PHOTOSYNTHESIS
 Biological process
 Energy or Light Energy is absorbed from the
sunlight
o Any source of light can power photosynthesis, not
only sunlight
 Reactants of Photosynthesis (carbon dioxide, water,
and light)
o 6CO2 + 6H2O  C6H12O6 + 6O2
Leaf as a Photosynthetic System
 The leaf is highly specialized to accommodate
photosynthesis
 Its flat surface increases the surface area, thereby
maximizing the absorption of light energy
 Mesophyll: photosynthetic tissue
o Palisade – contains the chloroplast; highly
compacted
 Chlorenchyma – cells which contain
chloroplast
o Spongy
Chloroplast
 Found inside the leaf
 Double-membraned
o Thylakoid – enclosed in a membrane called
thylakoid membrane
o Granum (plural: grana) – stack of thylakoids
o Stroma – where all the thylakoids are
embedded
Light can either be a particle or wave
 Wave
o Light wave is an example of a transverse
wave
 The direction of movement is
perpendicular to the wave (up and
down)
o Highest point is known as the crest
o Lowest point is the trough
o Wave – distance between the two crests
o Frequency – number of times a particular
particle passes through a certain point
o Increasing the wavelength decreases the
frequency. Thus, wavelength and frequency
are inversely proportional (W/F)
o Whenever the wavelength decreases, the
energy increases
o Thus, frequency and energy are directly
proportional (F=E)
o Not all wavelengths or frequencies are
absorbed by plants
 Visible spectrum – the only
spectrum absorbed by plants
 Blue wavelength = lower
wavelength, thus higher
energy and frequency
 Red wavelength = higher
wavelength, thus lower
energy and frequency
 Particle
o Photons
 Capable of lighting
 Contain energy (in the form of
quantum)
Theodor Engelmann’s Experiment
 German scientist who provided the explanation why
only a limited spectrum is absorbed by plants
 Conducted the experiment in deep water vents
 Found out that aerobic bacteria aggregated in area
with higher oxygen concentrations
o These aerobic bacteria aggregated with algal
cells
o They also tend to aggregate in areas wherein
blue & red lights were absorbed
 The red and blue wavelengths of light efficiently drive
photosynthesis
 Absorption spectrum
o Efficiently absorbed by plant cells
 Action spectrum
o Directly correlated to the rate of
photosynthesis
 Absorption and action spectrums must coincide
 Plants do not absorb green light, it only appears green
due to the green pigment, chlorophyll
What happens when light energy is absorbed?
 The chlorophyll gets excited
o When it gets excited, there is a high amount
of electrons
 The excited chlorophyll can dispose of its surplus
energy in three ways:
o Fluorescence
 Whenever the chlorophyll absorbs
the blue wavelength of light (high
energy), it can emit its available
energy in the form of photons
 photons – capable of light
o Direct conversion into heat
 Whenever the chlorophyll absorbs
the red wavelength of light (low
energy), it will eventually lose heat
o Photochemical
  Light with energy in it will power
chemical processes in a chloroplast
 One of the fastest mechanisms
known in all biological systems
 It is more beneficial that’s why it
needs to be faster (for competition)
o Serves as the antenna complex
o Composed of several pigments; can be
photosynthetic (chlorophyll a and b) or
accessory pigments (carotenoids)
o Chlorophyll a and b is in the ratio of 1:1
 Reaction Center Complex

In general, photosynthesis is a process of redox reactions

 OIL – oxidation is losing electrons
 RIG – reduction is gaining electrons
o Whenever electron is donated, received, and
transported, it is accompanied by hydrogen

TWO PHASES OF PHOTOSYNTHESIS

o Reaction Center: chlorophyll a (P680)
1. Light-Dependent Stage o Primary Electron Acceptor
 Directly needs the input of light energy
 Takes place in thylakoid membrane
 Also called the thylakoid reaction PS I
 Uses light energy to produce the end products, which  Light harvesting complex
are ATP (adenosine triphosphate) and NADPH o Chlorophyll a & b is in the ratio of 4:1
(nicotinamide adenine dinucleotide phosphate)  Reaction Center Complex
o These two molecules are highly energized o Reaction Center: P700
o These will be needed to power the next stage o Primary Electron Acceptor
of photosynthesis (Calvin cycle)
o Conversion of light energy into chemical
energy
 Photochemical reaction

