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AP Biology

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James Cunningham

on 15 June 2015

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Transcript of AP Biology

Epistasis: the phenotypic expression of one gene affects that of another






Polygenic Inheritance: A single phenotypic character is affected by two or genes
AP Biology
By James Cunningham
The Main Molecules of Life:
Membranes:
Metabolism
Respiration
Photosynthesis
Mitosis
Meiosis
Cells
Prokaryotic Cells
(NO NUCLEUS)
Eukaryotic
(NUCLEUS)
1.DNA in a nucleus surrounded by nuclear envelope
2.other membrane-bound organelles: mitochondria, ER, golgi apparatus, lysosomes, vacuoles, vesicles, cilia, and flagella
3.cytoplasm in region between plasma membrane and nucleus

1.No membrane-bound organelles
2.DNA in nucleoid (unbound region)
3.cytoplasm enclosed by plasma membrane; liquid portion is called cytosol
4.cell wall

BOTH:
1. Plasma Membrane
2. Cytoplasm
3. DNA
4. Ribosomes

Plant Cell:
Animal Cell:
1. Chloroplast- site of photosynthesis; contains...
A. thylakoids-stacked membranous discs containing chrophyll which takes in light
B. stroma- the internal fluid; comparable to cytoplasm
2. Cell Wall- protects cell and maintains its shape
3. Large Central Vacuole-holds organic material and water to be later recylced by the plant
4. Amyloplast- contains concentric layers of starch (amylopectin)

1. Centrioles- non membrane bound organelles; moves to poles of the cell and after mitosis forms mitotic spindles
BOTH:
1.
nucleus-
contains most DNA in cell
2.
nucleolus-
site of ribosmal DNA synthesis
3.
nuclear envelope-
surrounds nucleus and
4.
histones-
DNA molecule associated with proteins
5.
nucleosome-
region where DNA wraps around histones
6.
chromatin-
loosely coiled DNA and histones
7.
chromosomes-
made when chromatin is condensed and tightly coiled when a cell unergoes cell division
8.
ribosomes-
particles made of ribosomal RNA and proteins; site of protein synthesis
9.
plasma membrane-
a bilayer of phospholipids with proteins; selective barrier that allows sufficient passage IN OR OUT of oxygen, nutrients, and waste
10.
(ER)Endoplasmic Reticulum
- 'biosynthetic factory'
A.
Smooth ER
- detoxifies drugs and poisons in the cell, sythesizes lipids, metabolyzes carbs and stores calcium ions
B.
Rough ER
- (defined by containing ribosomes) protein synthesis of secretory proteins and glycoproteins
11.
glycoproteins-
combination of proteins and carb. chains
12.
transport vesicles-
sac that stores things inside and transports them elsewhere (ex: glycoproteins)
13.
secretory proteins-
any proteins secreted by the cell
14.
golgi apparatus-
contains cisternae which modifies products of ER, manufactures polysaccharides, as well as sorts various materials
15.
lysosomes-
(produced by golgi apparatus) memranous sca that contains hydrolytic enzymes that can digest inracellular macromolecules in vacuoles and can hydrolize proteins, fats, and nucleic acids
16.
vacuoles-
derived from the fusion of vesicles and are really only larger froms of them
17.
mitochondria-
have smooth outer and inner folded membranes called cristae which create larger surface are for enzymes that synthesize ATP; contain own DNA and free ribosomes
Chloroplast

Mitochondria
* Both contain own sets of DNA
* Both enveloped by double membrane
* Both believed to have once been free-living prokaryotes
-The Endosymbiont Theory: an early ancestor of eukaryotic cells engulfed an oxygen-using, non-photosythetic prokaryotic cell forming an endosybiant relationship and have merged into one organism which in later generations engulfed a photosythetic prokaryote, making the first ancestor of photosythetic eukaryotes

Some More Important Definitions:
1. exocytosis- process in which the plasma membrane discharges a transport vesicle's content (as secretions) and exits the cell
2. autophagy- process in which lysosomes degrade the cell's damaged organelles and protein
4. cyclosis-movement of the cytoplasm
5. fagocytosis-movement of the plasma membrane and the cytoplasm


