to form
ATP. There are three stages involved in this process, glycolysis, citric acid cycle (Krebs Cycle), and
electron transport with oxidative phosphorylation.
[First Stage] GLYCOLYSIS occurs in the cytoplasm and involves the oxidation or splitting
of glucose into pyruvate. Two molecules of ATP and two molecules of the high energy
NADH are also produced in glycolysis. In the presence of oxygen, pyruvate enters the
inner matrix of cell mitochondria and undergoes further oxidation in the Krebs cycle.

[Second Stage] KREBS CYCLE Two additional molecules of ATP are produced in this cycle
along with CO2, additional protons and electrons, and the high energy molecules NADH
and FADH2. Electrons generated in the Krebs cycle move across the folds in the inner
membrane (cristae) that separate the mitochondrial matrix (inner compartment) from
the intermembrane space (outer compartment). This creates an electrical gradient,
which helps the the electron transport chain pump hydrogen protons out of the matrix
and into the intermembrane space.

[Third Stage] ELECTRON TRANSPORT CHAIN a series of electron carrier protein

complexes within the mitochondrial inner membrane. NADH and FADH2 generated in
the Krebs cycle transfer their energy in the electron transport chain to transport protons
and electrons to the intermembrane space. The high concentration of hydrogen protons
in the intermembrane space is utilized by the protein complex ATP synthase to transport
protons back into the matrix. This provides the energy for the phosphorylation of ADP to
ATP. Electron transport and oxidative phosphorylation account for the formation of 34
molecules of ATP. Commented [JEV1]: No need to discuss in detail. Just
introduce these as ATP production steps.
 B. Anaerobic Respiration
This type of respiration occurs without oxygen and involves the consumption of another
molecule (nitrate, sulfur, iron, carbon dioxide, etc.) instead of oxygen. In aerobic organisms
undergoing respiration, electrons are shuttled to an electron transport chain, and the final
electron acceptor is oxygen. Molecular oxygen is a highly oxidizing agent and, therefore, is an
excellent electron acceptor. In anaerobes, other less-oxidizing substances such as sulphate
(SO42−), nitrate (NO3−), sulphur (S), or fumarate are used. These terminal electron acceptors
have smaller reduction potentials than O2, meaning that less energy is released per oxidized
molecule. Therefore, generally speaking, anaerobic respiration is less efficient than aerobic.

ANABOLIC REACTIONS

Anabolic reactions use up energy. They are endergonic. In an anabolic reaction small molecules join to
make larger ones. Example is during photosynthesis carbon dioxide and water are used to produce
glucose and oxygen:

PHOTOSYNTHESIS

Photosynthesis is a multi-step process that requires sunlight, carbon dioxide, and water as
substrates. It produces oxygen and glyceraldehyde-3-phosphate (G3P or GA3P), simple carbohydrate
molecules that are high in energy and can subsequently be converted into glucose, sucrose, or other sugar
molecules. These sugar molecules contain covalent bonds that store energy. Organisms break down these
molecules to release energy for use in cellular work.

Chlorophyll- absorbs solar energy to supply the

energy needed in the light reactions
Chloroplasts- site of photosynthesis for eukaryotes
 within the chloroplast are bodies called grana,
which consist of stacks of flattened membranes called
thylakoid disks
Thylakoid disks- where the trapping of light and
production of oxygen takes place
Stroma- lies within the inner membrane and outside
the thylakoid membrane
Figure 1: Parts of the Chloroplast
Photosynthesis takes place in two sequential stages:

1. The light-dependent reactions- requires sunlight

 take place in the thylakoid membranes in the granum (stack of thylakoids), within
the chloroplast.
 energy from sunlight is absorbed by chlorophyll and converted into stored chemical
energy, in the form of the electron carrier molecule NADPH (nicotinamide adenine
dinucleotide phosphate) and the energy currency molecule ATP (adenosine
triphosphate).

