Finals Biolec

GENERAL BIOLOGY
L ECTURE \ CAMSON
GENERAL BIOLOGY (LECTURE)
• Number of chromosomes = number of active

OUTLINE centromeres (constricted region of a chromosome
I L6: CELL DIVISION
that separates it into a short arm (p) and a long arm
II
(q))
• Number of DNA molecules = number of
chromatids (once they are separated during
CELL DIVISION anaphase, each will be called chromosome)
• Mitosis • The amount of DNA molecules increases only when
o type of cell division that occurs only in somatic cells DNA replicates (S-phase)
• any cell of a living organism • The amount of DNA molecules decreases only
other than the reproductive when the cell divides
cells
• Nuclear division STAGES OF MITOSIS
o Process by which the nucleus divides to produce
two new nuclei (karyokinesis) PROPHASE
• results in two daughter cells that are genetically identical to
• First stage of mitosis
each other and to the parental cell from which they came
• Follows the S and G2 phases of interphase
• Mitotic cell division or equational division
• Chromatin - begins to condense and becomes visible in the
o explains how you repair damage after an injury
light microscope as chromosomes
o how you replace the cells that you lose every day
and; • Nucleolus disappears
o how you grew from a single-celled zygote into an • Centrioles begin moving to opposite ends of the cell and
adult fibers extend from the centromeres.
o accounts for the growth and development of plants, • Some fibers cross the cell to form the mitotic spindle
mushrooms, and other multicellular eukaryotes • THE COMPLETION OF PROPHASE CAN BE MARKED BY
o for asexual reproduction in protists and many other THE FF:
eukaryotes o DNA material condenses to form compact mitotic
chromosomes.
HOMOLOGOUS CHROMOSOMES
o Chromosomes are seen to be composed of two
In a diploid cell:
chromatids attached together at the centromere.
• nuclei have two set of chromosomes:
o Initiation of the assembly of mitotic spindle or spindle
o one chromosome from your father
fibers composed of microtubule. As the cell's two
o one chromosome from your mother
centrosomes move toward opposite poles,
• somatic cells = diploid microtubules gradually assemble between them,
In a haploid cell: forming the network that will later pull the duplicated
• one copy of the chromosome or one set of chromosomes chromosomes apart.
• reproductive cells (eggs and sperm) = haploid
• Cells at the end of prophase, do not show golgi
2n = 6 in MITOSIS complexes, endoplasmic reticulum, nucleolus and the
• n = refers to the number of chromosomes nuclear envelope.
o how many different chromosomes there are in a cell
line PROMETAPHASE
• 2n = 2 times that number, and is written to indicate a given
• Nuclear membrane dissolves
cell line is diploid
• Spindle fibers connect to each chromosome
o having two homologous versions of each
• Kinetochore – a complex of proteins positioned at the
chromosome
centromere
• Humans = diploid
o N=23 ( 23 different chromosomes)
o 2n = 46 (except gametes, sex cells)
METAPHASE
• If a haploid cell has n chromosomes, a diploid cell has 2n • Complete disintegration of the nuclear envelope
(n represents a number, which is different for every species • The chromosomes are spread through the cytoplasm of the
cell
• Condensation of chromosomes is completed
YAWAAAAAAA KAPOYA NA OY 1
General Biology (LECTURE)
o spindle fibres attach to kinetochores of

chromosomes.
o Chromosomes are moved to spindle equator and get
aligned along metaphase plate. They are also
oriented by the spindle fibres to both poles. This
organization helps to ensure that in the next phase,
when the chromosomes are separated, each new
nucleus will receive one copy of each chromosome.
ANAPHASE
• each chromosome arranged at the metaphase plate is split
simultaneously and the two daughter chromatids, now
referred to as chromosomes of the future daughter nuclei,
begin their migration toward the two opposite poles
• paired chromosomes separate at the kinetochores
• move to opposite sides of the cell
o Centromeres split and chromatids separate.
o Chromatids move to opposite poles.
MEIOSIS I
TELOPHASE • homologous chromosomes are separated into two cells
such that there is one chromosome (consisting of two
• The chromosomes that have reached their respective poles
chromatids) per chromosome pair in each daughter cell,
decondense and lose their individuality.
o i.e., two chromosomes total
• Individual chromosomes can no longer be seen
• Chromatin material tends to collect in a mass in the two
PROPHASE I
poles
o Chromosomes cluster at opposite spindle poles and • chromosomes replicate to form sister chromatids
their identity is lost as discrete elements. • initially four chromatids (c) and two chromosomes (n) for
o Nuclear envelope assembles around the each of the 23 chromosome pairs (4c, 2n).
chromosome clusters. • The nuclear envelope disintegrates and the chromosomes
o Nucleolus, golgi complex and ER reform. begin to condense.
• Spindle fibres - appear which are important for successful
CYTOKINESIS division of the chromosomes.
• Mitosis accomplishes not only the segregation of duplicated • To increase genetic diversity:
chromosomes into daughter nuclei (karyokinesis), but the o homologous chromosomes exchange small parts of
cell itself is divided into two daughter cells by a separate themselves, such that one chromosome contains
process called cytokinesis at the end of which cell division both maternal and paternal DNA.
is complete. o This process is known as crossing over, and the
• Animal cells = achieved by the appearance of a furrow in points at which this occurs on a chromosome are
the plasma membrane referred to as chiasmata.
o Furrow gradually deepens and ultimately joins in the
center dividing the cell cytoplasm into two PROMETAPHASE I
• Plant cells = do not undergo cytokinesis bc of cell wall • Spindle fibres attach to the chromosomes at a points along
o wall formation starts in the center of the cell and the chromosomes called centromeres.
grows outward to meet the existing lateral walls. • While this is happening, the chromosomes continue to
o Cell-plate = represents the middle lamella between condense.
the wall of two adjacent cells
STAGES OF MEIOSIS
• Gametes are made
• begin with a cell with double the normal amount of DNA,
and end up with 4 non-identical haploid daughter
gametes after two divisions
• 6 stages
o Prophase
o Prometaphase
o Metaphase
o Anaphase
o Telophase
o Cytokinesis
METAPHASE I
• homologous chromosomes) align along the equator of the
cell
• A process called independent assortment occurs – this is • These stages are identical to their counterparts in meiosis
when maternal and paternal chromosomes line up randomly I.
align themselves on either side of the equator
• determines to which gamete chromosomes are allocated to, METAPHASE II
which leads to genetic diversity among offspring • chromosomes line up in single file along the equator of the
cell.
• in contrast to metaphase I, where chromosomes line up in
homologous pairs.
ANAPHASE I
• homologous chromosomes get pulled towards opposite
poles of the cell as the spindle fibres retract.
• This equally divides the DNA between the two cells which
will be formed. ANAPHASE II
• sister chromatids are pulled to opposite poles of the
equator
TELOPHASE I AND CYTOKINESIS I

