Biology Reviewer
Photosynthesis
Photosynthesis is the process by which
autotrophic organisms use light energy to make
sugar and oxygen gas from carbon dioxide and
water
6 C O2 +6 H 2 O→ C6 H 12 0 6+ 6 O2
Almost all plants are photosynthetic autotrophs,
as are some bacteria, algae, certain protists, and
some prokaryotes.
Autotrophs generate their own organic matter
through photosynthesis. Sunlight energy is
transformed to energy stored in the form of
chemical bonds
Chloroplast
Photosynthesis occurs in the leaves of a plant
structure, particularly cell structure makes the
reactions possible, enables integration of light
and dark reactions. Leaves contain millions of
chloroplasts.
Granum – are series of flattened,
interconnected sacs that looks like pancakes
stacked upon on top of each other
Thylakoid – each of those flattened sacs (venue
for light reaction)
Stroma – liquid part of the chloroplast (venue
for dark reaction)
Stomata – the tiny openings of the plants
Chlorophyll and Pigments
Chlorophyll – Absorbs the light energy from the
sun and used it to power the chemical reactions
of Photosynthesis
Chlorophyll a – is a bluish green and the most
abundant
Chlorophyll b – is a yellowish green, absorbs
light and transfers the energy to chlorophyll a
Chlorophyll c, d and e – take the place of
chlorophyll b in certain algae and other
photosynthetic bacteria.
Carotenoids – pigments that are Red, Orange or
Yellow
The 2 stages of Photosynthesis:
Light – dependent Reaction (Light Reaction) also
known as photolysis or hydrogen fixator
- Produces energy from solar power
(photons) in the form of ATP and
NADPH.
- Light hits the reaction centers of
chlorophyll, found in chloroplasts
- Light hits electrons in the cell of leaves
converting “excited” electrons in
phosphate thus creating ATP from ADP
- Chlorophyll vibrates and causes water
to break apart into Oxygen that is
released to the outside world and
Hydrogen that will be carried by NADP
to become NADPH
- End Product: Oxygen, ATP & NADPH
Light – independent Reaction (Dark Reaction)
also known as the Calvin cycle or carbon fixator
- Uses energy (ATP and NADPH) from
light reaction to make sugar (glucose).
- Occurs in the Stroma
- CO2 is added to the 5-C sugar RuDP by
the enzyme rubisco making it a 6-C
sugar
- This unstable 6-C compound splits to
two molecules of PGA or 3-C sugar
called phosphoglyceric acid
- PGA is converted to Glyceraldehyde or
PGAL (also known as 3-phosphate  or
G3P), two of which bond to form
glucose.
 - Once PGA becomes PGAL, it will bond
again form glucose, a stable form of 6-C
sugar.
- RuDP will be used again by another CO2
and the process continues
- In other words, CO2 in addition to the
Hydrogen from NADPH and energy from
ATP will become G3P (Glyceraldehyde
3-phosphate). G3P is comprised of 3
Carbon, 3 Oxygen (from CO2) and 6
Hydrogen. Doubling that would make it
C 6 H 12 06 AKA Glucose.
Respiration
occurs in both eukaryotic and prokaryotic
cells, with most reactions taking place in the
cytoplasm of prokaryotes and in the
mitochondria of eukaryotes.
Types of Cellular Respiration
Anaerobic respiration
- Does not involve Oxygen (also known as
Fermentation)
- NO Additional ATP is Formed
- Releasing Energy w/out Oxygen
Two Types:
Lactic Acid Fermentation
- bacteria, plants and most animals
- After glycolysis; 2 pyruvic acid changed
to lactic acid
- Sometimes happens in your muscles,
cramps, or during Exercise
Alcoholic Fermentation
- Bacteria and fungi (yeast)
- Ethyl alcohol and carbon dioxide are the
end products
- Process used to form beer, wine, and
other alcoholic beverages
- Also used to raise dough, bread
- Important in making kimchi, achara etc.
