Cell Division:

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Background on chromosomes:

Homologues/ homologous chromosomes- each organism contains two copies of each autosome, which are the same size and shape and code for the same genes
also, they have the same banding pattern (has to do with gene position) and the same centromere position
Sister chromatids- replicated chromosomes attached by a centromere
A sister chromatid is considered to be one chromosome, but when sister chromatids split apart, each sister chromatid is considered to be one chromosome
Haploid- describes one set of chromosomes
Represented by 1n
A haploid set of chromosomes has no homologues
Diploid- describes a set of chromosomes in which each chromosome has a homologue
Represented by 2n
all somatic cells are diploid
Triploidy- the condition of having 3 sets of chromosomes (3n)
This means that each each chromosome has two homologues instead of one
Polyploidy- the condition of having more than 2 sets of chromosomes (3n, 4n, 5n, etc...)
The cell cycle- the repeating set to events in the life of a cell
This is a continuous process
Mitosis- produces two daughter cells of about the same size with the same genetic information for the purposes of :
Growth, development, repair, asexual reproduction
Three main phases of the cell cycle:
Interphase- the part of the cell cycle that takes the greatest amount of time that occurs between divisions
Divided into three main stages:
G1
S
G2
The cell grows to its mature size
DNA is still in chromatin form


DNA is replicated: there are two copies of each chromosome


Cell prepares for division
Chromatin begins to condense


G0- the “resting phase” that cells enter when they stop dividing
Mitosis- the division of the nucleus
Four main stages:
Prophase- the longest stage of mitosis


Early prophase
Late prophase
Nuclear membrane and nucleolus begin to disintegrate


Centrosomes- structures that form the mitotic spindle (the spindle fibers that allow cell division to occur)
In animal cells, they contain centrioles
By late prophase, centrosomes reach opposite ends of the cell




Metaphase- chromosomes line up at the metaphase plate- this is the line down the center of the cell
Spindle fibers attach to the kinetochores (a disk-shaped protein) of chromosomes, located at their centromeres




Anaphase- centromeres divide as sister chromatids separate
Each sister chromatid is now considered to be a chromosome


Telophase- The nucleus has finished dividing
Spindle fibers disassemble
The nucleolus and nuclear envelope reform
DNA begins to return to chromatin form
A cleavage furrow appears- this is the fold that forms down the middle of the cell
Cytokinesis- the division of the cytoplasm
Cytokinesis starts towards the end of mitosis
Organelles distribute between both cells
The cleavage furrow fully forms, creating two daughter cells
In plant cells, a cell plate forms as the precursor to a cell wall


Cytokinesis in animal cells
Cytokinesis in plant cells






Binary fission- the process of cell division in prokaryotic cells
Meiosis- the process of creating gametes (haploid reproductive cells)
A diploid cells divides into four haploid cells


Interphase- occurs before meiosis so that the cell has a duplicate set of chromosomes
Meiosis involves two divisions: meiosis I and meiosis II
Meiosis I- homologues divide
Produces two haploid cells
Meiosis II- sister chromatids divide
Produces two haploid cells from each cell from meiosis I
Meiosis I:
Prophase I: Includes the same processes as prophase during mitosis: However, the difference is that synapsis occurs
Synapsis- homologous chromosomes line up next to each other and form a tetrad
Crossing-over- homologous chromosomes trade genetic information when parts break off


As a result, sister chromatids are no longer identical: this is known as genetic recombination
Metaphase I: Homologous chromosomes line up at the center of the cell and orient themselves randomly
This results in independent assortment- the random arrangement of chromosomes on either side of the cellular equator independently of one another


As a result, each gamete a parent produces is unique
Anaphase I: Homologous chromosomes split apart resulting in each side of the cell having one duplicated set of DNA (sister chromatids are still kept together)
Telophase I and Cytokinesis I: The cell finishes splitting apart into two haploid cells with a duplicated set of DNA
Meiosis II: this is basically the same process as mitosis
Prophase II- spindle fibers begin to form
Metaphase II- sister chromatids line up at the equator
Anaphase II- sister chromatids split apart
Telophase II/ Cytokinesis II- 4 haploid cells have formed
Spermatogenesis- the formation of sperm cells
Four sperm cells form from one diploid cell after meiosis
Oogenesis- the formation of egg cells
One egg cell is produced by meiosis
Three polar bodies, which are smaller, are also produced
These polar bodies will eventually degenerate
Genetics:
Mendel’s experiments
Gregor Mendel experimented with pea plants and discovered many things regarding heredity


Anther- the part of a plant that receives pollen
Stigma- the part of a plant that releases pollen
True breeding- describes a plant that will always produce offspring with a given trait when self- pollinating (if a pea plant has yellow pods and it self-pollinates then all of its offspring should have yellow pods if it is true-breeding)
This can be produced by self-pollinating plants for multiple generations
P generation- the parent generation
Mendel bred true-breeding parents for this generation
F1 generation- the offspring of the P generation
F2 generation- the offspring of the F1 generation
Mendel noticed that with many traits, one form appeared in all the offspring in the F1 generation, masking out the other
He also noticed that in the F2 generation, the other form of the trait reappeared, always with an approximate 3-1 ratio from the other trait to this previously masked-out trait
Example:


Mendel’s conclusion:
He believed that each trait is controlled by two “factors” (now known as alleles)
Some traits are controlled by dominant factors while others are controlled by recessive factors
He believed that dominant factors masked out recessive factors when inherited and this was why one trait always dominated in the F1 generation but then another reappeared
Law of segregation- the idea formed by Mendel that paired “factors” separate during the formation of reproductive cells (now known as meiosis)
This helped to explain why organisms had two factors for each trait when sex cells combined
Law of Independent Assortment- Mendel’s idea that factors separate independently of one another during the formation of gametes
Genetics- the field of biology devoted to understanding how characteristics are transferred from parents to offspring
Genotype- an organism’s genetic makeup consisting of alleles from both parents
Phenotype- the appearance of an organism
Phenotype does not always indicate genotype
Homozygous- when an organism has two of the same alleles for a trait
Heterozygous- when an organism has two different alleles for a trait
Monohybrid cross- a cross in which only one characteristic is tracked
Dihybrid cross- a cross in which two characteristics are tracked
Genotypic ratio- the ratio of the genotypes that appear in offspring
Phenotypic ratio- the ratio of the phenotypes that appear in offspring
Punnett squares- used to represent probability of certain genotypes
Example: A cross between a homozygous dominant purple pea plant and a homozygous recessive white pea plant


