Chapter 24 Reading Journal

What are the different definitions of species?
Biological- A group of organisms that can breed and produce viable and fertile offspring
Morphological- A group of organisms that has similar body shape and other structures
Ecological- A group of organisms that reacts in the same way to their environment, basically eats the same foods and resides in the same habitat
Phylogenetic- The smallest group of organisms that share a common ancestor (new branch on tree of life)

In the Biological species concept what barriers can separate different species?
The barriers that separate species in this concept are reproductive things that keep them from producing viable fertile offspring these are separated into two groups prezygotic (prevent a zygote from even being formed) and Postzygotic (keep the offspring from meeting the criteria of being viable and fertile.
Prezygotic:
Habitat isolation- organisms live in different habitats and therefore rarely come in contact with each other
Temporal isolation- Mating habits vary in time of day or time of year
Behavioral isolation- certain mating behaviors are specific to the group so they don’t attract members from the other group
Mechanical isolation- the organisms’ reproductive parts don’t fit together properly
Gamete isolation- fusing of the sperm and egg is unable to occur

Postzygotic-
Reduced hybrid viability- The new organism is less suited for the environment than either parent and will therefore be naturally selected against
Reduced hybrid fertility- The hybrid is sterile and therefore genes cannot flow between the two species keeping them isolated
Hybrid Breakdown- The first generation of the hybrid may be successful but when they breed with either parent species their offspring is not

What is the difference between allopatric and sympatric speciation?
Allopatric speciation occurs when a geographical barrier such as a canyon arises between to species. Over time the species evolve separately and once some type of reproductive isolation arises so that even if they were put into they same environment again they couldn’t reproduce new species have been formed
Sympatric speciation is more rare but it occurs within a population. This can happen when gene flow is reduced between certain sects of a population due to habitat differentiation, sexually selective behaviors, or polyploidy. Polyploidy is most common within plants where often times once they have an off number of chromosomes they cannot reproduce with either parent species but they can fertilize themselves. Speciation within a population can also occur when certain genetic traits allows some of the organisms to utilize a different food group or environmental resource creating habitat isolation. When mates are chosen for certain traits (sexual selection) species can faction off as well.
Facts:
-A hybrid zone is a region where different species overlap and mate producing hybrid offspring
-If the offspring in the hybrid zone are in some way less “fit” than the parent species over time reproductive barriers with strengthen this is called reinforcement
-If the hybrids are successful the opposite can happen and reproductive barriers may be reduced possibly eventually even leader to reverse speciation
-There are two patterns for the course of speciation in the fossil record punctuated equilibrium (stays the same for a very long time and then rapidly changes) Gradualism (long periods of time show small but consistent change which eventually constituted new species.
-In some cases speciation can occur from a change in a single gene such as with Japanese snails.



This is an example of sympatric speciation these two species of flies are not separated geographically at all but they have form different species because they both utilize a different food source and have therefore created a habitat isolation between themselves.

Summary: For the purpose of this book and the study of evolution the biological species concept was used, which is that, species are different if they cannot produce viable fertile offspring. Speciation can occur either because of a geographical separation (allopathic) or with the same geographical area due to polyploidy, sexual selection, or habitat shift. Hybrid zones are sometimes formed where two different species habitats overlap the offspring being unsuccessful can create more reproductive barriers but successful hybrids can reduce them. Speciation can occur at different rates sometimes even within one generation as is the case with autoplyoidy. Study of genetics has shown that as little as one gene difference can separate a species.

Chapter 25 Reading Journal

How do Scientists think life arose on earth?

They believe based on experiments done my Stanley Miller and Harold Urey that the early oceans had tons of organic molecules floating around and the energy from lightning and UV rays converted these molecules into macromolecules such as amino acids and nucleotides. Then protobionts which have some life like characteristics may have formed they would be contained in a membrane and maintain a separate composition from their surroundings. Eventually amino acids were able to form ribosomes and RNA was used as the first genetic material. Ribosomes that were able to self-replicate would be naturally selected for and therefore the environment would give rise to a genetic code.

How is the Fossil Record used for information about living things?