2. Light-Independent Stage
 Does not require light energy
 Occurs in the chloroplast stroma
 Also called stroma reaction or Photosynthetic carbon
reduction (PCR) Cycle or Calvin Cycle or C3 Cycle
 ATP and NADPH are used to produce
triosephosphate (end product of photosynthesis) in
the form of G3P or Glyceraldehyde-3-phosphate
 Three stages:
o Carbon fixation or the carboxylation phase
o Reduction Stage
o Regeneration Stage

LIGHT-DEPENDENT STAGE

Stages:
1. Light Harvesting stage – occurs in specialized
compartments embedded in thylakoid membranes
known as photosystems
2. Photolysis – occurs in specialized compartments
embedded in thylakoid membranes known as I. Light Harvesting Stage
photosystems o Light will be absorbed by the accessory and
3. Electron Transport Chain  NADPH the photosynthetic pigments
4. Photophosphorylation  ATP o Absorbed by PS 2
o Accessory pigments will funnel the electrons
Photosystems: down the reaction center
 If it weren’t funneled, it will lead to
PS II spontaneous combustion since the
 One which will be used first energy of sunlight is very high
 Light harvesting complex o The reaction center (chlorophyll a P680) is the
final destination of PS 2
  where light is transferred
II. Photolysis
o Whenever electron reaches the reaction
center, it will trigger photolysis
o Uses light to breakdown or split water
o 4 electrons, 4 molecules of hydrogen, and
one molecule of O2
III. Electron Transport
o Noncyclic ETC
 Whenever water is lysed or broken
down into its component molecules,
it will produce 4 molecules of
electrons
 These electrons will be transported
to different protein complexes
embedded in the thylakoid
membrane
 P680 (PS 2)  plastoquinone 
cytochrome b6f  plastocyanin 
P700 (PS 1)  Ferredoxin 
Ferrodoxin-NADPH reductase
 Whenever the electron will arise in
ferrodoxin-NADPH reductase, it will
power the reduction of NADP+ to
NADPH
 Thus, NADPH is produced
 Prevalent in higher vascular plants
o Cyclic ETC
 Absence of PS 2 and Ferrodoxin-
NADPH reductase (Thus no
NADPH is produced)
 PS 1  ferrodoxin 
plastoquinone  cytochrome b6f
 plastocyanin  PS 1
 The only product is ATP (no
NADPH since there’s no FNR
enzyme)
 Prevalent in lower vascular plants
IV. Photophosporylation
o Photo – light energy; phosphorylation –
conversion of ADP to ATP
o Whenever the electron gets to be transported
in the plastoquinone and cytochrome b6f,
there will be a pumping off of hydrogen
proteins from the stroma of chloroplast to
the thylakoid lumen
o When hydrogen proteins are pumped off,
there will be a buildup of electrochemical
potential and chemiosmotic potential
o This buildup will trigger one enzyme called
ATP synthase
o Hydrogen proteins will be transported back
to the stroma by the ATP synthase
o The pumping of ATP synthase will trigger
the phosphorylation of ADP to ATP
o The end product is ATP
LIGHT INDEPENDENT STAGE
 Also called as the Calvin cycle or Calvin-Benson cycle
Stages:
1. Carbon fixation – also called carboxylation stage;
CO2 will be utilized
2. Reduction phase
3. Regeneration stage
I. Carbon fixation
o Three CO2 and three RuBP will react in this
stage
 RuBP (ribulose-1,5-bisphosphate; 5-
carbon molecule composed of 2 phosphate)
 The enzyme involved in this stage is
RUBISCO (ribulose- 1,5-bisphosphate
carboxylase oxygenase)
o One CO2 will react to each of the three 5-
carbon molecules, RuBP, forming three
RuBP with 6 carbon molecules
o These three 6-carbon molecules are highly
unstable, therefore the plant needs to break
this molecule
o The 6-carbon molecule will be cleaved into
two components (each are comprised with
three carbon molecules)
o The resulting molecule is now called 3-
phosphoglycerate
II. Reduction phase
o The 3-phosphoglycerate will be
phosphorylated, therefore adding one
phosphate group to the product
o This leads to the production of 1,3-
Bisphosphogylcerate (3-carbon molecule and
2 phosphate group)
o The 1, 3-Bisphosphogylcerate are reduced
into G3P molecules (which means that one
molecule will be oxidized)
 The molecule which was oxidized is
NADPH
 NADPH is oxidized to NADP+
o Six G3Ps are produced
o One of these G3Ps will be used by the plant
to produce glucose and other carbohydrates
III. Regeneration
o The remaining five of G3Ps will be
regenerated to form three RuBP molecules
PHOTORESPIRATION
 Occurs when the CO2 level inside the leaf becomes
low
o During hot days, the stomata are closed to
prevent desiccation and transpiration
o Thus, CO2 molecules cannot enter the plant
o The plant continues to fix CO2 when its
