BIO 100 - Phylum

INTRODUCTION TO BIOLOGICAL - Kingdom

CONCEPTS Kingdoms: Animalia, Plantae, Fungi, Protista
Some Life’s Properties (eukaryotes), and Monera (prokaryotic)
A. Hierarchy of Organization A. Life Requires Energy
B. Metabolism ATP- Adenosine Triphosphate
C. Response to Environment Metabolism: The chemical process involved in
D. Homeostatsis the production of ATP, the primary organic
E. Reproduction compound used for energy
F. Growth and Development Plants- Photosynthesis
G. Evolutionary Adaptation Animals- Cellular Respiration
A. B. Life Responds to Environment
Hierarchy of Organization (I) Stimulus- Response
1. Atoms C. Life Requires Internal Balance
2. Micro- and Macro- Molecules (nucleotides) Homeostasis: ability of an organism to
3. Intracellular structures (organelles) maintain a steady internal environment that
Eukaryotes- organelles is optimal for physiological processes,
Prokaryotes- nucl despite the fluctuating external environment
Hierarchy of Organization (II) How? Feedback Mechanism
1. Cells Negative Feedback: output decreases the
2. Tissues input
3. Organs Example: The insulin decreases the levels of
4. Organ System glucose in the blood
Hierarchy of Organization (III) Positive Feedback: output increases the
1. Organism (some species) input
2. Population Example: Oxytocin increases the contraction during
3. Biological Community labor
4. Ecosystem D. Life Grows and Develops
Hierarchy of Organization (IV) Heritable program within the DNA directs
- Species organismal pattern of growth, producing an
- Genus organism that is characteristic of its species
- Family E. Life Evolves Through Adaptation
- Order F. Evolutionary Adaptation: a heritable
- Class change that occurs within an organism that
 allows them to adapt better on the
environment