The fossil record is mostly used to date organisms and the arrival of different species as well as by seeing them in chronological order enables scientists to guesstimate which species are descendents of other species. It also allows them to study at least the remnants of species that went extinct and see how creatures were adapted to the world as it used to be. They can date fossils either relatively by the position the strata that they are found but this only shows the age of fossils in relationship to other fossils. To get a more accurate age of fossils radiometric dating is used. Basically by using the half-life (time it takes for half the isotope to decay) of the isotope and then comparing it to the amount left in the fossil a more accurate age is given.

What is Adaptive Radiation and what causes it?

These are periods of sped up evolutionary change to fill new environmental needs. After each of the five major extinctions a mass adaptive radiation has occurred. The mammals underwent an adaptive radiation after the dinosaurs went extinct the mammals had to become more diverse to fill the ecological roles the dinosaurs had before. Adaptive radiation can also occur on a small scale usually when organisms settle in a generally desolate land they then undergo large structural changes and such to fill up to the uncharted land. Basically large changes of species occur when there are ecological niches not being utilized so larger behavioral or structural changes occur to take on these roles.

Facts:
- About 250 million years ago all the land masses on earth were connected they form Pangaea this new environment killed off many species but also gave rise to new ones it also accounts for fossils of the same species now found in lands separated by the ocean
- 2.7 billion years ago oxygen started to become present on the earth giving rise to species that utilized respiration
- The first eukaryotes came to be 2.1 billion years ago scientists believe this was due to endosymbiosis where smaller organisms were engulfed by larger ones and the symbiotic relationship is the reason for organelles
- The accumulation of O2 in the earth’s atmosphere about 2.2 billion years ago led to organisms that utilize respiration
- The arrival of creatures with totally different body structure than their ancestors is a result of change in DNA sequence and regulatory genes becoming inactive allow the display of different genes



This shows how human and chimp skulls are very similar during the fetal stage but chimps’ skulls continuing elongating where humans stop. This is an example of how changes in genes that control growth and development when altered can make large differences in the anatomy of a creature and therefore lead to macroevolution and new species.

Summary:
The early atmosphere of the earth was rich with organic molecules these gave rise to macromolecules such as amino acids and nucleotides. Once protobionts that maintained a different chemical composition than their surrounding arose Rna became a method for passing along genetic info it was later replaced by DNA because it had less error. The fossil record shows us animals of the past ect and they are dated by radiometric or relative dating. The first organisms were prokaryotes then eukaryotes became prominent with the addition of O2 organisms became more diverse and once organisms colonized land they underwent even more diversification. Large groups of organisms have come to be and gone extinct long before humans were even on the earth these major events were due to continental drift and large changes in environment or natural disasters that led to mass extinctions, to recover from this the organisms left have undergone adaptive radiations. Major changes in organisms physical structure is often due to changes in regulatory genes and developmental timing and patterns. Evolution has no desired result so the trends for evolving vary based on the environment as organisms try to make the best out of their ecological niche.

Chapter Thirteen Reading Journal

What accounts for genetic variation?
The fact that the chromosomal number is split during meiosis means that there are several possibilities of contribution from each parent that will come together. This refers to independent assortment of the chromosomes during meiosis 1 and random fertilization. The pairs of chromosomes are arranged independently and randomly along the metaphase plate for when they split during meiosis 1 this result in many combinations then they fertilize and combine with other gametes leaving endless possibilities for genes.

What are the distinct features of Meiosis?
Homolog pair during Meiosis 1 in mitosis sister chromatids are attached and they split. The kinetochore behavior is also unique because in meiosis both kineticores of the homolog pair attach to the same pole of the microtubles. In Mitosis the sister chromatids are attached to by cohesion, in meiosis the pairs are linked by the chaisma and then use the cohesion to keep the sister chromatids together until they spilt during meiosis 2.

What are the benefits and disadvantages of sexual reproduction?
The advantage is that there is more room for variation and therefore adaptation. With sexual reproduction organisms are not the same as their parents, which creates variety. In asexual reproduction parents make exact replicas of themselves, they do not need a second person to contribute this is an advantage, because it makes asexual reproduction easier to occur since they do not have to find a mate. This means though that if something in the environment changes an entire species of asexual reproducing organisms could die off, where sexually reproducing organisms would have certain people with enough variation for some to survive most likely. A disadvantage to sexual reproduction is also though that it is so variant because if a species is successful with certain characteristics their offspring may not have those same beneficial traits.