stomata are closed, the CO2 will then get
 used up and the O2 ratio in the leaf will
increase
 Photorespiration is defined as an aberrant use of
oxygen by chloroplast
o Since the O2 levels are higher inside, then it
will be used by the plant, instead of CO2
 It is the interference with carboxylation caused by
the deviant interaction of RUBISCO with oxygen
o Under normal conditions, RUBISCO will
attach CO2 to the ATP
o However, when the oxygen is higher, plants
will favor oxygen to be attached by the RuBP
 Factors affecting photorespiration: temperature,
stomatal resistance/conductance, stability of the
boundary air layer
 Negative Effects: Waste of ATP, waste of CO2
 Positive Effects: Photoprotection, possibility of
recovery of CO2
 RUBISCO reacts with O2 as well as CO2
o RUBISCO is both an oxygenase and
carboxylase
 Carboxylase = RuBP + CO2
 Oxygenase = RuBP + O2
 Thus, it will depend on the amount of CO2 and O2
 When O2 is used, it will lead to the production of two
molecules
o 3-phosphoglycerate or 3 PGA
o 2-phosphoglycolate
o The 2-phosphoglycolate is highly toxic, thus
the plant must have a mechanism in which it
will be converted into another form which is
nontoxic
 Key organelles: chloroplast,
peroxisome, and mitochondrion
o It will first be converted into glycolic acid or
glycolate en route from the chloroplast to the
peroxisome
o Phosphoglycolate  Glycolate 
Glyoxylate  Glycine  Serine 
Hydroxypyruvate  Glycerate  3-PGA
 Inside the mitochondrion, glycine
will be converted to serine
 Serine will be converted to 3-PGA
which will now enter the Calvin
cycle or C3 cycle
 3 PGA will be beneficial to the
production of glucose
 From a toxic substance, it became
beneficial to plants
Responses to Low CO2 Concentration (CO2 concentrating
mechanism):
Strategies for preventing photorespiration:
PLAN
1. Avoid RUBISCO; since under hot temperatures, it
favors the binding of O2 instead of CO2
2. Use an enzyme that does not react with O2 (it must
be highly reactive with CO2)
3. It has to fix CO2 in an environment shielded from
O2 (majority of the enzymes are highly reactive to
oxygen)
SOLUTION
1. CO2 fixing enzyme is PEP Carboxylase
o PEP Carboxylase will not react with O2
2. CO2 fixation occurs in mesophyll cells
OTHER TWO CARBOXYLATING MECHANISMS
 C4 pathway
o There will be a production of 4-carbon
molecule
o In general, C4 plants are monocots
 They are characterized by the
presence of pronounced bundle
sheath
o Phosphoenolpyruvate or PEP is the initial
reactant
o CO2 will be fixed or attached to the PEP (a
3-carbon molecule which has a higher
affinity)
o Hence, a 4-carbon molecule known as
oxaloacetate is produced
o Oxaloacetate will be converted into malate,
and malate will be transported into the
bundle sheath cell
o Malate will be decarboxylated, forming a 3-
carbon molecule pyruvate
o The carbon dioxide produced will now enter
the Calvin cycle wherein it will be fixed to
RuBP by RUBISCO enzyme
o In the bundle sheath cell, there is a low
amount of O2, thus CO2 from the
environment is produced in the mesophyll
cells
o Kranz Anatomy
 CAM pathway (Crassulacean Acid Metabolism)
o Temporal distribution of events
o Only happens in mesophyll
o 3 carbon molecules are produced (3
phosphoglycerate)
o uses the enzyme RUBISCO
o CO2  Phosphoenolpyruvate
Oxaloacetate  Malate
o PEP to malate happens at night (the stomata
are open)
o The plant will store malate, this malate will
be converted to CO2 and pyruvate in
daylight
o It will now proceed to G3P
o Pyruvate will be converted to PEP
 C3 C4 CAM  There’s always a participation of
Product G3P Malate Malate
Day & night Day & night night only
enzyme (e.g. PEP kinase)
Anatomy No bundle sheath Bundle sheath cell No bundle sheath II. Oxidative phosphorylation
No. of stomata 2000-31000 10000-160000 100-800 o Makes use of oxygen
Photorespiration Up to 40% Not detectable Not detectable o There will be a series of transport of
Species Wheat, rice, potato Sugar cane Pineapple, vanilla, cacti electrons, and the final electron acceptor is
the oxygen
Implications of having CO2 concentrating mechanisms: o Involved in redox reaction
 Allows the leaf to maintain high photosynthetic rates o Whenever the oxygen accepts electron,
at lower CO2 bioavailability ADP will be phosphorylated to form ATP
 This results to higher water use efficiency III. Photophosphorylation
o By the closing of stomata, water loss can be o There’s an input of light energy to power
prevented ATP to ADP
 Additional energy cost of the concentrating o Noncyclic and cyclic
mechanism (downside)
AEROBIC RESPIRATION