Aerobic respiration – Involves the use of oxygen
- In aerobic respiration, oxygen is
essential for ATP production. In this
process, sugar (in the form of glucose) is
oxidized (chemically combined with
oxygen) to yield carbon dioxide, water,
and ATP. The chemical equation for
aerobic cellular respiration is
C 6 H 12 O6 + 6O 2 → 6C O2+ 6 H 2 O+ 38 ATP
Stages of Cellular Respiration
1.) Glycolysis
- Start of respiration
- Process in which one Glucose molecule
is Converted into two (2) Pyruvic acid
molecules (also known as pyruvate)
- The process takes place in the
Cytoplasm of the cell and does not
require oxygen.
- End Products: 2 ATP and 2 NADH
- Steps
1. Two Phosphates are added to a
6-C sugar molecule and split
into two 3C sugars,
glyceraldehyde-3 -phosphate
(G3P)
2. Some hydrogen and energy are
removed from the G3P,
eventually producing 2
pyruvates.
3. Nicotinamide adenine
dinucleotide (NAD+), a
hydrogen acceptor which
becomes NADH, picks up
Hydrogen ions and electrons
are released.
2.) Krebs Cycle
- Also known as citric acid cycle
- Citric acid - formed in the cycle (2 turns
cycle)
 - Occurs in the inner matrix of Involved
Mitochondria Phosphoryla-
- Consists of the ff. process: tion &
ATP Photophos-
- Dehydration (removal of H2O) Oxidative
Production phorylation
- Hydration (addition of H2O) Phosphory-
- Decarboxylation (removal of lation
CO2) In Noncyclic
electron
- Dehydrogenation (removal of Immediate
transport: H2O
H2) source: NADH
Source of (undergoes
- One acid transformed to and FADH2.
Electron Photolysis to
another ACID Ultimate
for ETC yield
3.) Electron Transport Chain source:
electrons,
- Breakdown of glucose is complete Glucose
protons and
- 4 new ATP molecules are made Oxygen)
- Crestae of mitochondria takes place Type of
- Oxidative (FADH2 & NADH are oxidized) Metabolic Anabolism Catabolism
- Electrons that are removed from these Reaction
reduced H2 acceptors are transferred In Noncyclic
through a series of acceptors of lower electron
Terminal
energy levels (Coenzyme Q to transport: O2 (becomes
Electron
cytochromes b, c, a) NADP+ reduced to
acceptor
(becomes form H2O)
for ETC
Cytochromes reduced to
form NADPH)
- Are a class of Proteins that function as Part of Cell
electron transporter Chloroplast Mitochondria
Involved
- As electrons flow down the energy Type of
stairs, energy is released to Plants & One-
Organism
Celled All organisms
phosphorylate ADP to ATP. where it
Organisms
- Then O2 accepts H2 to form H2O or occurs
water. Breaking
Plants with the
down food
Photosynthesis Respiration use of light
molecules
Carbon energy and
Raw Glucose & Definition into
Dioxide & chlorophyll
Materials Oxygen of the chemical
Water produce
Process energy
Carbon Carbon
End Glucose & needed by
Dioxide & Dioxide
Products Oxygen cells to
Water and Water
function.
Electron NADP+ turns NAD turns to
Transfer to NADPH NADH+
Location of Mitochondrial Genetic Engineering
Electron Thylakoid inner
- involves the use of molecular
Transport Membrane membrane
techniques to modify the traits of a
Chain (cristae)
target organism. 
Organelle Chloroplast Mitochondria
- The modification of traits may involve:
  introduction of new traits into an
organism
 enhancement of a present trait by
increasing the expression of the
desired gene
 enhancement of a present trait by
disrupting the inhibition of the
desired genes’ expression.
- Genetic engineering aims to modify the
genes to enhance the capabilities of the
organism beyond what is normal.
Recombinant DNA
- is formed by joining nucleotide
sequences from two different sources
and often different species.
- One source contains the gene that will
be cloned.
- Another source is a gene carrier, called
a vector.
- Plasmids are small, circular DNA
molecules that replicate separately
from the much larger bacterial
chromosome; they are often used as
vectors.