• Telophase I – the nuclear envelope reforms and spindle
fibres disappear
• Cytokinesis I – cytoplasm and cell divides resulting in two TELOPHASE II
cells that are technically haploid – there is one chromosome • same as telophase I
and two chromatids for each chromosome (2c, n)
CYTOKINESIS
• The cytoplasm and cell divides producing 2 non-identical
haploid daughter cells.
• As this is happening in both cells produced by meiosis I, the
net product is 4 non-identical haploid daughter cells, each
containing one chromosome consisting of one chromatid
(1c, 1n).
• These are fully formed gametes.
MEIOSIS II
PROPHASE II AND PROMETAPHASE II
• Phospholipids are amphipathic molecules

o both a hydrophilic region and a hydrophobic region
SUMMARY OF MEIOSIS • Phosphate “head” end, with its polar covalent bonds –
attracted to water – hydrophilic
• “Tails” – hydrophobic
CELL MEMBRANE AND TRANSPORT MECHANISMS

• Cell membrane
o edge of life, the boundary that separates the living
cell from its surroundings and controls traffic into and
out of the cell it surrounds
o exhibits selective permeability;
• allows some substances to cross
it more easily than others MEMBRANE PROTEINS
• The ability of the cell to discriminate its chemical exchanges • most membrane proteins are amphipathic
with its environment is fundamental to life, and it is the cell • Such proteins can reside in the phospholipid bilayer with
membrane and its component molecules that make this their hydrophilic regions protruding.
selectivity possible. • This molecular orientation maximizes contact of hydrophilic
regions of proteins with water in the cytosol and
PHOSPHOLIPIDS extracellular fluid, while providing their hydrophobic parts
• Cell membranes are made up of a phospholipid bilayer with a nonaqueous environment.
• Lipids and proteins – staple ingredients of membranes
• Most abundant lipids – phospholipids
o organic molecules that resemble triglycerides
o But in a phospholipid, glycerol bonds to only two
fatty acids; the third carbon binds to a phosphate
group attached to additional atoms
• In this fluid mosaic model, the membrane is a mosaic of

protein molecules bobbing in a fluid bilayer of
phospholipids.
• The proteins are not randomly distributed in the membrane,

however. Groups of proteins are often associated in long-
lasting, specialized patches, where they carry out common
functions.
• The lipids themselves appear to form defined regions as
well.
WHAT CAN GO THROUGH THE CELL MEMBRANE?

• Molecules that are hydrophilic (water loving) are capable of
forming bonds with water and other hydrophilic molecules.
o They are called polar molecules.
• The opposite can be said for molecules that are hydrophobic
(water fearing), they are called nonpolar molecules.
• (1) Small, nonpolar molecules

o (ie. CO2 and O2)
o can pass through the lipid bilayer and do so by INTEGRAL PROTEINS
squeezing through the phospholipid bilayers. • Penetrate the hydrophobic interior of the lipid bilayer
o They don't need proteins for transport and can
• The majority are transmembrane proteins, which span the
diffuse across quickly.
membrane; other integral proteins extend only partway into
• (2) Small, polar molecules the hydrophobic interior. The hydrophobic regions of an
o (ie. H2O) integral protein consist of one or more stretches of nonpolar
o Recall that the interior of the phospholipid bilayer is amino acids usually coiled into a helices. The hydrophilic
made up of the hydrophobic tails. It won’t be easy for parts of the molecule are exposed to the aqueous solutions
the water molecules to cross, but they can cross on either side of the membrane. Some proteins also have
without the help of proteins. This is a somewhat one or more hydrophilic channels that allow passage
slower process. through the membrane of hydrophilic substances (even of
o To hasten the movement of water across the water itself).
membrane, transport o Transport proteins are embedded in the
proteins called aquaporins provide a polar channel for phospholipid bilayer that create passageways
water molecules. through which ions, glucose, and other polar
• (3) Large, nonpolar molecules substances pass into or out of the cell.
o These rings can pass through but it is also a slow o Glucose transporter(GLUT) is a facilitative
process. transport protein involved in glucose translocation
• (4) Large, polar molecules across the cell membrane.
o (ie. glucose and amino acids) and (5) Ions
o The charge of an ion, and the size and charge of large PERIPHERAL PROTEINS
polar molecules, makes it too difficult for them to • not embedded in the lipid bilayer at all;
pass through the nonpolar region of the phospholipid • they are appendages loosely bound to the surface of the
membrane without help of transport proteins (ion membrane, often to exposed parts of integral proteins.
channels, protein pump, GLUT transporter).
o Proteins/enzymes are transported via exocytosis RECOGNITION PROTEINS
due to their large size. • Carbohydrates attached to cell surface proteins serve as
"name tags" that help the body's immune system recognize
TYPES OF MEMBRANE PROTEINS AND THEIR its own cells. The immune system attacks cells with
FUNCTIONS unfamiliar surface molecules, which is why transplant
• Two major membrane proteins: recipients often reject donated organs. Surface proteins
o Integral proteins also distinctively mark specialized cells within an individual,
o Peripheral proteins so a bone cell's surface is different from that of a nerve cell
or a muscle cell.
o Glycoproteins are membrane carbohydrates that
are covalently bonded to proteins. Cells recognize
other cells by binding to molecules, often containing
carbohydrates, on the extracellular surface of the cell
membrane.
o Glycolipids are membrane carbohydrates that are
covalently bonded to lipids.
ADHESION PROTEINS
• These membrane proteins enable cells to stick to one
another.
RECEPTOR PROTEINS
• Receptor proteins bind to molecules outside the cell and • Without cholesterol, the phospholipids in your cells will start
trigger an internal response, a process called signal to get closer together when exposed to cold, making it more
transduction. difficult for small molecules, like gases to squeeze in
o i.e., when a hormone binds to a receptor, the between the phospholipids like they normally do.
resulting chain reaction produces the hormone’s • Without cholesterol, the phospholipids start to separate
effects on the cell. from each other, leaving large gaps.
SATURATED AND UNSATURATED FATTY ACIDS