Metabolism

Response to Environment

February 21, 2023

Modern Life Forms are Connected by an
Evolutionary History
 All living species evolved from interrelated
group of ancestors
 All forms of life can be placed in three large
domains called Bacteria, Archaea, and
Eukarya
 Based on similarities in ribosomal RNA,
the three domains are created.
Striking Similarities of the three domains:
- DNA is used as a genetic material
- All species use the same genetic code
- Messenger RNA encodes the information to
produce proteins (Central Dogma)
- Transfer RNAs and ribosomes are needed to
synthesize proteins
- All living cells are surrounded by a plasma
membrane
- Some metabolic pathways, such as
glycolysis, are found in all domains
The Central Dogma of Cellular and Molecular - Interior of the nucleus
Biology - Endomembrane system
Replication (DNA > DNA) - Semi-autonomous organelles
 by the DNA Polymerase -
Transcription (DNA>RNA) Cytoplasm
 by the RNA Polymerase - Typically occupies about 50% of the total
Translation (RNA > Protein) cell volume
 by the Ribosome  Important site of metabolic processes
Cell Theory  Synthesis of cellular proteins
1. All organisms are composed of cells  Contains the cytoskeletons that provide
2. Cells are the smallest unit of living cell organization, shape and movement
organisms Nucleus
3. Cells arise only from pre-existing cells - It is involved in the protection and
2 Types of Cells: organization of genetic material
-Prokaryotes - Surrounded by a nuclear envelope
-Eukaryotes composed of 2 phospholipid bilayers with
Prokaryotic Cells openings called nuclear pores.
- lack a membrane-bound nucleus - Contains the DNA; organized with proteins
- Genetic material is present in the nucleoid to form chromatin; forms chromosomes
- Two Types of Prokaryotes: archaea and during mitosis
bacteria - Where replication and transcription occurs
Prokaryotic Cells contain: Nucleolus
-genetic material in the nucleoid - It is the nuclear subdomain that assembles
- Cytoplasm ribosomal subunits in eukaryotic cells.
-plasma membrane Levels of DNA Packaging
-ribosomes - Supercoiling of DNA in prokaryotes
Eukaryotic Cells DNA Double Helix Strand > DNA wrapped
- possess a membrane-bound nucleus around histone > Nucleosomes coiled into a
- structurally more complex than prokaryotic chromatin fiber > Further condensation of
cells chromatin > Duplicated chromosome
- compartmentalize cellular functions within
organelles
Compartments of Eukaryotic Cells
- The cytoplasm Endomembrane System
 - Function: modify, package, and transport
proteins and lipids
- The organelles of the endomembrane system
are related through direct contact or by the
transfer of membrane segments as vesicles.
1. A. Rough Endoplasmic Reticulum (RER)
- The rough ER plays a key role in the initial
synthesis of proteins, initial sorting of
protein and glycosylation.
B. Smooth Endoplasmic Reticulum (SER)
-allows increased surface area for key
enzymes with metabolic roles
-detoxification of harmful substances
- carbohydrate metabolism
-synthesis and modification of lipids
2. Golgi Apparatus
-processing/modification of proteins, sorting,
packaging of secretory proteins
3. Lysosomes
- membrane bound vesicles containing digestive
enzymes to break down macromolecules
- contain acid hydrolases involved in hydrolytic
reactions
- destroy cells or foreign matter that the cell has
engulfed by phagocytosis.
-Vacuoles
-membrane-bound structures with various
functions depending on the cell type
- central vacuole in plant cells
-contractile vacuole of some protists
-phagocytic / food vacuoles
Semiautonomous Organelles
 Have their own genetic material
(DNA) and are capable of synthesizing
proteins required for their functioning
 Examples are mitochondria and
chloroplasts
Mitochondria
- present in all types of eukaryotic cells
-contain enzymes for transferring the energy
within macromolecules to ATP
- surrounded by 2 membranes
- smooth outer membrane
-folded inner membrane forming projections called
cristae
Cristae - increase the surface area of the
mitochondrial membrane
-intermembrane space is located between the two
membranes
-contain their own DNA
Chloroplasts
- Organelles present in cells of plants and
algae
- Contain chlorophyll for photosynthesis
- Surrounded by two membranes
- Thylakoids are membranous sacs within the
inner membrane
- Grana are stacks of thylakoids
Types of Plastids
-Chloroplasts contain chlorophyll
-Chromoplasts synthesize and store pigments
-Leucoplast contain no pigment
> Amyloplasts synthesize starch in roots and tubers
Endosymbiotic Theory
 - eukaryotic organelles evolved through a
symbiotic relationship
- a larger cell engulfed a smaller cell and a
symbiotic relationship developed.
Explanation:
Mitochondria and chloroplasts:
- Have 2 membranes
- Possess DNA and ribosomes
- Are about the size of a prokaryotic cell
- Divide by a process similar to bacteria
Peroxisome
- Consists of single-membrane that encloses
a fluid-filled lumen
- -catalyze chemical reactions by breaking
down molecules
 Mammalian liver cells have large
amounts of peroxisomes that
break down toxic molecules
Microtubules
- Hollow, cylindrical structures (~ 25 nm
diameter)
- The cellular location for microtubules could
vary among different cell types
- Important for cell shape and organization of
cell organelles, chromosome sorting,
intracellular movement of cargo proteins,
cell motility.
Intermediate filaments
- These proteins form a twisted and rope-like
structure (~10 nm diameter)
- Help maintain cell shape and rigidity
- Several types of related proteins can
assemble into intermediate filaments:
 Desmins – help maintain the
structure of sarcomeres which
are necessary for muscles to tense
(contract)
 Lamins – provide a platform for
the binding of proteins and
chromatin and confer
mechanical stability
 Keratins – form cytoskeletal
networks
Actin Filaments
- Composed of two strand of actin
monomers that spiral around each other
(~7nm diameter)
- They play a key role in cell strength and
shape as well as muscle contraction
-
Cell Movement
- Cell movement takes different forms
- Crawling is accomplished via actin
filaments and the protein myosin.
- Flagella undulate to move a cell
- Cilia can be arranged in rows on the surface
of a eukaryotic cell to propel a cell forward.
The cilia and flagella of eukaryotic cells have a
similar structure:
9-2 structure: 9 pairs of microtubules surrounded
by 2 central microtubules
-Cilia are usually more numerous than flagella on
a cell
Extracellular Structures
Extracellular structures include:
- Cell walls of plants, fungi, some protists
- Extracellular matrix surrounding animal cells
Cell Walls
-present surrounding the cells of plants, fungi, and Hypertonic Solution: a solution that has high
some protists solute concentration and low water concentration
-the carbohydrates present in the cell wall vary
depending on the cell type: Hypotonic Solution: a solution that has low solute
Plant and protist cell walls – cellulose concentration and highwater concentration
Fungal cell walls – chitin
Isotonic Solution: a solution that has an equal
concentration of solute and water relative to the
cell’s intracellular environment