Five Facts:
-A locus is a gene’s specific location on a chromosome
-Karyotyping involves mapping chromosomes
-Haploid cells are gametes and they contain half the chromosomes of diploid also known as somatic cells they make up the majority of the organism
-All sexual reproduction involves meiosis
- Meiosis halves the chromosome number so that offspring do not have double the genes of their parents.



This diagram shows the steps of meiosis. Essentially chromosomes replicate like they would in mitosis but instead of separating once they pair off into homologs cross over with other pairs and then separate. Then the sister chromatids which are still attached but may have some pieces from another chromosome separate halving the chromosome number.

Summary: In sexual reproduction offspring inherit half their chromosomes from each parent this creates variation and quicker adaptations. In asexual reproduction one parent exactly duplicates themselves. In somatic cells there are 2n chromosomes in gametes there are n chromosomes. Gametes are produced by meiosis and they combine with gametes from the opposite sex of the same organism to form a zygote, which is diploid and continues to replicate. Because of the genetic variation caused by crossing over and independent assortment with meiosis evolution is far more efficient.

Chapter Twelve Reading Journal

Questions:

What is the difference between mitosis and the cell cycle?
Mitosis includes prophase, prometaphase, metaphase, anaphase, and telophase this only makes up about 10% of the cell cycle the rest of the cell cycle is interphase that consists of G1, G2, and S phases. Mitosis is when the cell is actually in the process of dividing the other part of the cycle involves growth and DNA synthesis, which is most of the cells life. Although often the cells are in Go phase when they are told not to divide by the G1 checkpoint.

How do cells control the cell cycle?
Different cells divide at different rates and certain cells once in maturity never divide examples of these cells are muscle and nerve cells. The cell cycle has checkpoint after each of the sub phases of interphase and after mitosis. The checkpoint after G1 is called the restriction point and if it doesn’t receive the go ahead at this checkpoint it is sent into the non-dividing state called Go. Besides the checkpoints there are other molecules that regulate cell division mainly protein kinases and cyclin. Cyclin is constantly present but usually in the inactive form its active form is in higher concentration during S and G2 phases but is much lower during mitosis. Cells also regulate their cell cycles by knowledge of external factors such as surrounding density and anchorage.

What is known about how cancer cells differ from healthy cells?
Cancer cells don’t have good regulation of their cell cycles so they divide far too often. The fact that they are not anchorage dependant means that they can move from different parts of the organism and start growing in other places. The fact that they lack density dependency is the reason tumors form because the cells just layer on top of each other without stopping. They most also lack the cellular control of aptopsis or else they would self destruct because of their dysfunction.

Facts:
- Somatic cells contain 46 chromosomes gametes (reproductive cells) have 23 chromosomes
- Chromosomes are copied to from 2 sister chromatids which are attached at the centromere
- The five main phases of mitosis are prophase prometaphase metaphase anaphase and telophase the DNA needed for this division is produced during the S phase of interphase
- Microtubules play a major role in cell division because they attach to kinetochores and then shorten to separate the chromosomes that aligned in the middle during metaphase
- A benign tumor are cancer cells that stay in the place they started growing malignant tumors inhibit the function of major organs



This figure breaks down the various steps of mitosis. Doesn’t need much explaining I’m putting it on here because it explains.

Summary:
Cells are made up of genetic information that is packaged into chromosomes that are duplicated and then separated during cell division. The chromosomes duplicate to chromatids that are held together by the centromere. During interphase the cell grows and replicates DNA. It reaches several checkpoints before continuing and responds to many outside regulators. Cancer is somehow deficient in its regulation so its cell cycle malfunctions.

Chapter Eleven Reading Journal

Questions:

What are the three basic steps of Cell signaling?
Reception comes first when a chemical signal is detected by the cell this may happen because of direct contact or because the cell is receiving a signal that has already been passed along and is finally reaching the target cell. Transduction occurs when the message is converted so that it can be passed along to other signal molecules this is either done through the use of g-proteins, tyrosine kinasases, or ion channels. Response is when the cell behaves the way that the signal intended to make the cell.

How do G-Protein receptors work?
These receptor are in the membrane of cells and G proteins are either in the in active state of GDP or the active state of GTP when a phosphate has been added. When the g-protein receptor receives the signal molecule it changes the g-protein to the active form the g-protein then travels to an enzyme that it activates and often changes the shape of the enzyme once banded to it. This either immediately bringing about the cellular response or continuing to transfer the response through other enzymes. This is one of the most widespread cellular signaling functions.

