Chapter 19 & 20

1. Sympatric speciation & Microtubules

Sympatric speciation is when new species form within one environment without any geographical barriers getting in the way. One way that sympatric speciation can occur is through polyploidy (when an organism inherits three or more sets of every chromosome) and this happens through the nondisjunction of chromosomes during mitosis or meiosis. Nondisjunction is when spindle fibers, which are composed of microtubules, don’t attach correctly to a chromosome which causes the chromosome to defectively separate.

2. Endosymbiosis & Atmospheric Gases

Endosymbiosis is when an organism of one species lives out its life inside another host species, and the interaction benefits one or both of them. Chloroplast and mitochondria were formed through endosymbiosis. Chloroplasts are used for photosynthesis and photosynthesis uses Co2  and produces O2 and O2 is an atmospheric gas.

3. Adaptive Radiation & Character Displacement

Adaptive radiation occurs when many species emerge from one common ancestor and this occurs through character displacement. Character displacement is when only the individuals that have the best traits are able to survive and reproduce and therefore pass on their traits while the weaker individuals die and eventually become completely extinct. In character displacement, the allele frequencies change and this causes evolution.

4. Proto-cells & Uracil

Proto-cells are the transitional forms between simple organic compounds and the first living cells. These cells consist of membrane bound sacs which contain enzymes and systems of metabolism. Protocells are self-replicating meaning that they had DNA and RNA protein systems and in RNA there is uracil, a nucleotide base, which differs from RNA and DNA.

1.Prezygotic and Postzygotic isolation mechanisms:

Prezygotic

- Mechanical Isolation: physical incompatibilities which deter them from mating

- Temporal Isolation: Cannot mate because the timing of reproduction is different

- Behavioral Isolation: Courtship displays are ignored because they are not recognized

- Ecological Isolation: There are geographical separation which prevents them to mate

-Gamete morality: Gametes are incompatible, so no fertilization.

Postzygotic

-Hyprid inviability: Hybrid emboryo die early before they can reproduce

-  Hybrid sterility: Hybrid individuals can’t make functional gametes.

2. Compare and Contrast Gradualism and Punctuated Equilibrium:

Gradualism is when speciation occurs slowly through small changes over a long period of time while punctuated equilibrium is when that speciation occurs abruptly through directional selection, genetic drift, bottlenecks, and the founder effect.

3. Miller’s Experiment:

Water, methane, hydrogen, and ammonia are put into a reaction chamber and zapped with sparks which caused simulating lighting striking on earth. Then in a week, amino acids and other organic compounds formed inside the reaction chamber, which led to Miller suggesting that this was what occurred billions of years ago, defining chemical evolution.

4. Endosymbiosis:

- The mitochondria resembles bacteria in size and structure.

- Chloroplasts resembles the cunobacteria

- The amoeba’s were become symbiotic when they were infected by bacteria and led them to rely on bacteria to create an essential enzyme.

5. Cladogram

totals: kangaroo- 5

lamprey -1

rhesus monkey- 6

bullfrog-3

human-7

Snapping turtle-4

tuna-2

Chapter 17 & 18

Connections:

1.       Prophase I & Allele Frequency

The allele frequency is the section of all copies of a gene that consist of a particular gene trait (an allele).  During meiosis in prophase I, the two duplicated chromosomes connect and in this connection, they begin to exchange genetic information at junction points. The process of this crossing over results in genetic variation in genes and many different traits for each offspring. The crossing over and allele frequency are tied together for the crossing over influences the allele frequency between parents.

2.       Analogous structures & Natural Selection

Analogous structures are two structures that perform similar functions by a similar mechanism but evolved separately. Natural selection is the process of favorable traits eventually becoming the normative due to competition or survival of the fittest trait. Hence both of them occur because of the natural results of their surroundings and competition.

3.       Gene pool & Bottleneck

A gene pool is the entire unique group of alleles in a species or population.  Bottle neck is when the size of a population shoots down because of the environmental conditions. Hence, if a bottleneck were to occur, this would affect the gene pool and cause a low reproduction/population rate.