CELLULAR RESPIRATION Divided into four stages:

 The primary biological key player involved in cellular  Glycolysis – occurs in the cytosol
respiration is mitochondria  Krebs Cycle – matrix or cytosol
o Outer membrane, inner membrane,  ETC – occurs in the cristae of mitochondria
intermembrane, cristae
 The intermembrane region is I. Glycolysis
important in the third stage of  Also called Embden-Meyerhof pathway
cellular respiration (ETC)
 Takes place within the cytoplasm of most cells
 Organisms oxidize carbohydrates as their primary
 Involves the splitting of a six-carbon glucose into
energy source for catabolic reactions
two three-carbon pyruvate molecules
o Glucose – utilized carbohydrate by almost all
organisms  Substrate-level phosphorylation – direct transfer of
o Glucose is catabolized via two processes phosphate between two substrates
 Cellular respiration  Net gain of two ATP molecules, two molecules of
 Aerobic – typically NADH, and precursor metabolite pyruvate
exhibited by plants  Inefficient since it generates only a
(eukaryotes) net of 2 ATP for every 1 glucose
 Anaerobic – does not  Divided into three stages:
require oxygen; typically  Energy-investment
exhibited by bacteria  Lysis
(prokaryotes)  Energy-conserving
 Fermentation
1. Energy-investment stage
Cellular respiration  makes use of oxygen and gets rid o Glucose is phosphorylated by ATP to form
of carbon dioxide  Production of ATP glucose 6-phosphate
o The atoms of glucose 6-phosphate are
 The ultimate goal of cellular respiration is to produce
rearranged to form fructose 6-phosphate
energy in the form of ATP
o Fructose 6-phosphate is phosphorylated by
 All cells need energy to power cellular processes ATP to form fructose-1,6-bisphosphate
o Without cellular processes, cessation of cells o The gross ATP produced is 4
will happen
2. Lysis stage
PHOSPHORYLATION o Fructose 1,6-bisphosphate will be cleaved
 Addition of an organic phosphate to a substrate into glyceraldehyde-3-phosphate (G3P) and
 Usually, the substrate is in the form of ADP dihydroxyacetone phosphate (DHAP)
 Cells phosphorylate ADP to ATP in three ways: o DHAP is rearranged to form another G3P
 Substrate-level phosphorylation
 Oxidative phosphorylation 3. Energy-conserving stage
 Photophosphorylation (cyclic and noncyclic) o Inorganic phosphates are added to the two
G3P, forming 1,3-bisphosphoglyceric acid
I. Substrate-level phosphorylation  Two NAD+ are reduced to form
o There will be a transfer of a phosphate group two NADH
from a substrate to ADP
 o 1,3-bisphosphoglyceric acid was
diphosphorylated into 3-phosphoglyceric
acid
 Two ADP are phosphorylated by
substrate-level phosphorylation to
form two ATP
o 3-phosphoglyceric acid will be converted into
PEP
 The remaining phosphates are
moved to the middle carbons. A
water molecule is removed from
each substrate
o The PEP will be dephosphorylated to form
two pyruvic acid
 Two ADP are phosphorylated by
SLP to form two ATP
 The pyruvate is not yet ready to proceed to Krebs
cycle, thus there will be a transition stage
 4 molecules of ATP, 2 molecules of NADH, and 2
water molecules are produced
Transition Stage: formation of acetyl-coenzyme A
 pyruvate will be decarboxylated to from acetate
 acetate will bind to coenzyme A, forming acetyl-coA
 the carbon removed from pyruvate will be produced
as CO2, and the electrons and protons of the
hydrogen released combine with NAD+ to from
NADH
o 2 molecules of NADH and CO2 are formed
II. Krebs Cycle
o TCA (Tricarboxylic acid cycle) or the citric
acid cycle
o Occurs in cytosol of prokaryotes and in the
matrix of the mitochondria of eukaryotes
o Great amount of energy remains in the
bonds of Acetyl-coA
o Transfers much of this energy to coenzymes
NAD+ and FAD
 NAD+ will be reduced to NADH
 FAD will be reduced to FADH2
o The end product of Krebs cycle is NADH,
FADH2, and ATP
o Five Types of Reactions
 Anabolism of citric acid: 1
 Isomerization reactions: 2,7,8
 Rearrangement of the
structure of atoms
 Redox reactions: 3,4,6,8
 OILRIG
 Decarboxylation: 3,4
 Substrate-level phosphorylation: 5
1. Formation of citrate, a 6-carbon molecule
o Acetate will bind to a 4-carbon molecule
oxaloacetate, forming a 6-carbon molecule
known as citrate
 Acetate is a two-carbon molecule
which bears large amount of energy
2. Citrate will be isomerized to isocitrate
o Isocitric acid will be oxidized to alpha-
ketoglutarate
 There is a subsequent reaction of
NAD+ to NADH
o Along the way decarboxylation
3. Redox
4. Alpha-ketoglutarate will be oxidized into succinyl-coA
o Reduction process (NAD+ to NADH)
o Decarboxylation
5. Succinyl-coA will be converted to succinate
o Substrate level phosphorylation
o Where ATP is produced
6. Succinyl-coA will donate a phosphate group
(substrate)
7. Succinate will be oxidized to fumarate (Redox)
o The molecule that is reduced is FAD+, &
will be converted to FADH2 (Flavin
Adenine Dinucleotide)
8. Fumarate will be converted to malate
9. Malate is oxidized to oxaloacetate acid (Reduction)
