2.1 Atomic Bonds and Molecular Interactions
2.1 Covalent Bonds (Ashi)
A covalent bond is created as electrons from both participating atoms are shared
equally. A shared pair or bonding pair is the pair of electrons involved in this sort of
bonding. Covalent bonds are frequently referred to as molecular bonds. The sharing of
bonding pairs will ensure the atoms' outer shell stability.
Types of Covalent Bonds:
·
Single Bond - A single bond is formed when only one pair of electrons is shared
between the two participating atoms
·
Double Bond - If two electron pairs are shared as occurs in molecular oxygen
·
Triple Bond - if three pairs of electrons are shared, in molecular nitrogen
Polar and Nonpolar Molecules
Polar - Polar molecules contain one or more electronegative atoms, usually oxygen and
nitrogen. This form of covalent bond develops when the electronegativity of joining
atoms differs, resulting in uneven electron sharing. Electrons will be drawn to more
electronegative atoms. Molecules, such as water, that have an asymmetric distribution
of charge (or dipole) are referred to as polar molecules. Electronegativity is tendency of
an atom in a molecule to attract the shared pair of electrons towards itself. The strength
of a covalent bond is highly dependent on the electronegativities of the two bonded
atoms.
Nonpolar - Molecules that lack electronegative atoms and strongly polarized bonds,
such as molecules that consist entirely of carbon and hydrogen atoms, are said to be
nonpolar. This sort of covalent connection is established when two atoms share an
equal number of electrons. The difference in electronegativity between two atoms is
zero. It occurs whenever two atoms with equal electron affinities combine (diatomic
elements).
Ionization
Some atoms are so strongly electronegative that they can capture electrons from other
atoms during a chemical reaction. Cations are ions that are positively charged. When a
metal loses its electrons, they form. Anions are ions that are negatively charged. They
are created when a nonmetal obtains electrons.
2.2 The Human Perspective (Do Free Radicals Cause Aging) (ASHI)
Free radicals may be formed when a covalent bond is broken such that each portion
keeps one‐half of the shared electrons, or they may be formed when an atom or
molecule accepts a single electron transferred during an oxidation–reduction reaction.
Free radicals are extremely reactive and capable of chemically altering many types of
molecules, including proteins, nucleic acids, and lipids. This is illustrated by the fact that
certain cells of the immune system generate free radicals within their cytoplasm as a
means to kill bacteria that these immune cells have ingested.
The formation of hydroxyl radicals is probably a major reason that sunlight is so
damaging to skin. In 1969, Joe McCord and Irwin Fridovich of Duke University
discovered an enzyme, superoxide dismutase (SOD), whose sole function was the
destruction of the superoxide radical, a type of free radical formed when molecular
oxygen picks up an extra electron
Although these substances (antioxidants) may prove beneficial in the diet because of
their ability to destroy free radicals, studies with rats and mice have failed to provide
convincing evidence that they retard the aging process or increase maximum life span.
2.3 Noncovalent Bonds (ASHI)
Noncovalent bonds do not depend on shared electrons but rather on attractive forces
between atoms having an opposite charge. Individual noncovalent bonds are weak
(about 1 to 5 kcal/mol) and are thus readily broken and reformed.
·
holds the two strands of the DNA double helix together (hydrogen bonds)
● folds polypeptides into such secondary structures as the alpha helix and the beta
conformation
● enables enzymes to bind to their substrate
● enables antibodies to bind to their antigen
● enables transcription factors to bind to each other
● enables transcription factors to bind to DNA
● enables proteins (e.g. some hormones) to bind to their receptor
● permits the assembly of such macromolecular machinery as
○ ribosomes
○ actin filaments
○ microtubules
Ionic Bonds: Attractions between Charged Atoms
The ionic bond is the electrostatic force of attraction that holds two oppositely charged
ions together.
A chemical bond is formed between two atoms by the complete transfer of one or more
electrons from one atom to the other, causing the atoms to assume their closest inert
gas configuration.
Hydrogen Bonds
The formation of hydrogen bonds is a particular type of attractive intermolecular force
caused by the dipole-dipole interaction between a hydrogen atom bonded to a highly
electronegative atom and another highly electronegative atom in the vicinity of the
hydrogen atom. In water molecules (H2O), for example, hydrogen is covalently bound to
the more electronegative oxygen atom. As a result of dipole-dipole interactions between
the hydrogen atom of one water molecule and the oxygen atom of another H2O
molecule, hydrogen bonding occurs in water molecules.
Hydrophobic Interactions and van der Waals Forces
When nonpolar compounds are mixed with water, the nonpolar, hydrophobic (“water
fearing”) molecules are forced into aggregates, which minimizes their exposure to the
polar surroundings. This association of nonpolar molecules is called a hydrophobic
interaction. Van der Waals Forces is weak interaction of nonpolar molecules by the
shifting of electron density.
The Life‐Supporting Properties of Water
Life on Earth is totally dependent on water, and water may be essential to the existence
of life anywhere in the universe. Even though it contains only three atoms, a molecule of
water has a unique structure that gives the molecule extraordinary properties.
·
Water is a highly asymmetric molecule with the O atom at one end and the two H
atoms at the opposite end.
·
Each of the two covalent bonds in the molecule is highly polarized.
·
All three atoms in a water molecule are adept at forming hydrogen bonds.
2.4 Acids, Bases, and Buffers (ASHI)
A molecule that is capable of releasing (donating) a hydrogen ion is termed an acid.
Any molecule that is capable of accepting a proton is defined as a base. Acids and
bases exist in pairs, or couples. When the acid loses a proton (as when acetic acid
gives up a hydrogen ion), it becomes a base (in this case, acetate ion), which is termed
the conjugate base of the acid. Similarly, when a base (such as an —NH 2 group)
accepts a proton, it forms an acid (in this case —NH+ 3), which is termed the conjugate
acid of that base. Thus, the acid always contains one more positive charge than its
conjugate base.
Organisms, and the cells they comprise, are protected from pH fluctuations by buffers
—compounds that react with free hydrogen or hydroxyl ions, thereby resisting changes
in pH. Buffer solutions usually contain a weak acid together with its conjugate base.
2.2 Chemical Equilibrium
GAMO, ANGELINE MAE
3.1 The Laws of Thermodynamics
Energy is the capacity to do the work, the capacity to change or move something.
Thermodynamics is the study of the changes in energy that accompany events in the universe.
The First Law of Thermodynamics
The first law of thermodynamics states that energy can neither be created nor destroyed. It can,
however, be converted (transduced) from one form to another.
First Law of Thermodynamics: ΔE = Q – W
E – internal energy
ΔE – change during a transformation
Q – heat energy
W – mechanical work energy
W= Fd
F – force
d – distance
Exothermic is the reaction that loses heat.
Endothermic is the reaction that gains heat.
The Second Law of Thermodynamics
The second law of thermodynamics states that the total entropy of a system either increases or
remains constant in any spontaneous process; it never decreases.
Spontaneous indicates they are thermodynamically favorable and can occur without the input
of external energy.
Entropy is the measure of the system’s thermal energy per unit temperature that is unavailable
for doing useful work. TΔS
3.2 Free Energy
Free Energy – it is the energy-like property or state function of a system in thermodynamic
equilibrium. It is used to determine how systems change and how much work they can produce.
J. Williard Gibbs in 1878
ΔH = ΔG + TΔS
ΔG – change in free energy
ΔH – change in the enthalpy
T – absolute temperature (K= C + 273)
ΔS – change in the entropy of the system
Enthalpy – total energy content of a system
Rearranged version : ΔG = ΔH + TΔS
Exergonic refers to the process that can occur spontaneously, that is, processes that are
thermodynamically favored (have a – ΔG).
Endergonic refers to the processes that are thermodynamically unfavorable. It is also when ΔG
for a given process is positive, then it cannot occur spontaneously.
Free-Energy Changes in Chemical Reactions
A+B⇌C+D
The rate of the forward reaction is directly proportional to the product of the molar concentration
of A and B.
K1[A][B] (forward reaction)
K1 is the rate constant for the forward reaction
The rate of the backward reaction equals K2[C][D]
Equilibrium constant, Keq – ratio that quantifies the position of chemical equilibrium.
Dissociation Constant, Kd – a special type of equilibrium that measures how much two
molecules tend to stick together.
Standard Conditions:
1. 25 °C and 1 atm
2. All the reactants and products present at 1.0 M concentration
3. Except for water at 55.6 M, H+ at 10-7 M (pH 7.0)2
Standard Free-Energy Change ΔG° - free energy released when reactants are converted to
products under these standard conditions.
The relationship between the equilibrium constant and standard free-energy is given by the
equation:
ΔG° = - RTlnK’eq
ΔG° = -2.303RT log K’eq
R is the gas constant (1.987 cal/mol K)
T is the absolute temperature (298 K)3
Free-Energy Changes in Metabolic Reactions
ATP + H2O → ADP + P1
3.3 Coupling Endergonic and Exergonic Reactions
Reactions with large positive ΔG° values are typically driven by the input of energy.
Common Intermediate – the bridge between two reactions.
GAMBOA, MARY GRACE G.
3.4 Equilibrium versus Steady-State Metabolism
Equilibrium and Steady-State Metabolism are two different concepts related to biochemical
and physiological processes, particularly in the context of metabolic reactions within living
organisms. Let's explore each of these concepts:
1. Steady-State Metabolism: Refers to a dynamic, non-equilibrium condition in biological
systems where certain molecules' concentrations remain relatively constant over time despite
continuous turnover due to ongoing metabolic reactions. It is a state of balanced fluxes within a
system.
Characteristics:
- The system is typically open, meaning there is a continuous flow of materials in and out.
- While individual reactions within the system may not be at equilibrium, the overall system
maintains stability due to regulatory mechanisms.
- Steady-state conditions are essential for the proper functioning of living organisms, as it allows
them to maintain the necessary concentrations of molecules required for various processes.