Extra-Cellular Components:
*Cell Wall
*Extra-Cellular Matrix (ECM)- covers animal cells; bind to receptor proteins in plasma membranes called integrins
*integrins- are the bridges for cell to cell communication and ECM interactions (ex: influence gene activity or coordianting behavior of all cells within a certain tissue)
*Intercellular Junctions-form of communication in neighboring cells
-plasmodemata: allows water, salts, proteins, RNA to pass from cell-cell
-tight junctions: membranes of neighboring cells fused together, prevents fluid leakage
-desmosomes: fastens cells into strong tissues
-gap junctions: provides channels for small molecules

{
{
found only in animal cells
found only in plant cells
All living things are made up of 4 classes of moleules:
-lipids
-carbohydrates(carbs)
-proteins
-nucleic acids
{
polymers
*Macro-Molecules: large polymers built from monomers
*Polymer: a large molecule consisting of a chain of monomers; cannot diffuse through the cell
*Monomer: the 'building block' of molecules that can diffuse through a cell
Hydrolysis: the reaction that breaks a bond between two monomers by the addition of a water molecule
Synthesis makes it




Hydrolysis breaks it
hydrophilic:
moves toward
water










hydrophobic:
moves away from water
Dehydration Synthesis Reaction: process in which to synthesize polymers bonds two monomers together through the loss of a water molecule
*Monosaccharide- a sugar monomer
*Disaccharide- made up of 2 monosaccharides through dehydration synthesis
*Polysaccharide- made up of many sugar monomers monosaccharides that serve as energy storage and have structural roles

*glucose (C H O )- most common monosaccharide used by animals
A monosaccharide is classified by
-the # of carbons (determines length)
-location of the carboxyl group
-spatial arrangement
Most common dissachrides:
*sucrose (glucose+fructose)
*maltose (glucose+glucose)
*lactose (glucose+galactose)

6 12 6
Monosaccharides have molecular formulas in the ratio of 1:2:1
*starch: the energy storage polysaccharide of plants; a surplus of this results in their storage in granules within chloroplasts and other plastids
*amylose: the simplest form of starch
*cellulose: a major component of the cell wall of plant cells (cannot by most animals because few possess enzymes to break it down, thus aiding in digestion by passing through the digestive tract


ATP (Adenosine Triphosphate): a nucleotide that contains a large amount of chemical energy stored in its high-energy phosphate bonds. It releases energy when it is broken down.

*covalent bonds: when pairs of electrons are shared by atoms
*glycosidic linkage: the covalent bond linking disaccharides

*microfibrils: parallel cellulose molecules held together (this forms tough cell walls)
*chitin: a structural polysaccahride that is found in the exoskeleton of arthropods and is used to make a strong, flexible, and easily dissolved surgial thread




*triglyceride: consist of 3 fatty acids and one glycerol
*glycerol: an organic 3 carbon alcohol
*fatty acids: used constantly by the brain; replaces sugar in the production of ATP; consists of hydrocarbons
-saturated fatty acids: have single bonds between carbon and hydrogen molecules and therefore the maximum number of hydrogen molecules
-unsaturated fats: found in plant or fish oils; HEALTHIER type of fat; some aren't made by the human body and must be gained through diet
*hydrogenation: artificial process of making healthy, unsaturated fats into unhealthy saturated fats through the addition of a hydrogen
*steroids: lipids categorized by a carbon skeleton consisting of four rings
-cholesterol: an important steroid and is also a component in animal cell membranes as well as a precursor from which other steroids can be made
*LDL: low density proteins
*HDL: high density proteins
-high levels of LDL cholesterol leads to atherosclerosis and HDL removes excess LDL in vascular tissue

Lipids:
a large class of biological molecules that DON'T consist of polymers and that chemically have no affinity for water and includes fats, steroids, and phospholipids
Some More Important Information
Insulin and Glycogen:
-insulin's job is to produce glycogen from extra glucose in the blood, lowering blood sugar levels
-glycogen's job is to break down glycogen, releasing glucose into the bloodstream, raising blood sugar levels
H O
2
Concept 3: Active Transport uses Energy to move Solutes against their Gradients
Concept 2: Membrane Structure results in Selective Permeability
Concept 4: Bulk Transport across the Plasma Membrane occurs by Exocytosis and Endocytosis
Concept 1: Cellular Membranes are Fluid Mosaics of Lipids and Proteins
Reaction Process
Free Energy (G)
Progress of Reaction
Free Energy
Substrate Concentration
Rate of Reaction
Temperature
Rate of Reaction
Reaction Process
Exergonic Reaction (Energy Release)
[spontaneous!]
G<0 energy loss
E = activation energy
A
G>0
Endergonic Reaction (Energy Required)
[non-spontaneous]
energy gain
course of reaction WITH enzyme
course of reaction WITHOUT enzyme
Free Energy (G)
G is unaffected by enzyme
E changes
A
optimal temperature
Catabolic Reactions
(are Exergonic)
-release energy
-spontaneous
-negative delta G
-break down
(HYDROLYSIS)