4.       Balance polymorphism & Search Image

Balanced polymorphism can be defined as the number of selective processes by which different alleles and this occurs when natural selection eliminates individuals with detrimental phenotypes from a population.  A search image is the way an animal is able to see its prey only by senses and is necessary for same animals for their everyday habits and eating techniques. That is why balance polymorphism would be needed in order to allow these alleles to work.

Essentials:

1.       Observations made by Darwin

-          All populations by nature increase over time because of their need to reproduce.

-          Populations will be limited because of environmental constraints

-          A group of organisms will compete amongst themselves

-          Species  share a common gene pool with its population

-          Genetic variation is derived from alleles that come from mutations

-          Some traits are more helpful than other trait or alleles because of the environment.

-          Natural selection is the result of the variety of a population due to evolution.

2.       A. First the origin of photosynthetic cells

B.  Then the establishment of crusts of the earth that led to the environment where life can exists.

C. Molecular evolution that began life

D. oxygen in the atmosphere which led to the production of eukaryotic cells

E. Break up of Earth’s supercontinent which led to many different environments

3.       The phrase “individuals don’t evolve, populations do” is what evolution in actuality is because natural selection comes from the DNA changes of individuals and when they mate, their alleles or traits are passed down. That’s why new organisms with different traits are made because of their parents and these usually are based upon the environment and surroundings of the organism. When the child is affected by their parents, then the children mate with each other, the same alleles are passed down, therefore alternating or causing the process of evolution to the population.

4.       p²(AA) + 2pq(Aa) + q²(aa) = 1.0

p and q represent the frequencies of the alleles A and a.

The conditions that are needed are no mutations, the population is indefinitely large, the population is isolated, mating is random, and all individuals survive and produce the same number of offspring. 

Chapters 15,16,21

1.    1.    Lysogenic pathways are a latent period that extends through various replication cycles and these genes are integrated into the host chromosome and will stay there for a couple of divisions before being replicated. Binary fission is asexual reproduction and the body of a organism will split spontaneously. Binary fission and lysogenic reproduction is very different for the virus enters the host and stays there as they reproduce however binary fission splits spontaneously.

2.     2.   Conjugation is a mode of gene transfer that is possible whe one of the cells has an F plasmid among prokaryotic species while bacteria transformations is when a DNA is changed and therefore a bacteria is able to survive antibiotics. The way they fit together is that bacterial transformations may happen through conjugation because bacteria cells swap out with DNA to prevent the bacteria’s being destroyed.

3.     3.   A plasmid is a small bacterial DNA molecules that has a few genes and is replicated independently of the bacterial chromosome. A retrovirus is any of a group of viruses that contain two single-strand linear RNA molecules per virion and reverse transcriptase.   The plasmid is formed  many retroviruses which use enzymes to reverse transcriptase to form DNA and RNA.

4.   4.     An operator is a segment of DNA in which a repressor binds.  Hydrolysis is a reaction in which water reacts with a compound to produce another compound. Similar to each other, hydrolysis components attach to water molecules, the operator attaches to a protein.

5.     5.   An  okazaki fragment is a short fragment of DNA  which is created on a lagging strand during DNA replication. A restriction enzyme is an enzyme that cuts double stranderd or single stranded DNA. Hence an okazaki fragment comes from the cut strand that is cut from the restriction enzyme.

1.       Instructions for carrying out DNA molecules chromosomes lay in the hands of ribosome that are attached to membrane networks that snake their way through the cells. During protein synthesis, the amino acids are separated and bounded into new chains. Nuclosome packing is what determines if the section of DNA becomes transcribed leading to the regulation of genes that will be copied over. RNA interferences happens when RNA molecules pair themselves with themselves leading to t .

2.       The promoter is a DNA sequence t at allows a gene to be transcribed and RNA polymerase initiate this transcription. The operator is a segment of DNA that that a repressor binds to and it is located between the promoter and genes of operon. Repressors bind to the operators in DNA and it bends, blocking transcription.

3.       The gel electrophoresis separates the DNA fragment and in DNA fingerprinting a given sample is cut up with the restriction enzyme and run through the electrophoresis and that results in the DNA polymorphism being checked.