Example: Cellular metabolism is often in a steady-state condition. For instance, glucose is
continuously taken up by cells, metabolized through various pathways, and the products of
these pathways are used for energy production, biosynthesis, and other cellular functions.
Despite these continuous metabolic reactions, the concentration of key metabolites (e.g.,
glucose, ATP) is maintained relatively constant through feedback and regulatory mechanisms.
2. Equilibrium: In a chemical reaction, equilibrium is a state where the rate of the forward
reaction (conversion of reactants into products) equals the rate of the reverse reaction
(conversion of products back into reactants). At equilibrium, the concentrations of both reactants
and products remain constant over time.
Characteristics:
- The system is closed, meaning there's no net change in the concentration of reactants or
products.
- Equilibrium is a thermodynamically stable state.
- Chemical reactions can reach equilibrium when there is no external influence or when the
forward and reverse reactions occur at the same rate.
- Equilibrium is often described by the equilibrium constant (K), which depends on the specific
reaction and temperature.
Example: Consider the reaction A + B ⇌ C + D. At equilibrium, the concentrations of A, B, C,
and D no longer change, and the rate of A and B converting to C and D equals the rate of C and
D converting back to A and B.
In summary, equilibrium represents a state of balance in a closed chemical system, while
steady-state metabolism refers to the dynamic, non-equilibrium condition in open biological
systems where certain molecule concentrations are actively regulated and maintained despite
ongoing metabolic processes. Living organisms rely on steady-state conditions to carry out
essential functions while responding to changing external conditions.
3.5 Enzymes as Biological Catalysts
At the end of the nineteenth century, a debate was raging as to whether the process of ethanol
formation required the presence of intact yeast cells.
Justus von Liebig - organic chemist who argued that the reactions of fermentation that
produced the alcohol were no different from the types of organic reactions he had been studying
in the test tube
Louis Pasteur - biologist who argued that the process of fermentation could only occur within
the confines of an intact, highly organized, living cell
Hans Büchner (bacteriologist) and brother Eduard (chemist) - “yeast juice”—an extract made
by grinding yeast cells with sand grains and then filtering the mixture through filter paper
Eduard - discovered that fermentation was producing ethanol and bubbles of carbon dioxide
Büchner - had shown that fermentation did not require the presence of intact cells
Fermentation - required the presence of a unique set of catalysts that had no counterpart in the
nonliving world which is enzymes
Enzymes - catalysts (after the Greek for “in yeast”)
- are proteins, many of them are conjugated proteins
- mediators of metabolism, responsible for virtually every reaction that occurs in a cell
- without enzymes, metabolic reactions would proceed so slowly as to be imperceptible.
James Sumner of Cornell University (1926) - first evidence that enzymes are proteins was
obtained when he crystallized the enzyme urease from jack beans and determined its
composition.
Eventually, it became evident that certain biological reactions are catalyzed by RNA molecules.
For the sake of clarity, the term enzyme is still generally reserved for protein catalysts, while the
term ribozyme is used for RNA catalysts.
Conjugated Proteins - contain nonprotein components, called cofactors
Cofactors - may be inorganic (metals) or organic (coenzymes)
- important participants in the functioning of the enzyme, often carrying out activities for
which amino acids are not suited
Coenzymes - often the function of vitamins and their derivatives
(A.) The Properties of Enzymes
As is true of all catalysts, enzymes exhibit the following properties:
1. They are required only in small amounts;
2. They are not altered irreversibly during the course of the reaction, and therefore each
enzyme molecule can participate repeatedly in individual reactions; and
3. They have no effect on the thermodynamics of the reaction (important).
Enzymes - do not supply energy for a chemical reaction and therefore do not determine
whether a reaction is thermodynamically favorable or unfavorable
- do not determine the ratio of products to reactants at equilibrium
- can only accelerate the rate at which a favorable chemical reaction proceeds
Substrate - reactants bound by an enzyme
(B.) Overcoming the Activation Energy Barrier
Chemical transformations require that certain covalent bonds be broken within the reactants.
For this to occur, the reactants must contain sufficient kinetic energy (energy of motion) that they
overcome a barrier, called the activation energy (EA) —represented by the height of the
curves.
If a given reactant molecule acquires sufficient energy to overcome the activation barrier, then
the possibility exists that it will split into the two product molecules. The rate of the reaction
depends on the number of reactant molecules that contain the necessary kinetic energy at any
given time. One way to increase the reaction rate is to increase the energy of the reactants. This
is most readily done in the laboratory by heating the reaction mixture. In contrast, applying heat
to an enzyme‐mediated reaction leads to the rapid inactivation of the enzyme due to its
denaturation.
Reactants, when they are at the crest of the energy hump and ready to be converted to
products, are said to be at the transition state. At this point, the reactants have formed a
fleeting, activated complex in which bonds are being formed and broken.
Enzymes catalyze reactions by decreasing the magnitude of the activation energy barrier.
The differences in the geometry and bonding properties between the reactants and the
transition state are a focus of research in enzymatic mechanisms. The importance of the
transition state can be demonstrated in numerous ways. For example:
● Compounds that resemble the transition state of a reaction tend to be very effective inhibitors
of that reaction because they are able to bind so tightly to the catalytic region of the enzyme.
● Antibodies normally do not behave like enzymes but, rather, simply bind to molecules with
high affinity. However, antibodies that bind to a compound that resembles a transition state for a
reaction are often able to act like enzymes and catalyze the breakdown of that compound.
As the transition state is converted to products, the affinity of the enzyme for the bound
molecule(s) decreases and the products are expelled.
(C.) The Active Site
As catalysts, enzymes accelerate bond‐breaking and bond‐forming processes. To accomplish
this task, enzymes become intimately involved in the activities that are taking place among the
reactants.
Enzyme‐Substrate (ES) Complex - enzymes do this by forming a complex with reactants
In most cases, the association between enzyme and substrate is noncovalent, though many
examples are known in which a transient covalent bond is formed.
Active Site - part of the enzyme molecule that is directly involved in binding the substrate
- typically buried in a cleft or crevice that leads from the aqueous surroundings into the
depths of the protein
- When a substrate enters the active site cleft, it typically gives up its bound water
molecules (desolvation) and enters a hydrophobic environment within the enzyme.
The structure of the active site accounts not only for the catalytic activity of the enzyme, but also
for its specificity.
3.6 Mechanisms of Enzyme Catalysis
The formation of the enzyme–substrate complex allows the substrate(s) to be taken out of
solution and held onto the surface of the large catalyst molecule. Once there, the physical and
chemical properties of the substrate can be affected in a number of ways, several of which are
described in the following sections.
(A.) Substrate Orientation
Enzymes - lower the entropy of their substrates in a similar manner.
Substrates - bound to the surface of an enzyme are brought very close together in precisely the
correct orientation to undergo reaction
In contrast, when reactants are present in solution, they are free to undergo translational and
rotational movements, and even those possessing sufficient energy do not necessarily undergo
a collision that results in the formation of a transition‐state complex.
Translational Movement - involves the linear motion of an object or molecules from one
location to another. It is characterized by a change in position without altering the object's
orientation
Rotational Movement - involves the spinning or turning of an object around an axis and are
less common than translational movements but still play essential roles
Translational and rotational movements are essential for a wide range of cellular functions,
including the transport of molecules, cell motility, and organismal locomotion. These movements
are often coordinated and regulated by complex cellular machinery, including motor proteins,
cytoskeletal elements (such as microtubules and actin filaments), and energy sources like ATP.
Transition‐State - Complex - refers to a highly unstable and short-lived molecular structure
that occurs during enzymatic reactions
The transition-state complex is a critical concept in cellular biology because it represents the
high-energy intermediate state in enzymatic reactions. Enzymes play a vital role in catalysis by
stabilizing this transition-state complex, lowering the activation energy barrier, and facilitating
chemical reactions in biological systems. This allows cellular processes to occur with the
required speed and specificity, enabling life-sustaining biochemical transformations.
(B.) Changing Substrate Reactivity
Enzymes are composed of amino acids having a variety of different types of side chains, from
fully charged to highly nonpolar. When a substrate is bound to the surface of an enzyme, the
distribution of electrons within that substrate molecule is influenced by the neighboring side
chains of the enzyme. This influence increases the reactivity of the substrate and stabilizes the
transition‐state complex formed during the reaction. These effects are accomplished without the
input of external energy, such as heat.
The active sites of many enzymes contain side chains with a partial positive or negative charge.
Such groups are capable of interacting with a substrate to alter its electrostatic properties and
hence its reactivity. Such groups are also capable of reacting with a substrate to produce a
temporary, covalent enzyme–substrate linkage
Enzymes - adept (catalysts) at utilizing water molecules in the reactions they catalyze
- enzymes create their own electron‐accepting cofactor by chemically modifying one of
the amino acid residues situated in their active site.
(C.) Inducing Strain in the Substrate
Although the active site of an enzyme may be complementary to its substrate(s), various studies
reveal a shift in the relative positions of certain of the atoms of the enzyme once the substrate
has bound. In many cases, the conformation shifts so that the complementary fit between the
enzyme and reactants is improved (an induced fit ), and the proper reactive groups of the
enzyme move into place. An example of induced fit is shown in FIGURE 3.14 . These types of
movements within an enzyme molecule provide a good example of a protein acting as a
molecular machine. As these conformational changes occur, mechanical work is performed,
allowing the enzyme to exert a physical force on certain bonds within a substrate molecule.
This has the effect of destabilizing the substrate, causing it to adopt the transition state in which
the strain is relieved (Figure 3.12 c ). To fully understand the mechanism by which an enzyme
catalyzes a particular reaction, it is necessary to describe the various changes in atomic and
electronic structure in both the enzyme and the substrate(s) as the reaction proceeds.
Time‐resolved Crystallography - Observe the fleeting structural changes that take place in
the active site while an enzyme is catalyzing a single reaction cycle Ultra‐high‐intensity X‐ray
beams generated by a synchrotron
CASILIHAN, MHARINELA B.