Types of Cellular Transport

Passive Transport
2 Types:
Simple Diffusion
- Gasses (O2, Co2)
- Lipids (non-polar molecules)
- Substance passes between the phospholipids
- Can only move material in the direction of a
LECTURE 3: TRANSPORT SYSTEMS concentration gradient
Concepts to Know - Moves from high to low concentration
Diffusion Facilitated Diffusion
– movement of molecules from an area of high - Polar and charged molecules (ions)
concentration to a low concentration area - Amino acids, carbohydrates
- Water
Osmosis - Substance passes through specialized
-the movement of water (through a semi-permeable membrane channels formed by integral
membrane) from high concentration to low water membrane protein
concentration - Moves materials with and against
-hypotonic to hypertonic concentration gradient
-movement of water across membranes to balance - High to low concentration gradient
solute concentrations Active Transport
- unassisted membrane transport
 - Moving molecules against concentration
gradient; requires energy
- Bigger molecules
- Ions
- Low/high concentration gradient to high/low
concentration gradient
Primary Active Transport
-the energy is derived directly from the breakdown
of ATP through hydrolysis
- involves in the functioning of pumps that
directly use energy to transport solute against a
gradient
- A pump is a transporter that directly couples its
conformational changes to energy source such as
ATP hydrolysis
Secondary Active Transport
-Sodium is moving to another ….
- the energy is derived secondarily from energy that
has been stored in the form of ionic concentration
differences between the two sides of a membrane.
- a transported protein couples the movement of an
ion down its concentration gradient to uphill
movement of another molecule
 Na+ / glucose cotransporter found in the
small intestine and kidney tubules
Endocytosis
-engulfment of extracellular material through
invagination of the plasma membrane
-capturing a substance or particle from outside the
cell
- vesicular transport
TYPES: phagocytosis, pinocytosis, receptor-
mediated endocytosis
Example. Vesicle forms from a patch of inward-
sinking plasma membrane, enters cytoplasm.
FURTHER EXPLANATION
Exocytosis
-Transport of intracellular material outside of cell
through fusion of vesicles and the plasma
membrane.
Example. Vesicle in cytoplasm moves to plasma
membrane, fuses with it; contents released to the
outside.
-membrane-bound secretory vesicles are carried to
the cell membrane, and their content are secreted
into the extracellular environment
MEMBRANE TRANSPORT VERSION 2
 Jonathan Singer and Garth Nicholson in
1972 proposed the fluid-mosaic model of
membrane structure
 All biological membranes are constructed as
phospholipid bilayer
Phospholipid
Phospholipid structure consists of:
Glycerol - a 3-carbon polyalcohol acting as a
backbone for the phospholip
Fatty Acids – attached to the glycerol
Phosphate Group – attached to the glycerol
Membrane Proteins
-membrane proteins are attached to or embedded in
the phospholipid bilayer carry out most functions of
the membrane
- integral or intrinsic membrane proteins have
one or more regions that are physically embedded in
the hydrophobic region of phospholipid bilayer
- peripheral or extrinsic membrane proteins do
not interact with hydrophobic interior of the
phospholipid bilayer
Carbohydrates
- Are attached to membrane lipids and
proteins forming glycolipids and
glycoproteins, respectively.
Membrane Permeability
- The proteins allow membranes to be
selectively permeable by providing a
passageway for the movement of some but
not all substances across the membrane.
 Molecular size
 Polarity
 Charge
Assisted Membrane Transport
- Channels are transmembrane proteins
that form an open passageway for the
diffusion of ions and molecules across the
membrane
 Sodium, calcium, potassium
 Ligand-gated channel opens in
response to binding of ligand
 Voltage-gated channels open in
response to changes in the
amount of electric charge
Transporters or carriers bind solutes in a
hydrophilic pocket and undergo a conformational
change that switches the exposure of the pocket to
the other side of the membrane.
 Pump uses ATP to transport
molecules against its gradient
 Transport of organic molecules
such as sugars, amino acids, and
nucleotides.
Differences between Channels and Carriers
- A carrier is not open simultaneously to both
the extracellular and intracellular
environments
- Carriers have binding sides, but channels do
not
- Carrier proteins are more selective, often
only allowing one particular type of
molecules to cross
Assisted Membrane Transport
Facilitated diffusion is the process of passive
transport of molecules or ions across a biological
membrane via channel or carrier proteins.
 Glucose, amino acids, sodium
ions, chloride ions