Anabolic Reactions
(are Endergonic)
-consume energy
-non spontaneous
-positive delta G
-make-up
(DEHYDRATION
SYNTHESIS)
Induced Fit: Enzyme CHANGES SHAPE
Energy Coupling: an exergonic process drives an endergonic one
Factors that affect rate of enzyme action:
*concentration of substrate (thing 'entering' enzyme)
*temperature
-cooler---->slows
-warmer-->gradually decreases until denaturation
*pH
-above optimal level denaturation
-below optimal level slows function

Allosteric Regulation:
inhibitors stop enzyme...
-competitive-bind to active site and compete with substrate
-noncompetitive-bind to allosteric site and do NOT compete with substrate
motivators start up enzymes
< >
< >
< >
< >
< >
< >
< >
< >
< >
< >

< >

< >
< >
< >
< >
< >
< >

*Chromosomes become visible
*Crossing over occurs
*Nuclear Envelope breaks down
*
T
e
t
r
a
d
s
form

Prophase 1:
Metaphase 1:
*allignment of tetrads at metaphase plate(cell equator) lead to genetic variation
*2^n possibilities
Anaphase 1:
*tetrads seperate and move to different sides
*sister chromatids stay together
Telophase 1:
*2 daughter cells are formed
Cytokinesis:
Prophase 2:
*spindle aparatus forms
*sister chromatids move toward metaphase plate
Metaphase 2:
*Centromeres of chromosomes line up randomly at equator of cell
Anaphase 2:
*Centromere divides
*Sister chromatids seperate
Telophase 2:
*nuclear membrane forms around the chromosomes
Cytokinesis:
END RESULT: 4 GAMETES
2c 2n
4c 2n
2c n
1c n
Chromosome Number
PRIOR TO MEIOSIS
Genetic Content
23 pairs
23 tetrads
23 pairs
23 single
MEIOSIS 2 MEIOSIS 1
Spermatogenesis Oogenesis
..
polarbodies
egg
sperm
sperm
sperm
sperm
Fertilization
Mitosis
male gametogenesis
female gametogenesis
Meiosis
Meiosis
In plants, meiosis and fertilization alternate in every generation:
1st Generation:
2nd Generation:
Sporophyte(2n) spores(n) Gametophyte(n)
Gametophyte(n) zygote(2n) Sporophyte(2n)
(FERTILIZATION)
(MITOSIS)
(MITOSIS)
(MEIOSIS)
Tetrad
Crossing Over
chromatid
chromosome
(sister) chromatids
homologous chromosome
tetrad
Prophase:
*mitotic spindles begin to form
*nucleolus disappears but nucleus stays intact
Prometaphase:
*nuclear envelope fragments
*spindle microtubules attach to kinetochores of chromosomes
Metphase:
*spindle is complete
*chromosomealligned at metaphase plate(cell equator)
Anaphase:
*chromatids of each chromosome have seperated
*daughter chromosomes move to poles of cell
Telophase:
*daughter nuclei form
*cytokinesis begins
Cytokinesis:
< >
< >
< >
END RESULT: 2 DAUGHTER CELLS
Heredity:
Hybridization:
cross between two true breeding varieties
True-Breeding Organism:
an organism that always passes down a certain phenotypic trait to its offspring
Phenotype:
PHYSICAL appearance
Genotype:
GENETIC appearance
P Generation: the parent generation

F Generation: the offspring of the P generation

F Generation: produced when F generation self pollinates or cross pollinates with another F generation