3.7 ENZYME KINETICS
Michaelis-Menten Kinetics
Michaelis-Menten kinetics is a model of enzyme kinetics which explains how the rate of an
enzyme-catalyzed reaction depends on the concentration of the enzyme and its substrate. Let’s
consider a reaction in which a substrate (S) binds reversibly to an enzyme (E) to form an
enzyme-substrate complex (ES), which then reacts irreversibly to form a product (P) and
release the enzyme again.
S + E ⇌ ES → P + E
Two important terms within Michaelis-Menten kinetics are:
Vmax – the maximum rate of the reaction, when all the enzyme’s active sites are saturated with
substrate.
Km (also known as the Michaelis constant) – the substrate concentration at which the
reaction rate is 50% of the Vmax. Km is a measure of the affinity an enzyme has for its
substrate, as the lower the value of Km, the more efficient the enzyme is at carrying out its
function at a lower substrate concentration.
The Michaelis-Menten equation for the reaction above is:
This equation describes how the initial rate of reaction (V) is affected by the initial substrate
concentration ([S]). It assumes that the reaction is in the steady state, where the ES
concentration remains constant.
When a graph of substrate concentration against the rate of the reaction is plotted, we can see
how the rate of reaction initially increases rapidly in a linear fashion as substrate concentration
increases (1st order kinetics). The rate then plateaus, and increasing the substrate
concentration has no effect on the reaction velocity, as all enzyme active sites are already
saturated with the substrate (0 order kinetics).
Fig 2 – Graph of the rate of reaction against substrate concentration, demonstrating
Michaelis–Menten kinetics, with Vmax and Km highlighted.
This plot of the rate of reaction against substrate concentration has the shape of a rectangular
hyperbola. However, a more useful representation of Michaelis–Menten kinetics is a graph
called a Lineweaver–Burk plot, which plots the inverse of the reaction rate (1/r) against the
inverse of the substrate concentration (1/[S]).
This produces a straight line, allowing for the easier interpretation of various quantities and
values from the graph. For example, the y-intercept of the graph is equivalent to the Vmax. The
Lineweaver-Burk plot is also useful when determining the type of enzyme inhibition present by
comparing its effect on Km and Vmax.
Fig 3 – Different types of enzyme inhibition as shown on a Lineweaver-Burk plot
WHY IS IT IMPORTANT TO STUDY ENZYME KINETICS
-
Enzymes are essential for life and are one of the most important types of protein in
the human body. Studying enzyme kinetics provides information about the diverse
range of reactions in the human body, which we can use to understand and predict
the metabolism of all living things.
Enzyme inhibitors represent powerful tools for isolating specific enzyme activities in crude
homogenates (e.g., proteases; Berges and Falkowski, 1996), verifying assays, and determining
whether alternative metabolic pathways exist. They can also provide a means to differentiate the
roles of different taxa that perform identical reactions. For example, cyanobacterial assimilatory
nitrate reductases are quite distinct from eukaryotic forms and so the relative contributions of
the two groups to total nitrate assimilation might be distinguished using a carefully selected
inhibitor. Very few specific inhibitors are known (e.g., vanadate for nitrate reductase, methionine
sulfoximine [MSX] for GS, and azaserine for glutamate synthase), and so their use has been
limited.
1. Irreversible Inhibitors - inactivates an enzyme by bonding covalently to a particular group
at the active site. The inhibitor-enzyme bond is so strong that the inhibition cannot be
reversed by the addition of excess substrate.
2. Competitive Inhibitors - A molecule other than the substrate binds to the enzyme’s active
site, causing competitive inhibition. The inhibitor (molecule) has a structural and chemical
similarity to the substrate (hence able to bind to the active site). The competitive inhibitor
hinders substrate binding by blocking the active site. Since the inhibitor competes with the
substrate, increasing the substrate concentration reduces the inhibitor’s actions.
3. Noncompetitive Inhibitors – A chemical binds to a location other than the active site in
non-competitive inhibition (an allosteric site). When the inhibitor binds to the allosteric site,
the enzyme’s active site undergoes a structural shift. The active site and substrate no longer
share affinity as a result of this alteration, preventing the substrate from binding. Increased
substrate levels will not be able to reverse the inhibitor’s action since the inhibitor is not in
direct competition with the substrate.
The effects of inhibitors on enzyme kinetics. The effect of both competitive and noncompetitive
inhibitors is shown when the kinetics of the reactions are plotted as velocity of reaction versus
substrate concentration (a) or its reciprocal (b). The noncompetitive inhibitor reduces Vmax
without affecting KM, whereas the competitive inhibitor increases KM without affecting Vmax.
3.8 THE HUMAN PERSPECTIVE:
-The Growing Problem of Antibiotic Resistance
Most antibiotics are derived from natural products that are produced by microorganisms living in
the soil and readily cultivated in the lab. Table 1 lists the major classes of antibiotics, examples
of each class, the targets in the bacterial cells on which these compounds act, and the
mechanism by which bacteria have developed resistance to that class of compounds.
● Antibiotic resistance occurs when bacteria change in response to the use of these
medicines.
● Bacteria, not humans or animals, become antibiotic-resistant. These bacteria may
infect humans and animals, and the infections they cause are harder to treat than
those caused by non-resistant bacteria.
● Antibiotic resistance leads to higher medical costs, prolonged hospital stays, and
increased mortality. The world urgently needs to change the way it prescribes and
uses antibiotics. Even if new medicines are developed, without behavior change,
antibiotic resistance will remain a major threat. Behavior changes must also include
actions to reduce the spread of infections through vaccination, hand washing,
practicing safer sex, and good food hygiene.
● Antibiotic resistance is rising to dangerously high levels in all parts of the world. New
resistance mechanisms are emerging and spreading globally, threatening our ability
to treat common infectious diseases.
● When exposed to antibiotics, susceptible bacteria are killed; while excessive
antibiotic use or their use for the wrong reasons can cause bacteria to grow and
multiply.
● A growing list of infections – such as pneumonia, tuberculosis, blood poisoning,
gonorrhea, and foodborne diseases – are becoming harder, and sometimes
impossible, to treat as antibiotics become less effective. Where antibiotics can be
bought for human or animal use without a prescription, the emergence and spread of
resistance is made worse.
● Similarly, in countries without standard treatment guidelines, antibiotics are often
over-prescribed by health workers and veterinarians and over-used by the public.
Without urgent action, we are heading for a post-antibiotic era, in which common
infections and minor injuries can once again kill.
Problems being combatted:
● By having patients take several different drugs targeted at different viral enzymes. This greatly
reduces the likelihood that a variant will emerge that is resistant to all of the drugs.
● By designing drugs that interact with the most highly conserved portions of each targeted
enzyme, that is, those portions where mutations are most likely to produce a defective enzyme.
This point underscores the importance of knowing the structure and function of the target
enzyme and the manner in which potential drugs interact with that target.
3.9 AN OVERVIEW OF METABOLISM
The overall goals of metabolism are energy transfer and matter transport. Energy is transformed
from food macronutrients into cellular energy.
Most of this reaction can be grouped into Metabolic pathway - a series of connected chemical
reactions that feed one another. Each reaction is catalyzed by a specific enzyme, and the
product of one reaction is the substrate for the next.
The compounds formed in each step along the pathway are the Metabolic Intermediates
(metabolites) that lead ultimately to the formation of an end product.
Metabolic pathways can be broadly divided into two categories based on their effects.
Photosynthesis, which builds sugars out of smaller molecules, is a "building up," or anabolic,
pathway. In contrast, cellular respiration breaks sugar down into smaller molecules and is a
"breaking down," or catabolic, pathway.
Anabolic pathways build complex molecules from simpler ones and typically need an input of
energy. Building glucose from carbon dioxide is one example. Other examples include the
synthesis of proteins from amino acids, or of DNA strands from nucleic acid building blocks
(nucleotides). These biosynthetic processes are critical to the life of the cell, take place
constantly, and use energy carried by ATP and other short-term energy storage molecules.
Catabolic pathways involve the breakdown of complex molecules into simpler ones and
typically release energy. Energy stored in the bonds of complex molecules, such as glucose and
fats, is released in catabolic pathways. It's then harvested in forms that can power the work of
the cell (for instance, through the synthesis of ATP).
Oxidation and reduction: A matter of electrons
An oxidation–reduction or redox reaction is a reaction that involves the transfer of electrons
between chemical species (the atoms, ions, or molecules involved in the reaction). Redox
reactions are all around us: the burning of fuels, the corrosion of metals, and even the
processes of photosynthesis and cellular respiration involve oxidation and reduction.
During a redox reaction, some species undergo oxidation, or the loss of electrons, while others
undergo reduction, or the gain of electrons. For example, consider the reaction between iron
and oxygen to form rust:
4 Fe (s) + 3 O2(g) → 2 Fe2O3(s)
rusting of iron
In this reaction, neutral Fe loses electrons to form Fe3+ ions, neutral O2 gains electrons to form
O2- ions. In other words, iron is oxidized and oxygen is reduced. Importantly, oxidation and
reduction don’t occur only between metals and nonmetals. Electrons can also move between
nonmetals, as indicated by the combustion and photosynthesis examples above.
The substance that is oxidized during a redox reaction, that is, the one that loses electrons, is
called a reducing agent , and the one that is reduced, that is, the one that gains electrons, is
called an oxidizing agent .
-The Capture and Utilization of Energy
Energy is released when these molecules are burned in the presence of oxygen, converting
the carbons to more oxidized states, as in carbon dioxide and carbon monoxide gases. The
degree of reduction of a compound is also a measure of its ability to perform chemical work
within the cell. The more hydrogen atoms that can be stripped from a “fuel” molecule, the more
ATP that ultimately can be produced.