o Reduction of NAD+ to NADH
Glycolysis and Krebs Cycle strip off electrons from
glucose and transfer them to NADH and FADH2
In turn, these NADH and FADH2 pass these
electrons to the Electron Transport Chain
III. Electron Transport Chain
o Series of carrier molecules that pass
electrons from one to another to a final
electron acceptor
 ETC occurs in the membranes
 Carrier molecules = proteins
 In aerobic respiration, the final
electron acceptor is oxygen
 Whenever oxygen accepts
electron, it will form water
o Occurs in the cristae (inner
mitochondrial membrane) of eukaryotes
and in the cytoplasmic membrane of
prokaryotes
o Energy from electrons is used to pump
protons (H+) across the membrane,
establishing a proton gradient
o Most significant production of ATP
occurs from a series of redox reactions
o Basic functions:
 Facilitating the transfer of
electrons from the primary
donor to the terminal acceptor
 PD: NADH and
FADH2
o Participating in membrane events whose end
result is energy conservation
 Pertains to the production of
ATP
Categories of carrier molecules
o Flavoproteins – integral protein; bears with it
a particular molecule called Flavin (e.g. FMN
or Flavin mononucleotide)
 This FMN is the first carrier
molecule
o Ubiquinones – lipid-soluble proteins;
embedded in the hydrophobic part of the
membrane (non-polar tails)
o Metal-containing proteins – metals include
iron, sulfur, and copper
o Cyctochromes – composed of hemes
 Transfer of electrons
o High to low
o Liberation of energy
o The loss of energy from transferring
electrons will be used to synthesize ATP
MECHANISM
 Electrons coming from NADH will be passed to
FMN
 After which, electrons from FMN will be passed to
ubiquinone (coenzymeQ)
 Ubiquinone  cytochrome b6f
 After the passing of electrons, it will be passed to the
final electron acceptor which is oxygen
 After it is passed down, it will grab hydrogen protons,
eventually forming water
 Essentially, FADH2 follows the same path but
FADH2 will start with ubiquinone or coenzymeQ
o Thus, FADH2 will produce high amount of
ATP
 There is a subsequent pumping of protons from
mitochondrial matrix to intermembrane space
whenever electrons are transfer to FMN and
cytochrome
 Eventually, there will be a buildup of proton in the
intermembrane space
 Electro-chemical gradient (buildup)– has potential
energy known as proton motive force
o This proton motive force will be used to
synthesize ATP through ATP synthase
o Two components of ATP synthase
 CF1 – responsible for the
phosphorylation of ADP to ATP
 CF0 – responsible for the transfer
or pumping of protons to the
intermembrane space; will act as a
passageway
Summary
 1 NADH = 3 ATP
 1 FADH2 = 2 ATP
 10 NADH = 30 ATP
 2 FADH = 4 ATP
 Total: 34 ATP
 However, two of the NADH molecules were
produced in glycolysis
 Transporting them into ETC will require two
molecules of ATP
 Net produced = 32 ATP
ANAEROBIC RESPIRATION
 Involves electron transport, generation of a protein
motive force, and the activity of ATPase
 Since they do not utilize oxygen as the final electron
acceptor, some electron acceptors used are:
o Nitrate
o Sulfate
o Ferric Iron
o Carbonate (organic molecule; utilized by
methanogens and will be reduced to
methane)
 Fermentation
o Sometimes, cells cannot completely oxidize
glucose by cellular respiration
 Since there is no final electron
acceptor
o Cells require constant source of NAD+
 ATP production requires the
presence of NAD+
o NAD+ cannot be obtained simply using
glycolysis and Krebs cycle
o Fermentation pathways provide cells with
alternate source of NAD+
 NAD+ is only produced in ETC
o Partial oxidation of sugar (or other
metabolites) to release energy using an
organic molecule from within the cell as final
electron acceptor
Lactic Acid Fermentation
 Occurs when a person exercise until the oxygen
concentration is depleted
 Glucose will be oxidized into 2 pyruvate molecules
o There is a production of 2 net ATPs and 2
NAD+ molecules are reduced to NADH
 The pyruvate molecules are reduced to 2 lactic acid
(lactate)
o There will be an oxidation of NADH to 2
NAD+
Alcohol Fermentation in yeast
 One molecule of glucose produces 2 molecules of
pyruvate
 2 net ATP are produced and 2 NADH
 the pyruvate molecules are reduced to 2
acetylaldehyde
o Will be passed down to 2 ethanol
o There’s a regeneration of NAD+ to 2
NADH molecules
o Ethanol and lactate = waste molecules
o They will be used in producing food (cheese,
yogurt)
 SUMMARY  period of cell growth, when the cell synthesizes new
Aerobic Anaerobic Fermentation molecules and organelles
Oxygen Yes No No
Requirement
 uncondensed form
Type of Substrate Substrate- Substrate-level
Phosphorylation level level G1 Phase
Oxidative Oxidative o first gap phase or resting phase
Level level o Time between the end of the previous cell division
Final electron Oxygen Nitrate, Organic (interphase) and the beginning of DNA replication (S
acceptor sulfate, etc. molecules phase)
Molecules of ATP 38 2-36 2
produced S Phase
o DNA replication