Testcross- when an unknown genotype is crossed with a homozygous recessive genotype
If any offspring produced are recessive, then the unknown genotype has to be heterozygous
This is because this is the only possible way that both parents are able to pass a recessive allele
Complex patterns of inheritance:
While the pattern of inheritance that Mendel observed, known as complete dominance, holds true sometimes, more complex patterns also exist
Incomplete dominance- the inheritance pattern in which a phenotype between two phenotypes is produced when an offspring is heterozygous
Example: a gene for red flowers is passed by one parent while a gene for white flowers is passed by another, resulting in a phenotype of pink flowers


Codominance- both alleles for a gene are expressed when an organism is heterozygous
Example: people with AB blood have both A and B antigens on the surface of their red blood cells while people with A or B blood have red blood cells that contain only one of these antigens
Polygenic inheritance- traits that are influenced by multiple genes
These traits often exhibit a wider range of variation
Examples: skin color, eye color, height, hair color
Multiple alleles- inheritance with more than three alleles
Example: human blood type
Dihybrid crosses
Steps to making a punnett square for dihybrid crosses:


Blood type- this is based on the antigens (proteins) on the surface of red blood cells
ABO blood typing:
Type A- red blood cells with A antigens
Type B- red blood cells with B antigens
Type AB- red blood cells with both A and B antigens
Type O- red blood cells with neither A nor B antigens


Problems with donating blood to people of different blood types exist because of the fact that you have antibodies against any antigens that you do not have on your blood cells
For example:
If you have type A blood, this means that you do not have type B antigens on the surface of your blood, so you will have an immune response to any type B or AB blood that enters your body
People with type O blood will have an immune response to any other type of blood as a result
Alleles:
IA- the allele for type A blood
IB- the allele for type B blood
i- the allele for type O blood
The allele for type O blood (i) is recessive, while the other two are codominant
This means that you have type AB blood if you have IAIB as your genotype because you synthesize both proteins
Also, because the allele for type O blood is recessive, you need two copies of it in order to have type O blood (genotype of ii)
This means that you can have type A or B blood and still carry the allele for type O blood (genotypes IAi or IBi)


Blood type
Possible genotype(s)
A
IAIA or IAi
B
IBIB or IBi
AB
IAIB
O
ii


Rh factor- another form of blood type
You can be Rh positive or Rh negative (represented by alleles + or -)
Rh positive means that you have the Rh protein
Rh negative means that you have no Rh protein


Someone with Rh positive blood cannot donate to someone with Rh negative blood because antibodies will target their red blood cells for having foreign antigens
Someone with Rh negative blood can donate to someone with Rh positive blood because their blood contains no foreign antigens (assuming it’s a compatible ABO blood type)
Being Rh negative is recessive, while being Rh positive is dominant
Alleles:


Blood type
Possible genotype(s)
Rh positive
++ or +-
Rh negative
--


Having children with a different blood type:
this can sometimes be dangerous during second pregnancies, as after her first pregnancy, a mother may develop antibodies to her first child’s blood type and then send them to her child through blood during her second pregnancy
This is because blood is sent in one direction (to the baby) in the uterus, but some blood is traded in the other direction as the baby leaves the uterus
Chromosome mapping- The process through which the relative positions of genes on chromosomes are determined


Linked Genes- when genes tend to be inherited together
Linkage group- genes on the same chromosome
Incomplete linkage- when linkage groups break apart during crossing-over
Genes that are farther apart on a chromosome are more likely to be separated during crossing-over
Pedigree- a diagram that shows a trait is inherited over generations


A square represents a male
A circle represents a female
A half-filled circle represents a carrier- someone who has only one copy of a gene (this only applies to recessive traits because they can be “masked out”)
Autosomal traits
Dominant- for a child to have it, a parent must have it
There can be no carriers because the gene automatically masks out other genes
Recessive- it is possible for neither parent to have the trait and still pass it on
Both parents must be carriers (or have the disease) to pass the trait on to progeny


Sex-linked traits- traits coded for by genes on the x or y chromosome
X-linked recessive
A male only needs one parent to carry the gene in order to express the gene
Possible punnett squares for a trait denoted by T (dominant) and t (recessive):










In all cases, males have a higher or equal rate to females of expressing an x-linked recessive
Y-linked traits- only appear in males and are always passed from father to son
example: SRY
Karyotypes- a picture of someone’s set of chromosomes, showing how many copies of each gene someone has
This can be used to identify disorders in an individual’s number of chromosomes


Karyotype notation- a way of representing the information conveyed by a karyotype
It shows the amount of chromosomes an individual has, the sex chromosomes they have, and any deletions or additions of chromosomes
Format used: number of chromosomes, sex chromosomes, additions or deletions
Example: 47,XX,+10 for a female with a trisomy of chromosome 10


Genetic engineering/ technology:
Polymerase chain reaction- a process through which large amounts of DNA are replicated artificially for genetic technology purposes
Gel electrophoresis- separates DNA based on fragment size in order to create a DNA fingerprint