There are basically two stages in the catabolism of glucose, and they are virtually identical in all
aerobic organisms. The first stage, glycolysis , occurs in the soluble phase of the cytoplasm (the
cytosol) and leads to the formation of pyruvate. The second stage is the tricarboxylic acid (or
TCA) cycle , which occurs within the mitochondria of eukaryotic cells and the cytosol of
prokaryotes and leads to the final oxidation of the carbon atoms to carbon dioxide.Most of the
chemical energy of glucose is stored in the form of high‐energy electrons, which are removed
as substrate molecules are oxidized during both glycolysis and the TCA cycle. It is the energy of
these electrons that is ultimately used to synthesize ATP.
DINAMPO, NICOLE ANDRIA
3.10 Glycolysis and Fermentation
Glycolysis is a central metabolic pathway where glucose is broken down into simpler
compounds, generating energy (ATP). This process introduces the concept of thermodynamics
in metabolism, specifically focusing on ΔG (change in Gibbs free energy) and ΔG°’ (change in
standard Gibbs free energy). ΔG determines the direction of a reaction within a cell. ΔG is
highlighted as a critical factor in determining the spontaneity and direction of a chemical
reaction.
Most reactions in glycolysis have ΔG values near zero, indicating they are close to equilibrium.
However, three reactions have significantly different ΔG values, making them far from
equilibrium and essentially irreversible in the cell.
A negative ΔG implies that the reaction releases free energy It is exergonic, meaning it
releases free energy. This implies that the system has more potential to do work than before the
reaction, making it likely to proceed in the (favorable) forward direction spontaneously
A positive ΔG It is endergonic, meaning it requires an input of free energy. The reaction is less
likely to proceed spontaneously in the forward direction (not favorable)
In 1905, two British chemists, Arthur Harden and William Young, were studying glucose
breakdown by yeast cells, a process that generates bubbles of CO2 gas. Harden and Young
noted that the bub-bling eventually slowed and stopped, even though there was plenty of
glucose left to metabolize. Apparently, some other essential component of the broth was being
exhausted. After experimenting with a number of substances, the chemists found that adding
inorganic phosphates started the reaction going again. They concluded that the reaction was
exhausting phosphate, the first clue that phosphate groups played a role in metabolic
pathways. The importance of the phosphate group is illustrated by the initial reactions of
glycolysis.
GLYCOLYSIS 2 Phase:
1.
Energy investment phase
2.
Energy-Generation Phase:
STEP 1
1. Forward Reaction (Left to Right):
○ In this irreversible reaction, glucose is transformed into guloce-6-phosphate.
○ ATP is hydrolyzed (broken down) to ADP, releasing energy. This energy is used
to drive the formation of glucose 6-phosphate
○ The forward reaction is strongly favored because it releases free energy (ΔG<0)
and is crucial for glycolysis to proceed.
2. Reverse Reaction (Right to Left):
○ The reverse reaction (from right to left) would require the generation of ATP
(using ADP and inorganic phosphate) to convert glucose 6-phosphate back to
glucose. However, this is not energetically favorable under typical cellular
conditions
The irreversibility of these steps ensures a unidirectional flow of metabolites through glycolysis.
This is crucial for metabolic control and efficiency. These irreversible steps act as regulatory
points, allowing the cell to modulate and coordinate the rate of glycolysis based on energy
needs and metabolic conditions
STEP 3
Irreversibility importance
By committing fructose-6-phosphate to glycolysis through an irreversible step, the cell
maximizes the extraction of energy from glucose and ensures efficient ATP production;
significant energy investment, Once fructose-1,6-bisphosphate is formed, it is committed to
further metabolism within the glycolytic pathway, tie sure ATP production in the forward direction
STEP 6
Oxidation reduction (OIL RIG) Oxidation – loss of electron; Reduction- gain of electron
STEP 7
FIGURE 3.28 Ranking compounds by phosphate transfer potential.
CONCEPT OF transfer potential
Those phosphorylated compounds (are molecules that contain one or more phosphate
groups) on the scale, that is, ones with greater free energy (larger - ΔG°’), are molecules
with less affinity for the group being transferred than are ones lower on the scale. They are
more likely to donate.
Molecules with higher free energy (higher -ΔG°')= less affinity are more likely to serve as
donors
Molecules with lower free energy (lower ΔG°') = high affinity are more likely to serve as
acceptors
The less the affinity, the better the donor; the greater the affinity, the better the acceptor.
Thus, Since1,3‐bisphosphate glycerate has 2 phosphate group it has greater free energy
(larger - ΔG°’), therefore less affinity and serve as donor, so phosphate groups from
1,3‐bisphosphate glycerate is donate to ADP to form ATP.
SUMMARIZE:
Glucose- 2 pyruvate in the end
ATP= consumed 2 sa step 1,3 but produced 4 ATP sa step 7,10 therefore we have a net
ATP of 2 ATP
We used 2Pi and 2 NAD+ = 2 NADH and 2H+
H20 product sa step 9
Anaerobic Oxidation of Pyruvate: The Process of Fermentation
FERMENTATION
The product of fermentation varies from one type of cell or organism to another.
2 types: Ethanol Fermentation and Lactic Acid Fermentation
Ethanol Fermentation
EX. Yeast cells - anaerobic ; To regenerate NAD+ They convert pyruvate to ethanol
Lactic Acid Fermentation
Ex. When muscle cells are required to contract repeatedly, the oxygen level becomes too low to
keep pace with the cell’s metabolic demands. Under these conditions, skeletal muscle cells
regenerate
NAD+ by converting pyruvate to lactate.
Aerobic (need O2)
Pyruvate is converted to Acetyl CoA with the help of the enzyme Pyruvate dehydrogenase ->
krebs cycle/ the citric acid cycle (CO2 oxidized and NADH/FADH reduced) -> Electron transport
chain
3.11 Reducing Power
A cell’s reservoir of NADPH (Nicotinamide Adenine Dinucleotide Phosphate) represents its
reducing power , which is an important measure of the cell’s usable energy content. The use of
NADPH can be illustrated by one of the key reactions of photosynthesis:
In the reaction, NADPH donates a pair of high-energy electrons (e-) and a proton (H+) to
1,3-BPG. This transfer of electrons and a proton is a reduction reaction because 1,3-BPG
gains electrons and becomes reduced. NADPH is oxidized to NADP+
●
NADP+ is also formed from NAD+ through a phosphorylation reaction
In this reaction, NAD+ and ATP are reacting together to form NADP+ and ADP.
In here phosphorylation reaction happens,
ATP is losing one of its phosphate groups, converting it into ADP. This process releases energy
because the high-energy phosphate bond in ATP is broken. a phosphate group is added to
NAD+ to form NADP+
●
NADPH can then be formed by the reduction of NADP
reaction, which is catalyzed by the enzyme transhydrogenase
NADH is the reduced form of the coenzyme NAD+.
NADP+ is the oxidized form of the coenzyme NADPH
NADH: NADH is primarily involved in catabolic processes, particularly in the production of ATP
through oxidative phosphorylation
NADPH: NADPH, on the other hand, is primarily involved in anabolic (biosynthetic) processes. It
serves as a reducing agent,
In conditions where the cell has an abundant supply of energy, often in the form of ATP, it can
afford to prioritize the biosynthesis of complex molecules (anabolism), the production of
NADPH is favored, providing a supply of electrons needed for biosynthesis of new
macromolecules that are essential for growth.
In contrast, when the cell is facing energy scarcity or increased energy demands (e.g.,
during times of stress, starvation, or high energy expenditure), it may need to prioritize energy
production over biosynthesis. NADH, which is generated during the breakdown (catabolism) of
energy-rich molecules such as glucose, can be used to produce ATP through processes like
oxidative phosphorylation in the mitochondria.
In conclusion, Cells constantly balance their energy and biosynthetic needs based on their
current metabolic state and available resources. This balance is crucial for cell survival and
adaptation to changing conditions.
DELGADO, JHOLO
3.12 Metabolic Regulation
1. Metabolism - is the process by which the body changes food and drink into energy.
2. Metabolic Regulation - a term used to describe the process by which metabolic
pathways are regulated in mammals.
a. Metabolic pathways are often regulated by feedback inhibition. Some metabolic
pathways flow in a 'cycle' wherein each component of the cycle is a substrate for
the subsequent reaction in the cycle.
3.13 Separating Catabolic and Anabolic
1. Catabolic and Anabolic Pathways - Anabolic pathways are those that require energy
to synthesize larger molecules. Catabolic pathways are those that generate energy by
breaking down larger molecules. Both types of pathways are required for maintaining the
cell's energy balance.
a. A brief consideration of the anabolic pathway leading to the synthesis of glucose
(glucogenesis) will illustrate a few important aspects about synthetic pathways.
Most cells are able to synthesize glucose from pyruvate at the same time they
are oxidizing glucose as their major source of chemical energy.
2. How are the cells able to utilize these two opposing pathways?
a. The first important point is that, even though enzymes can catalyze a reaction in
both directions, the reactions of gluconeogenesis cannot proceed simply by the
reversal of the reactions of glycolysis.
b. Even if all the reactions of glycolysis could be reversed, it would be a very
undesirable way for the cell to handle its metabolic activities, because the two
pathways could not be controlled independently of one another. Thus, a cell
could not shut down glucose synthesis and crank up glucose breakdown
because the same enzymes would be active in both directions.
3.14 THE HUMAN PERSPECTIVE:
1. Altering enzyme Activity by Covalent Modification
a. During the mid‐1950s, Edmond Fischer and Edwin Krebs of the University of
Washington were studying glycogen phosphorylase, an enzyme found in muscle
cells that disassembles glycogen into its glucose subunits. The enzyme could
exist in either an inactive or an active state. Fischer and Krebs prepared a crude
extract of muscle cells and found that inactive enzyme molecules in the extract
could be converted to active ones simply by adding ATP to the test tube. Further
analysis revealed a second enzyme in the extract—a “con- verting enzyme,” as
they called it—that transferred a phosphate group from ATP to one of the 841
amino acids that make up the glycogen phosphorylase molecule. The presence
of the phosphate group altered the shape of the active site of the enzyme
molecule and increased its catalytic activity.