March 9, 2023
GENE EXPRESSION
The Structure of the Genetic Material
DNA Replication
The Flow of Genetic Information from DNA to RNA to
Protein
The Genetics of Viruses and Bacteria
Scientific Discovery: Experiment showed that DNA is the
genetic material
 It was known that DNA is a polymer of
nucleotides, each consisting of a nitrogenous bas, a
sugar, and a phosphate group.
 In 1950, Erwin Chargaff reported that DNA
composition varies from one species to the next.
 DNA are made up of nucleotides
 The number of Thymine is equal to the number of
Adenine
 Guanine and Cytosine hyberdize to each other
meaning they pair up with each other
Pyrimidines- Thymine and Cytosine (single structure)
Purines- Adenine and Guanine (double circular structure)
Purine + Pyrimidine - would fit that gap of 4 nanometers
between the two strand of the DNA
WHY DNA IS TWISTED?
This is because of the polarity of the backbone of the DNA
, the nitrogenous bases that makes up the step ladders, they
don’t want to be expose to water. They try to minimize the
space.
A nucleotide
DNA Replication
Before the cell divides, the DNA must be replicated so the
daughter cells would have a copy
A parental molecules of DNA > The parental strands
separate and serve as templates > Two identical
daughter molecules of DNA are formed
Replication bubble forms > each bubble has two
replication forks that moves into opposite >
DNA Polymerase only synthesizes Dna at the five prime
and 3 prime
DNA requires the three prime hydroxyl group
DNA polymerase always synthesizes the daughter
strand at 5’ to 3’ and reads the parental strand at the 3’
to 5’ direction and synthesizes them 5’ to 3’.
DNA is opened by the helicase and then single stranded
proteins binds to each strand of DNA. DNA polymerase
requires hydroxyl group
DNA is Antiparallel – one strand is 3’ to 5’ and the other is
5’ to 3’which is complementary. DNA polymerase adds
new daughter strand into 5’ to 3’ direction and needs to
read 3’ to 5’ template can be problematic because it is anti-
parallel.
Leading strand – the dna poly is reading the template 3
prime to 5 prime and synthesizing 5 prime to 3 prime
Synthesizes the DNA at the direction of the replication fork
Lagging strand – the primase will add on that RNA primers
and it will be removed and dna polymerase takes over,
adding on DNA from RNA primer. The rna primers are
removed creating fragments of DNA and refilled by DNA
polymerase. The fragments of DNA became ligated by
DNA ligase.
Primase- type of rna polymerase
DNA polymerase synthesizes away from the replication
fork.
DNA parental strands runs into 3’ to 5’ direction.
The nucleotides are added from 5’ to 3’
TRANSCRIPTION is the synthesis of RNA under the
direction of DNA
Transcription and Translation happens in the cytoplasm in
a bacterial cell
Transcription and Translation happens in the nucleus in a
eukaryotic cell
It synthesizes the DNA at the 5’ to 3’ direction and reads at
the 3’ to 5’ direction.
- Produces one strand of RNA transcript
- RNA splicing – removes introns and joins exons
Pre-mRNA > mRNA
Pre-mRNA- non-processed and are the ones not being
spliced out yet
mRNA – fully mature and processed
Introns – the ones being spliced out
Exons – capped after RNA process
Exons that have been left out in mRNA, not all of them are
also translated.
- Proteins are made up of a chain of amino acids.
- What sequence of amino acid is needed to produce
one specific type of protein?
- 3 stop codons that signals for the end of translation
- One codon can encode for multiple amino acids
meanwhile is also unambiguous
- There is 64 possible combinations of codons
Redundant – multiple codons can specify for a
specific amino acid
Unambiguous - This specific codon only specifies
for specific amino acids
Transfer RNA (tRNA) molecules function as a
language interpreter.
Ribosome synthesizes polypeptide chain.
First, initiation process where tRNA recognizes
the start codon
Genotype – nucleotides sequence that encodes for
a specific protein
Phenotype – are the traits expressed
For example, the skin color is a phenotype because
of pigment proteins and these are encoded by
specific genotype.

LECTURE 4: PHOTOSYNTHESIS
- Phototrophs utilize solar energy for energy
conservation. In most cases, CO2 is reduced into
organic molecules
Photosynthesis occurs in chloroplasts in plant cells
1) *** Plants, algae, and cyanobacteria uses
water and releases O2:
6 CO2 + 12 H2O + Light Energy ->
C6H12O6 + 6 H2O + 6 O2
2) Purple and green sulfur bacteria use H 2 S
and releases sulfur:
6 CO2 + 12 H 2 S + Light Energy ->
C6H12O6 + 6 H2O + 12 S
- Photosynthesis and cellular respiration are
complementary processes
Where do things happen? And how are things
acquired?
 Chloroplasts consist of an envelope of two
membranes, which encloses
- An inner compartment filled with a thick fluid
called stroma
- Contain a system of interconnected membranous
sacs called thylakoids
Thylakoids
 are often concentrated in stacks called grana and
 have an internal compartment called the thylakoid
space, which has functions analogous to the
intermembrane space of a mitochondrion.
 Thylakoid membranes also house much of the
machinery that converts light energy to chemical
energy.
Chlorophyll molecules
 are built into the thylakoid membrane and
 capture light energy.
Photosynthesis is a redox process
In photosynthesis,
 light energy is captured by chlorophyll molecules
to boost the energy of electrons,
 light energy is converted to chemical energy, and
  chemical energy is stored in the chemical bonds of  Chloroplasts contain several different pigments,
sugars. which absorb light of different wavelengths.
THE LIGHT REACTIONS: CONVERTING SOLAR – Chlorophyll a absorbs light with wavelengths of
ENERGY TO CHEMICAL ENERGY 430nm(blue) and 662nm(red).
Visible radiation absorbed by pigments drives the light – Chlorophyll b absorbs light of 453nm (blue)
reactions
and 642 nm (orange).
Sunlight contains energy called electromagnetic energy
– Carotenoids absorb light maximally between
or electromagnetic radiation.
460 nm and 550 nm
 Visible light is only a small part of the
 broaden the spectrum of colors that
electromagnetic spectrum, the full range of
can drive photosynthesis and provide
electromagnetic wavelengths.
photoprotection, absorbing and
 Electromagnetic energy travels in waves, and the dissipating excessive light energy.
wavelength is the distance between the crests of
- Absorption spectrum depicts the wavelengths of
two adjacent waves.
radiation absorbed by a pigment

 Light behaves as discrete packets of energy called Photosystems capture solar energy
photons.
Within a thylakoid membrane, chlorophyll and other
– A photon is a fixed quantity of light energy pigment molecules

 – absorb photons and

 – transfer the energy to other pigment molecules.