Steps:
DNA samples are cut with a restriction enzyme
These fragments are known as Variable Number Tandem Repeats (VNTRs)
DNA is placed in wells on a thick gel
DNA is negatively charged so it migrates to the positive end
The speed of the fragments’ migration is dependent upon the size of a fragment
Smaller fragments travel farther
DNA then forms a “fingerprint” in the gel
The standard amount of loci (points in the genome) used is 13
Practical applications:
The VNTRS are passed as alleles
As a result, they can help to determine parental relationships
DNA fingerprints are also used to identify people at crime scenes
Recombinant DNA- the result of joining DNA from two different organisms
Steps in creating recombinant DNA:
Isolate a plasmid and a segment of DNA that will be inserted inside of it
Plasmids- small rings of DNA found naturally in some bacterial cells in addition to their main chromosome
The DNA that will be inserted can be isolated using restriction enzymes
A restriction enzyme is also used to cut the plasmid so that the new DNA can be inserted
A restriction enzyme leaves behind sticky ends when it cuts, so this holds the new fragment of DNA and the bacterial plasmid together temporarily until ligase binds them permanently


when bacterial cells replicate, they also replicate their new DNA and create the proteins coded for by the DNA
Applications of this:
Inserting recombinant DNA into bacteria can help to synthesize proteins in large quantities
This was done with the human insulin gene to produce insulin as a treatment for diabetes
This has also been done with many other forms of medicine
Disadvantages of this:
This can have unknown consequences
Many people consider it unethical to combine DNA from between two organisms
Transgenic organisms/ GMOs
GMOs- An organism whose genetic material has been changed in a laboratory
Transgenic organisms- an organism in which genes have been transferred from another organism
This is possible with recombinant DNA
New DNA should be inserted into an organism’s genome in its earliest stages of life
Examples:
a gene to make corn produce a toxin against pests was inserted into the corn to deter pests from attacking the corn
Golden rice was produced by inserting the gene for beta carotene




Pros
Cons
Can increase crop quality and quantity


Can have unexpected consequences, create new allergens, bring new genes into the gene pool
Some people consider it unethical to manipulate nature in such ways


Human genome project- a research effort to sequence human DNA
It has sequenced the whole human genome
Pros
Cons
Helps to understand genetic diseases
A better understanding of the human genome allows for scientists to create better drugs
It may allow for customized treatments
Could help to compare normal genes with cancerous genes


Some people view this as an invasion of privacy (insurance companies could one day access information about your genome and deny you service if you are predisposed to any diseases)


Gene therapy- when a genetic disease is treated by inserting a new gene into patients’ cells
Steps:
Isolate a functional gene using a restriction enzyme
Insert the gene into a non-disease-causing virus: this is known as a viral vector
Infect the patient with the virus to produce a working protein for the gene
In vivo- when the virus infects a patient’s cells while they are in the body
Ex vivo- when the virus infects cultured cells




Pros
Cons
This could potentially be used as a treatment for any genetically-caused disease


Patients can suffer immune responses to gene therapy
The cures are not permanent because the treated cells may die and stop making the required protein


Cloning- uses somatic cell nuclear transfer
Steps:
Egg cells are extracted from the uterus
The egg cells are enucleated- this means that their nucleus is removed
An electric shock causes the enucleated egg cell to fuse with a somatic cell
Another electric pulse is used to stimulate cell division and create an embryo
The embryo is implanted into a surrogate mother
Problems with cloning:
Cloning can result in premature aging due to shortened telomeres- segments of DNA at the end of chromosomes
This is considered unethical by many people (for obvious reasons)
Artificial selection- selecting plants/ animals for specific traits and breeding those plants to increase the presence of those traits
Pros:
This can be used to produce more desirable crops
Cons:
This can decrease variation within a population. As a result, when diseases or other environmental factors come into place, they can completely wipe out a population
Evolution:
Biogenesis vs. Spontaneous Generation
Biogenesis- the idea that all living things come from other living things
Spontaneous generation- the idea that living things arise from nonliving things
Many experiments were carried out to test spontaneous generation
Pasteur’s was the conclusive experiment


He used a curved stem on a flask: this let air in, showing that if there was a vital force, it could make it in, though having a curved neck ensured that no microorganisms floating through the air could infiltrate.
He showed that by removing the neck and letting the microorganisms in, the bacteria began to appear
Darwinism vs. Lamarckism


Darwinism
Lamarckism
Believed in natural selection- the idea that environmental pressures made certain traits favorable and caused them to proliferate


Believed in inheritance of acquired traits- this means that if a parent gained a trait during his/her lifetime, its offspring would then have the trait as well
The classic (but wrong) example of this is giraffes stretching their necks to reach trees and having offspring with long necks
He theorized that all organisms descended from dead matter that spontaneously generated life


The origins of life
The first organisms most likely synthesized energy through chemosynthesis- CO2 is used as a carbon source used to put together organic compounds
Endosymbiosis- the theory that mitochondria and chloroplasts were originally independent prokaryotes that entered larger prokaryotes and formed eukaryotes


Vocabulary pertaining to evolution:
Evolution- the development of new types of organisms from preexisting organisms
Allele frequency- how common an allele is in a population
Genetic drift- when allele frequencies in a population change due to random chance
This is more severe in small populations
Macroevolution- large, complex changes in life that often creates new species
This type of evolution can be seen in the fossil record
Microevolution- any change in the frequency of alleles within a population, not necessarily a big change
Gene flow- the process of genes moving from one population to another
Immigration- the movement of individuals in a population
Emigration-the movement of individuals out of a population
Variation- differences between traits within a population
Sources of variation:
Mutation
Reshuffling of genes and the re pairing of gametes during sexual reproduction.
Natural selection- certain favorable variations of traits become more common, making organisms more likely to survive and reproduce
This results in a shift from the normal “bell curve” distribution of traits within a population
Darwin’s proposed reasons for natural selection:
Overproduction- organisms often produce more progeny than the amount that can survive due to limiting factors in the environment, resulting in only the most fit surviving
Genetic variation- organisms within a population have differing traits, some of which can be inherited or arise randomly
Struggle to survive- individuals must compete with each other, and some variations increase the chance that an organism will be successful
Adaptation- traits that will make an organism successful
This is different from acclimatization, which is adjusting during an organism’s lifetime
Differential Reproduction- Individuals that are best fit for their environment will survive and reproduce better than others, creating offspring that are also likely to be successful due to the variations of traits that they inherited
Types of natural selection:
Stabilizing selection- occurs when the average form of a trait is most favorable, resulting in an increase in the frequency of traits closer to average and a decrease in frequency of traits further from average


Disruptive selection- occurs when organisms with traits on either extreme are favored


The blue line represents the change from the bell curve
Directional selection- organisms that have traits that lean towards one extreme are more favorable, leading to a shift in one direction