G2 Phase
CELL CYCLE o Second phase or resting phase
 The cyclic series of events in the life of a dividing o Shorter relative to G1 and S phase
eukaryotic cell
 Initial cell  daughter cells II. Mitotic Phase

Meiosis VS Mitosis Mitosis

 Meiosis – sex cells (diploid  haploid)
 Mitosis – body cells or somatic cells (diploid  Prophase
diploid) o changes occur in both the nucleus and the cytoplasm
within the nucleus
The Chromosome o the chromatin fibers become more tightly coiled and
 Threadlike structures in a cell’s nucleus that are visible folded, forming discrete chromosomes
under the microscope during cell division
 Each chromosome consists of proteins and a single Prometaphase
large molecule of DNA that contains hundreds or o the nuclear envelope has disintegrated
thousands of different genes o the spindle fibers are specifically attached to a certain
chromosome
 Can be unduplicated or duplicated chromosomes
Metaphase
o Duplicated – sister chromatids
o chromosomes are lined up along the midplane of the
 Homologous chromosome – members of a cell initiated by the spindle fibers
chromosome pair that are similar in size, shape, and o mitotic spindle is fully formed, with its poles at
genetic constitution opposite ends of the cell
Anaphase
Parts of the chromosome o sister chromatids separate
 Telomere o one group of chromosomes moves toward each pole
 Centromere of the cell; the movement is powered by ATP
 Kinetochore o pushing and pulling creates invagination
o attachment site of the spindle microtubules; Telophase
the tighter the microtubules pull, the tighter o cell elongation that started in anaphase continues
the kinetochore holds on o daughter nuclei appear at the two poles of the cell as
nuclear envelopes form around the chromosomes
Chromosome Number
 Ploidy – refers to the number of sets/copy of Cytokinesis
chromosome in a cell  Animal Cell
o Haploid and diploid o Formation of cleavage furrow
o Contracting ring of microfilaments
Human Chromosomes
 The last pair of chromosomes will determine the sex  Plant cell
o Karyotype o Formation of cell plate