• Fatty acids are what make up the phospholipid tails.
• Saturated fatty acids are chains of carbon atoms that have
only single bonds between them.
• As a result, the chains are straight and easy to pack tightly.
Unsaturated fats are chains of carbon atoms that have
double bonds between some of the carbons.
• The double bonds create kinks in the chains, making it
harder for the chains to pack tightly.
3 MAIN FACTORS THAT INFLUENCE CELL
MEMBRANE FLUIDITY:
TEMPERATURE
• affect how the phospholipids move and how close together
they are found.
• Cold – found closer together
• Hot – move farther apart
PASSIVE TRANSPORT VS ACTIVE TRANSPORT
CONCENTRATION GRADIENT
• The regulation of membrane transport makes the interior of
a cell chemically different from the outside. Concentrations
of some dissolved substances (solutes) are higher inside
the cell than outside, and others are lower. Likewise, the
inside of each organelle in a eukaryotic cell may be
chemically quite different from the solution in the rest of the
CHOLESTEROL cell.
• The term gradient describes any such difference between
• The cholesterol molecules are randomly distributed across
two neighboring regions. In a concentration gradient, a
the phospholipid bilayer, helping the bilayer stay fluid in
solute is more concentrated in one region than in a
different environmental conditions.
neighboring region. If a substance moves from an area
• The cholesterol holds the phospholipids together so that
where it is more concentrated to an area where it is less
they don’t separate too far, letting unwanted substances in,
concentrated, it is said to be “moving down” or “following”
or compact too tightly, restricting movement across the
membrane.
its concentration gradient. As the solute moves, the gradient

dissipates-that is, it disappears.
PASSIVE TRANSPORT VERSUS ACTIVE

TRANSPORT
• Molecules and substances move in several ways that fall
within two categories: passive transport and active
transport. In passive transport, a substance moves across
a membrane without the direct expenditure of energy
because the net movement is down its concentration
gradient. In active transport, a cell uses a transport
protein to move a substance against its concentration
gradient—from where it is less concentrated to where it is
more concentrated. This requires the cell to expend its
energy reserves in the form of ATP.
• All forms of passive transport involve diffusion, the
spontaneous movement of a substance from a region
where it is more concentrated to a region where it is less
concentrated. Because diffusion represents the dissipation
of a chemical gradient—and the loss of potential energy—it
does not require energy input. Below is a familiar example
of diffusion.
PASSIVE TRANSPORT (SIMPLE DIFFUSION AND

OSMOSIS)
PASSIVE TRANSPORT: SIMPLE DIFFUSION

• a substance moves down its concentration gradient without
the use of a transport protein.
• Substances may enter or leave cells by simple diffusion only
if they can pass freely through the membrane.
• Lipids and small, nonpolar molecules such as oxygen (O 2)
and carbon dioxide (CO2), for example, diffuse easily across
the hydrophobic portion of a biological membrane.
• Water crosses the membrane until the solute

concentrations are equal on both sides.
• Solutions of equal solution concentration are said to
be isotonic.
• This only occurs when the solute concentration are the
same on both sides of the membrane.
PASSIVE TRANSPORT: OSMOSIS

• Two solutions of different concentrations may be separated
by a selectively permeable membrane through which water,
but not solutes, can pass.
• In that case, water will diffuse down its own gradient
toward the side with the high solute concentration. • Many cells are isotonic to the environment in order to avoid
• Osmosis is this simple diffusion of water across a selectively excessive inward and outward movement of water.
permeable membrane. • Other cells must constantly export water from their interior
to accommodate the natural inward movement.
• Most plants are hypertonic with respect to their immediate
environment.
PASSIVE TRANSPORT: OSMOSIS: TURGOR

PRESSURE
• Turgor pressure is the resulting force of water against the
cell wall.
• A limp, wilted piece of lettuce demonstrates the effect of
lost turgor pressure.
• But the leaf becomes crisp again if placed in water, as
individual cells expand like inflated balloons.
• Turgor pressure helps keep plants firm and stay upright.
PASSIVE TRANSPORT: OSMOSIS: ISTONIC,

HYPERTONIC, AND HYPOTONIC ENVIRONMENTS
• A solution with a higher concentration of solutes is said to
be hypertonic while a solution with a lower concentration
of solutes is hypotonic.
• In a hypertonic environment, a cell loses water, shrivels,
and may die.
• After a substance has diffused completely through a space

removing its concentration gradient, molecules will still
move around in the space, but there will be no net
movement of the number of molecules from one area to
another.
• This lack of a concentration gradient in which there is no net
movement of a substance is known as dynamic equilibrium.
• While diffusion will go forward in the presence of a
concentration gradient of a substance, several factors
affect the rate of diffusion:
o Extent of the concentration gradient:
• The greater the difference in
concentration, the more rapid
the diffusion.
• The closer the distribution of
the material gets to equilibrium,
the slower the rate of diffusion
becomes.
PASSIVE TRANSPORT (FACILITATED DIFFUSION)