Isolation:
Geographic isolation- a physical separation of members of a population such as rivers, deserts, or glaciers
Reproductive isolation- isolation that occurs when population groups cannot successfully mate and form fertile offspring
Types of reproductive isolation:
Prezygotic isolation- prevents hybrid offspring from being formed: this is isolation that prevents fertilization from ever occurring
Postzygotic isolation- occurs after fertilization and prevents hybrid offspring from surviving and reproducing
Habitat isolation- two populations of organisms each live in different environments, so the gene pools of the two populations are kept separate
Temporal isolation- when organisms mate at different times
Behavioral isolation- when two populations have different mating calls or activities
Mechanical isolation- when mating organs don’t fit together
Gametic isolation- gametes cannot combine to form offspring


Zygote mortality- zygote dies as soon as the egg is fertilized
Hybrid inavailability- hybrid offspring do not reach maturity and therefore cannot mate
Hybrid infertility (hybrid sterility)- hybrids cannot reproduce
Hybrid breakdown (F2 fitness)- second-generation hybrids have reduced fitness (offspring of two hybrids are less able to reproduce)


Causes of reproductive isolation:
Disruptive selection- two extremes diverge until they become reproductively isolated
Geographic isolation- this cuts off gene flow and causes populations to diverge from each other
Genetic equilibrium- the concept of allele frequencies staying constant throughout a population from generation to generation
Requirements for genetic equilibrium to occur:
A population must have no mutations occur
Gene flow does not occur-gene flow can change allele frequencies
A population must be infinitely large to make sure that genetic drift does not occur
A population must mate randomly so that certain alleles do not become more common
In order for genetic equilibrium to be existent, natural selection cannot occur due to its favoring of certain allele combinations and the resulting increases in these frequencies
Formula for genotypic frequencies when there is genetic equilibrium:
If genetic equilibrium exists within a population, which is nearly impossible, and a trait is coded for by two alleles, p and q, then p2+2pq+q2=1 will always represent the allele frequencies of a population, with p2 and q2 representing the frequency of being homozygous for the gene and 2pq representing the frequency of being heterozygous
Speciation- the process of forming new species
This occurs when members of a population can no longer successfully interbreed
This can take place if a population becomes divided and two groups of organisms no longer share a gene pool
Allopatric speciation- speciation that occurs when geographic isolation between two populations leads to speciation
after populations are isolated geographic isolation, gene flow disappears because the two populations can no longer interbreed
natural selection as well as genetic drift cause the populations to diverge and form new species
this is because as the two populations become more and more different, reproductive barriers can arise
Parapatric speciation- part of a population enters a new habitat that is right next to the original area of the parent species
memory aid: “para” means alongside
With parapatric speciation, some individuals from the different populations still mate, but most still stay in their original habitats


It occurs in neighboring habitats
because the two habitats may be different, this can lead to disruptive selection, because in one habitat, one phenotype might be more advantageous and in another, another phenotype might be more advantageous
Sympatric speciation- two subpopulations become reproductively isolated in the same geographic area
Rates of speciation
Gradualism- the idea that speciation occurs at a regular, gradual rate
Punctuated equilibrium- the idea that evolution occurs in short “bursts,” with short periods of a lot of change and long periods of no change


Types of evolution
Convergent evolution- different species evolve similar traits due to adapting to similar habitats that make similar traits more “fit”
Divergent evolution- one ancestor gives rise to multiple species that are better adapted to different environments
Adaptive radiation- when a population undergoes divergent evolution until it fills up different roles/niches in the environment


this is a type of divergent evolution
Coevolution- when two or more species adapt to each other’s influence
Examples:
Some plants evolve so that other organisms will pollinate them
“Arm’s race”- a predator and prey evolve to each other
Humans create antibiotic-resistant bacteria
Animals evolve mimicry- copying each other
Cladogram
shows relationships, similarities, differences, common ancestors
based on physical traits shared between organisms
example:


Group of organisms
Long stems
Seeds
Flowers
Mosses
no
no
no
Ferns
yes
no
no
Pine trees
yes
yes
no
Flowering plants
yes
yes
yes




Phylogenetic trees- diagrams that analyze evolutionary relationships


Evidence of evolution
The fossil record- shows the progression of life forms on Earth as part of the geologic time scale
The law of superposition- states that most recent strata (layers) are on top while older strata are on the bottom
This is used for relative dating to determine the relative age or organisms- their age compared to that of other organisms
Absolute dating- in some cases, radiometric dating can be used used to determine the exact ages of fossils
Homologous structures structures shared by species that originate from a common ancestor


Homologous structures are inherited from common ancestors
Homologous structures between two organisms may have similar structures but different functions
Homologous structures are evidence of how organisms diverged from a common ancestor, therefore illustrating paths of divergent evolution
Analogous structures- similar functions but different basic structures


They are not inherited from a common ancestor
They evolve independently but to similar environmental pressures, resulting in similar functions that are necessary
They are caused by convergent evolution, because organisms evolve similar traits without having a common ancestor
Vestigial structures- structures that still exist in organisms but have lost their primary function
Example: human tailbone
this shows evolution because it indicates how species descended from other species where vestigial structures may have been useful
Comparative embryology


In the early stages of development, many organisms look similar and show similar characteristics, indicating traits derived from a common ancestor by inheriting the genes
Biological molecules- organisms that share more similar amino acid, RNA, and DNA sequences are more closely related and evolved from a common ancestor more recently
This means that humans share more DNA with their more recent ancestors than with their more distant ancestors
Ecology:
Ecology- the study of the interactions between organisms and the living and nonliving elements of their environments
Interdependence- the word used to describe the concept of organisms’ survival depend on interactions with the environment and other organisms
Keystone species- a species that may affect many other species within a community due to the interdependence and interconnectedness of organisms
Example: sea otters feed on sea urchins, which feed on algae, so when sea otters are removed from an environment, sea urchins overgrow and destroy algae
Habitat- the environment in which an organism lives
Environmental factors:
Biotic factors- include all the living things that affect an organism
Abiotic factors- include all the non-living things that affect an organism

Cell Division:

Background on chromosomes:

Homologues/ homologous chromosomes- each organism contains two copies of each autosome, which are the same size and shape and code for the same genes

also, they have the same banding pattern (has to do with gene position) and the same centromere position

Sister chromatids- replicated chromosomes attached by a centromere

A sister chromatid is considered to be one chromosome, but when sister chromatids split apart, each sister chromatid is considered to be one chromosome

Haploid- describes one set of chromosomes

Represented by 1n

A haploid set of chromosomes has no homologues

Diploid- describes a set of chromosomes in which each chromosome has a homologue

Represented by 2n

all somatic cells are diploid

Triploidy- the condition of having 3 sets of chromosomes (3n)

This means that each each chromosome has two homologues instead of one

Polyploidy- the condition of having more than 2 sets of chromosomes (3n, 4n, 5n, etc...)