2. Altering enzyme Activity by Allosteric Modulation
a. Allosteric modulation is a mechanism whereby the activity of an enzyme is either
inhibited or stimulated by a compound that binds to a site, called the allosteric
site, that is spatially distinct from the enzyme’s active site. According to one view,
the binding of a compound to the allosteric site sends a “ripple” through the
protein, producing a defined change in the shape of the active site, which may be
located on the opposite side of the enzyme or even on a different polypeptide
within the protein molecule. Depending on the particular enzyme and the
particular allosteric modulator, the change in shape of the active site may either
stimulate or inhibit its ability to catalyze the reaction.
b. Cells are highly efficient manufacturing plants that do not waste energy and
materials producing compounds that are not utilized. One of the primary
mechanism cells use to shut down anabolic assembly lines is a type of allosteric
modulation called feedback inhibition.
3. Caloric Restriction and Longevity
a. The initial idea that reduced caloric intake could lead to longer life came from
studies in rats and mice. Feeding the animals 10–30 percent less food allowed
them to have longer lives, with an increase in both the average lifespan as well
as in the maximum lifespan.
4. What is the molecular and cellular mechanism of the effect?
a. The molecular mechanisms underlying this effect include a lower rate of accrual
of tissue oxidative damage that is associated with a significantly lower rate of
mitochondrial free radical generation in rodent species.
5. Would the same effect seen in humans?
a. The researchers found that people who cut their calories slowed the pace of their
aging by 2% to 3%, compared to people who were on a normal diet. That
translates, Belsky said, to a 10% to 15% reduction in the likelihood of dying early.
b. To ask whether caloric restriction was effective in animals more similar to humans
than the rodents that had previously been used, two large studies were begun in
the 1980s using rhesus monkeys, one at the Wisconsin National Primate
Research Center (WNPRC) and one at the National Institute of Aging (NIA), part
of the NIH. Because primates have much longer lifespans than mice or rats (not
to mention worms or fl ies) these experiments had to be run for decades. The two
studies gave different results: The WNPRC study showed an increased life span
in the calorie‐restricted monkeys while the NIA study showed no effect. One
important difference between the two studies is that the NIA study fed the
monkeys food based on natural ingredients while the WNPRC used a synthetic
food made from purified components such as lactalbumin and sucrose. Assuming
that more natural ingredients make for healthier food, perhaps cutting back on
unhealthy food in the WNPRC study may have had a positive impact on life span
by reducing deaths caused by heart disease and other ailments.
2.3 Biological Molecules
2.5 - The Nature of Biological Molecules (Alli)
The bulk of living organisms is water, and most of the dry weight is composed of
carbon-containing molecules. Originally called organic molecules, they were thought to be
unique to living organisms, but as chemists synthesized them in labs, the distinction faded.
These compounds produced by living organisms are now called biochemicals, and carbon is
central to the chemistry of life due to its ability to form an incredible variety of molecules.
Carbon's unique properties, such as having four outer-shell electrons and the ability to
bond with other carbon atoms, allow it to create diverse molecules with linear, branched, or
cyclic backbones. Silicon, which is similar but larger, cannot do this effectively. Understanding
biological molecules begins with hydrocarbons, which consist of only carbon and hydrogen
atoms. Ethane (C2H6) is a simple hydrocarbon, and as more carbons are added, organic
molecules become longer and more complex.
Functional Groups
Organic molecules in biology often contain functional groups, which are specific
arrangements of atoms that influence their physical properties, chemical reactivity, and solubility
in water. Some common functional groups include ester bonds and amide bonds, which connect
carboxylic acids to alcohols and amines, respectively. These functional groups typically contain
electronegative atoms like N, P, O, and/or S, making organic molecules more polar,
water-soluble, and reactive. Some functional groups can become positively or negatively
charged through ionization.
Functional groups can dramatically change the properties of organic molecules. For
instance, replacing a hydrogen atom in the hydrocarbon ethane with a hydroxyl group (—OH)
transforms it into ethanol, a palatable alcohol. Substituting a carboxyl group (—COOH) results in
acetic acid, a strong-tasting component of vinegar. Introducing a sulfhydryl group (—SH)
creates ethyl mercaptan (CH3CH2SH), a foul-smelling substance used in enzyme research.
Overall, functional groups play a crucial role in shaping the properties and reactivity of organic
molecules in biological systems.
A Classification of Biological Molecules by Function
​ 1. Macromolecules: These are large, highly organized molecules that form the
structural basis and perform essential functions within cells. Macromolecules can be
divided into four major categories: proteins, nucleic acids, polysaccharides, and certain
lipids. They are composed of monomers and their specific sequences give rise to the
diversity among organisms.
​ 2. Building Blocks of Macromolecules: Most macromolecules in cells have relatively
short lifetimes and are continually broken down and replaced. Cells maintain a pool of
small precursor molecules, including sugars, amino acids, nucleotides, and fatty acids,
which are used to build new macromolecules.
​ 3. Metabolic Intermediates (Metabolites): Cells synthesize complex molecules through
step-by-step chemical reactions, known as metabolic pathways. These pathways start
with specific starting materials and progress through intermediates until functional end
products are produced. The compounds formed along these pathways, which may not
have specific functions themselves, are called metabolic intermediates.
​ 4. Molecules of Miscellaneous Function: This category encompasses various
molecules with diverse roles, though they constitute a smaller portion of a cell's dry
weight compared to macromolecules. Examples include vitamins, hormones, energy
storage molecules like ATP, regulatory molecules like cyclic AMP, and metabolic waste
products like urea.
These different categories of organic molecules and their interactions play a fundamental role in
the chemistry of life and are crucial for the functioning of living organisms.
2.6 - Carbohydrates (Alli)
Carbohydrates, also known as glycans, encompass simple sugars called
monosaccharides and larger molecules composed of sugar building blocks. They primarily serve
as energy stores and structural materials in biological processes. Most sugars follow the general
formula (CH2O)n, with n values ranging from 3 to 7. Trioses have three carbons, tetroses have
four, pentoses have five, hexoses have six, and heptoses have seven carbons. These sugars
play essential roles in cellular metabolism and various biological functions
Thet Sructure of Simple Sugars
Sugars consist of carbon atoms forming a linear backbone linked by single bonds. Each
carbon in the backbone has a hydroxyl group, except one with a carbonyl group. If the carbonyl
is internal (ketone), it's called a ketose (e.g., fructose). If it's at one end (aldehyde), it's an
aldose (e.g., glucose).
Sugars are highly water-soluble due to their many hydroxyl groups. In solution, sugars
with five or more carbons spontaneously form closed ring structures. The open-chain form is
important in biochemistry, as it can react with proteins. In diabetes, open-chain sugars react with
hemoglobin to produce Hemoglobin A1c, used to monitor the condition.
Ring forms of sugars are usually depicted flat but exist in three-dimensional
conformations resembling a chair. The structures of fructose and glucose are examples of
ketoses and aldoses, respectively, with glucose's chair conformation being a more accurate
representation of its three-dimensional structure.
Sugars serve as essential building blocks for various carbohydrates, with their ring forms
predominantly found in biological processes.
Stereoisomerism
Carbon atoms can form bonds with four other atoms, resulting in a tetrahedral
arrangement. When a carbon atom is bonded to four different groups, it creates two
non-superimposable mirror image molecules called stereoisomers or enantiomers. They share
similar chemical reactivities but have mirrored structures, similar to right and left hands. For
example, d-glyceraldehyde has the hydroxyl group at carbon 2 projecting to the right, while
l-glyceraldehyde projects it to the left.
As the carbon backbone of sugar molecules lengthens, the number of asymmetric
carbon atoms and stereoisomers increases. For instance, aldohexoses have 16 different
stereoisomers. The designation of d or l depends on the arrangement of groups attached to the
asymmetric carbon farthest from the aldehyde group.
In ring structures, like pyranoses, a new center of asymmetry emerges at carbon 1 due
to its four different groups. This leads to α and β stereoisomers. α-pyranoses have the OH group
of the first carbon projecting below the ring plane, while β-pyranoses have it projecting upward.
These differences have significant biological implications, affecting the shapes and properties of
molecules like glycogen, starch, and cellulose.
Linking Sugars Together\
Sugars can form covalent glycosidic bonds to create larger molecules. These bonds
typically involve the reaction between carbon atom C1 of one sugar and the hydroxyl group of
another, resulting in a C-O-C linkage.
Disaccharides, composed of two sugar units, are a type of sugar molecule primarily
serving as readily available energy stores. For example, sucrose is found in plant sap,
transporting energy within plants, while lactose in mammalian milk provides fuel for newborns.
Some people lose the enzyme lactase, which breaks down lactose, causing digestive discomfort
when consuming dairy products.
Sugars can also join to form short chains called oligosaccharides. These are often
attached to lipids and proteins, converting them into glycolipids and glycoproteins, respectively.
Oligosaccharides are especially important on the surfaces of cells, where they play an
informational role, distinguishing one cell type from another and facilitating interactions with their
environment.
Polysaccharides
Claude Bernard, a 19th-century physiologist, investigated the cause of diabetes and the
source of elevated blood sugar levels. He discovered that glucose could be produced in the
body even without consuming dietary carbohydrates. Bernard identified the liver as the source
of glucose production, where an insoluble glucose polymer called glycogen was stored. His
hypothesis proposed that various food materials, including proteins, could be chemically
converted into glucose in the liver and stored as glycogen. When the body needed sugar for
energy, glycogen in the liver would be transformed back into glucose and released into the
bloodstream to meet the body's needs. This balance between glycogen formation and
breakdown in the liver was crucial in maintaining stable blood glucose levels. Bernard's
hypothesis was eventually confirmed, and glycogen was recognized as a type of
polysaccharide, a polymer of sugar units linked by glycosidic bonds.