• Ions and polar molecules cannot freely cross the
hydrophobic layer of a membrane; instead, transport
proteins form channels that help these solutes cross.
• Facilitated diffusion is a form of passive transport in which o Mass of the molecules diffusing:
a membrane protein assists the movement of a polar solute • Heavier molecules move more
down its concentration gradient. slowly; therefore, they diffuse
• Facilitated diffusion releases energy because the solute more slowly.
moves from where it is more concentrated to where it is less • The reverse is true for lighter
concentrated. molecules.
• Glucose moves into red blood cells via facilitated diffusion. o Temperature:
• This sugar is too hydrophilic to pass freely across the • Higher temperatures increase
membrane, but glucose transporter proteins form channels the energy and therefore the
that allow it in. movement of the molecules,
increasing the rate of diffusion.
• Lower temperatures decrease
the energy of the molecules,
thus decreasing the rate of
diffusion.
FACTORS THAT AFFECT THE RATE OF DIFFUSION

• A substance will tend to move into any space available to it
until it is evenly distributed throughout it.
o Solvent density: TYPES OF ACTIVE TRANSPORT

• As the density of a solvent
increases, the rate of diffusion Antiport Pumps
decreases.
• One type of
• The molecules slow down
transmembran
because they have a more e co-
difficult time getting through the transporter
denser medium. protein is
• If the medium is less dense, antiport
diffusion increases. pumps. While
o Solubility: moving
• Nonpolar or lipid-soluble another
materials pass through plasma substance in
membranes more easily than the opposite
polar materials, allowing a way, they
faster rate of diffusion. pump one
substance in
that direction.
These pumps
are extremely
efficient
because many
of them can
use one ATP
molecule to
fuel these two
different tasks.
• The sodium-
potassium
pump, which is
covered in
greater depth
under
"Examples of
o Surface area and thickness of the plasma Active
membrane: Transport," is
• Increased surface area one significant
increases the rate of diffusion, type of antiport
whereas a thicker membrane pump.
reduces it.
o Distance travelled: Symport Pumps
• The greater the distance that a • Diffusion
substance must travel, the gradients are
slower the rate of diffusion. used by
Symport
ACTIVE TRANSPORT pumps to
• In active transport, a cell uses a transport protein to move a transfer
substance against its concentration gradient—from where it materials.
is less concentrated to where it is more concentrated. Diffusion
• Because a gradient represents a form of potential energy, gradients are
the cell must expend energy to create it; this energy often concentration
comes from ATP. differences
that induce
substances to
migrate
naturally from
high
concentration
areas to low
concentration
areas.
• In the case of a
symport pump,
a substance the cell

that “wants” to membrane
move from an indents, a
area of high “bubble” of
concentration membrane
to low closes in on
concentration itself. The
down its formation and
concentration movement of
gradient is this vesicle
used to “carry” along the
another cytoskeleton’s
substance “tracks” require
against its energy.
concentration
gradient. • The three
forms of
Under "Examples endocytosis
of Active are
Transport," we pinocytosis,
mention one phagocytosis
symport pump and receptor-
example, the mediated
sodium- endocytosis.
glucose
transport • pinocytosis,
protein. the cell engulfs
Endocytosis small amounts
of fluids and
• Most dissolved
molecules substances.
dissolved in
water are • phagocytosis
small, and they , the cell
can cross cell captures and
membranes by engulfs large
simple particles, such
diffusion, as debris or
facilitated even another
diffusion, or cell (phag-
active means
transport. “eating”). The
Large vesicle then
particles, fuses with a
however, must lysosome,
enter and where
leave cells with hydrolytic
the help of a enzymes
transport dismantle the
vesicle—a cargo.
small sac that
can pinch off • Receptor-
of, or fuse with, mediated
a cell endocytosis
membrane. is a specialized
type of
• In pinocytosis
endocytosis, that enables
a cell the cell to
membrane acquire bulk
engulfs fluids quantities of
and large specific
molecules to substances,
bring them into even though
the cell. When those
substances EXAMPLES OF ACTIVE TRANSPORT

may not be
very Sodium – Potassium Pump
concentrated
in the
extracellular
fluid.
Embedded in
the plasma
membrane are
proteins with
receptor sites
exposed to the
extracellular
fluid. Specific
solutes bind to
the sites. The
receptor
proteins then
cluster in
coated pits,
and each
coated pit
forms a vesicle
containing the
bound Sodium-Glucose Transport Protein
molecules.
Exocytosis
The opposite
of endocytosis
is exocytosis
which uses
vesicles to
transport fluids
and large
particles out
of cells. Inside
a cell, the Golgi
apparatus
produces
vesicles filled
with
substances to
be secreted. PHOTOSYNTHESIS
The vesicle • provides not only food for the plant but also the energy, raw
moves to the materials, and O2 that support most heterotrophs.
cell membrane • Photosynthesis also uptakes CO2 a greenhouse gas from the
and joins with atmosphere alleviating global warming.
it, releasing the • The organisms that could use O2 in respiration (aerobic )
substance were then able to extract the most energy from food which
outside the started the emergence of multicellular organisms since
membrane. cellular division requires more ATP than glycolysis can
generate.
• Even the waste product of photosynthesis, O2, is essential
to much life on Earth.
ENERGY TRANSFORMATION
• Thermodynamics
o Study of energy transformations
o consists of laws that are useful to describe the energy
conversions important in living and in the nonliving
world.
o The law of energy conservation is the first law of o It contains a hydrophilic porphyrin ring head
thermodynamics. and hydrophobic tail.
o It describes energy as a property that cannot be o The porphyrin ring of the chlorophyll molecule
created or destroyed but can be converted to other contains Magnesium as its central portion and is
forms. Thus, the total amount of energy in the attached to the polar heads of the phospholipid
universe does not change. bilayer of the chloroplast thylakoid membrane while
the tails extend downwards together with the
Potential energy phospholipid hydrophobic tails.
• stored energy that includes chemical energy
in bonds and concentration gradient across a membrane ENDERGONIC VS EXERGONIC REACTIONS
• Second law of thermodynamics
Kinetic Energy o refers to energy lost to the surroundings as heat in
• energy of motion as observed in light, thermal energy and energy transformations that heads toward increasing
movement of molecules. disorder.
• Living cells constantly convert energy from one form to o Life remains ordered and complex because the sun is
another. constantly supplying energy to Earth.
o The entropy (measure of randomness or state of
SUNLIGHT disorder) of the universe, including the sun, is
• Photons increasing.
o are the fundamental particle of light energy from the • Metabolic reactions
sun which are absorbed by chlorophyll. and o Endergonic
converted by chloroplast into glucose or chemical o Exergonic
energy.
• The spectrum of white light absorbed ENDERGONIC
by chlorophyll and accessory pigments are in • Metabolic reactions that assemble or organizebasic or
the blue and red regions while reflecting green and yellow simpler units into complex ones (anabolism)
light making the leaves of plants green • they are not spontaneous and require an input of energy to
• Light with shorter wavelengths (distance between two proceed
waves) have higher frequency thus possess higher energy
EXERGONIC
• photoautotrophs, • catabolism which breaks down complex substances into
o chloroplasts are embedded in cells mostly found on simpler ones (disorder) are exergonic because they are
the leaves. spontaneous and release energy in the process
o Chloroplasts are found within palisade and spongy • Endergonic reactions use reactants that have lower energy
mesophyll cells that are specialized for than the product while it is the other way around in
photosynthetic function. exergonic reactions.
o They are organelles abundant with the green • A familiar example of endergonic reaction is
pigment chlorophyll. photosynthesis. In photosynthesis, glucose (C6H12O6) the
• Chlorophyll product, contains more potential energy than do carbon
o is the pigment which primarily absorbs light energy dioxide and water, the reactants.
from the sun. • The energy that powers this reaction is sunlight.
o i.e., breakdown of glucose to carbon dioxide and o The electron donor molecule being oxidized is like a
water gift-giver because its energy level is decreased by
• he products, carbon dioxide and water, contain less energy the loss.
than glucose. The process releases energy. o Reduction is the gain of electrons and energy and the
• Although the above reactions are generally classified as electron acceptor being reduced is similar to a
either of the two types of reactions, when examined closely, woman receiving the package.
both endergonic and exergonic reactions occur
simultaneously in all life processes.
• One providing energy, the other, requiring energy, which is
referred to as, energy coupling.
• An exergonic process is linked with an endergonic process