The cell cycle- the repeating set to events in the life of a cell

This is a continuous process

Mitosis- produces two daughter cells of about the same size with the same genetic information for the purposes of :

Growth, development, repair, asexual reproduction

Three main phases of the cell cycle:

Interphase- the part of the cell cycle that takes the greatest amount of time that occurs between divisions

Divided into three main stages:

G1

S

G2

The cell grows to its mature size

DNA is still in chromatin form

DNA is replicated: there are two copies of each chromosome

Cell prepares for division

Chromatin begins to condense

G0- the “resting phase” that cells enter when they stop dividing

Mitosis- the division of the nucleus

Four main stages:

Prophase- the longest stage of mitosis

Early prophase

Late prophase

Nuclear membrane and nucleolus begin to disintegrate

Centrosomes- structures that form the mitotic spindle (the spindle fibers that allow cell division to occur)

In animal cells, they contain centrioles

By late prophase, centrosomes reach opposite ends of the cell

Metaphase- chromosomes line up at the metaphase plate- this is the line down the center of the cell

Spindle fibers attach to the kinetochores (a disk-shaped protein) of chromosomes, located at their centromeres

Anaphase- centromeres divide as sister chromatids separate

Each sister chromatid is now considered to be a chromosome

Telophase- The nucleus has finished dividing

Spindle fibers disassemble

The nucleolus and nuclear envelope reform

DNA begins to return to chromatin form

A cleavage furrow appears- this is the fold that forms down the middle of the cell

Cytokinesis- the division of the cytoplasm

Cytokinesis starts towards the end of mitosis

Organelles distribute between both cells

The cleavage furrow fully forms, creating two daughter cells

In plant cells, a cell plate forms as the precursor to a cell wall

Cytokinesis in animal cells

Cytokinesis in plant cells

Binary fission- the process of cell division in prokaryotic cells

Meiosis- the process of creating gametes (haploid reproductive cells)

A diploid cells divides into four haploid cells

Interphase- occurs before meiosis so that the cell has a duplicate set of chromosomes

Meiosis involves two divisions: meiosis I and meiosis II

Meiosis I- homologues divide

Produces two haploid cells

Meiosis II- sister chromatids divide

Produces two haploid cells from each cell from meiosis I

Meiosis I:

Prophase I: Includes the same processes as prophase during mitosis: However, the difference is that synapsis occurs

Synapsis- homologous chromosomes line up next to each other and form a tetrad

Crossing-over- homologous chromosomes trade genetic information when parts break off

As a result, sister chromatids are no longer identical: this is known as genetic recombination

Metaphase I: Homologous chromosomes line up at the center of the cell and orient themselves randomly

This results in independent assortment- the random arrangement of chromosomes on either side of the cellular equator independently of one another

As a result, each gamete a parent produces is unique

Anaphase I: Homologous chromosomes split apart resulting in each side of the cell having one duplicated set of DNA (sister chromatids are still kept together)

Telophase I and Cytokinesis I: The cell finishes splitting apart into two haploid cells with a duplicated set of DNA

Meiosis II: this is basically the same process as mitosis

Prophase II- spindle fibers begin to form

Metaphase II- sister chromatids line up at the equator

Anaphase II- sister chromatids split apart

Telophase II/ Cytokinesis II- 4 haploid cells have formed

Spermatogenesis- the formation of sperm cells

Four sperm cells form from one diploid cell after meiosis

Oogenesis- the formation of egg cells

One egg cell is produced by meiosis

Three polar bodies, which are smaller, are also produced

These polar bodies will eventually degenerate

Genetics:

Mendel’s experiments

Gregor Mendel experimented with pea plants and discovered many things regarding heredity

Anther- the part of a plant that receives pollen

Stigma- the part of a plant that releases pollen

True breeding- describes a plant that will always produce offspring with a given trait when self- pollinating (if a pea plant has yellow pods and it self-pollinates then all of its offspring should have yellow pods if it is true-breeding)

This can be produced by self-pollinating plants for multiple generations

P generation- the parent generation

Mendel bred true-breeding parents for this generation

F1 generation- the offspring of the P generation

F2 generation- the offspring of the F1 generation

Mendel noticed that with many traits, one form appeared in all the offspring in the F1 generation, masking out the other

He also noticed that in the F2 generation, the other form of the trait reappeared, always with an approximate 3-1 ratio from the other trait to this previously masked-out trait

Example:

Mendel’s conclusion:

He believed that each trait is controlled by two “factors” (now known as alleles)

Some traits are controlled by dominant factors while others are controlled by recessive factors

He believed that dominant factors masked out recessive factors when inherited and this was why one trait always dominated in the F1 generation but then another reappeared

Law of segregation- the idea formed by Mendel that paired “factors” separate during the formation of reproductive cells (now known as meiosis)

This helped to explain why organisms had two factors for each trait when sex cells combined

Law of Independent Assortment- Mendel’s idea that factors separate independently of one another during the formation of gametes

Genetics- the field of biology devoted to understanding how characteristics are transferred from parents to offspring