 In the thylakoid membrane,

Plant pigments chlorophyll molecules are organized
along with other pigments and
 absorb some wavelengths of light and proteins into photosystems.

 reflect or transmit other wavelengths.

 We see the color of the wavelengths that are

transmitted or reflected. For example, chlorophyll
transmits green wavelengths.
Reaction center (chlorophyll A & electron acceptor) +
– accepted by NADP , reducing it to NADPH.
Light-harvesting complex (pigment molecules bounded to
 Between the two photosystems, the electrons
proteins)
– move down an electron transport chain and

– provide energy for the synthesis of ATP.

Two types of photosystems (photosystem I and

photosystem II) cooperate in the light reactions.

 Each type of photosystem has a characteristic

reaction center.

– Photosystem II, which functions first, is called

P680 because its pigment absorbs light with a
wavelength of 680 nm.

– Photosystem I, which functions second, is

called P700 because it absorbs light with a
wavelength of 700 nm.

Two photosystems connected by an electron transport

chain generate ATP and NADPH
 The electron carriers are arranged in accordance
In the light reactions, light energy is transformed into the with their redox potentials.
chemical energy of ATP and NADPH (Nicotinamide
adenine dinucleotide phosphate)  The products of the light reactions are
 To accomplish this, electrons are - NADPH,
– removed from water, - Oxygen
– passed from photosystem II to photosystem I, - ATP
and
Chemiosmosis powers ATP synthesis in the light
reactions
- Chemiosmosis involves ions moving down their
concentration gradient and their electrochemical
gradient. (Driving factor)

- ATP is generated because the electron transport

chain produces a concentration gradient of THE CALVIN CYCLE: REDUCING CO2 TO SUGAR
hydrogen ions across a membrane.
ATP and NADPH power sugar synthesis in the
 In photophosphorylation, using the initial Calvin Cycle
energy input from light,
To produce sugar, the necessary ingredients are
- the electron transport chain pumps H+ into the
thylakoid space, and – atmospheric CO2 and
– ATP and NADPH generated by the light reactions.
+
- the resulting concentration gradient drives H
 The Calvin cycle uses these three ingredients to
back out to the outer membrane (Chemiosmosis)
produce an energy-rich, three-carbon sugar
through ATP synthase, producing ATP.
called glyceraldehyde-3-phosphate (G3P).
- Cyclic vs Non-Cyclic photophosphorylation
 A plant cell may then use G3P to make glucose
and other organic molecules.

The steps of the Calvin cycle include

 carbon fixation,

 reduction,

 release of G3P, and

 regeneration of the starting molecule ribulose

bisphosphate (RuBP).
SUMMARY:

The two stages of photosynthesis are linked by ATP and

NADPH

Photosynthesis occurs in two metabolic stages.

1. The light reactions occur in the thylakoid membranes.

– water is split, providing a source of electrons and giving

off oxygen as a by-product,

– ATP is generated from ADP and a phosphate group, and

+
– the transfer of electrons and H from water to the
+
electron acceptor NADP produces NADPH.

2. The second stage is the Calvin cycle, which

occurs in the stroma of the chloroplast.
  – The Calvin cycle is a cyclic series of reactions  – Mitochondria use oxidative phosphorylation to
that assembles sugar molecules using CO2 and the transfer chemical energy from food into the
energy-rich products of the light reactions. chemical energy of ATP.

 – During the Calvin cycle, CO2 is incorporated  – Chloroplasts use photophosphorylation to

transfer light energy into the chemical energy of
into organic compounds in a process called ATP.
carbon fixation.
PHOTOSYNTHESIS (PROCESSES)

Photosystem I

- Generates NADPH

Photosystem II

-oxidizes water and transfer electrons to Photosystem I

- Both Photosystem I and II utilizes

photophosphorylation to generate ATP

- Photophosphorylation is the process of utilizing

light energy from photosynthesis to convert ADP
to ATP.

Light Reaction (Light-dependent reaction)