What are Second Messengers?
Typically small water-soluble molecules or ions that are used to spread the signal within the cell. cAMP usually activates protein kinase A which typically spreads the signal by adding phosphorous to other proteins. This happens because the first signal that occurs in the membrane increases the levels of Camp to pass the signal along within the cell. Other cellular signals increase levels of ions most typically Ca + IP3 or DAG these work similarly to Camp in that the original signal triggers an increase in the ions which triggers further responses. Second messenger is a general term used for non-proteins used in the transductions pathways.

Facts:
- Cells have to communicate because they need to regulate cellular processes and respond to their environment as well as reproduce
- Cells perform apoptosis basically cell suicide when their DNA is coded improperly or they are about to stop functioning they do this to prevent damage to other cells
- Cell signaling can also stimulate certain genes within the nucleus to produce certain RNA
- Earl Sutherland discovered second messengers and the use of cAMp in epinephrine
- Ligands bind to receptors to promote the cellular response



This shows how signals can be transferred over a long distance. The original receptor activates a molecule that is able to activate other protein kinases. This works because a phosphate is added to the protein activating it then deactivates be transferring its P to another kinase, which is activated. Thus the reaction can move from molecule to molecule.

Summary:
Cell signals are either local or long distance. The main signal receptors are G-protein tyrosine kinnases and ion gated channels. To get from reception and response cells must undergo transduction pathways that either use phosphorylation cascade or secondary messengers. The response helps regulate transcription and other cellular functions this also helps them identify surrounding cells. The also use signaling to know when to self-destruct to prevent damage to nearby cells.

Chapter Ten Reading Journal

Questions-

How does Photosynthesis relate to respiration?
The general equation of Photosynthesis is the reverse of respiration. Photosynthesis uses energy to build molecules of carbs for energy storage. Plants also use respiration when they need ATP for their cells but they are able to use sunlight to formulate the glucose needed unlike heterotrophs that have to consume this by eating other organisms often plants. Both respiration and photosynthesis have many similarities the product of the steps of photosynthesis are reactants of respiration. Photosynthesis only has two major steps instead of the three in respiration, and it also contains a cycle and an electron transport chain some ATP is also produced during this process.

Explain the concept of wavelengths visible light and how they relate to photosynthesis?
Light behaves like a wave and a particle; the particle is called a photon. The distance between peaks of a wave of light is called the wavelength the shorter the wavelength the higher the energy of light and the greater energy photons of that light contain. The visible light spectrum is from wavelengths of 380 to 750nm. The Chloroplasts contain chlorophyll molecules that absorb light. The most effective visible light is violet-blue and red and the least effective is green since chlorophyll reflects that color. Accessory pigments such as carotenoids and xanthophylls help the plant absorb more colors of light making the process more efficient. The membrane of the thylakoid contains light harvesting complexes that use these pigments to excite electron and send them to the primary electron acceptor sending the energy from Photosystem 2 to Photosystem 1.

What are the evolutionary advantages of CAM and C4 Plants?
Most plants can be called C3 plants because they use a 3-carbon compound to start the Calvin cycle. Unfortunately when not very much Co2 is present the Calvin cycle will bind to O2 to produce more Co2 this can be seen as very wasteful because it consumes ATP. C4 plants have adapted to hot dry climates because they use PEP carboxylase to which has a very high affinity for CO2 to fix CO2 in the mesophyll cells before sending CO2 to the more contained bundle-sheath cells where the Calvin cycle takes place. This eliminates photorespiration and also lessens water evaporation. CAM plants leave their stomata open only during the night to avoid the excessive amounts of water evaporation that would occur during the day. They fix co2 with and acid known as CAM during the night and then use it during the day when the light reactions are occurring.

Facts:
-The O2 released during photosynthesis is a result of the water spitting during the light reactions
-NADPH and ATP are formed during the light reactions and these energy molecules are needed to fix co2 during the Calvin cycle
-Stomata are the pores in the leaf stroma is the liquid inside the chloroplast
- Photosystem 2 occurs first and best absorbs light with a wavelength of 680 Photosystem 1 occurs second but can also function independently and best absorbs light with a wavelength of 700.
- ATP synthase is used during the electron transport chain from photosystem 2 to photosystem 1 when a H+ concentration is formed within the tylakoid pumping ATP into the stroma where the Calvin cycle occurs.




