L02 Lecture Video 10.11.

2021
Prof. Ronaldo A. Bigsang || September 2021 BIO107
Transcribers: Loyd Joredell H. Curit
Editors: Loyd Joredell H. Curit Cell and Molecular Biology

OUTLINE Outermost atom interacts with other outermost atoms of other molecules
which influences the bond between them.
They may share their outermost electron, or they may lore or gain an
Legend: electron in the process.
Remember Previous Trans Covalent bond – formed when atoms share electrons
Lecturer Book
(Exams) Trans Comm Ionic bond – when an atom losing or gaining electron
     These are two of the most important relation or links between atoms.

3.3 Noncovalent attractions help bring molecules together in cells

L02 Cell Chemistry and Bioenergetics
 Individually weak but can create an effective force between
Theme 3: Living things obey chemical and physical laws. molecules when together.
 Electrostatic attractions (ionic bonds)
Living things as systems, follow certain rules. o Attractive forces between oppositely charged atoms
 Hydrogen bonds (i.e. DNA)
 Cell chemistry is more complex than any other chemical system o Polar interaction in which an electropositive hydrogen
known. atom is partially shared by two electronegative atoms
 Van der Waals forces
Complexity is a universal property of cell. o Force produced by a flickering dipole due to
fluctuations in the electron cloud.
 Life is based on carbon compounds incorporated into enormous
 Hydrophobic force
polymeric molecules.
o Pushing of nonpolar surfaces out of the H-bonded
 The unique properties of these macromolecules enable cells
water network
and organisms to exhibit characteristics of life.
 Cells are 70% water allowing an array of chemical reactions
3.4 Water is the most abundant substance in cells
that depend largely on aqueous environment to proceed
 Properties of water:
3.1 Cells are made from a few types of atoms
o High specific heat capacity
 you have an increase in a gram of
 Matter is made up of elements or their combinations
molecule increasing 1 degree Celsius,
o Atoms are
amount of energy required to increase a
 Properties of living things depend on the way their atoms are gram of water.
linked together to form molecules  Important on living things having the ability
 C, H, O, N make up 96.5% of an organism’s weight to buffer; to survive in hot environments
o Versatile solvent (polarity)
These are the elements you mostly found on living organisms.  Can dissolve several substances; except
The type of bond influences the properties of living cells. for hydrophobic substances
o High surface tension
 Very important in species that walks on
water
 Several processes in body, like circulation;
distribution of substances
 Related to cohesion of water molecules
o Cohesion and adhesion
 Water molecules are cohesive; when
interacting with other water molecules they
can form a bond facilitating cohesion
 Adhesion is also important esp. in plants;
allows water to climb/move up in plant
vessels

Water has very important role to play in the processes of cells and to the
organisms as a whole.

3.2 The outermost electrons determine how atoms interact.

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LIPIDS
3.5 Cell contains four major families of small organic molecules

 disregarding water and inorganic ions, nearly all molecules in

the cell are based on carbon.

Cells are heavily carbon-based.

 Cells contain sugar, fatty acids, amino acids, nucleotides

o Carbon-based; 100-1000 molecular weight, 30 or so
carbon atoms
o Some serve as monomers to macromolecules
o Some serve as energy source

3.6 Macromolecules are polymers built from monomers

Does not have a particular monomer.

Basically, they are hydrophobic molecules.
Can be storage for energy.

Image is the typical structure of a phospholipid.

Dehydration reaction – polymer is formed from monomers due to the
removal of water from a short polymer and an unlinked polymer that forms
a new bond.
Hydrophilic phosphate head; hydrophobic phospholipid tail
Involved in the fluidity of plasma membrane.
POLYPEPTIDES

 Primary structure
o Sequence of amino acids
 Secondary structure
o H-bonds between atoms of polypeptide backbone
o Helices and sheets
 Tertiary structure
o Hydrophobic interactions between amino acids R
groups
o Van der Waals hold nonpolar R group
o Disulfide bridges
Hydrolysis – is breaking down a polymer by adding water which breaks  Quaternary structure
the bond between the polymer. o Association of polypeptides
POLYSACCHARIDES

This figure shows an example of different protein structures and how they
would look. (Normal vs Sickle cell hemoglobin)
A change in one component can be observed in higher level, as shown in
the change in amino acid sequence.