Polysaccharides are large molecules made of sugar units joined by glycosidic bonds.
They serve various functions in living organisms.
Glycogen and Starch: Glycogen is a branched polymer of glucose, serving as an energy store
in animals. It's primarily found in the liver and muscles. Starch, on the other hand, is the plant
equivalent of glycogen, stored in grains and tubers. It consists of two types of polymers,
amylose (unbranched) and amylopectin (branched).
Cellulose: Cellulose is a structural polysaccharide and a major component of plant cell walls. It
differs from glycogen and starch in that its glucose units are joined by β (1 → 4) linkages,
making it indigestible by most animals. Termites and certain animals rely on cellulase-producing
microorganisms to digest it.
Chitin: Chitin is an unbranched polymer of N-acetylglucosamine and serves as a structural
material in the exoskeletons of insects, spiders, and crustaceans. It is resilient and flexible.
Glycosaminoglycans (GAGs): GAGs are complex polysaccharides composed of alternating
sugar units. Heparin, a well-known GAG, inhibits blood coagulation by activating antithrombin.
Most GAGs are found in extracellular spaces and play various roles in the body.
These polysaccharides serve diverse functions, from energy storage (glycogen, starch) to
structural support (cellulose, chitin) and regulation (heparin, GAGs). They are crucial
components of biological systems.
2.7 - Lipids (Alli)
Lipids are a diverse group of nonpolar biological molecules characterized by their inability to
dissolve in water but ability to dissolve in organic solvents. Important lipid categories include
fats, steroids, and phospholipids.
Fats:
● Fats are composed of glycerol linked to three fatty acids, forming a molecule called a
triacylglycerol or triglyceride.
● Fatty acids are long hydrocarbon chains with a hydrophilic carboxyl group at one end
and a hydrophobic hydrocarbon chain at the other.
●
Fatty acids can be saturated (no double bonds) or unsaturated (contain double bonds),
affecting their physical properties.
● Hydrogenation converts unsaturated fats into saturated or trans-fats, which are
considered unhealthy.
● Fats serve as a concentrated energy source and are stored as lipid droplets, especially
in adipocytes.
Steroids:
● Steroids have a characteristic four-ringed hydrocarbon skeleton.
● Cholesterol is an important steroid present in animal cell membranes and a precursor for
steroid hormones.
● Steroids play essential roles in cellular function, including hormone regulation.
Phospholipids:
● Phospholipids are similar in structure to fats but have only two fatty acid chains and a
phosphate group.
● The phosphate group end is hydrophilic, while the fatty acid tail end is hydrophobic.
● Phospholipids are vital components of cell membranes and contribute to their unique
properties.
These lipid categories have various biological functions, including energy storage, membrane
structure, and hormone regulation, and they are essential for cellular processes.
2.8 - Building Blocks of Proteins (RV)
Proteins - synthesized by the cells through transcription and translation (quick review of
the central dogma)
Functions:
1) Enzymes
2) Structural cables
3) Hormones and growth factors
4) Gene activators
5) Membrane receptors and transporters
6) Contractile filaments
7) Molecular motors
*also as antibodies, serve as toxins, form blood clots, absorb or refract light,
transport
substances from one part of the body to another
Peptide formation
2.9 - Primary and Secondary Structure of Proteins (RV)
2.10 - Tertiary Structure of Proteins (RV)
2.11 - Quaternary Structure of Proteins (Ash)
The quaternary structure found in some proteins results from interactions between two
or more polypeptide chains – interactions that are usually the same as those that give
rise to the tertiary structure. A protein complex composed of two identical subunits is
described as a homodimer, whereas a protein complex composed of two nonidentical
subunits is a heterodimer. The Quaternary structure of protein is consist of two or more
polypeptide chains and are held together by noncovalent interactions (hydrogen bonds,
ionic bonds, and hydrophobic interactions) Subunits may either function independently
of each other, or may work cooperatively, as in hemoglobin, in which the binding of
oxygen to one subunit of the tetramer increases the attraction of the other subunits for
oxygen. Many proteins are made up of multiple polypeptide chains, often referred to as
protein subunits. The quaternary structure refers to how these protein subunits interact
with each other and arrange themselves to form a larger combined protein complex.
The final shape of the protein complex is once again stabilized by various interactions,
including hydrogen bonding, disulfide-bridges and salt bridges.
FIBROUS PROTEINS AND GLOBULAR PROTEINS
Globular proteins typically are approximately round in shape. They contain a mix of
amino acid types and contain differing sequences in their primary structures. Globular
proteins have many different functions, such as enzymes, cellular messengers, and
molecular transporters. These roles often require the proteins to be soluble in the
aqueous cellular environment. They are also sensitive to changes in their environment,
such as pH and temperature. Fibrous proteins are either long and narrow proteins or
assemble to form long and thin structures. The amino acids in the primary structure
often consist of repeating amino acid sequences. They are not typically soluble in water;
however, they may be soluble in strong acids or bases.
HEMOGLOBIN
The most common example used to illustrate quaternary structure is the hemoglobin
protein. Hemoglobin’s quaternary structure is the package of its monomeric subunits.
Hemoglobin is composed of four monomers. There are two alpha chains, each with 146
amino acids. Because there are two different subunits, hemoglobin exhibits
heteroquaternary structure. If all of the monomers in a protein are identical, there is
homoquaternary structure. Even though hemoglobin consists of four subunits, it is still
considered a single protein with a single function. Many examples are known in which
different proteins, each with a specific function, become physically associated to form a
much larger multiprotein complex which example is the pyruvate dehydrogenase
complex of bacterium E. coli.
2.12 - Protein Folding (Ash)
PROTEIN FOLDING
In 1956 by Christian Anfinsen at the National Institutes of Health studied the properties
of ribonuclease A, a small enzyme that consists of a single polypeptide chain of 124
amino acids with four disulfide bonds linking various parts of the chain. Protein folding is
the physical process by which a protein chain acquires its native 3-dimensional
structure, a conformation that is usually biologically functional, in an expeditious and
reproducible manner. It is the physical process by which a polypeptide folds into its
characteristic and functional three-dimensional structure from random coil. Each protein
exists as an unfolded polypeptide or random coil when translated from a sequence of
mRNA to a linear chain of amino acids. As the polypeptide chain is being synthesized
by the ribosome, the linear chain begins to fold into its three dimensional structure.
Folding begins to occur even during translation of the polypeptide chain. Amino acids
interact with each other to produce a well-defined three-dimensional structure, the
folded protein, known as the native state. The resulting three-dimensional structure is
determined by the amino acid sequence or primary structure (Anfinsen's dogma). The
energy landscape describes the folding pathways in which the unfolded protein is able
to assume its native state.
The correct three-dimensional structure is essential to function, although some parts of
functional proteins may remain unfolded, so that protein dynamics is important. Failure
to fold into native structure generally produces inactive proteins, but in some instances
misfolded proteins have modified or toxic functionality. Several neurodegenerative and
other diseases are believed to result from the accumulation of amyloid fibrils formed by
misfolded proteins. Many allergies are caused by incorrect folding of some proteins,
because the immune system does not produce antibodies for certain protein structures.
That’s why there are molecular chaperones also called as helper proteins that
selectively bind to short stretches of hydrophobic amino acids that tend to be exposed in
non-native proteins but buried in proteins having a native conformation.
MOLECULAR CHAPERONES
Not all proteins are able to assume their final tertiary structure by a simple process of
self‐assembly. This is not because the primary structure of these proteins lacks the
required information for proper folding, but rather because proteins undergoing folding
have to be prevented from interacting nonselectively with other molecules in the
crowded compartments of the cell. Several families of proteins have evolved whose
function is to help unfolded or misfolded proteins achieve their proper three‐dimensional
conformation. These “helper proteins” are called molecular chaperones, and they
selectively bind to short stretches of hydrophobic amino acids that tend to be exposed in
nonnative proteins but buried in proteins having a native conformation. They depicts the
activities of two families of molecular chaperones that operate in the cytosol of
eukaryotic cells. Molecular chaperones are involved in a multitude of activities within
cells, ranging from the import of proteins into organelles to the prevention and reversal
of protein aggregation.
2.13 - Protein Folding Can Have Deadly Consequences (Ash)
PROTEIN MISFOLDING
Misfolded proteins result when a protein follows the wrong folding pathway or
energy-minimizing funnel, and misfolding can happen spontaneously. Most of the time,
only the native conformation is produced in the cell. But as millions and millions of
copies of each protein are made during our lifetimes, sometimes a random event occurs
and one of these molecules follows the wrong path, changing into a toxic configuration.
This kind of conformational change is most likely to occur in proteins that have repetitive
amino acid motifs, such as polyglutamine; such is the case in Huntington's disease.
Remarkably, the toxic configuration is often able to interact with other native copies of
the same protein and catalyze their transition into the toxic state. Because of this ability,
they are known as infective conformations. The newly made toxic proteins repeat the
cycle in a self-sustaining loop, amplifying the toxicity and thus leading to a catastrophic
effect that eventually kills the cell or impairs its function.
Accumulation of misfolded proteins can cause disease, and unfortunately some of these
diseases, known as amyloid diseases, are very common. The most prevalent one is
Alzheimer's disease, which affects about 10 percent of the adult population over
sixty-five years old in North America. Parkinson's disease and Huntington's disease
have similar amyloid origins. These diseases can be sporadic (occurring without any
family history) or familial (inherited). Regardless of the type, the risk of getting any of
these diseases increases dramatically with age. The mechanistic explanation for this
correlation is that as we age (or as a result of mutations), the delicate balance of the
synthesis, folding, and degradation of proteins is perturbed, resulting in the production
and accumulation of misfolded proteins that form aggregates. Among the environmental
factors known to increase the risk of suffering degenerative diseases is exposure to
substances that affect the mitochondria, increasing the amount of oxidative damage to
proteins. However, it is clear that no single environmental factor determines the onset of
these disorders. In the case of Alzheimer's disease, and for other less common
neurodegenerative diseases, the genetics can be even more complicated, since
different mutations of the same gene and combinations of these mutations may
differently affect disease risk.