Genotype- an organism’s genetic makeup consisting of alleles from both parents

Phenotype- the appearance of an organism

Phenotype does not always indicate genotype

Homozygous- when an organism has two of the same alleles for a trait

Heterozygous- when an organism has two different alleles for a trait

Monohybrid cross- a cross in which only one characteristic is tracked

Dihybrid cross- a cross in which two characteristics are tracked

Genotypic ratio- the ratio of the genotypes that appear in offspring

Phenotypic ratio- the ratio of the phenotypes that appear in offspring

Punnett squares- used to represent probability of certain genotypes

Example: A cross between a homozygous dominant purple pea plant and a homozygous recessive white pea plant

Testcross- when an unknown genotype is crossed with a homozygous recessive genotype

If any offspring produced are recessive, then the unknown genotype has to be heterozygous

This is because this is the only possible way that both parents are able to pass a recessive allele

Complex patterns of inheritance:

While the pattern of inheritance that Mendel observed, known as complete dominance, holds true sometimes, more complex patterns also exist

Incomplete dominance- the inheritance pattern in which a phenotype between two phenotypes is produced when an offspring is heterozygous

Example: a gene for red flowers is passed by one parent while a gene for white flowers is passed by another, resulting in a phenotype of pink flowers

Codominance- both alleles for a gene are expressed when an organism is heterozygous

Example: people with AB blood have both A and B antigens on the surface of their red blood cells while people with A or B blood have red blood cells that contain only one of these antigens

Polygenic inheritance- traits that are influenced by multiple genes

These traits often exhibit a wider range of variation

Examples: skin color, eye color, height, hair color

Multiple alleles- inheritance with more than three alleles

Example: human blood type

Dihybrid crosses

Steps to making a punnett square for dihybrid crosses:

Blood type- this is based on the antigens (proteins) on the surface of red blood cells

ABO blood typing:

Type A- red blood cells with A antigens

Type B- red blood cells with B antigens

Type AB- red blood cells with both A and B antigens

Type O- red blood cells with neither A nor B antigens

Problems with donating blood to people of different blood types exist because of the fact that you have antibodies against any antigens that you do not have on your blood cells

For example:

If you have type A blood, this means that you do not have type B antigens on the surface of your blood, so you will have an immune response to any type B or AB blood that enters your body

People with type O blood will have an immune response to any other type of blood as a result

Alleles:

IA- the allele for type A blood

IB- the allele for type B blood

i- the allele for type O blood

The allele for type O blood (i) is recessive, while the other two are codominant

This means that you have type AB blood if you have IAIB as your genotype because you synthesize both proteins

Also, because the allele for type O blood is recessive, you need two copies of it in order to have type O blood (genotype of ii)

This means that you can have type A or B blood and still carry the allele for type O blood (genotypes IAi or IBi)

Blood type

Possible genotype(s)

A

IAIA or IAi

B

IBIB or IBi

AB

IAIB

O

ii

Rh factor- another form of blood type

You can be Rh positive or Rh negative (represented by alleles + or -)

Rh positive means that you have the Rh protein

Rh negative means that you have no Rh protein

Someone with Rh positive blood cannot donate to someone with Rh negative blood because antibodies will target their red blood cells for having foreign antigens

Someone with Rh negative blood can donate to someone with Rh positive blood because their blood contains no foreign antigens (assuming it’s a compatible ABO blood type)

Being Rh negative is recessive, while being Rh positive is dominant

Alleles:

Blood type

Possible genotype(s)

Rh positive

++ or +-

Rh negative

--

Having children with a different blood type:

this can sometimes be dangerous during second pregnancies, as after her first pregnancy, a mother may develop antibodies to her first child’s blood type and then send them to her child through blood during her second pregnancy

This is because blood is sent in one direction (to the baby) in the uterus, but some blood is traded in the other direction as the baby leaves the uterus

Chromosome mapping- The process through which the relative positions of genes on chromosomes are determined

Linked Genes- when genes tend to be inherited together

Linkage group- genes on the same chromosome

Incomplete linkage- when linkage groups break apart during crossing-over

Genes that are farther apart on a chromosome are more likely to be separated during crossing-over

Pedigree- a diagram that shows a trait is inherited over generations

A square represents a male

A circle represents a female

A half-filled circle represents a carrier- someone who has only one copy of a gene (this only applies to recessive traits because they can be “masked out”)

Autosomal traits

Dominant- for a child to have it, a parent must have it

There can be no carriers because the gene automatically masks out other genes

Recessive- it is possible for neither parent to have the trait and still pass it on

Both parents must be carriers (or have the disease) to pass the trait on to progeny

Sex-linked traits- traits coded for by genes on the x or y chromosome

X-linked recessive

A male only needs one parent to carry the gene in order to express the gene

Possible punnett squares for a trait denoted by T (dominant) and t (recessive):

In all cases, males have a higher or equal rate to females of expressing an x-linked recessive

Y-linked traits- only appear in males and are always passed from father to son

example: SRY

Karyotypes- a picture of someone’s set of chromosomes, showing how many copies of each gene someone has

This can be used to identify disorders in an individual’s number of chromosomes

Karyotype notation- a way of representing the information conveyed by a karyotype

It shows the amount of chromosomes an individual has, the sex chromosomes they have, and any deletions or additions of chromosomes

Format used: number of chromosomes, sex chromosomes, additions or deletions

Example: 47,XX,+10 for a female with a trisomy of chromosome 10

Genetic engineering/ technology:

Polymerase chain reaction- a process through which large amounts of DNA are replicated artificially for genetic technology purposes

Gel electrophoresis- separates DNA based on fragment size in order to create a DNA fingerprint

Steps:

DNA samples are cut with a restriction enzyme

These fragments are known as Variable Number Tandem Repeats (VNTRs)

DNA is placed in wells on a thick gel

DNA is negatively charged so it migrates to the positive end

The speed of the fragments’ migration is dependent upon the size of a fragment

Smaller fragments travel farther

DNA then forms a “fingerprint” in the gel

The standard amount of loci (points in the genome) used is 13

Practical applications:

The VNTRS are passed as alleles

As a result, they can help to determine parental relationships

DNA fingerprints are also used to identify people at crime scenes

Recombinant DNA- the result of joining DNA from two different organisms

Steps in creating recombinant DNA:

Isolate a plasmid and a segment of DNA that will be inserted inside of it

Plasmids- small rings of DNA found naturally in some bacterial cells in addition to their main chromosome

The DNA that will be inserted can be isolated using restriction enzymes

A restriction enzyme is also used to cut the plasmid so that the new DNA can be inserted

A restriction enzyme leaves behind sticky ends when it cuts, so this holds the new fragment of DNA and the bacterial plasmid together temporarily until ligase binds them permanently

when bacterial cells replicate, they also replicate their new DNA and create the proteins coded for by the DNA

Applications of this:

Inserting recombinant DNA into bacteria can help to synthesize proteins in large quantities

This was done with the human insulin gene to produce insulin as a treatment for diabetes

This has also been done with many other forms of medicine

Disadvantages of this:

This can have unknown consequences

Many people consider it unethical to combine DNA from between two organisms

Transgenic organisms/ GMOs

GMOs- An organism whose genetic material has been changed in a laboratory

Transgenic organisms- an organism in which genes have been transferred from another organism

This is possible with recombinant DNA

New DNA should be inserted into an organism’s genome in its earliest stages of life

Examples:

a gene to make corn produce a toxin against pests was inserted into the corn to deter pests from attacking the corn

Golden rice was produced by inserting the gene for beta carotene

Pros

Cons

Can increase crop quality and quantity

Can have unexpected consequences, create new allergens, bring new genes into the gene pool

Some people consider it unethical to manipulate nature in such ways

Human genome project- a research effort to sequence human DNA

It has sequenced the whole human genome

Pros

Cons

Helps to understand genetic diseases

A better understanding of the human genome allows for scientists to create better drugs

It may allow for customized treatments

Could help to compare normal genes with cancerous genes

Some people view this as an invasion of privacy (insurance companies could one day access information about your genome and deny you service if you are predisposed to any diseases)

Gene therapy- when a genetic disease is treated by inserting a new gene into patients’ cells

Steps:

Isolate a functional gene using a restriction enzyme

Insert the gene into a non-disease-causing virus: this is known as a viral vector

Infect the patient with the virus to produce a working protein for the gene

In vivo- when the virus infects a patient’s cells while they are in the body

Ex vivo- when the virus infects cultured cells

Pros

Cons

This could potentially be used as a treatment for any genetically-caused disease

Patients can suffer immune responses to gene therapy

The cures are not permanent because the treated cells may die and stop making the required protein

Cloning- uses somatic cell nuclear transfer

Steps:

Egg cells are extracted from the uterus

The egg cells are enucleated- this means that their nucleus is removed

An electric shock causes the enucleated egg cell to fuse with a somatic cell

Another electric pulse is used to stimulate cell division and create an embryo

The embryo is implanted into a surrogate mother

Problems with cloning:

Cloning can result in premature aging due to shortened telomeres- segments of DNA at the end of chromosomes

This is considered unethical by many people (for obvious reasons)

Artificial selection- selecting plants/ animals for specific traits and breeding those plants to increase the presence of those traits

Pros:

This can be used to produce more desirable crops

Cons:

This can decrease variation within a population. As a result, when diseases or other environmental factors come into place, they can completely wipe out a population

Evolution:

Biogenesis vs. Spontaneous Generation

Biogenesis- the idea that all living things come from other living things

Spontaneous generation- the idea that living things arise from nonliving things

Many experiments were carried out to test spontaneous generation

Pasteur’s was the conclusive experiment

He used a curved stem on a flask: this let air in, showing that if there was a vital force, it could make it in, though having a curved neck ensured that no microorganisms floating through the air could infiltrate.

He showed that by removing the neck and letting the microorganisms in, the bacteria began to appear

Darwinism vs. Lamarckism

Darwinism

Lamarckism

Believed in natural selection- the idea that environmental pressures made certain traits favorable and caused them to proliferate

Believed in inheritance of acquired traits- this means that if a parent gained a trait during his/her lifetime, its offspring would then have the trait as well

The classic (but wrong) example of this is giraffes stretching their necks to reach trees and having offspring with long necks

He theorized that all organisms descended from dead matter that spontaneously generated life

The origins of life

The first organisms most likely synthesized energy through chemosynthesis- CO2 is used as a carbon source used to put together organic compounds

Endosymbiosis- the theory that mitochondria and chloroplasts were originally independent prokaryotes that entered larger prokaryotes and formed eukaryotes

Vocabulary pertaining to evolution:

Evolution- the development of new types of organisms from preexisting organisms

Allele frequency- how common an allele is in a population

Genetic drift- when allele frequencies in a population change due to random chance

This is more severe in small populations

Macroevolution- large, complex changes in life that often creates new species

This type of evolution can be seen in the fossil record

Microevolution- any change in the frequency of alleles within a population, not necessarily a big change

Gene flow- the process of genes moving from one population to another

Immigration- the movement of individuals in a population

Emigration-the movement of individuals out of a population

Variation- differences between traits within a population

Sources of variation:

Mutation

Reshuffling of genes and the re pairing of gametes during sexual reproduction.

Natural selection- certain favorable variations of traits become more common, making organisms more likely to survive and reproduce

This results in a shift from the normal “bell curve” distribution of traits within a population

Darwin’s proposed reasons for natural selection:

Overproduction- organisms often produce more progeny than the amount that can survive due to limiting factors in the environment, resulting in only the most fit surviving

Genetic variation- organisms within a population have differing traits, some of which can be inherited or arise randomly

Struggle to survive- individuals must compete with each other, and some variations increase the chance that an organism will be successful

Adaptation- traits that will make an organism successful

This is different from acclimatization, which is adjusting during an organism’s lifetime

Differential Reproduction- Individuals that are best fit for their environment will survive and reproduce better than others, creating offspring that are also likely to be successful due to the variations of traits that they inherited

Types of natural selection:

Stabilizing selection- occurs when the average form of a trait is most favorable, resulting in an increase in the frequency of traits closer to average and a decrease in frequency of traits further from average

Disruptive selection- occurs when organisms with traits on either extreme are favored

The blue line represents the change from the bell curve

Directional selection- organisms that have traits that lean towards one extreme are more favorable, leading to a shift in one direction