in a redox reaction.
• Oxidation is exergonic
o because energized electrons are removed from the
electron donor. The electron donor has more energy
before it is oxidized than it does after the reaction is
complete. Thus, releasing energy. In reduction,
acceptor molecule gains electrons, so it ends up with
more energy than it had before the reaction started.
Hence, reduction is endergonic. Oxidations and
COUPLED REACTION PROCESSES reductions both occur simultaneously because
• Coupled reactions are simultaneous reactions in which one electrons removed from one molecule during
provides the energy that starts the other oxidation is gained by another molecule and is
• Endergonic and exergonic reaction occur simultaneously or reduced.
are coupled to initiate metabolic processes. • Corrosion of metal is a redox reaction. During corrosion, the
metal atoms lose electrons to form positive ions and oxygen
molecule gains electrons.
• Iron is the reducing agent

o because it causes the reduction of oxygen molecule
to oxide ion. Conversely, oxygen molecule is
the oxidizing agent causing iron to be oxidized to
ferric ion.
REDOX REACTIONS AND THE ELECTRON

TRANSPORT CHAIN (ETC)
• Electrons can carry energy which can transfer from one
molecule to another.
• These energy transformations in organisms occur in
oxidation–reduction (“redox”) reactions.
• Oxidation is the loss of electrons with loss of energy
o —from a molecule, an atom, or an ion.
Since electrons carry energy, they can be likened to
a gift.
• In an electron transport chain, each protein accepts an • It occurs in the thylakoid membrane of the granum.
electron from the molecule before it and passes it to the Harvesting of light energy occurs through two types of
next. As a result, each molecule in the chain is first reduced electron flow:
and then oxidized. o the non-cyclic
• Small amounts of energy are released at each step making it o the cyclic pathways.
an exergonic process, and the cell uses this energy in other
reactions. THE NONCYCLIC PATHWAY
• In cyanobacteria, plants, and all photosynthetic protists,
both photosystem types work together in the noncyclic
pathway.
• When electrons are ejected from photosystem II, they enter
an electron transfer chain in the thylakoid membrane
composed of plastoquinone (Pq), cytochrome
complex and plastocyanin (Pc).
• After the electrons have moved through the first electron
transfer chain, they are accepted by photosystem I. When
this photosystem absorbs light energy, its special pair of
chlorophylls in its reaction center emits electrons.
• These electrons enter a second, different electron transfer
chain.
• The electrons are first passed to a protein called ferredoxin
(Fd), then transferred to an enzyme called NADP reductase.
PHOTOSYSTEMS OF THE LIGHT REACTIONS

• Thylakoid membranes have two kinds of photosystems,
o type I (Photosystem I [PSI])
o type II (Photosystem II [PS II]),
• Both are protein complexes rich in chlorophyll (dark green

circles) which serve as either harvesting (green circles in
light green bean-shaped portion) or reaction centers (blue
middle portion).
• PSI is located at the outer surface of the thylakoid
membrane and contains chlorophylls and carotenoids
while PSII is located at the inner surface of the thylakoid
membrane, and contains chlorophyll
o b; chlorophyll
o a, phycobillins, and;
o xanthophylls. • At the end of this chain, the coenzyme NADP+ accepts
• The photosystems also contain a special pair of chlorophyll
molecules (dark green circles in the lower portion of the blue the electrons along with H+, so NADPH forms:
reaction center) found at the core of the photosystem.
• photosystem I is called P700,
• photosystem II is called P680.
• They are able to absorb light in different wavelengths but
they are best at absorbing light in wavelengths that • In the noncyclic pathway therefore, electrons have to be
correspond to their name or lambda max: 680 nm for replaced.
Photosystem 2 and 700 nm for photosystem 1, • Replacement of these two electrons comes
• thus they are called P680 and P700, respectively. from water which is split once electrons are ejected from
• Upon excitation, the pigments become strongly reduced photosystem II in a process called photolysis.
making them strong reducing agents that allow them to • Photosynthesis strips electrons from the oxygen atoms in
pass an electron to a primary electron acceptor found within H2O (i.e., the oxygen atoms are oxidized) and adds
the reaction center electrons to NADP storing energy in the electron carrier.
THE LIGHT REACTIONS SUMMARY OF THE NONCYCLIC PATHWAY