2.14 - Chaperones - Helping Proteins Reach Their Proper Folded State (Cass)
In order to become a useful protein, the polypeptide produced by a ribosome
during translation must be folded into a unique 3-dimensional configuration and must
bind any cofactors required for its activity. It might also need to be modified
appropriately by protein-modifying enzymes, such as protein kinases, or to correctly join
other protein subunits. Protein structures are evolved to fold rapidly into their final
shapes, and some proteins begin the folding process as the N-terminus emerges from
the ribosome.
Typically, this results in a flexible state termed a “molten globule”, which contains
secondary folding features – alpha helix and beta pleated sheets. While the molten
globule stage is usually complete within seconds, it is merely a starting point for the
then slow process of side-chain adjustments until the correct tertiary structure is
achieved. This slower process usually takes several minutes.
Misfolded, or aberrant proteins are not only a waste of energy for a cell, but they
are also dangerous. These aberrant proteins typically have exposed hydrophobic
regions, which cause them to clump together into aggregates, which accumulate and
can cause severe diseases.
The cell has two lines of defense against the formation of these dangerous
misfolded proteins – molecular chaperones, and the proteasome. Molecular chaperones
help proteins fold correctly, while the proteasome destroys misfolded proteins through
proteolysis. The molecular chaperones and proteasomes compete over these proteins.
The longer a protein remains misfolded, either because chaperones haven’t reached it,
or because they haven’t succeeded in fixing it, the more likely it is that a proteasome will
degrade it.
Chaperones work by binding to exposed hydrophobic patches on misfolded or
incompletely folded proteins and hydrolyzing ATP. Some of the energy expended by
chaperones is used to perform mechanical work, but much more is used to ensure the
accuracy of protein folding . The proteins that chaperones help fold properly are called
“client proteins”.
There are several families of molecular chaperones in eukaryotes, which function
in different organelles. This includes Hsp60 and Hsp70, each of which has a set of
associated proteins. Hsp stands for heat-shock proteins, because lots of them are
produced when a cell is exposed to elevated temperatures, responding to increased
amounts of misfolded proteins.
Hsp70 acts early on in the process of protein folding, binding to polypeptide chains
emerging from ribosomes where there is a chain of 7 hydrophobic amino acids. Hsp70
is aided by Hsp40s, and many cycles of ATP hydrolysis are generally required to fold a
single polypeptide chain correctly.
Hsp60 acts on fully synthesized proteins, forming a large barrel that serves to
isolate the protein and provide better conditions for folding. Hsp60, which is a type of
molecular chaperone called a chaperonin, initially captures proteins along the rim of one
of its barrels. Then, the binding of ATP and a protein cap increases the diameter of the
barrel and partly unfolds the protein. Inside the barrel, the protein has a chance to fold
in a more favorable environment. 15 seconds after ATP binds to the Hsp60, it
hydrolyzes, weakening the complex. The binding of another ATP molecule makes the
protein leave.
If the protein is still not folded correctly, it can repeat the cycle.
Proteasomes are so important that they constitute almost 1% of cell proteins.
They are dispersed throughout the nucleus and cytosol. If a protein folds correctly and
quickly, then none, or only a small bit of it gets degraded. A slowly-folding protein is at
risk for a longer time, and more of it might get destroyed before the remaining amino
acids attain the correctly folded state.
2.15 - Proteomics and Interacteomics (Cass)
Proteomics is the complete evaluation of the function and structure of proteins to
understand an organism’s nature. Mass spectrometry is an essential tool that is used for
profiling proteins in the cell. However, biomarker discovery remains the major challenge
of proteomics because of their complexity and dynamicity. Therefore, combining the
proteomics approach with genomics and bioinformatics will provide an understanding of
the information of biological systems and their disease alteration.
Proteomics has three main types: expression proteomics, structural proteomics, and
functional proteomics.
1. Expression proteomics is a novel approach that studies the quantitative and
qualitative expression of proteins. It aims to specify the difference in protein
expression between two conditions such as patients and control. In addition, it can
identify disease-specific proteins and new proteins in signal transduction. Expression
proteomics experiments are usually used to study the patterns of protein expression
in different cells. For example, a tumor tissue sample is compared to a normal tissue
sample to identify differences in the levels of proteins. Variations in protein
expression, which are present or missing in tumor tissue compared to normal tissue,
are detected using 2-DE and MS techniques.
2. Nuclear magnetic resonance spectroscopy and X-ray crystallography are used in
structural proteomics to determine the three-dimensional structure and structural
complexities of functional proteins. It specifies all protein interactions such as
membranes, cell organelles, and ribosomes in the mixture. The study of the nuclear
pore complex is an example of structural proteomics.
3. Functional proteomics is a type of proteomics. studies the protein functions and
molecular mechanisms in the cell and determines the protein partner’s interactions. In
particular, it investigates the interaction of an unknown protein with partners from a
specific protein complex involved in a particular process. This may indicate the
biological role of the protein. In addition, the elucidation of protein-protein interactions in
vivo can lead to comprehensive descriptions of cellular signaling pathways.
Interactomics is an interdisciplinary field of biology and bioinformatics refers to the
study of both the interactions among various proteins and other molecules within a cell,
and the consequences of such interactions. It aims to compare such networks of
interactions between and within species in order to find how the traits of such networks
are either preserved or varied.
The totality of protein-protein interactions taking place within a cell, organism, or a
specific biological context, is known as Interactome. The development of large-scale
protein-protein interaction (PPI) screening techniques, particularly high-throughput
affinity purification along with mass-spectrometry as well as the yeast two-hybrid assay,
has resulted in enormous amount of PPI data and the production of ever more complex
and complete interactomes.
Limitations: It is important to emphasize once more the limitations of available PPI
data. Our current knowledge of the interactome is both incomplete and noisy. PPI
detection methods have limitations as to how many truly physiological interactions they
can detect and they all find false positives and negatives.
Proteins play important roles in most biological processes, and their interactions with
each other precisely regulate biological function.Therefore, populating and
understanding specific interactomes is becoming extremely important.
Methods For PPI Analysis
In recent years, a number of approaches have been developed to detect protein–protein
interactions (PPIs). These approaches can be roughly divided into three groups: in
silico, in vivo and in vitro. Each group includes many different technologies
In silico methods - consist of text mining and computational analyses, are usually
carried out by computer simulation. Available public databases include the Munich
Information Center for Protein Sequence, the Molecular Interaction database, the
Human Protein Reference Database, bioGRID, CREDO, STRING and IntAct.
In vivo methods - include yeast two-hybrid (Y2H), protein-fragment complementation
assay (PCA) and mammalian protein–protein interaction trap (MAPPIT) and can be
performed on intact living organisms.
In vitro methods - refers to the experiments performed in a controlled environment
outside a living organism, and include methods such as tandem affinity
purification-mass
spectroscopy
(TAP-MS),
protein
microarray
and
the
luminescence-based mammalian interactome (LUMIER) technique.
Interactomics deals with various types of biological networks, which includes:
A. Metabolic Networks
Such networks map an attempt to comprehensively describe all possible biochemical
reactions for a particular cell or organism. In many representations of metabolic
networks, nodes are biochemical metabolites and edges are either the reactions that
convert one metabolite into another or the enzymes that catalyze these reactions.
Edges can be directed or undirected, depending on whether a given reaction is
reversible or not. In some particular cases of metabolic network modeling, the contrary
situation can be used, with nodes representing enzymes and edges pointing to adjacent
pairs of enzymes for which the product of one is the substrate of the other.
B. Protein-Protein Interaction Networks (PPINs)
In protein-protein interaction network maps, nodes represent proteins and edges
represent a physical interaction between two proteins. The edges are non-directed, as it
cannot be said which protein binds the other, i.e., which partner functionally influences
the other.
Methodologies to Map PPINs
There are many methodologies that can map protein-protein interactions, out of which
two are currently in wide use for large-scale mapping:
Yeast two-hybrid system - mapping of binary interactions is primarily carried out by
ever improving variations of the yeast two-hybrid (Y2H) system.
Mass Spectrometry (AP/MS) - mapping of membership in protein complexes,
providing indirect associations between proteins, is carried out by affinity-purification or
immuno-purification to isolate protein complexes, followed by some form of mass
spectrometry (AP/MS) to identify protein constituents of these complexes.
The graphs generated by these two approaches exhibit different global properties, such
as the relationships between gene essentiality and the number of interacting proteins.
Likewise, an empirical framework recently propagated for protein interaction mapping
now allows the estimation of overall accuracy and sensitivity for maps obtained using
high-throughput mapping approaches.
Four critical parameters need to be estimated:
Completeness - the number of physical protein pairs actually tested in a given search
space.
Assay sensitivity - which interactions can and cannot be detected by a particular
assay.
Sampling sensitivity - the fraction of all detectable interactions found by a single
implementation of any interaction assay.
Precision - the proportion of true biophysical interactors.
Careful contemplation of these parameters offers a quantitative idea of the
completeness and accuracy of a particular high-throughput interaction map, and allows
the comparison of multiple maps as long as standardized framework parameters are
used. On the contrary, comparing the results of small-scale experiments available in
literature curated databases is not possible, because there is simply no way to control
for accuracy, reproducibility, and sensitivity.
C. Gene Regulatory Networks
In most of the gene regulatory network maps, nodes either represent a transcription
factor or a putative DNA regulatory element, while directed edges represent the physical
binding of transcription factors to such regulatory elements. Edges can be:
Incoming - transcription factor binds a regulatory DNA element.
Outgoing - regulatory DNA element bound by a transcription factor.
Methodologies To Map Gene Regulatory Networks
At present, there are two general approaches compliant to large-scale mapping of gene
regulatory networks:
Yeast one-hybrid (Y1H) approaches - a putative cis-regulatory DNA sequence,
commonly a suspected promoter region, is used as bait to capture transcription factors
that bind to that sequence.