4.       Eukaryotic cells have a nucleus and a double membrane. The prokaryote has no nucleus. In a prokaryote every organelle is attached to a membrane whereas a eukaryotic cell is composed of a cytoplasm filled with many organelles because they are more complex.  DNA replication in prokaryotes happens when a bacteria chromosome connects itself to the cell plasma membrane creating DNA replication. The cell makes proteins and lipids and the membrane grows while the two DNA molecules pull apart giving each DNA one. The final step is when the membranes divide.

5.       The difference between a lytic and lysogenic is that the lytic cycle is when a virus enters through the membrane to get into a cell and the lysogenic cycle is when a virus enters a cell through the host cell.

Chapter 13 & 14

Connection: 

1. 5’ end when describing DNA is the end of the stand that has no amino acids bonding to the stand and it is low in electronegativity. The reason that the 5’ DNA is low in electronegativity is because electronegativity is attached to amino acids and hence when the DNA strand is done, it no longer attracts the amino acids.

2.  A start codon is the codon at which translation of mRNA into protein starts and it encodes the first amino acid. The groups of these amino acids are different for each organism and vary from each other however they still work together. Similarly, incomplete dominance works the same for there are traits that are not all similar, yet they work together, mixing, to make another combination of traits.

3. Semiconvsevative replication means that half of each parent molecule would be present in each daughter molecule. The barr body is the inactive sex chromosome in a male or female. Therefore because there is an inactive sex chromosome, the chromosome goes through the process of replication by going through semiconservative chromosome.

4. RNA polymerase is the enzyme that copies DNA into RNA and this copying occurs the place that the RNA is located in which is the nucleolus.

5. DNA polymerase is the enzyme which is responsible for replicating DNA. By replicating the DNA it is necessary that the enzyme forms glycosidic linkages between itself and the amino acid to start the replication process.

6. Helicases are a class of enzymes that are necessary for all living organisms and it is required for DNA unwinding. The G2 karyotupe shows the condense replicated DNA which is what the helicases break down.

Essentials: 

1. The antiparallelism shown in the 5’3’ pattern is the reason that DNA polymerase moves away from the 3’5’ strand. They move in different directions, therefore being deemed as antiparallelism. The DNA plymearse goes back to the replication fork and keeps on creating new segments hence the complication is solved.

2. The structural differences between RNA and DNA is that RNA is a single-stranded nucleic acid while DNA is double-stranded. Rna also has a ribose sugar instead of a deoxyribose sugar like dna. Lastly, RNA nucleotides have a uracil base as oppose to a thymine.

3. The messenger RNA is the template for protein synthesis and it forms RNA that carries information form DNA in the nucleus to the ribosome sites of protein synthesis. Ribosomal RNA is the central component of the ribosome and it is the protein manufacturing machinery, responsible for protein synthesis. Transfer RNA is the RNA molecules present in the cell that attatch the correct amino acid to the protein chain that is being synthesized.

4. a. Transcription:

- First the RNA polymerase binds to the DNA strand at a promoter

- unwinds the two strands of DNA and uses one of the DNa strands as a template.

-Matches new nucleotide with their components on the DNA strand, G-C, A-U

-binds new RNA nucleotides to form a copy of the DNA strand (mRNA – polymerase)

-Stops when the sequence stops also known as the stop codon.

b. RNA splicing

- Introns start from the GU sequence and end in the AG sequence. 5’3’.

-Elogation of the RNA molecule happens

- One DNA strand is transcriped

c. Translation:  

- Transfers RNA in sequence of mRNA nucleotide

- The anticodon recognizes the area on mRNA as the codon.

- RNA is transferred. 