Hybrid:
offspring of two different breeds, varieties, species or genera
Dominant:
the trait that is expressed and that masks the recessive (Dd, DD)
Recessive:
trait that IS masked and is lowercase of its dominant counterpart (Dd, dd)
Homozygous:
has same allele expressed twice
Homozygous Dominant- DD
Homozygous Recessive- dd
Heterozygous:
has two different alleles (Dd)
2
1
1
Monohybrid Cross:
R R
r



r
Rr
Rr
Rr
Rr
*Produces 100% heterozygotes
A cross between a homozygous dominant and homozygous recessive
Dihybrid Cross:
YyRr
YR Yr yR yr
YR

Yr

yR

yr
YYRR YYRr YyRR YyRr


YYRr YYrr YyRr Yyrr



YyRR YyRr yyRR yyRr



YyRr Yyrr yyRr yyrr
YyRr
a cross between F1 offspring of two individuals that differ in two traits of particular interest.
RR
Rr
Rr
rr
R r
R


r
*produces 3:1 phenotype of allele R
*Produces a 9:3:3:1 phenotypic ratio
Complete Dominance: Heterozygous phenotype is the same as that of the homozygous dominant



Incomplete Dominance: Heterozygous phenotype intermediate between the two homozygous phenotypes



Codominance: Both phentypes expressed in heterozygotes



Multiple Alleles: In the whole population, some genes have more than two alleles




Pleiotropy: One gene is able to affect multiple phenotypic characteristics:
Relationship among 2 or more genes
Relationship among alleles of a single gene
:
Chromosomal Basis of Inheritance
Sex Chromosomes:
X Y
XX-female male-XY
sex linked gene-gene located on either sex chromosome
X-Linked Genes:
RECESSIVE-
*affects more males
Ex: color blindness, muscular dystrophy, and hemophilia
DOMINANT-
*affects more females
Ex: Rett Syndrome
Gene Linkage:


Given....
a-b = 32%
a-d = 4%
d-c = 20%
c-b = 8%
a d c b
(4%) (20%) (8%)
start w/ biggest number
}
32%
-if sum of rest of the numbers is less than or equal to largest number then all letters are contained within the largest distance
-if sum of rest of the numbers is greater than the largest number then the letters can be outside of the largest distance
(32%)
Non-Disjunction
n+1 n+1 n-1 n-1
n+1 n-1 n n
Monosomic Zygote:
(2n-1)
Trisomic Zygote:
(2n+1)


-Down Syndrome
(trisomy)

-Turner Syndrome
(sex monosomy) X

-Klinefelter Syndrome
(sex trisomy) XXY
a failure of homologous chromosomes to separate during meiosis
Barr Bodies
Genomic
Imprinting
DNA
Sturcture:
G and A
-purines

T and C
-pyrimidines
Gene Expression by Protein Synthesis
Gene:
-a unit of heritage that affects phenotype
-a region of DNA that can be expressed to produce a final functional product
(polypeptide or RNA molecule)
-genetic code is nearly universal
RNA: Ribonucleic Acid

-single strand of nucleotides which consists of
1)phosphate
2)ribose [5 carbon sugar]
3)nitrogenous base
Adenine + Uracil (NOT THYMINE)
Guanine + Cytosine
mRNA (messenger RNA)
-carries info specifying amino acid sequences
-codon- 3 base sequence in mRNA that specifies for an amino acid or a stop signal ending translation
-many amino acids have more than 1 codon
-there are 64 codons
*AUG (start codon)
*UAA
*UAG
*UGA




}
(stop codon)
formation of ATP
Redox Reaction-transfer of electrons
L G
E E
O R

osing aining
lectrons lectrons
xidized educed

Aerobic Cellular Respiration
1






2A

Glycolsis (sugar splitting)
-no oxygen
-glucose made into pyruvates by enzymes in cytoplasm
-yields 2ATP, 2NADH, & H


-gain of 2ATP
-inhibition: (ATP is inhibitor of PFK) if there is no need for more ATP, production stops

+
Glucose+2ATP+2NAD +4H 2 Pyruvates+4ATP+2NADH+2H
+
+
Pyruvative Oxidation (prepatory for Citrid Acid Cycle)
-pyruvates are oxidized during transport to acetyl CoA by CoA (coenzyme A)
-2CO is produced and released as well
-2NADH & 2H are produced and transported to ETC