Chromatin immunoprecipitation (ChIP) approaches - antibodies raised against
transcription factors of interest, or against a peptide tag used in fusion with potential
transcription factors, are used to immunoprecipitate potentially interacting cross-linked
DNA fragments.
2.16 - Protein Engineering (Cass)
PROTEIN ENGINEERING
Protein engineering is the process by which a researcher modifies a protein sequence
through substitution, insertion, or deletion of nucleotides in the encoding gene.
with the goal of obtaining a modified protein that is more suitable for a particular
application or purpose than the unmodified protein.
● Targeted mutagenesis, or site-directed mutagenesis is a method whereby a
specific site within a gene sequence is altered. Such alterations can be
performed for engineering purposes, as in protein engineering, or for examining
the effect of specific mutations in a gene.
●
Application of Protein Engineering
1. Industrial Applications
A broad range of enzymes are being used in different industries like food, paper,
leather, cosmetic, pharmaceutical and chemical industry.
● Principally, the food industry spends a diversity of enzymes like proteases,
lipases, amylases etc. in food processing.
Proteases are employed in numerous industrial processes for example in paper industry
as biofilm removal, in food industry in milk clotting, meat tenderization and to add up
flavors and also used in detergents as protein stain removal
● Proteins engineers are working to develop engineered proteases, which have the
ability to act more efficiently at low temperature and alkaline pH.
Amylases are used in many industries to multiply functions for example it is used in food
industry to soften bread, adjust flour, for liquefaction and scarification of starch and juice
treatment.
● In the detergent and paper industry, these enzymes are used to remove starch
stains and de-inking.
● For the production of different food and industrial products starch is converted
into bioethanol or into food ingredients like fructose, glucose and organic acids in
microbial fermenters which require biocatalysts such amylase for the liquefaction
and scarification. So to improve the activity and stability of amylases at harsh
conditions, protein engineering and DNA recombinant technology have been
used.
Lipases are also used intensively by food and detergent industries such as for lipid stain
removal, cheese flavor, dough stability and as contaminants controller in paper & pulp
industry.
These processes require mostly high temperature, different pH range and also many
other compounds are present there, which can inhibit/hinder enzyme activity. So, to
overcome these problems and to further enhance their production and activity,
properties of enzymes, which include specificity, thermos-stability and catalytic activity,
are improved by making the use of new approaches of protein engineering.
1. Environmental Applications
Oxygenases, laccases and peroxidases are three major classes of enzymes, which
have significant roles in environmental applications for biodegradation of organic and
toxic pollutants. But mostly, these enzymes face problems like enzyme denaturation by
toxic compounds, inhibition of ES (enzyme- substrate) complex and low catalytic
activity. Scientists have done intensive work to overcome these problems by developing
engineered enzymes by recombinant technology and rational enzyme design.
2. Medical and Clinical Applications
Protein engineering has enormous applications in the area of therapeutics. Mutation,
DNA shuffling and recombinant DNA approach were used in protein engineering to get
improved results of therapeutic protein. Later advancements in protein engineering
resulted in production of secreted therapeutic proteins such as interferon, insulin, and
also development in gene therapy by inducing recombination using mega nucleases
and DNA double-strand breaks.
● Development of therapeutics against cancer is the major field of interest in
protein engineering. One of potential treatments recommended for cancer is
pre-targeted immunotherapy in which radiation toxicity is thought to be
minimized. By using protein engineering, the use of this pre-targeted
immunotherapy was expected to be an efficient treatment for cancer.
● Advancements in recombinant DNA technology and protein engineering enable
the synthesis of novel antibodies, which can be used as anti-cancer drugs. These
unique antibodies are engineered such a way that they precisely identify and
bind with higher affinity with their cancerous antigenic markers, and aid in
eliminating the cancerous cell with greater accuracy.
3. Other Emerging Applications
Innovative proteins known as affibody binding proteins, which are of
non-immunoglobulin (Ig) origin, have been developed using protein engineering
techniques. They have high affinity and are used in diagnostics, viral targeting,
bioseparation and tumor imaging.
2.17 - Protein Adaptation and Evolution (Paul)
Adaptations are traits that improve the likelihood that an organism will survive in a
particular environment. As in other characteristics, proteins are also subject to
adaptations.
- explain how comparing evolutionary characteristics between homologous
(related) proteins can prove this (ex. Halophilic archaebacteria)
- These homologous proteins may exhibit virtually identical shapes and folding
patterns, but show strikingly different amino acid sequences.
- the greater the evolutionary distance between these proteins, the more
different their amino acid sequences are
- Secondary and tertiary structures of proteins change much more slowly during
evolution compared to their primary structures.
- flashback to protein structuring from previous reporters (i.e. primary
structure – linear sequence of amino acids in a protein, secondary
structure – primary structure folds, tertiary structure – in 3d shape or entire
polypeptide)
- This does not mean, however, that minor changes in a primary structure
will not majorly affect the protein’s conformation.
- explain how each amino acid play an important role in a
protein’s function; flashback to protein folding from previous
reporters (i.e. a protein’s fold do more than just hold its
shape, it has effects on its functions too)
- If mutations of this magnitude occur in nature, it may even
create an entire new protein with new functional properties,
and thus may serve as an ancestral form of an entirely new
family of proteins.
Going back to adaptations, we have seen how evolution has produced different versions
of proteins in different organisms (e.g. protein malate dehydrogenase in halophilic
archaebacteria as mentioned above). However, evolution also produces different
versions of proteins in individual organisms. Different versions of a protein is called
isoforms.
- an example of this is globin or collagen (several versions of each are encoded in
the human body)
- another example of this is the cytoskeletal (provides support and shape) protein
actin. the human body produces six different isoforms of actin – two of which are
found in smooth muscle, one in skeletal muscle, one in heart muscle, and the
other two in virtually all types of cells.
Now that a large number of amino acid sequences and tertiary structures have been
reported, it is clear that proteins are members of families (or superfamilies). They are
thought to have originated from an ancestral gene and over long periods of time,
diverged from each other to create new proteins. The expansion of these families are
responsible for much of the protein diversity encoded in the genomes of present day
plants and animals.
2.18 - Nucleic Acids (Paul)
Nucleic acids are macromolecules made up of long chains of monomers called
nucleotides.
- they function mainly for storage and transmission of genetic information, but may
also have structural or catalytic roles.
There are two types of nucleic acids found in living organisms, namely deoxyribonucleic
acid (DNA) and ribonucleic acid (RNA).
- DNA serves as the carrier of genetic material of cellular organisms, though RNA
carries this role for many viruses.
In this discussion, we will examine the basic structure of nucleic acids using a
single-stranded RNA as a representative model.
- A nucleotide is the building block of nucleic acids and it consists of three parts:
(1) a phosphate, (2) a sugar, and (3) a nitrogenous base.
- Nucleotides of RNA contain the sugar ribose, while nucleotides of DNA contain
the sugar deoxyribose. The difference between the two is that in deoxyribose, a
hydrogen atom is bonded to the second carbon atom instead of a hydroxyl group
found in ribose.
Nucleotides are joined together to form a strand by strong covalent bonds that link the 3’
hydroxyl group of one sugar with the 5’ phosphate group of the adjoining sugar. These
bonds are described as 3’-5’-phosphodiester bonds because the phosphate atom is
esterified to two oxygen atoms, one from each sugar.
A strand of DNA (or RNA) contains four different nucleotides distinguished by their
nitrogenous bases – either a purine or a pyrimidine. Pyrimidines are smaller molecules
consisting only of one ring, while purines are larger molecules which consist of two
rings.
- RNAs contain two different purines (adenine and guanine) and two different
pyrimidines (cytosine and uracil). In DNAs, the pyrimidine uracil is replaced by
thymine.
Nucleotides are not only important as building blocks of nucleic acids, they also have
important functions in their own right. Most of the energy being put to use at any given
moment in any organism is derived from the nucleotide adenosine triphosphate (ATP).
2.19 - The Formation of Complex Macromolecules (Paul)
In this lesson, I will discuss how different subunits of cellular structures assemble
themselves. The assembly of cellular organelles is poorly understood, but it is apparent
from the following examples that different types of subunits can self‐assemble to form
higher‐order arrangements.
A. The Assembly of Tobacco Mosaic Virus Particles
- In 1955, Heinz Fraenkel‐Conrat and Robley Williams of the University of
California, Berkeley demonstrated that TMV particles were capable of self
assembly.
- TMV particles consist of one long RNA molecule wound within a helical
capsule made up of identical protein subunits.
- In their experiment, they purified RNA and protein separately, mixed them
together, and recovered mature, infective particles after a short period of
incubation. This is perhaps the most convincing evidence that
self-assembly is directed and may occur in vitro under physiological
conditions when the only macromolecules present are those that make up
the final structure.
B. The Assembly of Ribosomal Subunits
- One of the milestones in the study of ribosomes came in the mid‐1960s,
when Masayasu Nomura and his co‐workers at the University of
Wisconsin succeeded in reconstituting complete, fully functional 30S
-
bacterial subunits by mixing the 21 purified proteins of the small subunit
with purified small‐subunit ribosomal RNA.
- explain that ribosomes may be 50S or 30S. 50s comprise of 2 RNA
molecules and approximately 32 different proteins. 30s comprise of
1 RNA molecule and 21 different proteins.
- Going back to the experiment, it is found that intermediates forming
in different stages at reconstitution during the in vitro process
closely parallel the step-by-step manner that occur in vivo.
It must be noted, however, that formation of ribosomes within a eukaryotic
cell requires the transient association of many proteins that do not end up
in the final particle, as well as the removal of approximately half the
nucleotides of the large ribosomal RNA precursor.
- Thus, it can be concluded that mature eukaryotic cells no longer
possess the information necessary to reconstitute themselves in
vitro.