Chapter 11 & 12

a) Gene locus & disulfide bridge

The disulfide bond is a strong covalent bond that is important in linking polypeptide chains in proteins that form during the tertiary structure of protein synthesis. A gene locus is the DNA site of a gene, and a certain part of it could be called an allele which codes for certain traits. The disulfide bond holds together the chromosome that is composed of DNA.

b) Nondisjunction & 9-triplet pattern

The nondisjunction is a failure of sister chromatids to move apart in meiosis or mitosis, therefore resulting in daughter cells getting too little or too many chromosomes. The nine triplet pattern is the organization and structure of microtubules in cells, therefore when the sister chromatids fail to separate in this process, it is called a nondisjunction.

c) Autosome & Steroid

Autosome is of a sexually reproducing species, any chromosome of a type that is the same in both males and females. A steroid is a class of organic compounds that can have functions ranging from fat cholesterol in order to be like hormones. The two are similar for they function similarly.

d) Polygenic & Glycocalyx

Polygenic is the term that means of or relating to an inheritable character that is controlled by several genes at once. Glycocalyx is a general term referring to extracellular polymeric material that is produced by some bacteria. Therefore, polygenic can contribute to traits such as glycocalyx because an example of glycocalyx is the slime on fish, which is the outer cells of fish.

a.

- Mendal’s law of segregation:

In Mendal’s law of segregation mendal explains how traits are passed from parents to offspring through gene transmission. He said that genes that consists of DNA are located on the chromosomes. The DNA is passed from parents to their offspring by reproduced. His four main concept was that organisms could inherit two alleles for each trait, a gene can have more than one form, when meiosis occurs and gametes are produced, allele pairs separate which leaves each cell with a single trait, and when two alleles of a pair are different, one becomes dominant and the other recessive.

-Mendal’s law of independent assortment:

Mendal’s law of independent assortment says that allel pairs separate by themselves s (independently) while they are forming gametes. Therefore, the traits are transferred to the offspring independently of one another. 

Chapter 10

Connection:

a. carrying capacity and biotic potential: The biotic potential is the maximum rate that a population can grow under ideal conditions. The carrying capacity is the maximum number of individuals an environment can contain. These work together because the biotic potential may have to yield to the carrying capacity and therefore the environment must be able to sustain the whole population or many will die.

b. biological magnification and trophic level: The trophic level is all organisms having the same number of transfer steps away from the energy input into an ecosystem while the biological magnification is the increasing concentration of a slowly degradable or non degradable substance in body tissues as it is passing along in the food chains. Both processes deal with energy being inputted into a larger system. In addition each species is put on a trophic level as a smaller organism is eaten by a bigger one and the process continues, this can lead to a biological magnification.

c. Detrivores and autotrophs: Detrivores are animals that feed on decomposing matter or organisms and an autotroph is an organism that synthesizes its own food from simple inorganic compounds in its environment with energy from the sun. These two are similar for instead of feeding off of living organisms, they find their food through what the ecosystem provides for them, autotrophs being the sun and detrivores feeding off organism that are already decomposed.

A)

45.4: limits on the Growth of Populations

1) Density-Dependent Limiting Factors

a) Many times the environmental factors keep a certain population of species from growing to its biotic potential

b) When resources of a specie or organism is lower in numbers, this supply is called the limiting factor

          - This can be extrensively detrimental to a population and one factor can affect the whole population

2) Carrying Capacity and Logistic Growth

     a) In the end, it is the sustainable supply of resources that will determine population   size

     b) the carrying capacity is the maximum number of individuals of a population given   the sustainable supply

     c) The pattern of logistic growth is used to show how the carrying capacity can affect           a population size

     d) When exponential or logistic growth are overcrowded, factors function as density-  dependent controls putting an individual’s survival over the population.

3) Density-Independent Limiting Factors

     a) Density-independent factos cause more deaths and fewer birth rates

B)

Survivorship curve: a graph line that emerges when ecologists plot a cohort’s age-specific survival habit.

Type I: Type I These curves are used to indicate population and it curves when there is a drop of survival during their lifetime.

Ex. The population of people in America who have easy access to health insurance as opposed to some of the starving children in Africa then the curve would drop because of the population, if the whole world is taken into consideration, will drop.

Type II: This curve reflects the death rate of all ages this includes all organisms.

Ex. The death of snowy egrets is very constant.

Type III: This curve is used to describe organisms with high death rate at an early stage in life.

Ex. Sea star larvae die at a very early age.