-transported to make proton gradient across inner mitochondrial membrane
Citric Acid Cycle (Krebs Cycle)
-completes breakdown of acetyl CoA






[Phospho-fructose Kinase]
+
2
2 Pyruvates+2CoA+2NAD 2 acetyl CoA+2NADH+2H +2CO
+
+
2
2B




fluid mosaic model: description of the membrane of a cell where ‘fluid’ refers to the phospholipids of a cell membrane and the ‘mosaic’ referring to the proteins embedded in the phospholipid layer
The membrane exhibits selective permeability, allowing some substances to cross it more easily than others, and results from the phospholipids and many types of proteins in the membrane
Selective permeability: property that allows membranes to regulate the passage of substances in them
Phospholipids have both a hydrophobic and hydrophilic region (amphipathic)
The membrane is NOT a barrier to harmful things in the cell (determines entry on size)
A: The Fluidity of Membranes
the membrane must be fluid for proper function and is fluid due to the phospholipids
most lipids ‘vibrate’
proteins are immobile due to attachment to cytoskeleton or extra-cellular membrane
B: Temperature and Cholesterol affect Fluidity
changes in temperature can cause changes in fluidity (cholesterol minimizes changes in fluidity)
1. cooler temperatures- solidification; fluid state---solid state (less permeable)
2. warmer temperatures- becomes “too fluid”
C: Evolution of Differences in Membrane Lipid Composition
Differences in lipid composition are adaptations to specific environments and natural selection favors these organisms whose lipids can ensure the appropriate fluidity of the membrane
D: Membrane Proteins
Different types of cells contain different sets of membrane proteins which determine most of the membrane’s specific functions
1. Peripheral proteins- are bound to the outer surface of the membrane and are not embedded at all
2. Integral Proteins- transmembrane proteins that contain both hydrophobic and hydrophilic regions, which correspond to the membranes same regions (glycoproteins)
Major functions of membrane proteins:
1. Transport (facilitated diffusion, active transport)
2. Enzymatic Activity (hydrolytic, metabolic)
3. Signal transduction (cell communication)
4. Cell-cell recognition (tissues, antibodies)
5. Intercellular Joining (junctions)
6. Attachment to the cytoskeleton and ECM (cell shape)
E: The Role of Membrane Carbohydrates in cell-cell recognition
Cells recognize one another by binding to surface receptors with carbohydrate located on the extracellular surface of the plasma membrane
Membrane carbohydrates form glycolipids when covalently bonded to lipids and glycoproteins when covalently bonded to proteins
Carbohydrates on the external side of the plasma membrane vary among cell types and species
F: Synthesis and Sidedness of Membranes
Membranes have distinct inside cytoplasmic and outside extracellular faces
The uneven distribution of proteins, lipids, and associated carbohydrates is determined when the membrane is built by the ER and the golgi apparatus
1. The ER makes membrane proteins and lipids and when the carbohydrates are added to the trans-membrane proteins, they are made into glycoproteins
2. Inside the golgi apparatus, the glycoproteins undergo further carbohydrate modification, and lipids acquire carbohydrates, making them glycolipids
To survive, a cell must receive external substances, which is controlled by selective permeability
Small nonpolar molecules move easily through the membrane through passive transport
Passive transport: the movement of small molecules from an area of high concentration to an area of low concentration until dynamic equilibrium is reached
Polar molecules do not cross the membrane easily and can use transport proteins
Transport Proteins assist in the process known as facilitated diffusion
Facilitated diffusion: the passage of ions or molecules down their electrochemical gradient across a biological membrane with the assistance of specific transmembrane proteins, requires no energy expenditure
Channel proteins function by having a hydrophilic channel that certain small polar molecules can use as a tunnel to get to the membrane
Carrier proteins bind to molecules and change their shape to shuttle them across the membrane
THESE TRANPORT PROTEINS ARE NOT NEEDED BUT HELP SPEED THINGS UP
Osmosis and Water Balance
OSMOSIS-
Osmosis: the diffusion of free water across (IN AND OUT OF) a selectively permeable membrane
LOW SOLUTES=HIGH CONC.
HIGH SOLUTES=LOW CONC.
Water can pass though the membrane but aquaporins speed up the process
WATER BALANCE-
Tonicity is the ability of a surrounding solution to cause a cell to gain or lose water
ISOTONIC SOLUTION: water conc. is the same as that inside the cell; NO NET MOVEMENT
HYPERTONIC SOLUTION: water conc. is LESS than that inside the cell, solute conc. is greater; cell loses water  cell shrinks (plasmylosis)
HYPOTONIC SOLUTION: water conc. is GREATER than that inside the cell, solute conc. is less; cell gains water AC-explosion PC-turgid