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POLYNUCLEOTIDES  A metabolic pathway begins with a specific molecule and ends

with a product
 Each step is catalyzed by a specific enzyme

The products of each reaction is a requirement for another until a product

is formed. Specific enzymes catalyze the enzyme activity for each
reaction

METABOLIC PATHWAYS

 Catabolic pathways release energy to break down complex

molecules into simpler compounds
 Anabolic pathways consume energy to synthesize complex
molecules from simpler ones.
 Bioenergetics is the study of how organisms manage their
energy resources.

FOUR BASIC MACROMOLECULES IN THE CELL:

 Polysaccharides
 Lipids
 Polypeptides
 Polynucleotides
Breaking down a substance
Theme 4: Cells create and maintain order through a never-ending stream will also break the bond that
of chemical reactions. will also release the energy
within the bond.

ENERGY AND LIVING SYSTEMS

 Energy is the ability to do work.

 Metabolism is the totality of an organism’s chemical reaction
 Metabolism is an emergent property of life that arises from
interaction between molecules within the cell.
 Energy exists in various forms, some of which can perform work
o Kinetic energy is associated with motion
 Heat is kinetic energy associated with
random movement of atoms or molecules
o Potential energy is energy that matters possess
because of its location or structure
 Chemical energy is potential energy
available for release in a chemical reaction.
 Energy can be converted from one form to another.
Energy can’t be created nor destroyed; just transformed into another
form.

Used in acquiring energy to sustain processes inside the cell.

4.1 Cell metabolism is organized by enzymes

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 Organisms also replace ordered forms of matter and energy
with less ordered form
 Energy flows in an ecosystem in the form of light and exits
in the form of heat.

4.3 The free-energy change of a reaction tells us whether the

reaction occurs spontaneously

 The change in free energy (∆G) during a process is related to

the change in enthalpy, or change in total energy (∆H), change
in entropy (∆S), and temperature in Kelvin (T)

 Free Energy = Total Energy Unusable Energy

 Only processes with a negative ∆G are spontaneous
 Spontaneous processes can be harnessed to perform work

FREE ENERGY, STABILITY, AND EQUILIBRIUM

 Free energy is a measure of a system’s instability, its tendency

to change to a more stable state
 During a spontaneous change, free energy decreases and the
stability of a system increases
 Equilibrium is a state of maximum stability
 A process is spontaneous and can perform work only when it is
moving toward equilibrium
LAWS OF THERMODYNAMICS

 Energy can be converted from one form to another

 Thermodynamics is the study of energy transformations
 In an open system, energy and matter can be transferred
between the system and its surrounding.
o Organisms are open systems

 According to the first law of thermodynamics, the energy of the

universe is constant
o Energy can be transferred and transformed, but it
cannot be created nor destroyed
 During every energy transfer or transformation, some energy is
unusable, and is often lost as heat.
 According to the second law of thermodynamics
o Every energy transfer or transformation increases the
entropy (disorder) of the universe.
 Reactions in a closed system eventually reach equilibrium and
then do no work
 Cells are not in equilibrium; they are open systems
experiencing a constant flow of materials
 A defining feature of life is that metabolism is never at
equilibrium
 A catabolic pathway in a cell releases free energy in a series of
reactions

4.4 Free energy changes in exergonic and endergonic reactions

4.2 Biological order is made possible by the release of heat energy
from cells  Exergonic reaction ΔG is negative; net release of energy;
spontaneous
 Living things unavoidably convert organized forms of energy to  Endergonic reaction ΔG is positive; absorbs energy;
heat nonspontaneous
 Spontaneous processes occur without energy input; they can
happen quickly or slowly
 For a process to occur without energy input, it must increase
the entropy of the universe

 Cell creates ordered structures from less ordered materials.