C)

a. Negative Growth: A negative growth population has a small amount of individuals in its pre-productive time with a higher amount when it is productive and after the productive stage is when the largest number of individuals can exist.

b. No Growth: A population with no growth steadily declines but as it gets older, it would have a smaller population.

c. Rapid Growth: A population with rapid growth has a dramatic increase in its population as the years go on.

d. Slow Growth: A population with slow growth is when the growth of a population decreases at a consistent rate.

D) The nitrogen cycle is when gaseous nitrogen is changed into ammonia (N2 à NH3). This occurs when the ammonia created by nitrogen-fixing bacteria in the soil and nitrogen fixation happen. Then the organisms use the two forms, nitrate and ammonium to live. Then as organisms pass on, they decompose and nitrogen enters back into the soil. And in the soil, the nitrogen is absorbed and nitrate is converted to gaseous nitrogen again. 

Chapter 45 & 47

Connection:

a. carrying capacity and biotic potential: The biotic potential is the maximum rate that a population can grow under ideal conditions. The carrying capacity is the maximum number of individuals an environment can contain. These work together because the biotic potential may have to yield to the carrying capacity and therefore the environment must be able to sustain the whole population or many will die.

b. biological magnification and trophic level: The trophic level is all organisms having the same number of transfer steps away from the energy input into an ecosystem while the biological magnification is the increasing concentration of a slowly degradable or non degradable substance in body tissues as it is passing along in the food chains. Both processes deal with energy being inputted into a larger system. In addition each species is put on a trophic level as a smaller organism is eaten by a bigger one and the process continues, this can lead to a biological magnification.

c. Detrivores and autotrophs: Detrivores are animals that feed on decomposing matter or organisms and an autotroph is an organism that synthesizes its own food from simple inorganic compounds in its environment with energy from the sun. These two are similar for instead of feeding off of living organisms, they find their food through what the ecosystem provides for them, autotrophs being the sun and detrivores feeding off organism that are already decomposed.

A)

45.4: limits on the Growth of Populations

1) Density-Dependent Limiting Factors

a) Many times the environmental factors keep a certain population of species from growing to its biotic potential

b) When resources of a specie or organism is lower in numbers, this supply is called the limiting factor

          - This can be extrensively detrimental to a population and one factor can affect the whole population

2) Carrying Capacity and Logistic Growth

     a) In the end, it is the sustainable supply of resources that will determine population   size

     b) the carrying capacity is the maximum number of individuals of a population given   the sustainable supply

     c) The pattern of logistic growth is used to show how the carrying capacity can affect           a population size

     d) When exponential or logistic growth are overcrowded, factors function as density-  dependent controls putting an individual’s survival over the population.

3) Density-Independent Limiting Factors

     a) Density-independent factos cause more deaths and fewer birth rates

B)

Survivorship curve: a graph line that emerges when ecologists plot a cohort’s age-specific survival habit.

Type I: Type I These curves are used to indicate population and it curves when there is a drop of survival during their lifetime.

Ex. The population of people in America who have easy access to health insurance as opposed to some of the starving children in Africa then the curve would drop because of the population, if the whole world is taken into consideration, will drop.

Type II: This curve reflects the death rate of all ages this includes all organisms.

Ex. The death of snowy egrets is very constant.

Type III: This curve is used to describe organisms with high death rate at an early stage in life.

Ex. Sea star larvae die at a very early age.

C)

a. Negative Growth: A negative growth population has a small amount of individuals in its pre-productive time with a higher amount when it is productive and after the productive stage is when the largest number of individuals can exist.

b. No Growth: A population with no growth steadily declines but as it gets older, it would have a smaller population.

c. Rapid Growth: A population with rapid growth has a dramatic increase in its population as the years go on.

d. Slow Growth: A population with slow growth is when the growth of a population decreases at a consistent rate.

D) The nitrogen cycle is when gaseous nitrogen is changed into ammonia (N2 à NH3). This occurs when the ammonia created by nitrogen-fixing bacteria in the soil and nitrogen fixation happen. Then the organisms use the two forms, nitrate and ammonium to live. Then as organisms pass on, they decompose and nitrogen enters back into the soil. And in the soil, the nitrogen is absorbed and nitrate is converted to gaseous nitrogen again.