1. Photon will come down from light or any other

energy source and hit photosystem II

2. It is absorbed by the light harvesting complexes

Question to consider after Week 4 – Cellular Respiration
bounced it and then eventually hits P680 (680 nm-
 How does photophosphorylation compare with red light).
oxidative phosphorylation?
3. P680 needs an electron from a water molecules 14. The electron moves up energy states into the
H2O and the way to get its electron is to split up reaction center and the primary electron acceptor
the water molecule into oxygen and hydrogen ions 15. From here, the electrons moved down the second
(1/2 O2 + H +¿¿ ). The ½ oxygen molecule will electron transport chain into the complex called
join another oxygen molecule and become O2) Ferredoxins (FD)
16. NADP+ reductase then takes in the complex and 1
4. The photon and electron is now all inside the electron is produced. However, but NADP+
P680. reductase required 2 hydrogen electrons in order to
be complete.
5. The photon now excites this electron and the
17. After repeating the process and gaining another
electron moves up in energy states into this
one electron, it produces NADPH
primary electron acceptor e−¿¿
18. Combining ATP and NADPH, it produces a sugar
6. It then moves down this electron transport chain complex which then produces a glucose molecule.
through proteins called Plastoquinone(PQ). From
PQ to b6f complex (Cytochrome) and then travels
down to PC (Plastocyanin). The energy state gets  Light reactions occur in the thylakoid
lower and lower as the electron travels from membranes
protein to protein.  During the light reaction, there are two
7. During the electron transport chain, the energy possible routes for electron flow:
gets absorbed by ATP as the energy of electron - Cyclic Electron Flow
lowers. - Noncyclic Electron Flow
8. Electron transport chain provides energy for -
synthesis of ATP by chemiosmosis
9. The b6f complex main function is to link the
electron from photosystem II to photosystem I. POSSIBLE QUESTIONS (Light Reaction):
10. Now in photosystem I, photon is absorbed into the
complex from an exterior source (most likely the Cyclic Electron Flow
sun)
11. It then bounces from light harvesting complex
until it reaches the complex P700 (700 nm
wavelength - red)
12. For the whole process (Photosystem I and II), all
light colors are absorbed except for green which is
the reason why plant leaves colors are green.
13. The electron that moves from photosystem II to
photosystem I is then excited by the energy
produced by the photon that was absorbed and Non-cyclic Electron Flow
P700.

Calvin Cycle ( Light-independent reaction or dark
reactions)
 Takes place in the fluid surrounding the
thylakoids called stroma.
 ATP provides the energy and NADPH
provides the electrons and hydrogens that
are needed to reduce carbon dioxide to
build sugars.
The Whole Process:
1. Phase 1: Carbon fixation, an enzyme
called Rubisco takes CO2 from the air
and adds it to a five carbon compound
called RuBP(ribulose-1,5- bisphosphate).
This makes a six carbon compound that
immediately splits in half to make two
molecules of 3-phosphoglycerate (3-
PGA). Notice that we did carbon fixation
for three molecules of CO2.
2. Phase 2: Reduction, ATP from light
reactions provide energy to make an
intermediate compound (I.3
bisphosphoglycerate). This reactive
intermediate can then be reduced or gain
electrons and hydrogen.
3. The electrons and hydrogens come from
NADPH and are used to reduce the
intermediate compound to make
glyceraldehyde 3-phosphate (G3P) or
sometimes trios phosphate.
 Notice: For every three molecules of CO2
brought into the cycle, there is a net gain
of one G3P. Three Carbons in and three
carbons out.

4. Phase 3: Regeneration, notice that only

one G3P is removed from the cycle,
leaving 5 G3Ps behind. These 5 G3P
molecules get converted back to the
starting compound RuBP.

5. The balanced photosynthesis equation has

six carbon dioxide to produce 1 molecule
of glucose. Therefore, two repeated
Calvin cycle is needed to produce
glucose. Two G3Ps is needed to make
glucose.