Cell Cycle Checkpoints in the Cell Cycle

 90% interphase phase (G1, S, G2)  G1 checkpoint: check for nutrients, growth
 10% mitotic phase (Mitosis & cytokinesis) factors, and DNA damage
 Metaphase checkpoint: check for chromosome
I. Interphase spindle attachment
  G2 checkpoint: check for cell size and DNA chromosomes were duplicated prior to Meiosis I, thus
replication each chromosome consists of two chromatids
o In Meiosis II, the sister chromatids separate and
Types of Chromatin distributed into two different nuclei, thereby forming
o Heterochromatin – inactive sites four haploid cells
o Euchromatin – active site
Chromosomal Aberrations
Meiosis  Variation in chromosome number
o One single cell  4 haploid cells o Aneuploidy: change in the number of one or
o No interphase (DNA will only be replicated once: S a few chromosomes but not a complete set
Phase in Mitosis) (e.g. 2n+1)
o Euploidy: change in the number of complete
Steps of the Meiotic Phase sets of chromosomes (e.g. 3n, 4n)
o Reduction Division  Structural Aberrations
o Equational Division o Deletions:
o Duplications
Homologous Chromosome or tetrad o Inversions: happen in synapsis
o Homologous chromosomes will form tetrad through o Translocations
synaptonemal complex; same location of centromere o Fragile sites
o Homologous: same genes at the same loci but
different alleles
Aneuploidy may arise through:
 Loss of the centromere leading to acentric
Meiosis I chromosomes
 Nondisjunction
Prophase I  Loss of the small chromosome generated thru a
o Crossing over occurs; there is an exchange of genetic Robertsonian translocation
materials Types:
o Chiasma: site of crossing over  Nullisomy: loss of both members of a homolgous
o Thus, increasing variation (variation  uniqueness) chromosomes; 2n+2
Metaphase 1  Monosomy: loss of a single chromosome: 2n-1, e.g.
o Instead of a duplicated chromosome, homologous XO
chromosomes are aligned  Trisomy: addition / gain of a single chromosome;
o Metaphase plate 2n+1 e.g. XXY, XXX, XYY
Anaphase 1
 Tetrasomy: gain or addition of two homologous
o Pushing and pulling spindle fibers, thus creating
chromosomes; 2n+2; e.g. XXXX, XXXY
spindle fibers
o Sister chromatids remain attached
o Autosomal Trisomy: Down Syndrome: Trisomy 21
Telophase 1 and cytokinesis
(47, XX + 21 or 41, XY + 21)
o The genetic material in most eukaryotic cells does not
o Edward Syndrome: Trisomy 18
uncoil
o Patau syndrome: Trisomy 13
o Trisomy 8
Meiosis II
o Polyploidy: common in plants
o Autopolyploidy: all chromosome sets are from a
Prophase II
single species
o no pairing of homologous chromosomes, and no
o Allopolyploidy: chromosome sets are from two
crossing over occurs
different species
o new spindle microtubules form, and the nuclear
envelope breaks down
Significance of polyploidy
Metaphase II
o increase in chromosome number causes increase in
o two sister chromatids line up on the midplane
cell size
Anaphase II
o sister chromatids separate and will move to opposite
Mitosis vs Meiosis
poles
Telophase II and cytokinesis
o four haploid daughter cells are formed