Occurs through exocytosis and endocytosis and requires energy
EXOCYTOSIS-cells release substances with transport vesicleThese vesicles go fuse with the membrane and release their contents and then the vesicle membrane becomes part of the plasma membrane
ENDOCYTOSIS-cells take in macromolecules by forming vesicles from the membrane
1) Phagocytosis- a cell surrounds and engulfs a large molecule by wrapping around it and enclosing it with a vesicle
2) Pinocytosis- ingests extracellular fluid and its dissolved solutes
3) Receptor-mediated Endocytosis- inward budding of vesicles containing proteins with receptor sites specific to the molecules being taken in
Moves substances against concentration gradient (low-high)
Requires energy (ATP)
Allows cells to maintain conc. gradient that differ from their external environment and produce a membrane potential
Membrane potential: the electrical difference between the inside of the cell and the surrounding extracellular fluid (+ on one side/-on the other)
Requires certain carrier transport proteins known as “pumps” that use ATP to maintain the membrane potential of a plasma membrane
2 most common pumps:
SODIUM POTASSSIUM PUMPS: pump out sodium and take in potassium
PROTON PUMPS: transports hydrogen ions out of a cell
Acetyl group+Oxaloacetate Citric Acid+2ATP+CO +6NADH+FADH +H
2
+
2
acetyl CoA+oxaloacetate citric acid
3
Oxidative Phosphorylation:
A)electron transport chain
electrons are passed through proteins to provide energy for pumping H to provide energy to make ATP
B)chemiosmosis uses proton gradient to drive H into ATP sythase
C)ATP sythase
at the end of the electron transport chain
Location:
Eukaryotes-Intermembrane Space (mitochondria)
Prokaryotes-Plasma Membrane
uses H to power ATP sythase to combine ADP and a single phosphate

+
Reaction Process
Free Energy (G)
Exergonic Reaction (Energy Release)
[spontaneous!]
G<0 energy loss
E = activation energy
A
Reaction Process
G>0
Endergonic Reaction (Energy Required)
[non-spontaneous]
energy gain
Free Energy (G)
+
10 NAHD+2FADH +H +O 38ATP+H O
+
2
2
2
PRODUCT OF AEROBIC CELLULAR RESPIRATION:
38 MAXIMUM ATP! (excluding byproducts)

Anaerobic Cellular Respiration (Fermentation)
Alcohol Fermentation:
1) Glycolysis
2) Fermentation


Lactid Acid Fermentation
1) Glycolysis
2) Fermentation

glucose+NAD pyruvate+2ATP+NADH CO +ethanol+NAD
2
+
+
glucose+NAD pyruvate+2ATP+NADH lactic acid+ethanol
+
6CO +6H O+light C H O +6O
2
2
6
6
12
6
Autotrophs: producers Heterotrophs: consumers
photoautotrphs: light self-nourishment
chemoautotrophs: chemcical self-nourishment
spongy
mesophyll
palisade
air space
}
MESOPHYLL: where most photosynthesis occurs
{
grana
chlorophyll a:
chlorophyll b:
carotenoids:
(absorb damaging wavelengths)
}
photosynthetic pigment that absorbs light
Calvin Cycle:
6CO +6RuBP 12 PGA
2
12 PGA+ATP+NADPH 12G3P+ADP+P+NADP
+
chromatid
chromosome
(sister) chromatids
homologous chromosome
Prophase

Prometaphase

Metaphase

Anaphase

Telophase
G1 phase the first (gap/)growth phase of the cell cycle consisting of the portion of interphase before DNA synthesis begins

S phase (synthesis) replication of DNA/chromatin

G2 phase the second (gap/) growth phase consisting of the portion of interphase AFTER DNA synthesis has occured
Interphase: cell grows, performs normal fnuctions, and prepares for division consisting of G1, S and G2 phases
Full transcript