• Light reactions utilize light or solar energy to produce ATP • (1) Light reactions begin in Photosystem IIwhere
and uses water to replace the excited electrons from chlorophyll molecules and accessory pigments absorb light
chlorophyll molecule.
energy that is passed to the special pair of

chlorophyll molecules in the reaction center making one
of their electrons excited.
• (2) Upon excitation, the pigments become strongly reduced
making them strong reducing agents that allow them
to pass an electron to a primary electron acceptor found
within the reaction center.
• (3) The electron lost by Photosystem II to the ETC is
replaced by splitting water . One of its hydrogens will
replace the electron while the other hydrogen will contribute
to the proton gradient.
• (4) The electron in no. 2 travels through an electron
transport chain where its energy is released and used to
create a proton gradient until it reaches its ground state
and occupies the reaction center of Photosystem I.
• (5) The proton gradient created from the energy released is
used to fuel ADP phosphorylation by ATP synthase as it
forms ATP by allowing protons to move down their
gradient (chemiosmosis).
• (6) Electron reaches ground state and occupies the vacant
chlorophyll molecule in Photosystem I, it is again
energized due to the light energy absorbed by the
surrounding chlorophyll molecules. SUMMARY OF THE CYCLIC PATHWAY
• (7) The electron will pass through an electron transport • (1) In photosystem I, chlorophyll molecules absorb light
chain again. energy that is passed to the special pair of chlorophyll
• (8) The terminal electron acceptor in Photosystem I molecules in the reaction center making one of their
is NADP which becomes NADPH after accepting electrons excited.
the electron and will also serve as energy source in the • (2) The electron will be passed
Calvin's cycle. from ferridoxin to plastocycanin before reaching the
ground state releasing energy. These steps are repeated to
THE CYCLIC PATHWAY constitute the cyclic electron flow.
• (3) The proton gradient created from the energy released
• On its own, the noncyclic pathway does not yield enough
is used to fuel ADP phosphorylationby ATP synthase as
ATP to balance NADPH use in sugar production pathways.
it forms ATP by allowing protons to move down their
• The cyclic pathway produces additional ATP for this
gradient (chemiosmosis).
purpose.
• The electrons that are ejected from photosystem I enter a
SUMMARY OF LIGHT REACTIONS
portion of the electron transfer chain of photosystem II, and
then return to photosystem I (shown in yellow arrows in the
left figure).
• The electrons are passed to ferridoxin (Fd), which are then
accepted by cytochrome complex and
ultimately, plastocyanin (Pc) before reaching their ground
state.
• The cycle begins again when electrons become excited as REDOX REACTIONS IN THE LIGHT REACTIONS
light is absorbed by chlorophyll pigments. • “Oxidation”
• As in the noncyclic pathway, the electron transfer chain uses o means that electrons (or H+ ions) are removed from
electron energy to move hydrogen ions into the thylakoid an atom or a molecule;
compartment, and the resulting hydrogen ion gradient • “reduction”
drives ATP formation. o means electrons are added.
• Redox reactions happen during electron transport when
electrons are passed from one acceptor to another starting
from the excitation of the electron in the special pair of
chlorophyll molecules in the reaction center, its transport in
the electron transport chain until it reaches the terminal
electron acceptor NADP.
• Even photolysis is a redox reaction since electrons are
transferred from water to the special pair of chlorophyll
molecules in photosystem II.
ATP FORMATION IN THE LIGHT REACTIONS

• Electron transfer chains (ETC) can harvest the energy of
electrons in a series of redox reactions.
• Redox happens when components of the ETC pass
electrons from one another.
• A component is reduced when it accepts electrons from the with the release of the energy from the electron transport
previous component which is oxidized in the process. In the chainserving as the exergonic reaction.
accompanying illustration (fig. 8.71), the electron is shown • Another instance when energy coupling occurs is during
to move through the different acceptors in decreasing ATP synthesis by ATP synthase which utilizes the energy
energy levels (descending in a staircase) showing the released from the exergonic process of the chemiosmosis of
release of energy as electrons are allowed to move. In this protons to fuel the endergonic ATP formation.
case, molecules of the electron transport chain use the • Lastly, during the ATP formation, we can observe the ATP-
released energy to actively transport hydrogen ions (H+) ADP cycle (fig 8.73). Energy from chemiosmosis served as
across the membrane, from the stroma to the thylakoid the exergonic reaction while ADP phosphorylation was the
compartment or lumen creating a hydrogen ion endergonic reaction. During Calvin's cycle energy in ATP
gradient across the thylakoid membrane. will be utilized to transform carbon dioxide to glucose
(endergonic reaction) forming ADP (exergonic reaction).
ATP FORMATION IN THE LIGHT REACTIONS:
CHEMIOSMOSIS
• The hydrogen ion gradient is a type of potential energy that
can be tapped to make ATP.
• The H+ ions want to follow their concentration gradient by
moving back into the stroma, but ions cannot diffuse
through the lipid bilayer. H+ leaves the thylakoid
compartment only by flowing through proteins called ATP
synthases embedded in the thylakoid membrane. An ATP
synthase is both a transport protein and an enzyme.
• When hydrogen ions flow through its interior from an area of
high concentration to an area of low concentration, the
protein phosphorylates ADP using the energy released by
the movement of hydrogen ions down their concentration
gradient, so ATP forms in the stroma.
• The coupling of ATP formation to the release of energy from
a proton gradient is called chemiosmotic
phosphorylation because it is the addition of a phosphate to
ADP (phosphorylation) using energy from the movement of
chemicals, particularly, protons across a membrane
(chemiosmosis).
ENERGY COUPLING IN THE LIGHT REACTIONS