Meiosis I vs Meiosis II
o In Meiosis I, chromosomes will first join together,
then separate and move into different nuclei. These
CENTRAL DOGMA
GENE
 Gene is the sequence of nucleotides within a portion
Phenotype vs Genotype:
of DNA that codes for a peptide or a functional RNA
Phenotype
o Sum of all genes: genome
o anatomical, morphological, behavioral, sexual,
physiological traits
Flow of Information
Genotype
o Codes for phenotype  Replication: DNA  DNA
 Transcription: DNA  RNA
James Watson and Francis Crick  Translation: RNA  Protein
o DNA is a double helix
o The double helix is antiparallel DNA REPLICATION
 Semiconservative replication
DNA o Old strand, and new strand
 Nucleotide  phosphate + nucleoside o New strand is ½ parent template and ½ new
Nitrogenous bases DNA
 Pyrimidines – 6 rings (cytosine, thymine, uracil)  Through complementary base pairing
 Purines – 9 rings (adenine, guanine)  Multiple origin of replication
 Adenine  thymine o Replication bubble: where DNA starts to
 Guanine  cytosine replicate and where DNA bases are added
 Uracil (adenine  uracil) if DNA-RNA hybrid  DNA Replication occurs in S phase
Sugar Component
Interaction of enzymes
 D-ribose: RNA
 DNA Helicase – with the use of energy, it will open
 2’-deoxyribose: DNA (water molecule cannot enter
the DNA molecule; serves as molecular scissors
since there is no OH)
Phosphate  DNA Gyrase – reduces the coiling of DNA; will cut
DNA to reduce coiling then attach it again
 phosphodiester linkage: negative charge protects
phosphorus from attack by H20  Single stranded binding proteins (SSBP)– will
DNA Backbone attach to the DNA to stabilize the single strand DNA
o to avoid the binding of DNA when it was
 Backbone: sugar and phosphate linked by
cut by the DNA gyrase
phosphodiester bonds
 DNA Polymerase III – adds nucleotide; most
 Leading strand: 5’3
important because it builds the pairing of DNA;
 Lagging strand: 3’5 however, it can only put on a strand with 3’ OH end;
 Polar: backbone there must be an RNA Primer
 Nonpolar: nitrogenous bases  RNA primer – (RNA primase- enzyme used); it starts
the process of DNA polymerase III; Leading strand
RNA o Leading strand – continuous elongation (3’
o Distributable throughout the cell, most commonly in to 5’)
the ribosomes o Lagging strand – Okazaki fragments
o ribosomal RNA (80-90) -major component of  DNA Ligase – will join the Okazaki fragments; acts
ribosomes, together with proteins as the molecular glue
 messenger RNA -carries genetic information to sites  DNA Polymerase I – will remove the primer and
for protein synthesis change it into nucleotide; also proofreads and repairs
 transfer RNA - transports specific amino acids in mismatched bases
protein synthesis; translates nucleic acid language into  Telomerase – can add DNA bases at 5’ end
protein language
 Both mRNA and tRNA have transient existence, DNA TRANSCRIPTION
smaller than rRNA  Mechanism by which the template strand of DNA is
utilized by specific RNA polymerases to make one of
DNA vs RNA the three different types of RNA
Primary structure: o Template strand is used to make mRNA (3’
o the sugar component of RNA is ribose while to 5’)
DNA has deoxyribose o Does not need a primer to start
o Pyrimidine base U replaces the T of DNA o Divided into three stages: initiation,
Secondary structure: elongation, termination
o DNA is a double helix Initiation
o Most RNA molecules are single-stranded
 RNA polymerase unwinds the DNA double helix
  Transcription starts when RNA polymerase binds to a o Start codon – AUG (methionine)
specific DNA which it recognizes as a start signal o Stop codons – UGA, UAA, UAG
Elongation
 Additional nucleotides are added to the RNA  Universal
molecules o The same sequences of 3 bases encode the
 DNA double helix re-forms following transcription same amino acids in all life forms
Termination  Polarity
 RNA polymerase recognizes a stop signal  Commaless
 RNA molecule and RNA polymerase then separate o There is no signal to indicate the end of one
completely from the DNA strand codon and the beginning of the next
 Chain Initiation Codons
Post transcriptional processing (mRNA processing)  Chain Termination Codons
 RNA Capping – removes the interfering introns
 Polyadenylation 4 Levels of protein structure
 Splicing – highly precise removal of intron sequences;  Primary – sequence of amino acids
performed by spliceosomes  Secondary – interactions between adjacent amino
o Introns – junk DNAs acids
o Exons – the real gene; expressed DNA  Tertiary – 3D folding of the polypeptide
 Quaternary – arrangement of multiple polypeptides
Difference of transcriptional control in prokaryotes and eukaryotes:
Wobble Base Pairing
Prokaryotes  Wobble hypothesis
 Genes are usually switched ‘on’ by default  The two first bases are important
 Repressor proteins needed to ‘stop’ transcription o They are specific, whereas the third letter has
a relaxed state
Eukaryotes
 Genes are usually switched ‘off’ by default Sickle-cell phenotype
 Transcriptional activators are needed to induce  GAG  GTG
transcription
 Regulated by chromatin structure

DNA TRANSLATION
 Occurs in the cytosol and ER
 Initiation and elongation – RNA will attach to the
small subunit, will recognize the start codon (AUG)
and will attach to the large subunit
o A site – amino acyl site; will receive new
tRNA
o P site – peptidyl site; where peptide bonds
are formed
o E site – where RNA exits
 The process will stop when there’s an interaction
between the stop codon (UGA, UAA, UAG)

The Genetic Code

 A triplet code called codon could make a genetic code
for 64 different combinations
 Non-overlapping
o The same letter is not used for two different
codons
 Unambiguous
o 1 codon: 1 amino acid
o e.g. ACG – threonine
 Degenerate
o The same amino acid is coded by more than
one base triplet
o One amino acid is coded by several codons
o 64 codons: 20 amino acids
o e.g. UCU, UCC, UCA, UCG – serine