This depicts the relationship between Photosystem 1 and Photosystem 2. Photosystem 2 absorbs light and splits water to send the excited electron to the electron transport chain that produces ATP while sending the electron to Photosystem 1. Photosystem 1 uses this energy to from NADPH, but it can also independently absorb light and form NADPH. This is why Photosystem 2 is said to use non-cyclic electron flow and Photosystem 1 uses cyclic electron flow.

Summary:
Plants are said to be the producers because they don’t need to live off other organisms they use photosynthesis to produce glucose. Inside the chloroplasts within the membrane of the thylakoid light energy is absorbed by the photosystems that produce NADPH and ATP the energy storing molecules needed for the Calvin cycle. The Calvin cycle uses CO2 to combine with Rubisco ATP and NADPH power the cycle and are recycled to NADP+ and ADP to be reused in the light reactions. The Calvin cycle produces G3P, which is converted into energy storing molecules.

Chapter Nine Reading Journal

Questions:
What is the basic summary of respiration?

The first step is glycolysis, which breaks down glucose and produces NADH, ATP and Pyruvate. In the energy investment phase the cell uses ATP to break glucose in G3P. In the energy pay off phase NADH and are produced along with Pyruvate, which makes it possible to move into the Krebs cycle. Through active transport the Pyruvate is moved into the mitochondria, once Coenzyme A is added CO2 and NADH are released forming Acetyl CoA. Acetyl CoA combines with oxaloacetate to start the Krebs cycle forming NADH and FADH2. These molecules are used as the electron transport chain, which creates a concentration gradient powering ATP synthase, which produces ATP.

What are the different types of fermentation?

Alcohol fermentation: Ethanol is converted to Pyruvate first CO2 is released forming acetaldehyde then its reduced by NADH to ethanol this recycles the NAD+ so the glycolysis can continue. Many bacteria and yeast use this for energy production.

Lactic Fermentation: Pyruvate is reduced to NADH forming Lactate. This is also used in bacteria and fungi, but also used in animal cells when they are short of oxygen. In humans lactate is taken to the liver and converted back to Pyruvate.

How does ATP synthase work?
NADH and FADH2 release their H+ ions to proteins in the membrane that pump the H ions across the membrane to create a concentration gradient. The H ions move back across the membrane to reach equilibrium through the protein ATP synthase that by the energy provided attaches P to ADP forming ATP. This is called oxidative phosphorylation. About 36 ATP are made through this process for every NADH 3 ATP can be produced and for every FADH2 2 ATP can be produced.

Facts:
*Glycolysis is one of the most wide spread metabolic pathways and is therefore the oldest.
*Cells are able to trigger the production of more ATP or make the process slow because of feedback inhibition.
* O2 acts as the final acceptor in the electron transport chain
* The general equation for glycolysis is C6H12O6 + 6O2 → 6CO2+ H20 + energy hydrogen is oxidized and the Oxygen is Reduced
* The majority of ATP is produced during ATP synthase/ electron transport chain, but it is made other times during respiration






This shows the Krebs cycle also known as the citric acid cycle. Acetyl CoA combines with the oxaloacetate to form citrate. As the cycle continues NADH and FADH2 are released as NAD+ and FADH are reduced. This is also the step in respiration where Co2 is released and it is considered a cycle because the same products will be produced every time allowing it to occur again in other words oxaloacetate will be produced allowing acetyl CoA to combine with it theoretically allowing it to continue forever.


Summary:
All cells need energy and they undergo a process called respiration to produce this energy. Respiration involves glycolysis, which can also be used for anaerobic respiration (respiration without O2) if O2 is present glycolysis moves to the Krebs cycle and then to the electron transport chain performing oxidative phosphorylation thus completing aerobic respiration. Fermentation is used in organism that produce energy either without the presence of a mitochondria or when O2 levels are depleted. Since glucose is not always available cells must perform respiration using other molecules such as fats and proteins by breaking them into either G3P, Acetyl CoA or as the case is only in proteins moving directly into the citric acid cycle.