• Since reduction reactions
are endergonic and oxidation reactions are exergonic,
energy coupling occurs during the electron transport
chain during which, both reactions happen.
• Furthermore, the proton gradient creation required an input
of energy when protons were actively transported against
their gradient (from the stroma where it has low
concentration to the lumen where it has high concentration),
the reaction is considered an endergonic reaction paired
ATP-ADP CYCLE
• Energy is temporarily stored in the covalent bonds of
adenosine triphosphate (ATP) which is considered as the
energy currency of the cell. It is released in exergonic
reactions like the digestion of an energy bar enough to
power muscle contraction. Mitochondria, a cell organelle
produces most of a cell’s ATP. The muscles and brain,
contain the most mitochondria because they require more
energy.
• ATP is classified as a nucleotide (figure 8.74). It has a

nitrogen-containing base adenine, the five-carbon sugar
ribose, and three phosphate groups. Each phosphate group
has a negatively charged oxygen atom. The negative
charges on neighboring phosphate groups repel one
another, making the molecule unstable. Thus, releasing Structure of ATP
energy when the bonds between the phosphates break.
• When a cell requires energy for an endergonic reaction, it

uses ATP by removing one of phosphate groups (figure
8.75). The products of this hydrolysis reaction are
adenosine diphosphate (ADP, in which only two phosphate
groups remain attached to ribose), the liberated phosphate
group, and a burst of energy. In a reverse situation, energy
can be temporarily stored by adding a phosphate to ADP,
forming ATP and water Hydrolysis of ATP to ADP
• A cell uses ATP (figure 8.76) as an energy source by

transferring its phosphate group to another molecule which
can energize the target molecule. In addition, the process
makes the target molecule more likely to bond with other
molecules. Another way that the cell uses ATP is by
changing the shape of the target molecule as in muscle
contraction or in the movement of chromosomes during cell
division. Lastly, ATP is also the source of energy fuelling
active transport like the sodium-potassium pump. A human
cell uses the equivalent of 2 billion ATP molecules a minute
just to stay alive. If you ran out of ATP, you would die
instantly.
• ATP’s high-energy phosphate bonds make the molecule too

unstable for long-term storage. Thus, cells also store
energy-rich molecules such as fats, starch, and glycogen.
When ATP supplies become low, cells use lipid and
carbohydrate reserves for cellular processes.
Uses of ATP: phosphorylation (top), change its shape in a

useful way (middle) or active transport (bottom)
THE CARBON REACTIONS PRODUCE

CARBOHYDRATES
•
THE CALVIN’S CYCLE
ATP-ADP Cycle
• The Calvin's cycle (Fig. 8.81) makes use of SUMMARY OF CALVIN’S CYCLE
the ATP and NADPH formed by the light reactions to fuel
the reduction of CO2 to glceraldehyde-3-phosphate
(G3P) or phosphoglyceraldehyde (PGAL). The cycle has 3
steps when CO2 undergoes fixation (first
step) and reduction (second step ) to convert 3-
phosphoglycerate (3-PGA) to G3P or PGAL. The third step
involves the regeneration of ribulose biphosphate
(RuBP) which reacts with CO2 in the first step or fixation
thus calling the entire reaction as a cycle. First step is called SUMMARY OF PHOTOSYNTHESIS
fixation because inorganic carbon dioxide is converted to
an organic molecule by reacting with RuBP.
•
REDOX AND COUPLED REACTIONS IN
PHOTOSYNTHESIS
• The electrons that leave from the chlorophyll of
Photosystem II are replaced by the electrons produced from
the splitting of water. Water therefore, acts an a reducing
agent and is oxidized with oxygen as the product. The
electrons removed from water travel through the non-cyclic
pathway until they are added to NADP electron carrier
reducing it into NADPH. The electrons carried by NADPH
are eventually used to reduce the carbon in CO2. Electrons
or H+ ions from water are removed, therefore it is oxidized
while carbon dioxide is added with the electrons or H+ ions
from water, therefore it is reduced. When a molecule is
reduced, its energy level is increased, thus, photosynthesis
produces a high-energy, more complex molecule G3P.
• Photosynthesis is actually a series of coupling
of endergonic and exergonic reactions. However, light
• The second step is referred to as reduction because of the reactions in general are exergonic processes producing
addition of H+ to the 3-phosphoglycerate ( ATP and NADPH which are used for the endergonic Calvin
• 3-PGA) molecule from NADPH making the cycle.
product glyceraldehyde-3-phosphate (G3P) a high-energy
molecule. The carboxylic group (COOH) of 3-PGA is reduced
to an aldehyde group (CHO) in G3P by the replacement of OH
by H (fig 8.82).
• To be able to form one G3P molecule, three turns of the
cycle is needed consuming three molecules of carbon
dioxide which will produce 6 molecules of G3P, five (5
molecules x 3 carbon atoms/molecule = 15 carbon atoms)
of which will proceed to the third phase which is the
regeneration of the three 5-carbon atom RuBP (3 molecules
x 5 carbon atoms/molecule = 15 carbon atoms). Two
G3P molecules are needed in making CELLULAR RESPIRATION
one glucose molecule. • Cellular respiration is a metabolic pathway that uses
glucose to produce adenosine triphosphate (ATP), an
organic compound the body can use for energy. One
molecule of glucose can produce a net of 30-32 ATP. There
are three main steps of cellular respiration: glycolysis,
the citric acid cycle, and oxidative phosphorylation.
Glycolysis takes place in the cytosol, the citric acid cycle
occurs in the mitochondrial matrix, and oxidative
phosphorylation occurs on the inner mitochondrial
membrane. Several diseases can affect cellular respiration.
Since cellular respiration is so vital to bodily functions,
many of these diseases severely affect individuals.
• In general, a cell contains only enough ATP to sustain from