GLYCOLYSIS

1. The first reaction that takes place is

conversion of glucose to glucose-6-
phosphate (ATP to ADP). The enzyme
that catalyzes this reaction is called
hexokinase (the word hexo means six
denoting the six carbon compound
glucose and the kinases are a group of
enzymes that catalyze the phosphorylation
reactions).
2. So the enzyme hexokinase transfers a
molecule of phosphate from ATP to
glucose and converts glucose to glucose
6-phosphate
3. In this reaction ATP is converted into a
molecule of ADP. Hence it utilizes one
molecule of ATP.
4. Next the glucose-6-phosphate is
converted into its isomer, the fructose
6-phosphate by the enzyme isomerase.
This is a simple rearrangement reaction.
5. In the next step the fructose-6-
phosphate is converted to fructose 1,6-
bisphosphate (ATP to ADP). That is
addition of another phosphate group as the
first carbon of the fructose ring. This
reaction is catalyzed by the enzyme
phospho-fructo-kinase( another kinase
enzyme which transfers a group of
phosphate from ATP to fructose-6-
phosphate and again ATP is converted
into ADP, hence another ATP is utilized
in the reaction.
6. Next the fructose-1-6 bisphosphate is
split into two molecules the
glyceraldehyde-3-phosphate and
dihydroxyacetone phosphate. These
both are 3 carbon compounds and the
enzyme that catalyzes this reaction is
called aldolase. These are reactions that
composed the first phase of the glycolysis
and as you can see energy is actually
utilized in this process in the form of two
ATP's. The two compounds
glyceraldehyde-3-phosphate and
dihydroxyacetone phosphate are actually
isomers and can be interconverted into
each other by the enzyme isomerase but
since the glyceraldehyde 3-phosphate is
further utilized in the process of
glycolysis, the equilibrium of this
isomerization reaction is always towards
the glyceraldehyde 3-phosphate. We
should also keep in mind that every
molecule of glucose is split into two
molecules. Every reaction of the second
phase happens twice and produces
twice the products.
7. In the next reaction, the glyceraldehyde
-3-phosphate is converted to 1,3-
bisphospho-glycerate (NAD+ to NADH)
This involves addition of a phosphate
group at the first position of the
phosphoglycerate. The enzyme that
catalyzes this reaction is the
glyceraldehyde-3-phosphate
dehydrogenase and in this reaction,
nicotinamide adenine dinucleotide
(NAD+) which is the coenzyme is
reduced to NADH which is further
utilized in the electron transport chain to
produce more energy. Also this reaction
utilizes a molecule of inorganic
phosphate.
8. The 1,3-bisphospho-glycerate is
converted to 3-phospho-glycerate (ADP
to ATP) by the enzyme
phosphoglycerate kinase (this kinase
enzyme transfers the phosphate group at
the first position of phosphoglycerate to
adenosine diphosphate and in this process
a molecule of ATP is generated.
9. Next, the 3 phosphoglycerate is
converted to 2-phosphoglycerate. this is
a simple rearrangement reaction that
happens with the help of the enzyme
phosphoglycerate mutase.
10. Next, the 2-phosphoglycerate is
converted to phosphoenolpyruvate. The
enzyme involved is enolase and
 magnesium ions are also utilized in this
reaction.
11. In the final step, the phosphoenol
pyruvate (PEP) is converted to
pyruvate (ADP to ATP) by the enzyme
pyruvate kinase. The phosphate group at
the phosphoenol pyruvate is transferred to
ADP and converted to ATP.
Glycolysis summary:
 4 ATPs are produced in phase II, 2 ATPs are used
in phase 1. Therefore, only 2 ATPs are in the final
equation
 Since 2 ADPs are produced in Phase 1 and 4
ADPs are used in Phase II, only 2 are used in the
equation.
 Since NAD+ and NADH are only present in phase
II, it produces 2 NADH molecules from 2 NAD+
Glycolysis end products:
- 2 pyruvic acid
- 2 NADH
- 2 ATP
Transition Reaction (oxidation of pyruvic acid)
In the transition reaction, for 2 molecules of pyruvate:
- 2 CO2 is released and 2 NADH is produced
KREBS CYCLE
- occurs in mitochondria of eukaryotes
- Occurs in cytosol of prokaryotes
1. Pyruvate (3-C compound) is oxidized into Acetyl-
CoA (2-C compound) through enzyme pyruvate
dehydrogenase complex. In this reaction, a
molecule of carbon dioxide and a molecule of
NADH is generated.
2. The Acetyl-CoA combines with Oxaloacetate
(4-C compound) to form citrate (6-C compound).
This reaction is catalyzed by Citrate synthase.
3. The citrate is isomerized into isocitrate by the
enzyme Aconitase.
4. Isocitrate is oxidized into Alpha-Ketoglutarate
(5-C compound) by enzyme Isocitrate
Dehydrogenase (NAD+ to NADH and release 1
molecule of CO2). Since 1 molecule of CO2 is
released, it becomes a 5-C compound).
5. Alpha-Ketoglutarate is converted into Succinyl
COA (4-C compound) by the enzyme Alpha-
Ketoglutarate dehydrogenase (NAD+ to NADH
and release 1 molecule of CO2)
6. Succinyl COA converted to Succinate by
enzyme Succinyl COA Synthase (releases ATP
(adenine triphosphate)).
7. Succinate is converted to Fumrate by the
enzyme Succinate dehydrogenease (produces
QH2(ubiquinol) which then is responsible for
producing FADH2).
8. Fumrate is converted into Malate by the enzyme
Fumrase.
9. Malate is converted to Oxaloacetate by the
enzyme Malate Dehydrogenase (NAD+ to
NADH).
Results of Krebs Cycle (2 cycles is needed to
produce glucose, 6 carbon is needed. Therefore, two
pyruvate is needed to produce a glucose).
6 NADH
 2 FADH2 - The ETP is a series of proteins and other
2 ATP molecules embedded in the inner membrane
4 CO2 of the mitochondrion
- These molecules transport electrons
1. NADH that electron carrier we have been
making delivers its electrons to the first
protein in the electron transport chain
2. As the electrons move through this protein
complex, energy is gradually released.
This energy is used to pump hydrogen
ions or protons across the inner membrane
After glycolysis, pyruvate oxidation, and Krebs cycle, from the matrix into the inter-membrane
glucose has been oxidized to: space
- 6 CO2
- 4 ATP
- 10 NADH
- 2 FADH2
These electron carriers proceed to the electron
transport chain.