Isolation:

Geographic isolation- a physical separation of members of a population such as rivers, deserts, or glaciers

Reproductive isolation- isolation that occurs when population groups cannot successfully mate and form fertile offspring

Types of reproductive isolation:

Prezygotic isolation- prevents hybrid offspring from being formed: this is isolation that prevents fertilization from ever occurring

Postzygotic isolation- occurs after fertilization and prevents hybrid offspring from surviving and reproducing

Habitat isolation- two populations of organisms each live in different environments, so the gene pools of the two populations are kept separate

Temporal isolation- when organisms mate at different times

Behavioral isolation- when two populations have different mating calls or activities

Mechanical isolation- when mating organs don’t fit together

Gametic isolation- gametes cannot combine to form offspring

Zygote mortality- zygote dies as soon as the egg is fertilized

Hybrid inavailability- hybrid offspring do not reach maturity and therefore cannot mate

Hybrid infertility (hybrid sterility)- hybrids cannot reproduce

Hybrid breakdown (F2 fitness)- second-generation hybrids have reduced fitness (offspring of two hybrids are less able to reproduce)

Causes of reproductive isolation:

Disruptive selection- two extremes diverge until they become reproductively isolated

Geographic isolation- this cuts off gene flow and causes populations to diverge from each other

Genetic equilibrium- the concept of allele frequencies staying constant throughout a population from generation to generation

Requirements for genetic equilibrium to occur:

A population must have no mutations occur

Gene flow does not occur-gene flow can change allele frequencies

A population must be infinitely large to make sure that genetic drift does not occur

A population must mate randomly so that certain alleles do not become more common

In order for genetic equilibrium to be existent, natural selection cannot occur due to its favoring of certain allele combinations and the resulting increases in these frequencies

Formula for genotypic frequencies when there is genetic equilibrium:

If genetic equilibrium exists within a population, which is nearly impossible, and a trait is coded for by two alleles, p and q, then p2+2pq+q2=1 will always represent the allele frequencies of a population, with p2 and q2 representing the frequency of being homozygous for the gene and 2pq representing the frequency of being heterozygous

Speciation- the process of forming new species

This occurs when members of a population can no longer successfully interbreed

This can take place if a population becomes divided and two groups of organisms no longer share a gene pool

Allopatric speciation- speciation that occurs when geographic isolation between two populations leads to speciation

after populations are isolated geographic isolation, gene flow disappears because the two populations can no longer interbreed

natural selection as well as genetic drift cause the populations to diverge and form new species

this is because as the two populations become more and more different, reproductive barriers can arise

Parapatric speciation- part of a population enters a new habitat that is right next to the original area of the parent species

memory aid: “para” means alongside

With parapatric speciation, some individuals from the different populations still mate, but most still stay in their original habitats

It occurs in neighboring habitats

because the two habitats may be different, this can lead to disruptive selection, because in one habitat, one phenotype might be more advantageous and in another, another phenotype might be more advantageous

Sympatric speciation- two subpopulations become reproductively isolated in the same geographic area

Rates of speciation

Gradualism- the idea that speciation occurs at a regular, gradual rate

Punctuated equilibrium- the idea that evolution occurs in short “bursts,” with short periods of a lot of change and long periods of no change

Types of evolution

Convergent evolution- different species evolve similar traits due to adapting to similar habitats that make similar traits more “fit”

Divergent evolution- one ancestor gives rise to multiple species that are better adapted to different environments

Adaptive radiation- when a population undergoes divergent evolution until it fills up different roles/niches in the environment

this is a type of divergent evolution

Coevolution- when two or more species adapt to each other’s influence

Examples:

Some plants evolve so that other organisms will pollinate them

“Arm’s race”- a predator and prey evolve to each other

Humans create antibiotic-resistant bacteria

Animals evolve mimicry- copying each other

Cladogram

shows relationships, similarities, differences, common ancestors

based on physical traits shared between organisms

example:

Group of organisms

Long stems

Seeds

Flowers

Mosses

no

no

no

Ferns

yes

no

no

Pine trees

yes

yes

no

Flowering plants

yes

yes

yes

Phylogenetic trees- diagrams that analyze evolutionary relationships

Evidence of evolution

The fossil record- shows the progression of life forms on Earth as part of the geologic time scale

The law of superposition- states that most recent strata (layers) are on top while older strata are on the bottom

This is used for relative dating to determine the relative age or organisms- their age compared to that of other organisms

Absolute dating- in some cases, radiometric dating can be used used to determine the exact ages of fossils

Homologous structures structures shared by species that originate from a common ancestor

Homologous structures are inherited from common ancestors

Homologous structures between two organisms may have similar structures but different functions

Homologous structures are evidence of how organisms diverged from a common ancestor, therefore illustrating paths of divergent evolution

Analogous structures- similar functions but different basic structures

They are not inherited from a common ancestor

They evolve independently but to similar environmental pressures, resulting in similar functions that are necessary

They are caused by convergent evolution, because organisms evolve similar traits without having a common ancestor

Vestigial structures- structures that still exist in organisms but have lost their primary function

Example: human tailbone

this shows evolution because it indicates how species descended from other species where vestigial structures may have been useful

Comparative embryology

In the early stages of development, many organisms look similar and show similar characteristics, indicating traits derived from a common ancestor by inheriting the genes

Biological molecules- organisms that share more similar amino acid, RNA, and DNA sequences are more closely related and evolved from a common ancestor more recently

This means that humans share more DNA with their more recent ancestors than with their more distant ancestors

Ecology:

Ecology- the study of the interactions between organisms and the living and nonliving elements of their environments

Interdependence- the word used to describe the concept of organisms’ survival depend on interactions with the environment and other organisms

Keystone species- a species that may affect many other species within a community due to the interdependence and interconnectedness of organisms

Example: sea otters feed on sea urchins, which feed on algae, so when sea otters are removed from an environment, sea urchins overgrow and destroy algae

Habitat- the environment in which an organism lives

Environmental factors:

Biotic factors- include all the living things that affect an organism

Abiotic factors- include all the non-living things that affect an organism