Photosystems- multiprotein complex that converts light into chemical energy. There are
two types embedded in the thylakoid membrane.
 photosystem I (PSI)
o reduction of NADP1 to NADPH.
o can be excited by light of wavelengths shorter than 700 nm
o electron comes from the chloroplast electron transport chain.
 photosystem II (PSII)
o oxidation of water to produce oxygen
o the electron comes from the splitting of water, which releases oxygen as a
waste product
o light of wavelengths shorter than 680 nm for excitation

2. The light-independent reactions, or Calvin Cycle.

 the energized electrons from the
light-dependent reactions provide
the energy to form carbohydrates
from carbon dioxide molecules.
 It is a cyclical nature of the process.
 Do not use light as a reactant and
may take place at day or night
 The process requires the products
of the light-dependent reactions to
function.
 The light-independent molecules
depend on the energy carrier
molecules, ATP and NADPH, to drive the construction of new carbohydrate
molecules. After the energy is transferred, the energy carrier molecules return to
 the light-dependent reactions to obtain more energized electrons. In addition,
several enzymes of the light-independent reactions are activated by light.

BIOSYNTHESIS Commented [JEV2]: You may discuss this but not so

much in detail. Focus more on the catabolic and anabolic
Biosynthesis refers to the production of a complex chemical compound from simpler precursors processes.
in a living organism. It is usually involving enzymes that will catalyze the reaction) and energy source (e.g.
ATP). Examples of biosynthesis include photosynthesis, chemosynthesis, amino acid synthesis, nucleic
acid synthesis, and ATP synthesis. In particular, photosynthesis is the synthesis of complex organic
material using carbon dioxide, water, inorganic salts, and light energy (from sunlight) captured by light-
absorbing pigments, such as chlorophyll and other accessory pigments

Basic Equation:

Terminologies

Precursor compounds: these compounds are the starting molecules or substrates in a reaction.
These may also be viewed as the reactants in a given chemical process.
Chemical energy: chemical energy can be found in the form of high energy molecules. These
molecules are required for energetically unfavorable reactions. Furthermore, the hydrolysis of
these compounds drives a reaction forward. High energy molecules, such as ATP, have three
phosphates. Often, the terminal phosphate is split off during hydrolysis and transferred to
another molecule.
Catalytic enzymes: these molecules are special proteins that catalyze a reaction by increasing
the rate of the reaction and lowering the activation energy.
Coenzymes or cofactors: cofactors are molecules that assist in chemical reactions. These may be
metal ions, vitamin derivatives such as NADH and acetyl CoA, or non-vitamin derivatives such as
ATP. In the case of NADH, the molecule transfers a hydrogen, whereas acetyl CoA transfers an
acetyl group, and ATP transfers a phosphate.In the simplest sense, the reactions that occur in
biosynthesis have the following format.

Variation of the equations:

1. Simple compounds which are converted into other compounds, usually as part of a multiple
step reaction pathway. Two examples of this type of reaction occur during the formation
of nucleic acids and the charging of tRNA prior to translation. For some of these steps,
chemical energy is required:
 2. Simple compounds that are converted into other compounds with the assistance of
cofactors. For example, the synthesis of phospholipids requires acetyl CoA, while the
synthesis of another membrane component, sphingolipids, requires NADH and FADH for
the formation the sphingosine backbone. The general equation for these examples is:

3. Simple compounds that join together to create a macromolecule. For example, fatty
acids join together to form phospholipids. In turn, phospholipids
and cholesterol interact noncovalently in order to form the lipid bilayer. This reaction may
be depicted as follows:

Examples of Biosynthesis

 Lipids- e.g Steps of cholesterol synthesis

o The synthesis of isopentenyl pyrophosphate, the "building block" of cholesterol
o The formation of squalene via the condensation of six molecules of isopentenyl
phosphate
o The conversion of squalene into cholesterol via several enzymatic reactions
 Proteins-
o Protein synthesis occurs via a process called translation
o genetic material called mRNA is read by ribosomes to generate a protein polypeptide
chain
o This process requires transfer RNA (tRNA) which serves as an adaptor by binding amino
acids on one end and interacting with mRNA at the other end; the latter pairing between
the tRNA and mRNA ensures that the correct amino acid is added to the chain
o Occurs in three phases: initiation, elongation, and termination