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PHOSPHORYLATION

4.5  ATP drives endergonic reactions by phosphorylation,

transferring a phosphate group to some other molecule (e.g.,
reactant
 The recipient molecule is now called a phosphorylated
intermediate

ATP powers cellular work by coupling exergonic reactions to

endergonic reactions

 A cell does three main kinds of work chemical, transport,

mechanical
Many cellular reactions are endergonic
 To do work, cells manage energy resources by energy
coupling, the use of an exergonic process to drive an
endergonic one
 Most energy coupling in cells is mediated by ATP

ADENOSINE TRIPHOSPHATE

 ATP is a high energy molecule that serves as the cell’s main
energy shuttle
 ATP is composed of ribose (a sugar), adenine (a nitrogenous
base), and three phosphate groups
 The hydrolysis of ATP releases phosphate in a strongly
exergonic reaction tha t drives endergonic reactions to
completion
REGENERATION OF ATP
 ATP is a renewable resource that is regenerated by addition of
a phosphate group to adenosine diphosphate (ADP)
 The energy to phosphorylate ADP comes from catabolic
reactions in the cell

4.6 Enzymes speed up metabolic reactions by lowering energy

barriers

 A catalyst is a chemical agent that speeds up a reaction without

being consumed by the reaction
 An enzyme is a catalytic protein exhibits great specificity for the
reaction catalyzed and the molecules acted on

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ACTIVATION ENERGY
 Every chemical reaction between molecules involves bond
breaking and bond forming
 The initial energy needed to start a chemical reaction is called
the free energy of activation, or activation energy (EA)
 Activation energy is often supplied in the form of thermal energy
that the reactant molecules absorb from their surroundings
 Enzymes catalyze reactions by lowering the EA barrier
 Enzymes do not affect the change in free energy (∆G); instead,
they hasten reactions that would occur eventually
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SUBSTRATE SPECIFITY
 The reactant that an enzyme acts on is called the substrate
 The enzyme binds to its substrate, forming an enzyme
substrate (ES) complex
 The active site is the region on the enzyme where the substrate
binds
o The lock-and-key model portrays an enzyme as
conformationally rigid and able to bond only to
substrates that exactly fit the active site
o Induced fit of a substrate brings chemical groups of
the active site into positions that enhance their ability
to catalyze flexibility) the reaction
CATALYSIS IN THE ENZYME’S ACTIVE SITE
 In an enzymatic reaction, the substrate binds to the active site
of the enzyme
 The active site can lower an EA barrier by
o Orienting substrates correctly
o Straining substrate bonds
o Providing a favorable microenvironment
o Covalently bonding to the substrate
[BIO107] L02 – Prof. Bigsang
o Noncompetitive inhibitors bind to another part of an
enzyme, causing the enzyme to change shape and
making the active site less effective
 Examples of inhibitors include toxins, poisons, pesticides, and
antibiotics

EVOLUTION OF ENZYMES

 Enzymes are proteins encoded by genes

 Changes (mutations) in genes lead to changes in amino acid
composition of an enzyme
 Altered amino acids in enzymes may alter their substrate
specificity
 Under new environmental conditions a novel form of an enzyme
might be favored

EFFECT OF LOCAL CONDITIONS ON ENZYME ACTIVITY

 An enzyme’s activity can be affected by

o General environmental factors, e.g., temperature and 4.7
pH
o Chemicals that specifically influence the enzyme
 Optimal conditions favor the most active shape for the
enzyme molecule
 Temperature
o collision between enzyme and substrate
o low temperature – low collision
o high temperature – enzyme denaturation
 pH
o causes denaturation of enzymes
o optimum enzyme action at pH 6-8

Regulation of enzyme activity helps control metabolism

 Chemical chaos would result if a cell’s metabolic pathways were

not tightly regulated
 A cell does this by switching on or off the genes that encode
specific enzymes or by regulating the activity of enzymes

 Allosteric regulation may either inhibit or stimulate an

enzyme’s activity
 Allosteric regulation occurs when a regulatory molecule binds to
a protein at one site and affects the protein’s function at another
site

 Substrate concentration
o low substrate concentration – slow reaction
o high substrate concentration – faster reaction
 Cofactors
o cofactors are nonprotein enzyme helpers
o cofactors may be inorganic (such as a metal in ionic
form) or organic
o an organic cofactor is called a coenzyme, g .,
vitamins

 Enzyme inhibitors
o Competitive inhibitors bind to the active site of an
enzyme, competing with the substrate; usually
resemble normal substrates but cannot form products

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 In feedback inhibition, the end product of a metabolic pathway shuts
down
the

pathway
 Feedback inhibition prevents a cell from wasting chemical
resources by synthesizing more product than is needed

 Cooperativity is a form of allosteric regulation that can amplify

enzyme activity
 One substrate molecule primes an enzyme to act on additional
substrate molecules more readily

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