30 seconds to a few minutes of normal activity. Because it
has such high potential energy, ATP is unstable and is not
stored. As a result, most cells are making ATP all the time.
Much of the ATP your cells produce is made using the
chemical energy from glucose. How do cells obtain
glucose? Photosynthetic organisms can produce glucose
from the products of photosynthesis, where the energy in
sunlight is used to reduce carbon dioxide (CO2). These
organisms will either use the glucose to make ATP or store
it in other energy-rich molecules like starch. When
photosynthetic organisms are eaten or decompose, their
glucose molecules are obtained by animals, fungi, and
many bacteria and archaea.
• Storage carbohydrates, such as starch and glycogen, act

like savings accounts for chemical energy. ATP, in contrast,
is like cash. To withdraw chemical energy from the accounts
to get cash, storage carbohydrates are first hydrolyzed into
their glucose monomers. The glucose is then used to
produce ATP through one of two general processes: cellular
respiration or fermentation. The primary difference between
these two processes lies in the degree to which glucose is • Decarboxylation: Removes a carboxyl group and releases
oxidized. carbon dioxide (CO2)
• Dehydrogenation: Hydrogen atoms are transferred to a
coenzyme
REACTION TYPES IN CELLULAR RESPIRATION • Redox Reaction: Oxidation -the process by which
• Preparatory Reaction: Molecules are rearranged in electrons are removed from atoms or ions; Reduction- the
preparation for dehydrogenation or decarboxylation. gaining of electrons by one of the atoms involved in the
reaction. The electron transport chain is an example of a
series of redox reactions.
ANAEROBIC RESPIRATION & FERMENTATION

• Life thrives without O2 in waterlogged soils, deep puncture
wounds, sewage treatment plants, and your own digestive
tract, to name just a few places. In the absence of O2, the
microbes in these habitats generate ATP using anaerobic
metabolic pathways.
o Two examples are
o anaerobic respiration
o and fermentation.
• Phosphorylation: Addition of phosphate to an organic

compound
o Substrate level phosphorylation - an enzyme
transfers a phosphate group directly from a high-
energy "donor" molecule to ADP. Examples of
processes involving SLP are Glycolysis and Krebs
Cycle.
o Oxidative level phosphorylation - when ATP is
generated from the oxidation of NADH and FADH2
and the subsequent transfer of electrons and
pumping of protons. The electron transport chain and FERMENTATION
chemiosmosis make up oxidative phosphorylation.
o i.e., Mercury
o Mercury stops oxidation–reduction reaction early in
the electron transport chain
• ET INHIBITORS
o i.e., Cyanide
o Cyanide blocks the final transfer of electrons to O2.
When proteins in the electron transport chain have
no place to “dump” their electrons, the process
grinds to a halt.
• ET INHIBITORS
o i.e., Carbon Monoxide
o Carbon Monoxide blocks the final transfer of
electrons to O2
ALCOHOLIC FERMENTATION
• pyruvate is converted to ethanol and CO2, while NADH is
oxidized to produce NAD+.
• Alcoholic fermentation produces wine from grapes, beer
from barley, and cider from apples.
LACTIC ACID FERMENTATION

• A cell uses NADH to reduce pyruvate, but in this case, the
products are NAD+ and lactic acid or its close relative,
lactate.
• The bacterium Lactobacillus, for example, ferments the
lactose in milk, producing the lactic acid that gives yogurt
its sour taste.
• Bacteria can also ferment sugars in cabbage to produce Yawaa kapoya ato
the acids in sauerkraut.
CHEMICALS THAT INHIBIT RESPIRATION

• Many toxic chemicals kill by blocking one or more reactions
in respiration. Here are a few examples:
• KREBS CYCLE INHIBITOR

o i.e., Arsenic
o Arsenic binds to part of a molecule needed for the
formation of acetyl CoA
• CHEMIOSMOTIC PHOSPHORYLATION
o i.e., 2,4- Dinitrophenol (DNP)
o DNP kills by making the inner mitochondrial
membrane permeable to protons
• ET INHIBITORS

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GENERAL BIOLOGY

GENERAL BIOLOGY (LECTURE)

• Number of chromosomes = number of active

o spindle fibres attach to kinetochores of

TELOPHASE I AND CYTOKINESIS I

• Phospholipids are amphipathic molecules

CELL MEMBRANE AND TRANSPORT MECHANISMS

• In this fluid mosaic model, the membrane is a mosaic of

• The proteins are not randomly distributed in the membrane,

WHAT CAN GO THROUGH THE CELL MEMBRANE?

• (1) Small, nonpolar molecules

SATURATED AND UNSATURATED FATTY ACIDS

PASSIVE TRANSPORT VS ACTIVE TRANSPORT

its concentration gradient. As the solute moves, the gradient

PASSIVE TRANSPORT VERSUS ACTIVE

PASSIVE TRANSPORT (SIMPLE DIFFUSION AND

PASSIVE TRANSPORT: SIMPLE DIFFUSION

• Water crosses the membrane until the solute

PASSIVE TRANSPORT: OSMOSIS

PASSIVE TRANSPORT: OSMOSIS: TURGOR

PASSIVE TRANSPORT: OSMOSIS: ISTONIC,

• After a substance has diffused completely through a space

PASSIVE TRANSPORT (FACILITATED DIFFUSION)

FACTORS THAT AFFECT THE RATE OF DIFFUSION

o Solvent density: TYPES OF ACTIVE TRANSPORT

a substance the cell

substances EXAMPLES OF ACTIVE TRANSPORT

• An exergonic process is linked with an endergonic process

• Iron is the reducing agent

REDOX REACTIONS AND THE ELECTRON

PHOTOSYSTEMS OF THE LIGHT REACTIONS

• Both are protein complexes rich in chlorophyll (dark green

THE LIGHT REACTIONS SUMMARY OF THE NONCYCLIC PATHWAY

energy that is passed to the special pair of

ATP FORMATION IN THE LIGHT REACTIONS

ENERGY COUPLING IN THE LIGHT REACTIONS

• ATP is classified as a nucleotide (figure 8.74). It has a

• When a cell requires energy for an endergonic reaction, it

• A cell uses ATP (figure 8.76) as an energy source by

• ATP’s high-energy phosphate bonds make the molecule too

Uses of ATP: phosphorylation (top), change its shape in a

THE CARBON REACTIONS PRODUCE

• In general, a cell contains only enough ATP to sustain from

• Storage carbohydrates, such as starch and glycogen, act

ANAEROBIC RESPIRATION & FERMENTATION

• Phosphorylation: Addition of phosphate to an organic

LACTIC ACID FERMENTATION

CHEMICALS THAT INHIBIT RESPIRATION

• KREBS CYCLE INHIBITOR

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