The following are the steps in cloning a gene:
1. Plasmid DNA is isolated.
2. DNA containing the gene of interest is
isolated.
3. Plasmid DNA is treated with a
restriction enzyme that cuts in one
place, opening the circle.
4. DNA with the target gene is treated
with the same enzyme, and many
fragments are produced.
5. Plasmid and target DNA are mixed and
associate with each other.
6. Recombinant DNA molecules are
produced when the enzyme DNA ligase
joins plasmid and target segments
together.
7. The recombinant plasmid containing
the target gene is taken up by a
bacterial cell. 
8. The bacterial cell reproduces to form a
clone, a group of genetically identical
cells descended from a single ancestral
cell.
Recombinant DNA Technology Outline
i. cutting or cleavage of DNA by restriction
enzymes (REs)
ii. selection of an appropriate vector or
vehicle which would propagate the
recombinant DNA ( eg. circular plasmid
in bacteria with a foreign gene of
interest)
iii. ligation (join together) of the gene of
interest (eg. from animal) with the
vector ( cut bacterial plasmid)
iv. transfer of the recombinant plasmid
into a host cell (that would carry out
replication to make huge copies of the
recombined plasmid)
v. selection process to screen which cells
actually contain the gene of interest
vi. sequencing of the gene to find out the
primary structure of the protein
Process (Ways of introducing plasmids)
1. Biolistic
- In this technique, a “gene gun” is used
to fire DNA-coated pellets on plant
tissues.
- Cells that survive the bombardment,
and are able to take up the expression
plasmid coated pellets and acquire the
ability to express the designed protein.
2. Heat Shock Treatment. 
- is a process used to transfer plasmid
DNA into bacteria. 
- The target cells are pre-treated before
the procedure to increase the pore sizes
of their plasma membranes. 
 - This pretreatment (usually with CaCl2)
is said to make the cells “competent”
for accepting the plasmid DNA
- After the cells are made competent,
they are incubated with the desired
plasmid at about 4°C for about 30min.
The plasmids concentrate near the cells
during this time. Afterwards, a “Heat
Shock” is done on the plasmid-cell
solution by incubating it at 42°C for 1
minute then back to 4°C for 2 minutes.
- The rapid rise and drop of temperature
is believed to increase and decrease the
pore sizes in the membrane.  mummy, establish paternity or
- The plasmid DNA near the membrane
surface are taken into the cells by this
process.
-  The cells that took up the plasmids
acquire new traits and are said to be
“transformed”.
Genetically Modified Organisms (GMOs)
3. Electroporation. 
- This technique follows a similar
methodology as Heat Shock Treatment,
but the expansion of the membrane
pores is done through an electric
“shock”.  -
- This method is commonly used for
insertion of genes into mammalian
cells.
Polymerase chain reaction (PCR)
- is a method widely used in molecular
biology to make many copies of a
specific DNA segment.
- Using PCR, a single copy (or more) of a
DNA sequence is exponentially
amplified to generate thousands to
millions of more copies of that
particular DNA segment. PCR is now a
common and often indispensable
technique used in medical laboratory
and clinical laboratory research for a
broad variety of applications including
biomedical research and criminal
forensics.
- PCR was developed by Kary Mullis
- To do PCR, the original DNA that one
wishes to copy need not be pure or
abundant. It can be pure but it also can
be a minute part of a mixture of
materials.
- PCR has found widespread and
innumerable uses -- to diagnose genetic
diseases, do DNA fingerprinting, find
bacteria and viruses, study human
evolution, clone the DNA of an Egyptian
biological relationships, etc..
Accordingly, PCR has become an
essential tool for biologists, DNA
forensics labs, and many other
laboratories that study genetic material.
- With the ability to insert gene
sequences, comes the possibility of
providing new traits for these target
organisms. 
This has allowed the development of
GMOs.
- Some of these genetic modifications
promise higher product yield for their
targets. 
- These include the Flavr-Savr Tomato
and Bt-Corn