-ATP Synthase is a membrane-bound enzyme that

The Electron Transport Chain uses the energy of the proton gradient to synthesize
- utilizes 4 protein complexes (Cytochrome I- ATP from ADP + Pi.
IV) Whole Mitosis Process:
- 2 mobile carriers (Ubiquinone and https://www.khanacademy.org/science/ap-biology/c
Cytochrome C) ell-communication-and-cell-cycle/cell-cycle/a/
phases-of-mitosis

Electron Transport Chain Process:

- The vast majority of the ATP is made
 strand binding proteins react with the
single stranded regions of the DNA and
stabilize it.
2. DNA polymerase 3 is the major enzyme
involved in DNA replication.
DNA polymerase 3 can only add a nucleotide to the three
prime end of a pre-existing chain of nucleotides and it
cannot initiate a nucleotide chain, therefore an RNA
polymerase called a primase constructs an RNA primer a
sequence of about 10 nucleotides complementary to the
parent DNA.
3. DNA polymerase 3 can then add
deoxyribonucleotides to synthesize the
new complementary strand of DNA
because the two parent strands of dna are
anti-parallel (they are oriented in opposite
directions and must therefore be elongated
by different mechanisms).
4. The leading strand elongates toward the
replication fork by adding nucleotides
continuously to its growing three prime
end.
5. In contrast ,the lagging strand which
elongates away from the replication fork
is synthesized discontinuously as a series
of short segments called Okazaki
fragments.
6. When the DNA polymerase 3 reaches the
RNA primer on the lagging strand, it is
replaced by DNA polymerase 1 which
removes the RNA and replaces it with
DNA. DNA ligase then attaches and
forms phosphodiester bonds.
REPLICATION OF DNA PROCESS: 7. The DNA is further unwound, new
1. The replication of DNA begins at a primers are made, and DNA polymerase 3
sequence of nucleotides called the origin jumps ahead to begin synthesizing another
of replication. Helicase unwinds the okazaki fragment.
double-stranded DNA helix and single-
 8. For simplicity, DNA polymerase 3 has
been depicted as separate units. One
acting on the leading strand and the other
acting on the lagging strand.
9. The current view of DNA polymerase III
is that the two subunits function together
with the DNA on the lagging strand
folding to allow the dimeric DNA
polymerase molecule to replicate both
strands of the parental DNA duplex
simultaneously
10. Proteins other than DNA polymerase 3 are
not shown.
TRANSCRIPTION PROCESS:
- Process by which enzymes use one of the
strands of DNA within a gene as a template to
produce a messenger RNA (mRNA)
1. RNA Polymerase with the help of proteins
called transcription factors, binds to a specific
sequence within the gene, which is called the
promoter, and pries the two strands apart.
One of the strands will serve as the template
strand, or antisense strand, meaning it will be
used to generate the mRNA, and the other is
the non-template strand or the sense strand.
RNA polymerase doesn't need a primer.
2. It simply initiates mRNA synthesis at the start
codon (AUG), and then moves downstream
along the gene in a process called elongation,
synthesizing the mRNA as it goes, reading
the antisense strand from 3' to 5' and
generating the mRNA from the 5' end,
attaching RNA nucleotides to the 3' end as
it goes.
In DNA replication, thymine binds with
adenine. But in RNA transcription, the RNA
produced contains uracil instead of thymine.
Unlike replication, RNA polymerase zips DNA
back up as it goes, keeping only 10 to 20 bases exposed at
a time.
3. Once RNA polymerase reaches the end of the
gene, termination occurs, the enzyme
detaches from the gene and the DNA is
returned to its original state. But we have
produced an mRNA. This carries with it the
information encoded in the gene, and after a
few quick modifications during RNA
processing it will leave the nucleus, where all
the genetic material or chromatin is, and
move into the cytoplasm, where it will find
a ribosome.
4. This is where translation occurs (ribosome).
The mRNA acts as a code for a specific
protein. This happens because each set of
three bases on the mRNA, which we call
codons, will code for a specific anticodon,
which will be carried by a specific transfer
RNA, or tRNA, and each different tRNA is
covalently linked to a particular amino acid.
The arrangement of the nucleotides into these
codons is called the reading frame. Since there
are four bases and each codon has three
letters, 4^3 gives us 64 different possible
codons, which is more than enough to code for
all the amino acids we need.
5. AUG is the start codon, which initiates
translation by coding for methionine, and
these three are stop codons (UAG, UGA,
UAA). These are the ones that terminate
translation.
6. Translation will occur inside a ribosome. The
small ribosomal subunit binds to an mRNA
and an initiator tRNA, which adheres to the
 start codon. Then the large ribosomal subunit
joins to complete the translation initiation
complex. Then, the tRNA that corresponds to
the next codon after the start codon will enter
the ribosome. This will carry with it an amino
acid, which becomes covalently bound to the
methionine from the initiator tRNA. The first
tRNA detaches and leaves the ribosome,
which has shifted over, making room for the
next tRNA.
7. The new amino acid links to the first two, and
this process continues all the way down the
mRNA. As tRNAs enter and exit the ribosome
in a sequence that is dictated by the codons on
the mRNA, a polypeptide chain will grow.
This continues until a stop codon is reached, at
which point the completed polypeptide will
swim away, most likely entering one of the
cell organelles for folding and further
modification. So in this two-step process,
DNA is transcribed into an mRNA, and then
this mRNA is translated into a protein, all
simply by obeying the base pairing that occurs
in nucleic acids, and since every gene codes
for a specific protein, and proteins make up
most of what you are, from your muscle tissue
and organ tissue, to all of your receptors and
enzymes, this is how DNA carries the code for
a living organism.